Chiang, Mao-Hsiung; Lin, Hao-Ting
2011-01-01
This study aimed to develop a novel 3D parallel mechanism robot driven by three vertical-axial pneumatic actuators with a stereo vision system for path tracking control. The mechanical system and the control system are the primary novel parts for developing a 3D parallel mechanism robot. In the mechanical system, a 3D parallel mechanism robot contains three serial chains, a fixed base, a movable platform and a pneumatic servo system. The parallel mechanism are designed and analyzed first for realizing a 3D motion in the X-Y-Z coordinate system of the robot's end-effector. The inverse kinematics and the forward kinematics of the parallel mechanism robot are investigated by using the Denavit-Hartenberg notation (D-H notation) coordinate system. The pneumatic actuators in the three vertical motion axes are modeled. In the control system, the Fourier series-based adaptive sliding-mode controller with H(∞) tracking performance is used to design the path tracking controllers of the three vertical servo pneumatic actuators for realizing 3D path tracking control of the end-effector. Three optical linear scales are used to measure the position of the three pneumatic actuators. The 3D position of the end-effector is then calculated from the measuring position of the three pneumatic actuators by means of the kinematics. However, the calculated 3D position of the end-effector cannot consider the manufacturing and assembly tolerance of the joints and the parallel mechanism so that errors between the actual position and the calculated 3D position of the end-effector exist. In order to improve this situation, sensor collaboration is developed in this paper. A stereo vision system is used to collaborate with the three position sensors of the pneumatic actuators. The stereo vision system combining two CCD serves to measure the actual 3D position of the end-effector and calibrate the error between the actual and the calculated 3D position of the end-effector. Furthermore, to
Combinatorial 3D Mechanical Metamaterials
NASA Astrophysics Data System (ADS)
Coulais, Corentin; Teomy, Eial; de Reus, Koen; Shokef, Yair; van Hecke, Martin
2015-03-01
We present a class of elastic structures which exhibit 3D-folding motion. Our structures consist of cubic lattices of anisotropic unit cells that can be tiled in a complex combinatorial fashion. We design and 3d-print this complex ordered mechanism, in which we combine elastic hinges and defects to tailor the mechanics of the material. Finally, we use this large design space to encode smart functionalities such as surface patterning and multistability.
Parallel 3-D method of characteristics in MPACT
Kochunas, B.; Dovvnar, T. J.; Liu, Z.
2013-07-01
A new parallel 3-D MOC kernel has been developed and implemented in MPACT which makes use of the modular ray tracing technique to reduce computational requirements and to facilitate parallel decomposition. The parallel model makes use of both distributed and shared memory parallelism which are implemented with the MPI and OpenMP standards, respectively. The kernel is capable of parallel decomposition of problems in space, angle, and by characteristic rays up to 0(104) processors. Initial verification of the parallel 3-D MOC kernel was performed using the Takeda 3-D transport benchmark problems. The eigenvalues computed by MPACT are within the statistical uncertainty of the benchmark reference and agree well with the averages of other participants. The MPACT k{sub eff} differs from the benchmark results for rodded and un-rodded cases by 11 and -40 pcm, respectively. The calculations were performed for various numbers of processors and parallel decompositions up to 15625 processors; all producing the same result at convergence. The parallel efficiency of the worst case was 60%, while very good efficiency (>95%) was observed for cases using 500 processors. The overall run time for the 500 processor case was 231 seconds and 19 seconds for the case with 15625 processors. Ongoing work is focused on developing theoretical performance models and the implementation of acceleration techniques to minimize the number of iterations to converge. (authors)
Parallel contact detection algorithm for transient solid dynamics simulations using PRONTO3D
Attaway, S.W.; Hendrickson, B.A.; Plimpton, S.J.
1996-09-01
An efficient, scalable, parallel algorithm for treating material surface contacts in solid mechanics finite element programs has been implemented in a modular way for MIMD parallel computers. The serial contact detection algorithm that was developed previously for the transient dynamics finite element code PRONTO3D has been extended for use in parallel computation by devising a dynamic (adaptive) processor load balancing scheme.
Parallelization of Program to Optimize Simulated Trajectories (POST3D)
NASA Technical Reports Server (NTRS)
Hammond, Dana P.; Korte, John J. (Technical Monitor)
2001-01-01
This paper describes the parallelization of the Program to Optimize Simulated Trajectories (POST3D). POST3D uses a gradient-based optimization algorithm that reaches an optimum design point by moving from one design point to the next. The gradient calculations required to complete the optimization process, dominate the computational time and have been parallelized using a Single Program Multiple Data (SPMD) on a distributed memory NUMA (non-uniform memory access) architecture. The Origin2000 was used for the tests presented.
Parallel algorithm for computing 3-D reachable workspaces
NASA Astrophysics Data System (ADS)
Alameldin, Tarek K.; Sobh, Tarek M.
1992-03-01
The problem of computing the 3-D workspace for redundant articulated chains has applications in a variety of fields such as robotics, computer aided design, and computer graphics. The computational complexity of the workspace problem is at least NP-hard. The recent advent of parallel computers has made practical solutions for the workspace problem possible. Parallel algorithms for computing the 3-D workspace for redundant articulated chains with joint limits are presented. The first phase of these algorithms computes workspace points in parallel. The second phase uses workspace points that are computed in the first phase and fits a 3-D surface around the volume that encompasses the workspace points. The second phase also maps the 3- D points into slices, uses region filling to detect the holes and voids in the workspace, extracts the workspace boundary points by testing the neighboring cells, and tiles the consecutive contours with triangles. The proposed algorithms are efficient for computing the 3-D reachable workspace for articulated linkages, not only those with redundant degrees of freedom but also those with joint limits.
Parallelization of ARC3D with Computer-Aided Tools
NASA Technical Reports Server (NTRS)
Jin, Haoqiang; Hribar, Michelle; Yan, Jerry; Saini, Subhash (Technical Monitor)
1998-01-01
A series of efforts have been devoted to investigating methods of porting and parallelizing applications quickly and efficiently for new architectures, such as the SCSI Origin 2000 and Cray T3E. This report presents the parallelization of a CFD application, ARC3D, using the computer-aided tools, Cesspools. Steps of parallelizing this code and requirements of achieving better performance are discussed. The generated parallel version has achieved reasonably well performance, for example, having a speedup of 30 for 36 Cray T3E processors. However, this performance could not be obtained without modification of the original serial code. It is suggested that in many cases improving serial code and performing necessary code transformations are important parts for the automated parallelization process although user intervention in many of these parts are still necessary. Nevertheless, development and improvement of useful software tools, such as Cesspools, can help trim down many tedious parallelization details and improve the processing efficiency.
CALTRANS: A parallel, deterministic, 3D neutronics code
Carson, L.; Ferguson, J.; Rogers, J.
1994-04-01
Our efforts to parallelize the deterministic solution of the neutron transport equation has culminated in a new neutronics code CALTRANS, which has full 3D capability. In this article, we describe the layout and algorithms of CALTRANS and present performance measurements of the code on a variety of platforms. Explicit implementation of the parallel algorithms of CALTRANS using both the function calls of the Parallel Virtual Machine software package (PVM 3.2) and the Meiko CS-2 tagged message passing library (based on the Intel NX/2 interface) are provided in appendices.
A parallel algorithm for solving the 3d Schroedinger equation
Strickland, Michael; Yager-Elorriaga, David
2010-08-20
We describe a parallel algorithm for solving the time-independent 3d Schroedinger equation using the finite difference time domain (FDTD) method. We introduce an optimized parallelization scheme that reduces communication overhead between computational nodes. We demonstrate that the compute time, t, scales inversely with the number of computational nodes as t {proportional_to} (N{sub nodes}){sup -0.95} {sup {+-} 0.04}. This makes it possible to solve the 3d Schroedinger equation on extremely large spatial lattices using a small computing cluster. In addition, we present a new method for precisely determining the energy eigenvalues and wavefunctions of quantum states based on a symmetry constraint on the FDTD initial condition. Finally, we discuss the usage of multi-resolution techniques in order to speed up convergence on extremely large lattices.
Parallel Optimization of 3D Cardiac Electrophysiological Model Using GPU
Xia, Yong; Wang, Kuanquan; Zhang, Henggui
2015-01-01
Large-scale 3D virtual heart model simulations are highly demanding in computational resources. This imposes a big challenge to the traditional computation resources based on CPU environment, which already cannot meet the requirement of the whole computation demands or are not easily available due to expensive costs. GPU as a parallel computing environment therefore provides an alternative to solve the large-scale computational problems of whole heart modeling. In this study, using a 3D sheep atrial model as a test bed, we developed a GPU-based simulation algorithm to simulate the conduction of electrical excitation waves in the 3D atria. In the GPU algorithm, a multicellular tissue model was split into two components: one is the single cell model (ordinary differential equation) and the other is the diffusion term of the monodomain model (partial differential equation). Such a decoupling enabled realization of the GPU parallel algorithm. Furthermore, several optimization strategies were proposed based on the features of the virtual heart model, which enabled a 200-fold speedup as compared to a CPU implementation. In conclusion, an optimized GPU algorithm has been developed that provides an economic and powerful platform for 3D whole heart simulations. PMID:26581957
Parallel PAB3D: Experiences with a Prototype in MPI
NASA Technical Reports Server (NTRS)
Guerinoni, Fabio; Abdol-Hamid, Khaled S.; Pao, S. Paul
1998-01-01
PAB3D is a three-dimensional Navier Stokes solver that has gained acceptance in the research and industrial communities. It takes as computational domain, a set disjoint blocks covering the physical domain. This is the first report on the implementation of PAB3D using the Message Passing Interface (MPI), a standard for parallel processing. We discuss briefly the characteristics of tile code and define a prototype for testing. The principal data structure used for communication is derived from preprocessing "patching". We describe a simple interface (COMMSYS) for MPI communication, and some general techniques likely to be encountered when working on problems of this nature. Last, we identify levels of improvement from the current version and outline future work.
3D seismic imaging on massively parallel computers
Womble, D.E.; Ober, C.C.; Oldfield, R.
1997-02-01
The ability to image complex geologies such as salt domes in the Gulf of Mexico and thrusts in mountainous regions is a key to reducing the risk and cost associated with oil and gas exploration. Imaging these structures, however, is computationally expensive. Datasets can be terabytes in size, and the processing time required for the multiple iterations needed to produce a velocity model can take months, even with the massively parallel computers available today. Some algorithms, such as 3D, finite-difference, prestack, depth migration remain beyond the capacity of production seismic processing. Massively parallel processors (MPPs) and algorithms research are the tools that will enable this project to provide new seismic processing capabilities to the oil and gas industry. The goals of this work are to (1) develop finite-difference algorithms for 3D, prestack, depth migration; (2) develop efficient computational approaches for seismic imaging and for processing terabyte datasets on massively parallel computers; and (3) develop a modular, portable, seismic imaging code.
Shared Memory Parallelism for 3D Cartesian Discrete Ordinates Solver
NASA Astrophysics Data System (ADS)
Moustafa, Salli; Dutka-Malen, Ivan; Plagne, Laurent; Ponçot, Angélique; Ramet, Pierre
2014-06-01
This paper describes the design and the performance of DOMINO, a 3D Cartesian SN solver that implements two nested levels of parallelism (multicore+SIMD) on shared memory computation nodes. DOMINO is written in C++, a multi-paradigm programming language that enables the use of powerful and generic parallel programming tools such as Intel TBB and Eigen. These two libraries allow us to combine multi-thread parallelism with vector operations in an efficient and yet portable way. As a result, DOMINO can exploit the full power of modern multi-core processors and is able to tackle very large simulations, that usually require large HPC clusters, using a single computing node. For example, DOMINO solves a 3D full core PWR eigenvalue problem involving 26 energy groups, 288 angular directions (S16), 46 × 106 spatial cells and 1 × 1012 DoFs within 11 hours on a single 32-core SMP node. This represents a sustained performance of 235 GFlops and 40:74% of the SMP node peak performance for the DOMINO sweep implementation. The very high Flops/Watt ratio of DOMINO makes it a very interesting building block for a future many-nodes nuclear simulation tool.
3D finite-difference seismic migration with parallel computers
Ober, C.C.; Gjertsen, R.; Minkoff, S.; Womble, D.E.
1998-11-01
The ability to image complex geologies such as salt domes in the Gulf of Mexico and thrusts in mountainous regions is essential for reducing the risk associated with oil exploration. Imaging these structures, however, is computationally expensive as datasets can be terabytes in size. Traditional ray-tracing migration methods cannot handle complex velocity variations commonly found near such salt structures. Instead the authors use the full 3D acoustic wave equation, discretized via a finite difference algorithm. They reduce the cost of solving the apraxial wave equation by a number of numerical techniques including the method of fractional steps and pipelining the tridiagonal solves. The imaging code, Salvo, uses both frequency parallelism (generally 90% efficient) and spatial parallelism (65% efficient). Salvo has been tested on synthetic and real data and produces clear images of the subsurface even beneath complicated salt structures.
A parallel algorithm for 3D dislocation dynamics
NASA Astrophysics Data System (ADS)
Wang, Zhiqiang; Ghoniem, Nasr; Swaminarayan, Sriram; LeSar, Richard
2006-12-01
Dislocation dynamics (DD), a discrete dynamic simulation method in which dislocations are the fundamental entities, is a powerful tool for investigation of plasticity, deformation and fracture of materials at the micron length scale. However, severe computational difficulties arising from complex, long-range interactions between these curvilinear line defects limit the application of DD in the study of large-scale plastic deformation. We present here the development of a parallel algorithm for accelerated computer simulations of DD. By representing dislocations as a 3D set of dislocation particles, we show here that the problem of an interacting ensemble of dislocations can be converted to a problem of a particle ensemble, interacting with a long-range force field. A grid using binary space partitioning is constructed to keep track of node connectivity across domains. We demonstrate the computational efficiency of the parallel micro-plasticity code and discuss how O(N) methods map naturally onto the parallel data structure. Finally, we present results from applications of the parallel code to deformation in single crystal fcc metals.
Parallel 3D Mortar Element Method for Adaptive Nonconforming Meshes
NASA Technical Reports Server (NTRS)
Feng, Huiyu; Mavriplis, Catherine; VanderWijngaart, Rob; Biswas, Rupak
2004-01-01
High order methods are frequently used in computational simulation for their high accuracy. An efficient way to avoid unnecessary computation in smooth regions of the solution is to use adaptive meshes which employ fine grids only in areas where they are needed. Nonconforming spectral elements allow the grid to be flexibly adjusted to satisfy the computational accuracy requirements. The method is suitable for computational simulations of unsteady problems with very disparate length scales or unsteady moving features, such as heat transfer, fluid dynamics or flame combustion. In this work, we select the Mark Element Method (MEM) to handle the non-conforming interfaces between elements. A new technique is introduced to efficiently implement MEM in 3-D nonconforming meshes. By introducing an "intermediate mortar", the proposed method decomposes the projection between 3-D elements and mortars into two steps. In each step, projection matrices derived in 2-D are used. The two-step method avoids explicitly forming/deriving large projection matrices for 3-D meshes, and also helps to simplify the implementation. This new technique can be used for both h- and p-type adaptation. This method is applied to an unsteady 3-D moving heat source problem. With our new MEM implementation, mesh adaptation is able to efficiently refine the grid near the heat source and coarsen the grid once the heat source passes. The savings in computational work resulting from the dynamic mesh adaptation is demonstrated by the reduction of the the number of elements used and CPU time spent. MEM and mesh adaptation, respectively, bring irregularity and dynamics to the computer memory access pattern. Hence, they provide a good way to gauge the performance of computer systems when running scientific applications whose memory access patterns are irregular and unpredictable. We select a 3-D moving heat source problem as the Unstructured Adaptive (UA) grid benchmark, a new component of the NAS Parallel
Dissipation mechanism in 3D magnetic reconnection
Fujimoto, Keizo
2011-11-15
Dissipation processes responsible for fast magnetic reconnection in collisionless plasmas are investigated using 3D electromagnetic particle-in-cell simulations. The present study revisits the two simulation runs performed in the previous study (Fujimoto, Phys. Plasmas 16, 042103 (2009)); one with small system size in the current density direction, and the other with larger system size. In the case with small system size, the reconnection processes are almost the same as those in 2D reconnection, while in the other case a kink mode evolves along the current density and deforms the current sheet structure drastically. Although fast reconnection is achieved in both the cases, the dissipation mechanism is very different between them. In the case without kink mode, the electrons transit the electron diffusion region without thermalization, so that the magnetic dissipation is supported by the inertia resistivity alone. On the other hand, in the kinked current sheet, the electrons are not only accelerated in bulk, but they are also partly scattered and thermalized by the kink mode, which results in the anomalous resistivity in addition to the inertia resistivity. It is demonstrated that in 3D reconnection the thickness of the electron current sheet becomes larger than the local electron inertia length, consistent with the theoretical prediction in Fujimoto and Sydora (Phys. Plasmas 16, 112309 (2009)).
A 3D parallel model of Ganymede's exosphere
NASA Astrophysics Data System (ADS)
Leclercq, Ludivine; Turc, Lucile; François, Leblanc; Ronan, Modolo
2013-04-01
Ganymede is a unique object : it is the biggest moon of our solar system, and the only satellite which has its own intrinsic magnetic field. Its surface is covered by water ice and by regolith. Some previous observations suggest that below its surface may exist an ocean of liquid water. The atmosphere of the planet is poorly known but should be composed essentially of water, hydrogen and oxygen (Marconi et al., Icarus, 2007). These atmospheric particles mainly originate from the surface thanks to sublimation of water-ice and sputtering, a process driven by the magnetospheric Jovian particles impacting Ganymede surface and leading to ejection of atoms and molecules into Ganymede atmosphere. We developed a model of Ganymede's atmosphere based on a 3D Monte Carlo description of the fate of the ejected particles from the surface. This model has been parallelized allowing a much better statistical, spatial and temporal description of Ganymede's environment. This model includes the main sources of the neutral atmosphere and is able to calculate all its characteristics. It was successfully compared to the few known observations as well as to previous modeling. In this presentation, we will present the main characteristics of this model and what it tells us on Ganymede's atmosphere, in terms of spatial structure, composition, temporal variability and relations with both magnetosphere and surface.
Parallel ALLSPD-3D: Speeding Up Combustor Analysis Via Parallel Processing
NASA Technical Reports Server (NTRS)
Fricker, David M.
1997-01-01
The ALLSPD-3D Computational Fluid Dynamics code for reacting flow simulation was run on a set of benchmark test cases to determine its parallel efficiency. These test cases included non-reacting and reacting flow simulations with varying numbers of processors. Also, the tests explored the effects of scaling the simulation with the number of processors in addition to distributing a constant size problem over an increasing number of processors. The test cases were run on a cluster of IBM RS/6000 Model 590 workstations with ethernet and ATM networking plus a shared memory SGI Power Challenge L workstation. The results indicate that the network capabilities significantly influence the parallel efficiency, i.e., a shared memory machine is fastest and ATM networking provides acceptable performance. The limitations of ethernet greatly hamper the rapid calculation of flows using ALLSPD-3D.
Mechanical properties of 3D ceramic nanolattices
NASA Astrophysics Data System (ADS)
Meza, Lucas
Developments in advanced nanoscale fabrication techniques have allowed for the creation of 3-dimensional hierarchical structural meta-materials that can be designed with arbitrary geometry. These structures can be made on length scales spanning multiple orders of magnitude, from tens of nanometers to hundreds of microns. The smallest features are controllable on length scales where materials have been shown to exhibit size effects in their mechanical properties. Combining novel nanoscale mechanical properties with a 3-dimensional architecture enables the creation of new classes of materials with tunable and unprecedented mechanical properties. We present the fabrication and mechanical deformation of hollow tube alumina nanolattices that were fabricated using two-photon lithography direct laser writing (DLW), atomic layer deposition (ALD), and oxygen plasma etching. Nanolattices were designed in a number of different geometries including octet-truss, octahedron, and 3D Kagome. Additionally, a number of structural parameters were varied including tube wall thickness (t) , tube major axis (a) , and unit cell size (L) . The resulting nanolattices had a range of densities from ρ = 4 to 250 mg/cm3. Uniaxial compression and cyclic loading tests were performed on the nanolattices to obtain the yield strength and modulus. In these tests, a marked change in the deformation response was observed when the wall thickness was reduced below 20nm; thick-walled nanolattices (t>20nm) underwent catastrophic, brittle failure, which transitioned to a gradual, ductile-like deformation as wall thickness was reduced. Thick-walled nanolattices also exhibited no recovery after compression, while thin-walled structures demonstrated notable recovery, with some recovering by 98% after compression to 50% strain and by 80% when compressed to 90% strain. Across all geometries, unit cell sizes, and wall thicknesses, we found a consistent power law relation between strength and modulus with
Parallel adaptive mesh refinement within the PUMAA3D Project
NASA Technical Reports Server (NTRS)
Freitag, Lori; Jones, Mark; Plassmann, Paul
1995-01-01
To enable the solution of large-scale applications on distributed memory architectures, we are designing and implementing parallel algorithms for the fundamental tasks of unstructured mesh computation. In this paper, we discuss efficient algorithms developed for two of these tasks: parallel adaptive mesh refinement and mesh partitioning. The algorithms are discussed in the context of two-dimensional finite element solution on triangular meshes, but are suitable for use with a variety of element types and with h- or p-refinement. Results demonstrating the scalability and efficiency of the refinement algorithm and the quality of the mesh partitioning are presented for several test problems on the Intel DELTA.
Arbitrary and Parallel Nanofabrication of 3D Metal Structures with Polymer Brush Resists.
Chen, Chaojian; Xie, Zhuang; Wei, Xiaoling; Zheng, Zijian
2015-12-01
3D polymer brushes are reported for the first time as ideal resists for the alignment-free nanofabrication of complex 3D metal structures with sub-100 nm lateral resolution and sub-10 nm vertical resolution. Since 3D polymer brushes can be serially fabricated in parallel, this method is effective to generate arbitrary 3D metal structures over a large area at a high throughput. PMID:26439441
Parallel deterministic neutronics with AMR in 3D
Clouse, C.; Ferguson, J.; Hendrickson, C.
1997-12-31
AMTRAN, a three dimensional Sn neutronics code with adaptive mesh refinement (AMR) has been parallelized over spatial domains and energy groups and runs on the Meiko CS-2 with MPI message passing. Block refined AMR is used with linear finite element representations for the fluxes, which allows for a straight forward interpretation of fluxes at block interfaces with zoning differences. The load balancing algorithm assumes 8 spatial domains, which minimizes idle time among processors.
New 3D parallel SGILD modeling and inversion
Xie, G.; Li, J.; Majer, E.
1998-09-01
In this paper, a new parallel modeling and inversion algorithm using a Stochastic Global Integral and Local Differential equation (SGILD) is presented. The authors derived new acoustic integral equations and differential equation for statistical moments of the parameters and field. The new statistical moments integral equation on the boundary and local differential equations in domain will be used together to obtain mean wave field and its moments in the modeling. The new moments global Jacobian volume integral equation and the local Jacobian differential equations in domain will be used together to update the mean parameters and their moments in the inversion. A new parallel multiple hierarchy substructure direct algorithm or direct-iteration hybrid algorithm will be used to solve the sparse matrices and one smaller full matrix from domain to the boundary, in parallel. The SGILD modeling and imaging algorithm has many advantages over the conventional imaging approaches. The SGILD algorithm can be used for the stochastic acoustic, electromagnetic, and flow modeling and inversion, and are important for the prediction of oil, gas, coal, and geothermal energy reservoirs in geophysical exploration.
FIBROBLAST MECHANICS IN 3D COLLAGEN MATRICES
Rhee, Sangmyung; Grinnell, Frederick
2007-01-01
Connective tissues provide mechanical support and frameworks for the other tissues of the body. Type 1 collagen is the major protein component of ordinary connective tissue, and fibroblasts are the cell type primarily responsible for its biosynthesis and remodeling. Research on fibroblasts interacting with collagen matrices explores all four quadrants of cell mechanics: pro-migratory vs. pro-contractile growth factor environments on one axis; high tension vs. low tension cell-matrix interactions on the other. The dendritic fibroblast – probably equivalent to the resting tissue fibroblast – can be observed only in the low tension quadrant and generally has not been appreciated from research on cells incubated with planar culture surfaces. Fibroblasts in the low tension quadrant require microtubules for formation of dendritic extensions, whereas fibroblasts in the high tension quadrant require microtubules for polarization but not for spreading. Ruffling of dendritic extensions rather than their overall protrusion or retraction provides the mechanism for remodeling of floating collagen matrices, and floating matrix remodeling likely reflects a model of tissue mechanical homeostasis. PMID:17825456
Time efficient 3-D electromagnetic modeling on massively parallel computers
Alumbaugh, D.L.; Newman, G.A.
1995-08-01
A numerical modeling algorithm has been developed to simulate the electromagnetic response of a three dimensional earth to a dipole source for frequencies ranging from 100 to 100MHz. The numerical problem is formulated in terms of a frequency domain--modified vector Helmholtz equation for the scattered electric fields. The resulting differential equation is approximated using a staggered finite difference grid which results in a linear system of equations for which the matrix is sparse and complex symmetric. The system of equations is solved using a preconditioned quasi-minimum-residual method. Dirichlet boundary conditions are employed at the edges of the mesh by setting the tangential electric fields equal to zero. At frequencies less than 1MHz, normal grid stretching is employed to mitigate unwanted reflections off the grid boundaries. For frequencies greater than this, absorbing boundary conditions must be employed by making the stretching parameters of the modified vector Helmholtz equation complex which introduces loss at the boundaries. To allow for faster calculation of realistic models, the original serial version of the code has been modified to run on a massively parallel architecture. This modification involves three distinct tasks; (1) mapping the finite difference stencil to a processor stencil which allows for the necessary information to be exchanged between processors that contain adjacent nodes in the model, (2) determining the most efficient method to input the model which is accomplished by dividing the input into ``global`` and ``local`` data and then reading the two sets in differently, and (3) deciding how to output the data which is an inherently nonparallel process.
Parallel processing for efficient 3D slope stability modelling
NASA Astrophysics Data System (ADS)
Marchesini, Ivan; Mergili, Martin; Alvioli, Massimiliano; Metz, Markus; Schneider-Muntau, Barbara; Rossi, Mauro; Guzzetti, Fausto
2014-05-01
We test the performance of the GIS-based, three-dimensional slope stability model r.slope.stability. The model was developed as a C- and python-based raster module of the GRASS GIS software. It considers the three-dimensional geometry of the sliding surface, adopting a modification of the model proposed by Hovland (1977), and revised and extended by Xie and co-workers (2006). Given a terrain elevation map and a set of relevant thematic layers, the model evaluates the stability of slopes for a large number of randomly selected potential slip surfaces, ellipsoidal or truncated in shape. Any single raster cell may be intersected by multiple sliding surfaces, each associated with a value of the factor of safety, FS. For each pixel, the minimum value of FS and the depth of the associated slip surface are stored. This information is used to obtain a spatial overview of the potentially unstable slopes in the study area. We test the model in the Collazzone area, Umbria, central Italy, an area known to be susceptible to landslides of different type and size. Availability of a comprehensive and detailed landslide inventory map allowed for a critical evaluation of the model results. The r.slope.stability code automatically splits the study area into a defined number of tiles, with proper overlap in order to provide the same statistical significance for the entire study area. The tiles are then processed in parallel by a given number of processors, exploiting a multi-purpose computing environment at CNR IRPI, Perugia. The map of the FS is obtained collecting the individual results, taking the minimum values on the overlapping cells. This procedure significantly reduces the processing time. We show how the gain in terms of processing time depends on the tile dimensions and on the number of cores.
Prediction of parallel NIKE3D performance on the KSR1 system
Su, P.S.; Zacharia, T.; Fulton, R.E.
1995-05-01
Finite element method is one of the bases for numerical solutions to engineering problems. Complex engineering problems using finite element analysis typically imply excessively large computational time. Parallel supercomputers have the potential for significantly increasing calculation speeds in order to meet these computational requirements. This paper predicts parallel NIKE3D performance on the Kendall Square Research (KSR1) system. The first part of the prediction is based on the implementation of parallel Cholesky (U{sup T}DU) matrix decomposition algorithm through actual computations on the KSRI multiprocessor system, with 64 processors, at Oak Ridge National Laboratory. The other predictions are based on actual computations for parallel element matrix generation, parallel global stiffness matrix assembly, and parallel forward/backward substitution on the BBN TC2000 multiprocessor system at Lawrence Livermore National Laboratory. The preliminary results indicate that parallel NIKE3D performance can be attractive under local/shared-memory multiprocessor system environments.
A parallel multigrid-based preconditioner for the 3D heterogeneous high-frequency Helmholtz equation
Riyanti, C.D. . E-mail: C.D.Riyanti@tudelft.nl; Kononov, A.; Erlangga, Y.A.; Vuik, C.; Oosterlee, C.W.; Plessix, R.-E.; Mulder, W.A.
2007-05-20
We investigate the parallel performance of an iterative solver for 3D heterogeneous Helmholtz problems related to applications in seismic wave propagation. For large 3D problems, the computation is no longer feasible on a single processor, and the memory requirements increase rapidly. Therefore, parallelization of the solver is needed. We employ a complex shifted-Laplace preconditioner combined with the Bi-CGSTAB iterative method and use a multigrid method to approximate the inverse of the resulting preconditioning operator. A 3D multigrid method with 2D semi-coarsening is employed. We show numerical results for large problems arising in geophysical applications.
Design of 3D-Printed Titanium Compliant Mechanisms
NASA Technical Reports Server (NTRS)
Merriam, Ezekiel G.; Jones, Jonathan E.; Howell, Larry L.
2014-01-01
This paper describes 3D-printed titanium compliant mechanisms for aerospace applications. It is meant as a primer to help engineers design compliant, multi-axis, printed parts that exhibit high performance. Topics covered include brief introductions to both compliant mechanism design and 3D printing in titanium, material and geometry considerations for 3D printing, modeling techniques, and case studies of both successful and unsuccessful part geometries. Key findings include recommended flexure geometries, minimum thicknesses, and general design guidelines for compliant printed parts that may not be obvious to the first time designer.
Implementation of parallel matrix decomposition for NIKE3D on the KSR1 system
Su, Philip S.; Fulton, R.E.; Zacharia, T.
1995-06-01
New massively parallel computer architecture has revolutionized the design of computer algorithms and promises to have significant influence on algorithms for engineering computations. Realistic engineering problems using finite element analysis typically imply excessively large computational requirements. Parallel supercomputers that have the potential for significantly increasing calculation speeds can meet these computational requirements. This report explores the potential for the parallel Cholesky (U{sup T}DU) matrix decomposition algorithm on NIKE3D through actual computations. The examples of two- and three-dimensional nonlinear dynamic finite element problems are presented on the Kendall Square Research (KSR1) multiprocessor system, with 64 processors, at Oak Ridge National Laboratory. The numerical results indicate that the parallel Cholesky (U{sup T}DU) matrix decomposition algorithm is attractive for NIKE3D under multi-processor system environments.
Parallel robot for micro assembly with integrated innovative optical 3D-sensor
NASA Astrophysics Data System (ADS)
Hesselbach, Juergen; Ispas, Diana; Pokar, Gero; Soetebier, Sven; Tutsch, Rainer
2002-10-01
Recent advances in the fields of MEMS and MOEMS often require precise assembly of very small parts with an accuracy of a few microns. In order to meet this demand, a new approach using a robot based on parallel mechanisms in combination with a novel 3D-vision system has been chosen. The planar parallel robot structure with 2 DOF provides a high resolution in the XY-plane. It carries two additional serial axes for linear and rotational movement in/about z direction. In order to achieve high precision as well as good dynamic capabilities, the drive concept for the parallel (main) axes incorporates air bearings in combination with a linear electric servo motors. High accuracy position feedback is provided by optical encoders with a resolution of 0.1 μm. To allow for visualization and visual control of assembly processes, a camera module fits into the hollow tool head. It consists of a miniature CCD camera and a light source. In addition a modular gripper support is integrated into the tool head. To increase the accuracy a control loop based on an optoelectronic sensor will be implemented. As a result of an in-depth analysis of different approaches a photogrammetric system using one single camera and special beam-splitting optics was chosen. A pattern of elliptical marks is applied to the surfaces of workpiece and gripper. Using a model-based recognition algorithm the image processing software identifies the gripper and the workpiece and determines their relative position. A deviation vector is calculated and fed into the robot control to guide the gripper.
NASA Astrophysics Data System (ADS)
Popov, Anton; Kaus, Boris
2015-04-01
This software project aims at bringing the 3D lithospheric deformation modeling to a qualitatively different level. Our code LaMEM (Lithosphere and Mantle Evolution Model) is based on the following building blocks: * Massively-parallel data-distributed implementation model based on PETSc library * Light, stable and accurate staggered-grid finite difference spatial discretization * Marker-in-Cell pedictor-corector time discretization with Runge-Kutta 4-th order * Elastic stress rotation algorithm based on the time integration of the vorticity pseudo-vector * Staircase-type internal free surface boundary condition without artificial viscosity contrast * Geodynamically relevant visco-elasto-plastic rheology * Global velocity-pressure-temperature Newton-Raphson nonlinear solver * Local nonlinear solver based on FZERO algorithm * Coupled velocity-pressure geometric multigrid preconditioner with Galerkin coarsening Staggered grid finite difference, being inherently Eulerian and rather complicated discretization method, provides no natural treatment of free surface boundary condition. The solution based on the quasi-viscous sticky-air phase introduces significant viscosity contrasts and spoils the convergence of the iterative solvers. In LaMEM we are currently implementing an approximate stair-case type of the free surface boundary condition which excludes the empty cells and restores the solver convergence. Because of the mutual dependence of the stress and strain-rate tensor components, and their different spatial locations in the grid, there is no straightforward way of implementing the nonlinear rheology. In LaMEM we have developed and implemented an efficient interpolation scheme for the second invariant of the strain-rate tensor, that solves this problem. Scalable efficient linear solvers are the key components of the successful nonlinear problem solution. In LaMEM we have a range of PETSc-based preconditioning techniques that either employ a block factorization of
Li, Yong Gang; Yang, Yang; Short, Michael P.; Ding, Ze Jun; Zeng, Zhi; Li, Ju
2015-01-01
SRIM-like codes have limitations in describing general 3D geometries, for modeling radiation displacements and damage in nanostructured materials. A universal, computationally efficient and massively parallel 3D Monte Carlo code, IM3D, has been developed with excellent parallel scaling performance. IM3D is based on fast indexing of scattering integrals and the SRIM stopping power database, and allows the user a choice of Constructive Solid Geometry (CSG) or Finite Element Triangle Mesh (FETM) method for constructing 3D shapes and microstructures. For 2D films and multilayers, IM3D perfectly reproduces SRIM results, and can be ∼102 times faster in serial execution and > 104 times faster using parallel computation. For 3D problems, it provides a fast approach for analyzing the spatial distributions of primary displacements and defect generation under ion irradiation. Herein we also provide a detailed discussion of our open-source collision cascade physics engine, revealing the true meaning and limitations of the “Quick Kinchin-Pease” and “Full Cascades” options. The issues of femtosecond to picosecond timescales in defining displacement versus damage, the limitation of the displacements per atom (DPA) unit in quantifying radiation damage (such as inadequacy in quantifying degree of chemical mixing), are discussed. PMID:26658477
NASA Astrophysics Data System (ADS)
Li, Yong Gang; Yang, Yang; Short, Michael P.; Ding, Ze Jun; Zeng, Zhi; Li, Ju
2015-12-01
SRIM-like codes have limitations in describing general 3D geometries, for modeling radiation displacements and damage in nanostructured materials. A universal, computationally efficient and massively parallel 3D Monte Carlo code, IM3D, has been developed with excellent parallel scaling performance. IM3D is based on fast indexing of scattering integrals and the SRIM stopping power database, and allows the user a choice of Constructive Solid Geometry (CSG) or Finite Element Triangle Mesh (FETM) method for constructing 3D shapes and microstructures. For 2D films and multilayers, IM3D perfectly reproduces SRIM results, and can be ∼102 times faster in serial execution and > 104 times faster using parallel computation. For 3D problems, it provides a fast approach for analyzing the spatial distributions of primary displacements and defect generation under ion irradiation. Herein we also provide a detailed discussion of our open-source collision cascade physics engine, revealing the true meaning and limitations of the “Quick Kinchin-Pease” and “Full Cascades” options. The issues of femtosecond to picosecond timescales in defining displacement versus damage, the limitation of the displacements per atom (DPA) unit in quantifying radiation damage (such as inadequacy in quantifying degree of chemical mixing), are discussed.
Gust Acoustics Computation with a Space-Time CE/SE Parallel 3D Solver
NASA Technical Reports Server (NTRS)
Wang, X. Y.; Himansu, A.; Chang, S. C.; Jorgenson, P. C. E.; Reddy, D. R. (Technical Monitor)
2002-01-01
The benchmark Problem 2 in Category 3 of the Third Computational Aero-Acoustics (CAA) Workshop is solved using the space-time conservation element and solution element (CE/SE) method. This problem concerns the unsteady response of an isolated finite-span swept flat-plate airfoil bounded by two parallel walls to an incident gust. The acoustic field generated by the interaction of the gust with the flat-plate airfoil is computed by solving the 3D (three-dimensional) Euler equations in the time domain using a parallel version of a 3D CE/SE solver. The effect of the gust orientation on the far-field directivity is studied. Numerical solutions are presented and compared with analytical solutions, showing a reasonable agreement.
An improved parallel SPH approach to solve 3D transient generalized Newtonian free surface flows
NASA Astrophysics Data System (ADS)
Ren, Jinlian; Jiang, Tao; Lu, Weigang; Li, Gang
2016-08-01
In this paper, a corrected parallel smoothed particle hydrodynamics (C-SPH) method is proposed to simulate the 3D generalized Newtonian free surface flows with low Reynolds number, especially the 3D viscous jets buckling problems are investigated. The proposed C-SPH method is achieved by coupling an improved SPH method based on the incompressible condition with the traditional SPH (TSPH), that is, the improved SPH with diffusive term and first-order Kernel gradient correction scheme is used in the interior of the fluid domain, and the TSPH is used near the free surface. Thus the C-SPH method possesses the advantages of two methods. Meanwhile, an effective and convenient boundary treatment is presented to deal with 3D multiple-boundary problem, and the MPI parallelization technique with a dynamic cells neighbor particle searching method is considered to improve the computational efficiency. The validity and the merits of the C-SPH are first verified by solving several benchmarks and compared with other results. Then the viscous jet folding/coiling based on the Cross model is simulated by the C-SPH method and compared with other experimental or numerical results. Specially, the influences of macroscopic parameters on the flow are discussed. All the numerical results agree well with available data, and show that the C-SPH method has higher accuracy and better stability for solving 3D moving free surface flows over other particle methods.
Massively parallel regularized 3D inversion of potential fields on CPUs and GPUs
NASA Astrophysics Data System (ADS)
Čuma, Martin; Zhdanov, Michael S.
2014-01-01
We have recently introduced a massively parallel regularized 3D inversion of potential fields data. This program takes as an input gravity or magnetic vector, tensor and Total Magnetic Intensity (TMI) measurements and produces 3D volume of density, susceptibility, or three dimensional magnetization vector, the latest also including magnetic remanence information. The code uses combined MPI and OpenMP approach that maps well onto current multiprocessor multicore clusters and exhibits nearly linear strong and weak parallel scaling. It has been used to invert regional to continental size data sets with up to billion cells of the 3D Earth's volume on large clusters for interpretation of large airborne gravity and magnetics surveys. In this paper we explain the features that made this massive parallelization feasible and extend the code to add GPU support in the form of the OpenACC directives. This implementation resulted in up to a 22x speedup as compared to the scalar multithreaded implementation on a 12 core Intel CPU based computer node. Furthermore, we also introduce a mixed single-double precision approach, which allows us to perform most of the calculation at a single floating point number precision while keeping the result as precise as if the double precision had been used. This approach provides an additional 40% speedup on the GPUs, as compared to the pure double precision implementation. It also has about half of the memory footprint of the fully double precision version.
Spatial parallelism of a 3D finite difference, velocity-stress elastic wave propagation code
Minkoff, S.E.
1999-12-01
Finite difference methods for solving the wave equation more accurately capture the physics of waves propagating through the earth than asymptotic solution methods. Unfortunately, finite difference simulations for 3D elastic wave propagation are expensive. The authors model waves in a 3D isotropic elastic earth. The wave equation solution consists of three velocity components and six stresses. The partial derivatives are discretized using 2nd-order in time and 4th-order in space staggered finite difference operators. Staggered schemes allow one to obtain additional accuracy (via centered finite differences) without requiring additional storage. The serial code is most unique in its ability to model a number of different types of seismic sources. The parallel implementation uses the MPI library, thus allowing for portability between platforms. Spatial parallelism provides a highly efficient strategy for parallelizing finite difference simulations. In this implementation, one can decompose the global problem domain into one-, two-, and three-dimensional processor decompositions with 3D decompositions generally producing the best parallel speedup. Because I/O is handled largely outside of the time-step loop (the most expensive part of the simulation) the authors have opted for straight-forward broadcast and reduce operations to handle I/O. The majority of the communication in the code consists of passing subdomain face information to neighboring processors for use as ghost cells. When this communication is balanced against computation by allocating subdomains of reasonable size, they observe excellent scaled speedup. Allocating subdomains of size 25 x 25 x 25 on each node, they achieve efficiencies of 94% on 128 processors. Numerical examples for both a layered earth model and a homogeneous medium with a high-velocity blocky inclusion illustrate the accuracy of the parallel code.
Spatial Parallelism of a 3D Finite Difference, Velocity-Stress Elastic Wave Propagation Code
MINKOFF,SUSAN E.
1999-12-09
Finite difference methods for solving the wave equation more accurately capture the physics of waves propagating through the earth than asymptotic solution methods. Unfortunately. finite difference simulations for 3D elastic wave propagation are expensive. We model waves in a 3D isotropic elastic earth. The wave equation solution consists of three velocity components and six stresses. The partial derivatives are discretized using 2nd-order in time and 4th-order in space staggered finite difference operators. Staggered schemes allow one to obtain additional accuracy (via centered finite differences) without requiring additional storage. The serial code is most unique in its ability to model a number of different types of seismic sources. The parallel implementation uses the MP1 library, thus allowing for portability between platforms. Spatial parallelism provides a highly efficient strategy for parallelizing finite difference simulations. In this implementation, one can decompose the global problem domain into one-, two-, and three-dimensional processor decompositions with 3D decompositions generally producing the best parallel speed up. Because i/o is handled largely outside of the time-step loop (the most expensive part of the simulation) we have opted for straight-forward broadcast and reduce operations to handle i/o. The majority of the communication in the code consists of passing subdomain face information to neighboring processors for use as ''ghost cells''. When this communication is balanced against computation by allocating subdomains of reasonable size, we observe excellent scaled speed up. Allocating subdomains of size 25 x 25 x 25 on each node, we achieve efficiencies of 94% on 128 processors. Numerical examples for both a layered earth model and a homogeneous medium with a high-velocity blocky inclusion illustrate the accuracy of the parallel code.
Parallel computation of 3-D Navier-Stokes flowfields for supersonic vehicles
NASA Technical Reports Server (NTRS)
Ryan, James S.; Weeratunga, Sisira
1993-01-01
Multidisciplinary design optimization of aircraft will require unprecedented capabilities of both analysis software and computer hardware. The speed and accuracy of the analysis will depend heavily on the computational fluid dynamics (CFD) module which is used. A new CFD module has been developed to combine the robust accuracy of conventional codes with the ability to run on parallel architectures. This is achieved by parallelizing the ARC3D algorithm, a central-differenced Navier-Stokes method, on the Intel iPSC/860. The computed solutions are identical to those from conventional machines. Computational speed on 64 processors is comparable to the rate on one Cray Y-MP processor and will increase as new generations of parallel computers become available.
Description of a parallel, 3D, finite element, hydrodynamics-diffusion code
Milovich, J L; Prasad, M K; Shestakov, A I
1999-04-11
We describe a parallel, 3D, unstructured grid finite element, hydrodynamic diffusion code for inertial confinement fusion (ICF) applications and the ancillary software used to run it. The code system is divided into two entities, a controller and a stand-alone physics code. The code system may reside on different computers; the controller on the user's workstation and the physics code on a supercomputer. The physics code is composed of separate hydrodynamic, equation-of-state, laser energy deposition, heat conduction, and radiation transport packages and is parallelized for distributed memory architectures. For parallelization, a SPMD model is adopted; the domain is decomposed into a disjoint collection of subdomains, one per processing element (PE). The PEs communicate using MPI. The code is used to simulate the hydrodynamic implosion of a spherical bubble.
Kolotilina, L.; Nikishin, A.; Yeremin, A.
1994-12-31
The solution of large systems of linear equations is a crucial bottleneck when performing 3D finite element analysis of structures. Also, in many cases the reliability and robustness of iterative solution strategies, and their efficiency when exploiting hardware resources, fully determine the scope of industrial applications which can be solved on a particular computer platform. This is especially true for modern vector/parallel supercomputers with large vector length and for modern massively parallel supercomputers. Preconditioned iterative methods have been successfully applied to industrial class finite element analysis of structures. The construction and application of high quality preconditioners constitutes a high percentage of the total solution time. Parallel implementation of high quality preconditioners on such architectures is a formidable challenge. Two common types of existing preconditioners are the implicit preconditioners and the explicit preconditioners. The implicit preconditioners (e.g. incomplete factorizations of several types) are generally high quality but require solution of lower and upper triangular systems of equations per iteration which are difficult to parallelize without deteriorating the convergence rate. The explicit type of preconditionings (e.g. polynomial preconditioners or Jacobi-like preconditioners) require sparse matrix-vector multiplications and can be parallelized but their preconditioning qualities are less than desirable. The authors present results of numerical experiments with Factorized Sparse Approximate Inverses (FSAI) for symmetric positive definite linear systems. These are high quality preconditioners that possess a large resource of parallelism by construction without increasing the serial complexity.
Advanced quadratures and periodic boundary conditions in parallel 3D S{sub n} transport
Manalo, K.; Yi, C.; Huang, M.; Sjoden, G.
2013-07-01
Significant updates in numerical quadratures have warranted investigation with 3D Sn discrete ordinates transport. We show new applications of quadrature departing from level symmetric (S{sub 2}o). investigating 3 recently developed quadratures: Even-Odd (EO), Linear-Discontinuous Finite Element - Surface Area (LDFE-SA), and the non-symmetric Icosahedral Quadrature (IC). We discuss implementation changes to 3D Sn codes (applied to Hybrid MOC-Sn TITAN and 3D parallel PENTRAN) that can be performed to accommodate Icosahedral Quadrature, as this quadrature is not 90-degree rotation invariant. In particular, as demonstrated using PENTRAN, the properties of Icosahedral Quadrature are suitable for trivial application using periodic BCs versus that of reflective BCs. In addition to implementing periodic BCs for 3D Sn PENTRAN, we implemented a technique termed 'angular re-sweep' which properly conditions periodic BCs for outer eigenvalue iterative loop convergence. As demonstrated by two simple transport problems (3-group fixed source and 3-group reflected/periodic eigenvalue pin cell), we remark that all of the quadratures we investigated are generally superior to level symmetric quadrature, with Icosahedral Quadrature performing the most efficiently for problems tested. (authors)
Comparison of Parallel MRI Reconstruction Methods for Accelerated 3D Fast Spin-Echo Imaging
Xiao, Zhikui; Hoge, W. Scott; Mulkern, R.V.; Zhao, Lei; Hu, Guangshu; Kyriakos, Walid E.
2014-01-01
Parallel MRI (pMRI) achieves imaging acceleration by partially substituting gradient-encoding steps with spatial information contained in the component coils of the acquisition array. Variable-density subsampling in pMRI was previously shown to yield improved two-dimensional (2D) imaging in comparison to uniform subsampling, but has yet to be used routinely in clinical practice. In an effort to reduce acquisition time for 3D fast spin-echo (3D-FSE) sequences, this work explores a specific nonuniform sampling scheme for 3D imaging, subsampling along two phase-encoding (PE) directions on a rectilinear grid. We use two reconstruction methods—2D-GRAPPA-Operator and 2D-SPACE RIP—and present a comparison between them. We show that high-quality images can be reconstructed using both techniques. To evaluate the proposed sampling method and reconstruction schemes, results via simulation, phantom study, and in vivo 3D human data are shown. We find that fewer artifacts can be seen in the 2D-SPACE RIP reconstructions than in 2D-GRAPPA-Operator reconstructions, with comparable reconstruction times. PMID:18727083
Parallel Imaging of 3D Surface Profile with Space-Division Multiplexing
Lee, Hyung Seok; Cho, Soon-Woo; Kim, Gyeong Hun; Jeong, Myung Yung; Won, Young Jae; Kim, Chang-Seok
2016-01-01
We have developed a modified optical frequency domain imaging (OFDI) system that performs parallel imaging of three-dimensional (3D) surface profiles by using the space division multiplexing (SDM) method with dual-area swept sourced beams. We have also demonstrated that 3D surface information for two different areas could be well obtained in a same time with only one camera by our method. In this study, double field of views (FOVs) of 11.16 mm × 5.92 mm were achieved within 0.5 s. Height range for each FOV was 460 µm and axial and transverse resolutions were 3.6 and 5.52 µm, respectively. PMID:26805840
NASA Astrophysics Data System (ADS)
Chang, Yau-Zen; Hou, Jung-Fu; Tsao, Yi Hsiang; Lee, Shih-Tseng
2011-09-01
This paper proposes a scheme for finding the correspondence between uniformly spaced locations on the images of human face captured from different viewpoints at the same instant. The correspondence is dedicated for 3D reconstruction to be used in the registration procedure for neurosurgery where the exposure to projectors must be seriously restricted. The approach utilizes structured light to enhance patterns on the images and is initialized with the scale-invariant feature transform (SIFT). Successive locations are found according to spatial order using a parallel version of the particle swarm optimization algorithm. Furthermore, false locations are singled out for correction by searching for outliers from fitted curves. Case studies show that the scheme is able to correctly generate 456 evenly spaced 3D coordinate points in 23 seconds from a single shot of projected human face using a PC with 2.66 GHz Intel Q9400 CPU and 4GB RAM.
A Parallelized 3D Particle-In-Cell Method With Magnetostatic Field Solver And Its Applications
NASA Astrophysics Data System (ADS)
Hsu, Kuo-Hsien; Chen, Yen-Sen; Wu, Men-Zan Bill; Wu, Jong-Shinn
2008-10-01
A parallelized 3D self-consistent electrostatic particle-in-cell finite element (PIC-FEM) code using an unstructured tetrahedral mesh was developed. For simulating some applications with external permanent magnet set, the distribution of the magnetostatic field usually also need to be considered and determined accurately. In this paper, we will firstly present the development of a 3D magnetostatic field solver with an unstructured mesh for the flexibility of modeling objects with complex geometry. The vector Poisson equation for magnetostatic field is formulated using the Galerkin nodal finite element method and the resulting matrix is solved by parallel conjugate gradient method. A parallel adaptive mesh refinement module is coupled to this solver for better resolution. Completed solver is then verified by simulating a permanent magnet array with results comparable to previous experimental observations and simulations. By taking the advantage of the same unstructured grid format of this solver, the developed PIC-FEM code could directly and easily read the magnetostatic field for particle simulation. In the upcoming conference, magnetron is simulated and presented for demonstrating the capability of this code.
A 3D parallel simulator for crystal growth and solidification in complex alloy systems
NASA Astrophysics Data System (ADS)
Nestler, Britta
2005-02-01
A 3D parallel simulator is developed to numerically solve the evolution equations of a new non-isothermal phase-field model for crystal growth and solidification in complex alloy systems. The new model and the simulator are capable to simultaneously describe the diffusion processes of multiple components, the phase transitions between multiple phases and the development of the temperature field. Weak and facetted formulations of both, surface energy and kinetic anisotropies are incorporated in the phase-field model. Multicomponent bulk diffusion effects including interdiffusion coefficients as well as diffusion in the interfacial region of phase or grain boundaries are considered. We introduce our parallel simulator that is based on a finite difference discretization including effective adaptive strategies and multigrid methods to reduce computation time and memory usage. The parallelization is realized for distributed as well as shared memory computer architectures using MPI libraries and OpenMP concepts. Applying the new computer model, we present a variety of simulated crystal structures such as dendrites, grains, binary and ternary eutectics in 2D and 3D. The influence of anisotropy on the microstructure evolution shows the formation of facets in preferred crystallographic directions. Phase transformations and solidification processes in a real multi-component alloy can be described by incorporating the physical data (e.g. surface tensions, kinetic coefficients, specific heat, heat and mass diffusion coefficients) and the specific phase diagram (in particular latent heats and melting temperatures) into the diffuse interface model via the free energies.
Parallel graph search: application to intraretinal layer segmentation of 3D macular OCT scans
NASA Astrophysics Data System (ADS)
Lee, Kyungmoo; Abràmoff, Michael D.; Garvin, Mona K.; Sonka, Milan
2012-02-01
Image segmentation is of paramount importance for quantitative analysis of medical image data. Recently, a 3-D graph search method which can detect globally optimal interacting surfaces with respect to the cost function of volumetric images has been introduced, and its utility demonstrated in several application areas. Although the method provides excellent segmentation accuracy, its limitation is a slow processing speed when many surfaces are simultaneously segmented in large volumetric datasets. Here, we propose a novel method of parallel graph search, which overcomes the limitation and allows the quick detection of multiple surfaces. To demonstrate the obtained performance with respect to segmentation accuracy and processing speedup, the new approach was applied to retinal optical coherence tomography (OCT) image data and compared with the performance of the former non-parallel method. Our parallel graph search methods for single and double surface detection are approximately 267 and 181 times faster than the original graph search approach in 5 macular OCT volumes (200 x 5 x 1024 voxels) acquired from the right eyes of 5 normal subjects. The resulting segmentation differences were small as demonstrated by the mean unsigned differences between the non-parallel and parallel methods of 0.0 +/- 0.0 voxels (0.0 +/- 0.0 μm) and 0.27 +/- 0.34 voxels (0.53 +/- 0.66 μm) for the single- and dual-surface approaches, respectively.
NASA Astrophysics Data System (ADS)
Jung, Jaewoon; Kobayashi, Chigusa; Imamura, Toshiyuki; Sugita, Yuji
2016-03-01
Three-dimensional Fast Fourier Transform (3D FFT) plays an important role in a wide variety of computer simulations and data analyses, including molecular dynamics (MD) simulations. In this study, we develop hybrid (MPI+OpenMP) parallelization schemes of 3D FFT based on two new volumetric decompositions, mainly for the particle mesh Ewald (PME) calculation in MD simulations. In one scheme, (1d_Alltoall), five all-to-all communications in one dimension are carried out, and in the other, (2d_Alltoall), one two-dimensional all-to-all communication is combined with two all-to-all communications in one dimension. 2d_Alltoall is similar to the conventional volumetric decomposition scheme. We performed benchmark tests of 3D FFT for the systems with different grid sizes using a large number of processors on the K computer in RIKEN AICS. The two schemes show comparable performances, and are better than existing 3D FFTs. The performances of 1d_Alltoall and 2d_Alltoall depend on the supercomputer network system and number of processors in each dimension. There is enough leeway for users to optimize performance for their conditions. In the PME method, short-range real-space interactions as well as long-range reciprocal-space interactions are calculated. Our volumetric decomposition schemes are particularly useful when used in conjunction with the recently developed midpoint cell method for short-range interactions, due to the same decompositions of real and reciprocal spaces. The 1d_Alltoall scheme of 3D FFT takes 4.7 ms to simulate one MD cycle for a virus system containing more than 1 million atoms using 32,768 cores on the K computer.
Nguyen, B.T.; Hutchinson, S.A.
1995-07-01
The upwind leapfrog scheme for electromagnetic scattering is briefly described. Its application to the 3D Maxwell`s time domain equations is shown in detail. The scheme`s use of upwind characteristic variables and a narrow stencil result in a smaller demand in communication overhead, making it ideal for implementation on distributed memory parallel computers. The algorithm`s implementation on two message passing computers, a 1024-processor nCUBE 2 and a 1840-processor Intel Paragon, is described. Performance evaluation demonstrates that the scheme performs well with both good scaling qualities and high efficiencies on these machines.
Parallel goal-oriented adaptive finite element modeling for 3D electromagnetic exploration
NASA Astrophysics Data System (ADS)
Zhang, Y.; Key, K.; Ovall, J.; Holst, M.
2014-12-01
We present a parallel goal-oriented adaptive finite element method for accurate and efficient electromagnetic (EM) modeling of complex 3D structures. An unstructured tetrahedral mesh allows this approach to accommodate arbitrarily complex 3D conductivity variations and a priori known boundaries. The total electric field is approximated by the lowest order linear curl-conforming shape functions and the discretized finite element equations are solved by a sparse LU factorization. Accuracy of the finite element solution is achieved through adaptive mesh refinement that is performed iteratively until the solution converges to the desired accuracy tolerance. Refinement is guided by a goal-oriented error estimator that uses a dual-weighted residual method to optimize the mesh for accurate EM responses at the locations of the EM receivers. As a result, the mesh refinement is highly efficient since it only targets the elements where the inaccuracy of the solution corrupts the response at the possibly distant locations of the EM receivers. We compare the accuracy and efficiency of two approaches for estimating the primary residual error required at the core of this method: one uses local element and inter-element residuals and the other relies on solving a global residual system using a hierarchical basis. For computational efficiency our method follows the Bank-Holst algorithm for parallelization, where solutions are computed in subdomains of the original model. To resolve the load-balancing problem, this approach applies a spectral bisection method to divide the entire model into subdomains that have approximately equal error and the same number of receivers. The finite element solutions are then computed in parallel with each subdomain carrying out goal-oriented adaptive mesh refinement independently. We validate the newly developed algorithm by comparison with controlled-source EM solutions for 1D layered models and with 2D results from our earlier 2D goal oriented
PARALLEL 3-D SPACE CHARGE CALCULATIONS IN THE UNIFIED ACCELERATOR LIBRARY.
D'IMPERIO, N.L.; LUCCIO, A.U.; MALITSKY, N.
2006-06-26
The paper presents the integration of the SIMBAD space charge module in the UAL framework. SIMBAD is a Particle-in-Cell (PIC) code. Its 3-D Parallel approach features an optimized load balancing scheme based on a genetic algorithm. The UAL framework enhances the SIMBAD standalone version with the interactive ROOT-based analysis environment and an open catalog of accelerator algorithms. The composite package addresses complex high intensity beam dynamics and has been developed as part of the FAIR SIS 100 project.
NASA Technical Reports Server (NTRS)
Luke, Edward Allen
1993-01-01
Two algorithms capable of computing a transonic 3-D inviscid flow field about rotating machines are considered for parallel implementation. During the study of these algorithms, a significant new method of measuring the performance of parallel algorithms is developed. The theory that supports this new method creates an empirical definition of scalable parallel algorithms that is used to produce quantifiable evidence that a scalable parallel application was developed. The implementation of the parallel application and an automated domain decomposition tool are also discussed.
Billion-atom synchronous parallel kinetic Monte Carlo simulations of critical 3D Ising systems
Martinez, E.; Monasterio, P.R.; Marian, J.
2011-02-20
An extension of the synchronous parallel kinetic Monte Carlo (spkMC) algorithm developed by Martinez et al. [J. Comp. Phys. 227 (2008) 3804] to discrete lattices is presented. The method solves the master equation synchronously by recourse to null events that keep all processors' time clocks current in a global sense. Boundary conflicts are resolved by adopting a chessboard decomposition into non-interacting sublattices. We find that the bias introduced by the spatial correlations attendant to the sublattice decomposition is within the standard deviation of serial calculations, which confirms the statistical validity of our algorithm. We have analyzed the parallel efficiency of spkMC and find that it scales consistently with problem size and sublattice partition. We apply the method to the calculation of scale-dependent critical exponents in billion-atom 3D Ising systems, with very good agreement with state-of-the-art multispin simulations.
Parallel 3D Finite Element Numerical Modelling of DC Electron Guns
Prudencio, E.; Candel, A.; Ge, L.; Kabel, A.; Ko, K.; Lee, L.; Li, Z.; Ng, C.; Schussman, G.; /SLAC
2008-02-04
In this paper we present Gun3P, a parallel 3D finite element application that the Advanced Computations Department at the Stanford Linear Accelerator Center is developing for the analysis of beam formation in DC guns and beam transport in klystrons. Gun3P is targeted specially to complex geometries that cannot be described by 2D models and cannot be easily handled by finite difference discretizations. Its parallel capability allows simulations with more accuracy and less processing time than packages currently available. We present simulation results for the L-band Sheet Beam Klystron DC gun, in which case Gun3P is able to reduce simulation time from days to some hours.
Billion-atom synchronous parallel kinetic Monte Carlo simulations of critical 3D Ising systems
NASA Astrophysics Data System (ADS)
Martínez, E.; Monasterio, P. R.; Marian, J.
2011-02-01
An extension of the synchronous parallel kinetic Monte Carlo (spkMC) algorithm developed by Martinez et al. [J. Comp. Phys. 227 (2008) 3804] to discrete lattices is presented. The method solves the master equation synchronously by recourse to null events that keep all processors' time clocks current in a global sense. Boundary conflicts are resolved by adopting a chessboard decomposition into non-interacting sublattices. We find that the bias introduced by the spatial correlations attendant to the sublattice decomposition is within the standard deviation of serial calculations, which confirms the statistical validity of our algorithm. We have analyzed the parallel efficiency of spkMC and find that it scales consistently with problem size and sublattice partition. We apply the method to the calculation of scale-dependent critical exponents in billion-atom 3D Ising systems, with very good agreement with state-of-the-art multispin simulations.
The 3D model: explaining densification and deformation mechanisms by using 3D parameter plots.
Picker, Katharina M
2004-04-01
The aim of the study was to analyze very differently deforming materials using 3D parameter plots and consequently to gain deeper insights into the densification and deformation process described with the 3D model in order to define an ideal tableting excipient. The excipients used were dicalcium phosphate dihydrate (DCPD), sodium chloride (NaCl), microcrystalline cellulose (MCC), xylitol, mannitol, alpha-lactose monohydrate, maltose, hydroxypropyl methylcellulose (HPMC), sodium carboxymethylcellulose (NaCMC), cellulose acetate (CAC), maize starch, potato starch, pregelatinized starch, and maltodextrine. All of the materials were tableted to graded maximum relative densities (rhorel, max) using an eccentric tableting machine. The data which resulted, namely force, displacement, and time, were analyzed by the application of 3D modeling. Different particle size fractions of DCPD, CAC, and MCC were analyzed in addition. Brittle deforming materials such as DCPD exhibited a completely different 3D parameter plot, with low time plasticity, d, and low pressure plasticity, e, and a strong decrease in omega values when densification increased, in contrast to the plastically deforming MCC, which had much higher d, e, and omega values. e and omega values changed only slightly when densification increased for MCC. NaCl showed less of a decrease in omega values than DCPD did, and the d and e values were between those of MCC and DCPD. The sugar alcohols, xylitol and mannitol, behaved in a similar fashion to sodium chloride. This is also valid for the crystalline sugars, alpha-lactose monohydrate, and maltose. However, the sugars are more brittle than the sugar alcohols. The cellulose derivatives, HPMC, NaCMC, and CAC, are as plastic as MCC, however, their elasticity depends on substitution indicated by lower (more elastic) or higher (less elastic) omega values. The native starches, maize starch and potato starch, are very elastic, and pregelatinized starch and maltodextrine are
Parallel 3D Multi-Stage Simulation of a Turbofan Engine
NASA Technical Reports Server (NTRS)
Turner, Mark G.; Topp, David A.
1998-01-01
A 3D multistage simulation of each component of a modern GE Turbofan engine has been made. An axisymmetric view of this engine is presented in the document. This includes a fan, booster rig, high pressure compressor rig, high pressure turbine rig and a low pressure turbine rig. In the near future, all components will be run in a single calculation for a solution of 49 blade rows. The simulation exploits the use of parallel computations by using two levels of parallelism. Each blade row is run in parallel and each blade row grid is decomposed into several domains and run in parallel. 20 processors are used for the 4 blade row analysis. The average passage approach developed by John Adamczyk at NASA Lewis Research Center has been further developed and parallelized. This is APNASA Version A. It is a Navier-Stokes solver using a 4-stage explicit Runge-Kutta time marching scheme with variable time steps and residual smoothing for convergence acceleration. It has an implicit K-E turbulence model which uses an ADI solver to factor the matrix. Between 50 and 100 explicit time steps are solved before a blade row body force is calculated and exchanged with the other blade rows. This outer iteration has been coined a "flip." Efforts have been made to make the solver linearly scaleable with the number of blade rows. Enough flips are run (between 50 and 200) so the solution in the entire machine is not changing. The K-E equations are generally solved every other explicit time step. One of the key requirements in the development of the parallel code was to make the parallel solution exactly (bit for bit) match the serial solution. This has helped isolate many small parallel bugs and guarantee the parallelization was done correctly. The domain decomposition is done only in the axial direction since the number of points axially is much larger than the other two directions. This code uses MPI for message passing. The parallel speed up of the solver portion (no 1/0 or body force
Three-dimensional parallel UNIPIC-3D code for simulations of high-power microwave devices
NASA Astrophysics Data System (ADS)
Wang, Jianguo; Chen, Zaigao; Wang, Yue; Zhang, Dianhui; Liu, Chunliang; Li, Yongdong; Wang, Hongguang; Qiao, Hailiang; Fu, Meiyan; Yuan, Yuan
2010-07-01
This paper introduces a self-developed, three-dimensional parallel fully electromagnetic particle simulation code UNIPIC-3D. In this code, the electromagnetic fields are updated using the second-order, finite-difference time-domain method, and the particles are moved using the relativistic Newton-Lorentz force equation. The electromagnetic field and particles are coupled through the current term in Maxwell's equations. Two numerical examples are used to verify the algorithms adopted in this code, numerical results agree well with theoretical ones. This code can be used to simulate the high-power microwave (HPM) devices, such as the relativistic backward wave oscillator, coaxial vircator, and magnetically insulated line oscillator, etc. UNIPIC-3D is written in the object-oriented C++ language and can be run on a variety of platforms including WINDOWS, LINUX, and UNIX. Users can use the graphical user's interface to create the complex geometric structures of the simulated HPM devices, which can be automatically meshed by UNIPIC-3D code. This code has a powerful postprocessor which can display the electric field, magnetic field, current, voltage, power, spectrum, momentum of particles, etc. For the sake of comparison, the results computed by using the two-and-a-half-dimensional UNIPIC code are also provided for the same parameters of HPM devices, the numerical results computed from these two codes agree well with each other.
BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations
Ghaffarizadeh, Ahmadreza; Friedman, Samuel H.; Macklin, Paul
2016-01-01
Motivation: Computational models of multicellular systems require solving systems of PDEs for release, uptake, decay and diffusion of multiple substrates in 3D, particularly when incorporating the impact of drugs, growth substrates and signaling factors on cell receptors and subcellular systems biology. Results: We introduce BioFVM, a diffusive transport solver tailored to biological problems. BioFVM can simulate release and uptake of many substrates by cell and bulk sources, diffusion and decay in large 3D domains. It has been parallelized with OpenMP, allowing efficient simulations on desktop workstations or single supercomputer nodes. The code is stable even for large time steps, with linear computational cost scalings. Solutions are first-order accurate in time and second-order accurate in space. The code can be run by itself or as part of a larger simulator. Availability and implementation: BioFVM is written in C ++ with parallelization in OpenMP. It is maintained and available for download at http://BioFVM.MathCancer.org and http://BioFVM.sf.net under the Apache License (v2.0). Contact: paul.macklin@usc.edu. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26656933
3D-radiative transfer in terrestrial atmosphere: An efficient parallel numerical procedure
NASA Astrophysics Data System (ADS)
Bass, L. P.; Germogenova, T. A.; Nikolaeva, O. V.; Kokhanovsky, A. A.; Kuznetsov, V. S.
2003-04-01
Light propagation and scattering in terrestrial atmosphere is usually studied in the framework of the 1D radiative transfer theory [1]. However, in reality particles (e.g., ice crystals, solid and liquid aerosols, cloud droplets) are randomly distributed in 3D space. In particular, their concentrations vary both in vertical and horizontal directions. Therefore, 3D effects influence modern cloud and aerosol retrieval procedures, which are currently based on the 1D radiative transfer theory. It should be pointed out that the standard radiative transfer equation allows to study these more complex situations as well [2]. In recent year the parallel version of the 2D and 3D RADUGA code has been developed. This version is successfully used in gammas and neutrons transport problems [3]. Applications of this code to radiative transfer in atmosphere problems are contained in [4]. Possibilities of code RADUGA are presented in [5]. The RADUGA code system is an universal solver of radiative transfer problems for complicated models, including 2D and 3D aerosol and cloud fields with arbitrary scattering anisotropy, light absorption, inhomogeneous underlying surface and topography. Both delta type and distributed light sources can be accounted for in the framework of the algorithm developed. The accurate numerical procedure is based on the new discrete ordinate SWDD scheme [6]. The algorithm is specifically designed for parallel supercomputers. The version RADUGA 5.1(P) can run on MBC1000M [7] (768 processors with 10 Gb of hard disc memory for each processor). The peak productivity is equal 1 Tfl. Corresponding scalar version RADUGA 5.1 is working on PC. As a first example of application of the algorithm developed, we have studied the shadowing effects of clouds on neighboring cloudless atmosphere, depending on the cloud optical thickness, surface albedo, and illumination conditions. This is of importance for modern satellite aerosol retrieval algorithms development. [1] Sobolev
Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA.
Mrozek, Dariusz; Brożek, Miłosz; Małysiak-Mrozek, Bożena
2014-02-01
Searching for similar 3D protein structures is one of the primary processes employed in the field of structural bioinformatics. However, the computational complexity of this process means that it is constantly necessary to search for new methods that can perform such a process faster and more efficiently. Finding molecular substructures that complex protein structures have in common is still a challenging task, especially when entire databases containing tens or even hundreds of thousands of protein structures must be scanned. Graphics processing units (GPUs) and general purpose graphics processing units (GPGPUs) can perform many time-consuming and computationally demanding processes much more quickly than a classical CPU can. In this paper, we describe the GPU-based implementation of the CASSERT algorithm for 3D protein structure similarity searching. This algorithm is based on the two-phase alignment of protein structures when matching fragments of the compared proteins. The GPU (GeForce GTX 560Ti: 384 cores, 2GB RAM) implementation of CASSERT ("GPU-CASSERT") parallelizes both alignment phases and yields an average 180-fold increase in speed over its CPU-based, single-core implementation on an Intel Xeon E5620 (2.40GHz, 4 cores). In this paper, we show that massive parallelization of the 3D structure similarity search process on many-core GPU devices can reduce the execution time of the process, allowing it to be performed in real time. GPU-CASSERT is available at: http://zti.polsl.pl/dmrozek/science/gpucassert/cassert.htm. PMID:24481593
PORTA: A Massively Parallel Code for 3D Non-LTE Polarized Radiative Transfer
NASA Astrophysics Data System (ADS)
Štěpán, J.
2014-10-01
The interpretation of the Stokes profiles of the solar (stellar) spectral line radiation requires solving a non-LTE radiative transfer problem that can be very complex, especially when the main interest lies in modeling the linear polarization signals produced by scattering processes and their modification by the Hanle effect. One of the main difficulties is due to the fact that the plasma of a stellar atmosphere can be highly inhomogeneous and dynamic, which implies the need to solve the non-equilibrium problem of generation and transfer of polarized radiation in realistic three-dimensional stellar atmospheric models. Here we present PORTA, a computer program we have developed for solving, in three-dimensional (3D) models of stellar atmospheres, the problem of the generation and transfer of spectral line polarization taking into account anisotropic radiation pumping and the Hanle and Zeeman effects in multilevel atoms. The numerical method of solution is based on a highly convergent iterative algorithm, whose convergence rate is insensitive to the grid size, and on an accurate short-characteristics formal solver of the Stokes-vector transfer equation which uses monotonic Bezier interpolation. In addition to the iterative method and the 3D formal solver, another important feature of PORTA is a novel parallelization strategy suitable for taking advantage of massively parallel computers. Linear scaling of the solution with the number of processors allows to reduce the solution time by several orders of magnitude. We present useful benchmarks and a few illustrations of applications using a 3D model of the solar chromosphere resulting from MHD simulations. Finally, we present our conclusions with a view to future research. For more details see Štěpán & Trujillo Bueno (2013).
Design and verification of an ultra-precision 3D-coordinate measuring machine with parallel drives
NASA Astrophysics Data System (ADS)
Bos, Edwin; Moers, Ton; van Riel, Martijn
2015-08-01
An ultra-precision 3D coordinate measuring machine (CMM), the TriNano N100, has been developed. In our design, the workpiece is mounted on a 3D stage, which is driven by three parallel drives that are mutually orthogonal. The linear drives support the 3D stage using vacuum preloaded (VPL) air bearings, whereby each drive determines the position of the 3D stage along one translation direction only. An exactly constrained design results in highly repeatable machine behavior. Furthermore, the machine complies with the Abbé principle over its full measurement range and the application of parallel drives allows for excellent dynamic behavior. The design allows a 3D measurement uncertainty of 100 nanometers in a measurement range of 200 cubic centimeters. Verification measurements using a Gannen XP 3D tactile probing system on a spherical artifact show a standard deviation in single point repeatability of around 2 nm in each direction.
Time-dependent 3-D dterministic transport on parallel architectures using Dantsys/MPI
Baker, R.S.; Alcouffe, R.E.
1996-12-31
In addition to the ability to solve the static transport equation, we have also incorporated time dependence into our parallel 3-D S{sub {ital N}} code DANTSYS/MPI. Using a semi-implicit scheme, DANTSYS/MPI is capable of performing time-dependent calculations for both fissioning and pure source driven problems. We have applied this to various types of problems such as nuclear well logging and prompt fission experiments. This paper describes the form of the time- dependent equations implemented, their solution strategies in DANTSYS/MPI including iteration acceleration, and the strategies used for time-step control. Results are presented for a model nuclear well logging calculation.
3-D readout-electronics packaging for high-bandwidth massively paralleled imager
Kwiatkowski, Kris; Lyke, James
2007-12-18
Dense, massively parallel signal processing electronics are co-packaged behind associated sensor pixels. Microchips containing a linear or bilinear arrangement of photo-sensors, together with associated complex electronics, are integrated into a simple 3-D structure (a "mirror cube"). An array of photo-sensitive cells are disposed on a stacked CMOS chip's surface at a 45.degree. angle from light reflecting mirror surfaces formed on a neighboring CMOS chip surface. Image processing electronics are held within the stacked CMOS chip layers. Electrical connections couple each of said stacked CMOS chip layers and a distribution grid, the connections for distributing power and signals to components associated with each stacked CSMO chip layer.
Ruh, Dominic; Tränkle, Benjamin; Rohrbach, Alexander
2011-10-24
Multi-dimensional, correlated particle tracking is a key technology to reveal dynamic processes in living and synthetic soft matter systems. In this paper we present a new method for tracking micron-sized beads in parallel and in all three dimensions - faster and more precise than existing techniques. Using an acousto-optic deflector and two quadrant-photo-diodes, we can track numerous optically trapped beads at up to tens of kHz with a precision of a few nanometers by back-focal plane interferometry. By time-multiplexing the laser focus, we can calibrate individually all traps and all tracking signals in a few seconds and in 3D. We show 3D histograms and calibration constants for nine beads in a quadratic arrangement, although trapping and tracking is easily possible for more beads also in arbitrary 2D arrangements. As an application, we investigate the hydrodynamic coupling and diffusion anomalies of spheres trapped in a 3 × 3 arrangement. PMID:22109012
NASA Astrophysics Data System (ADS)
Yang, Dikun; Oldenburg, Douglas W.; Haber, Eldad
2014-03-01
Airborne electromagnetic (AEM) methods are highly efficient tools for assessing the Earth's conductivity structures in a large area at low cost. However, the configuration of AEM measurements, which typically have widely distributed transmitter-receiver pairs, makes the rigorous modelling and interpretation extremely time-consuming in 3-D. Excessive overcomputing can occur when working on a large mesh covering the entire survey area and inverting all soundings in the data set. We propose two improvements. The first is to use a locally optimized mesh for each AEM sounding for the forward modelling and calculation of sensitivity. This dedicated local mesh is small with fine cells near the sounding location and coarse cells far away in accordance with EM diffusion and the geometric decay of the signals. Once the forward problem is solved on the local meshes, the sensitivity for the inversion on the global mesh is available through quick interpolation. Using local meshes for AEM forward modelling avoids unnecessary computing on fine cells on a global mesh that are far away from the sounding location. Since local meshes are highly independent, the forward modelling can be efficiently parallelized over an array of processors. The second improvement is random and dynamic down-sampling of the soundings. Each inversion iteration only uses a random subset of the soundings, and the subset is reselected for every iteration. The number of soundings in the random subset, determined by an adaptive algorithm, is tied to the degree of model regularization. This minimizes the overcomputing caused by working with redundant soundings. Our methods are compared against conventional methods and tested with a synthetic example. We also invert a field data set that was previously considered to be too large to be practically inverted in 3-D. These examples show that our methodology can dramatically reduce the processing time of 3-D inversion to a practical level without losing resolution
NASA Astrophysics Data System (ADS)
Rastogi, Richa; Srivastava, Abhishek; Khonde, Kiran; Sirasala, Kirannmayi M.; Londhe, Ashutosh; Chavhan, Hitesh
2015-07-01
This paper presents an efficient parallel 3D Kirchhoff depth migration algorithm suitable for current class of multicore architecture. The fundamental Kirchhoff depth migration algorithm exhibits inherent parallelism however, when it comes to 3D data migration, as the data size increases the resource requirement of the algorithm also increases. This challenges its practical implementation even on current generation high performance computing systems. Therefore a smart parallelization approach is essential to handle 3D data for migration. The most compute intensive part of Kirchhoff depth migration algorithm is the calculation of traveltime tables due to its resource requirements such as memory/storage and I/O. In the current research work, we target this area and develop a competent parallel algorithm for post and prestack 3D Kirchhoff depth migration, using hybrid MPI+OpenMP programming techniques. We introduce a concept of flexi-depth iterations while depth migrating data in parallel imaging space, using optimized traveltime table computations. This concept provides flexibility to the algorithm by migrating data in a number of depth iterations, which depends upon the available node memory and the size of data to be migrated during runtime. Furthermore, it minimizes the requirements of storage, I/O and inter-node communication, thus making it advantageous over the conventional parallelization approaches. The developed parallel algorithm is demonstrated and analysed on Yuva II, a PARAM series of supercomputers. Optimization, performance and scalability experiment results along with the migration outcome show the effectiveness of the parallel algorithm.
In situ patterned micro 3D liver constructs for parallel toxicology testing in a fluidic device.
Skardal, Aleksander; Devarasetty, Mahesh; Soker, Shay; Hall, Adam R
2015-09-01
3D tissue models are increasingly being implemented for drug and toxicology testing. However, the creation of tissue-engineered constructs for this purpose often relies on complex biofabrication techniques that are time consuming, expensive, and difficult to scale up. Here, we describe a strategy for realizing multiple tissue constructs in a parallel microfluidic platform using an approach that is simple and can be easily scaled for high-throughput formats. Liver cells mixed with a UV-crosslinkable hydrogel solution are introduced into parallel channels of a sealed microfluidic device and photopatterned to produce stable tissue constructs in situ. The remaining uncrosslinked material is washed away, leaving the structures in place. By using a hydrogel that specifically mimics the properties of the natural extracellular matrix, we closely emulate native tissue, resulting in constructs that remain stable and functional in the device during a 7-day culture time course under recirculating media flow. As proof of principle for toxicology analysis, we expose the constructs to ethyl alcohol (0-500 mM) and show that the cell viability and the secretion of urea and albumin decrease with increasing alcohol exposure, while markers for cell damage increase. PMID:26355538
Comparison of 3-D synthetic aperture phased-array ultrasound imaging and parallel beamforming.
Rasmussen, Morten Fischer; Jensen, Jørgen Arendt
2014-10-01
This paper demonstrates that synthetic aperture imaging (SAI) can be used to achieve real-time 3-D ultrasound phased-array imaging. It investigates whether SAI increases the image quality compared with the parallel beamforming (PB) technique for real-time 3-D imaging. Data are obtained using both simulations and measurements with an ultrasound research scanner and a commercially available 3.5- MHz 1024-element 2-D transducer array. To limit the probe cable thickness, 256 active elements are used in transmit and receive for both techniques. The two imaging techniques were designed for cardiac imaging, which requires sequences designed for imaging down to 15 cm of depth and a frame rate of at least 20 Hz. The imaging quality of the two techniques is investigated through simulations as a function of depth and angle. SAI improved the full-width at half-maximum (FWHM) at low steering angles by 35%, and the 20-dB cystic resolution by up to 62%. The FWHM of the measured line spread function (LSF) at 80 mm depth showed a difference of 20% in favor of SAI. SAI reduced the cyst radius at 60 mm depth by 39% in measurements. SAI improved the contrast-to-noise ratio measured on anechoic cysts embedded in a tissue-mimicking material by 29% at 70 mm depth. The estimated penetration depth on the same tissue-mimicking phantom shows that SAI increased the penetration by 24% compared with PB. Neither SAI nor PB achieved the design goal of 15 cm penetration depth. This is likely due to the limited transducer surface area and a low SNR of the experimental scanner used. PMID:25265174
3D magnetospheric parallel hybrid multi-grid method applied to planet-plasma interactions
NASA Astrophysics Data System (ADS)
Leclercq, L.; Modolo, R.; Leblanc, F.; Hess, S.; Mancini, M.
2016-03-01
We present a new method to exploit multiple refinement levels within a 3D parallel hybrid model, developed to study planet-plasma interactions. This model is based on the hybrid formalism: ions are kinetically treated whereas electrons are considered as a inertia-less fluid. Generally, ions are represented by numerical particles whose size equals the volume of the cells. Particles that leave a coarse grid subsequently entering a refined region are split into particles whose volume corresponds to the volume of the refined cells. The number of refined particles created from a coarse particle depends on the grid refinement rate. In order to conserve velocity distribution functions and to avoid calculations of average velocities, particles are not coalesced. Moreover, to ensure the constancy of particles' shape function sizes, the hybrid method is adapted to allow refined particles to move within a coarse region. Another innovation of this approach is the method developed to compute grid moments at interfaces between two refinement levels. Indeed, the hybrid method is adapted to accurately account for the special grid structure at the interfaces, avoiding any overlapping grid considerations. Some fundamental test runs were performed to validate our approach (e.g. quiet plasma flow, Alfven wave propagation). Lastly, we also show a planetary application of the model, simulating the interaction between Jupiter's moon Ganymede and the Jovian plasma.
A 3D Parallel Beam Dynamics Code for Modeling High Brightness Beams in Photoinjectors
Qiang, Ji; Lidia, S.; Ryne, R.D.; Limborg, C.; /SLAC
2006-02-13
In this paper we report on IMPACT-T, a 3D beam dynamics code for modeling high brightness beams in photoinjectors and rf linacs. IMPACT-T is one of the few codes used in the photoinjector community that has a parallel implementation, making it very useful for high statistics simulations of beam halos and beam diagnostics. It has a comprehensive set of beamline elements, and furthermore allows arbitrary overlap of their fields. It is unique in its use of space-charge solvers based on an integrated Green function to efficiently and accurately treat beams with large aspect ratio, and a shifted Green function to efficiently treat image charge effects of a cathode. It is also unique in its inclusion of energy binning in the space-charge calculation to model beams with large energy spread. Together, all these features make IMPACT-T a powerful and versatile tool for modeling beams in photoinjectors and other systems. In this paper we describe the code features and present results of IMPACT-T simulations of the LCLS photoinjectors. We also include a comparison of IMPACT-T and PARMELA results.
A 3d Parallel Beam Dynamics Code for Modeling High BrightnessBeams in Photoinjectors
Qiang, J.; Lidia, S.; Ryne, R.; Limborg, C.
2005-05-16
In this paper we report on IMPACT-T, a 3D beam dynamics code for modeling high brightness beams in photoinjectors and rf linacs. IMPACT-T is one of the few codes used in the photoinjector community that has a parallel implementation, making it very useful for high statistics simulations of beam halos and beam diagnostics. It has a comprehensive set of beamline elements, and furthermore allows arbitrary overlap of their fields. It is unique in its use of space-charge solvers based on an integrated Green function to efficiently and accurately treat beams with large aspect ratio, and a shifted Green function to efficiently treat image charge effects of a cathode. It is also unique in its inclusion of energy binning in the space-charge calculation to model beams with large energy spread. Together, all these features make IMPACT-T a powerful and versatile tool for modeling beams in photoinjectors and other systems. In this paper we describe the code features and present results of IMPACT-T simulations of the LCLS photoinjectors. We also include a comparison of IMPACT-T and PARMELA results.
Xie, G.; Li, J.; Majer, E.; Zuo, D.
1998-07-01
This paper describes a new 3D parallel GILD electromagnetic (EM) modeling and nonlinear inversion algorithm. The algorithm consists of: (a) a new magnetic integral equation instead of the electric integral equation to solve the electromagnetic forward modeling and inverse problem; (b) a collocation finite element method for solving the magnetic integral and a Galerkin finite element method for the magnetic differential equations; (c) a nonlinear regularizing optimization method to make the inversion stable and of high resolution; and (d) a new parallel 3D modeling and inversion using a global integral and local differential domain decomposition technique (GILD). The new 3D nonlinear electromagnetic inversion has been tested with synthetic data and field data. The authors obtained very good imaging for the synthetic data and reasonable subsurface EM imaging for the field data. The parallel algorithm has high parallel efficiency over 90% and can be a parallel solver for elliptic, parabolic, and hyperbolic modeling and inversion. The parallel GILD algorithm can be extended to develop a high resolution and large scale seismic and hydrology modeling and inversion in the massively parallel computer.
The 3-D inelastic analyses for computational structural mechanics
NASA Technical Reports Server (NTRS)
Hopkins, D. A.; Chamis, C. C.
1989-01-01
The 3-D inelastic analysis method is a focused program with the objective to develop computationally effective analysis methods and attendant computer codes for three-dimensional, nonlinear time and temperature dependent problems present in the hot section of turbojet engine structures. Development of these methods was a major part of the Hot Section Technology (HOST) program over the past five years at Lewis Research Center.
3D parallel computations of turbofan noise propagation using a spectral element method
NASA Astrophysics Data System (ADS)
Taghaddosi, Farzad
2006-12-01
A three-dimensional code has been developed for the simulation of tone noise generated by turbofan engine inlets using computational aeroacoustics. The governing equations are the linearized Euler equations, which are further simplified to a set of equations in terms of acoustic potential, using the irrotational flow assumption, and subsequently solved in the frequency domain. Due to the special nature of acoustic wave propagation, the spatial discretization is performed using a spectral element method, where a tensor product of the nth-degree polynomials based on Chebyshev orthogonal functions is used to approximate variations within hexahedral elements. Non-reflecting boundary conditions are imposed at the far-field using a damping layer concept. This is done by augmenting the continuity equation with an additional term without modifying the governing equations as in PML methods. Solution of the linear system of equations for the acoustic problem is based on the Schur complement method, which is a nonoverlapping domain decomposition technique. The Schur matrix is first solved using a matrix-free iterative method, whose convergence is accelerated with a novel local preconditioner. The solution in the entire domain is then obtained by finding solutions in smaller subdomains. The 3D code also contains a mean flow solver based on the full potential equation in order to take into account the effects of flow variations around the nacelle on the scattering of the radiated sound field. All aspects of numerical simulations, including building and assembling the coefficient matrices, implementation of the Schur complement method, and solution of the system of equations for both the acoustic and mean flow problems are performed on multiprocessors in parallel using the resources of the CLUMEQ Supercomputer Center. A large number of test cases are presented, ranging in size from 100 000-2 000 000 unknowns for which, depending on the size of the problem, between 8-48 CPU's are
MESA: A 3-D Eulerian hydrocode for penetration mechanics studies
Mandell, D.A.; Holian, K.S.; Henninger, R.
1991-01-01
We describe an explicit, finite-difference hydrocode, called MESA, and compare calculations to metal and ceramic plate impacts with spall and to Taylor cylinder tests. The MESA code was developed with support from DARPA, the Army and the Marine Corps for use in armor/anti-armor problems primarily, but the code has been used for a number of other applications. MESA includes 2-D and 3-D Eulerian hydrodynamics, a number of material strength and fracture models, and a programmed burn high explosives model. 15 refs., 4 figs.
Dharmaraj, Christopher D.; Thadikonda, Kishan; Fletcher, Anthony R.; Doan, Phuc N.; Devasahayam, Nallathamby; Matsumoto, Shingo; Johnson, Calvin A.; Cook, John A.; Mitchell, James B.; Subramanian, Sankaran; Krishna, Murali C.
2009-01-01
Three-dimensional Oximetric Electron Paramagnetic Resonance Imaging using the Single Point Imaging modality generates unpaired spin density and oxygen images that can readily distinguish between normal and tumor tissues in small animals. It is also possible with fast imaging to track the changes in tissue oxygenation in response to the oxygen content in the breathing air. However, this involves dealing with gigabytes of data for each 3D oximetric imaging experiment involving digital band pass filtering and background noise subtraction, followed by 3D Fourier reconstruction. This process is rather slow in a conventional uniprocessor system. This paper presents a parallelization framework using OpenMP runtime support and parallel MATLAB to execute such computationally intensive programs. The Intel compiler is used to develop a parallel C++ code based on OpenMP. The code is executed on four Dual-Core AMD Opteron shared memory processors, to reduce the computational burden of the filtration task significantly. The results show that the parallel code for filtration has achieved a speed up factor of 46.66 as against the equivalent serial MATLAB code. In addition, a parallel MATLAB code has been developed to perform 3D Fourier reconstruction. Speedup factors of 4.57 and 4.25 have been achieved during the reconstruction process and oximetry computation, for a data set with 23 × 23 × 23 gradient steps. The execution time has been computed for both the serial and parallel implementations using different dimensions of the data and presented for comparison. The reported system has been designed to be easily accessible even from low-cost personal computers through local internet (NIHnet). The experimental results demonstrate that the parallel computing provides a source of high computational power to obtain biophysical parameters from 3D EPR oximetric imaging, almost in real-time. PMID:19672315
Dharmaraj, Christopher D; Thadikonda, Kishan; Fletcher, Anthony R; Doan, Phuc N; Devasahayam, Nallathamby; Matsumoto, Shingo; Johnson, Calvin A; Cook, John A; Mitchell, James B; Subramanian, Sankaran; Krishna, Murali C
2009-01-01
Three-dimensional Oximetric Electron Paramagnetic Resonance Imaging using the Single Point Imaging modality generates unpaired spin density and oxygen images that can readily distinguish between normal and tumor tissues in small animals. It is also possible with fast imaging to track the changes in tissue oxygenation in response to the oxygen content in the breathing air. However, this involves dealing with gigabytes of data for each 3D oximetric imaging experiment involving digital band pass filtering and background noise subtraction, followed by 3D Fourier reconstruction. This process is rather slow in a conventional uniprocessor system. This paper presents a parallelization framework using OpenMP runtime support and parallel MATLAB to execute such computationally intensive programs. The Intel compiler is used to develop a parallel C++ code based on OpenMP. The code is executed on four Dual-Core AMD Opteron shared memory processors, to reduce the computational burden of the filtration task significantly. The results show that the parallel code for filtration has achieved a speed up factor of 46.66 as against the equivalent serial MATLAB code. In addition, a parallel MATLAB code has been developed to perform 3D Fourier reconstruction. Speedup factors of 4.57 and 4.25 have been achieved during the reconstruction process and oximetry computation, for a data set with 23 x 23 x 23 gradient steps. The execution time has been computed for both the serial and parallel implementations using different dimensions of the data and presented for comparison. The reported system has been designed to be easily accessible even from low-cost personal computers through local internet (NIHnet). The experimental results demonstrate that the parallel computing provides a source of high computational power to obtain biophysical parameters from 3D EPR oximetric imaging, almost in real-time. PMID:19672315
Sofronov, I.D.; Voronin, B.L.; Butnev, O.I.
1997-12-31
The aim of the work performed is to develop a 3D parallel program for numerical calculation of gas dynamics problem with heat conductivity on distributed memory computational systems (CS), satisfying the condition of numerical result independence from the number of processors involved. Two basically different approaches to the structure of massive parallel computations have been developed. The first approach uses the 3D data matrix decomposition reconstructed at temporal cycle and is a development of parallelization algorithms for multiprocessor CS with shareable memory. The second approach is based on using a 3D data matrix decomposition not reconstructed during a temporal cycle. The program was developed on 8-processor CS MP-3 made in VNIIEF and was adapted to a massive parallel CS Meiko-2 in LLNL by joint efforts of VNIIEF and LLNL staffs. A large number of numerical experiments has been carried out with different number of processors up to 256 and the efficiency of parallelization has been evaluated in dependence on processor number and their parameters.
NASA Astrophysics Data System (ADS)
Meléndez, A.; Korenaga, J.; Sallarès, V.; Miniussi, A.; Ranero, C. R.
2015-10-01
We present a new 3-D traveltime tomography code (TOMO3D) for the modelling of active-source seismic data that uses the arrival times of both refracted and reflected seismic phases to derive the velocity distribution and the geometry of reflecting boundaries in the subsurface. This code is based on its popular 2-D version TOMO2D from which it inherited the methods to solve the forward and inverse problems. The traveltime calculations are done using a hybrid ray-tracing technique combining the graph and bending methods. The LSQR algorithm is used to perform the iterative regularized inversion to improve the initial velocity and depth models. In order to cope with an increased computational demand due to the incorporation of the third dimension, the forward problem solver, which takes most of the run time (˜90 per cent in the test presented here), has been parallelized with a combination of multi-processing and message passing interface standards. This parallelization distributes the ray-tracing and traveltime calculations among available computational resources. The code's performance is illustrated with a realistic synthetic example, including a checkerboard anomaly and two reflectors, which simulates the geometry of a subduction zone. The code is designed to invert for a single reflector at a time. A data-driven layer-stripping strategy is proposed for cases involving multiple reflectors, and it is tested for the successive inversion of the two reflectors. Layers are bound by consecutive reflectors, and an initial velocity model for each inversion step incorporates the results from previous steps. This strategy poses simpler inversion problems at each step, allowing the recovery of strong velocity discontinuities that would otherwise be smoothened.
Chang, H.; Solano, M.; VanDyke, J.P.; McMechan, G.A.; Epili, D.
1998-03-01
Portable, production-scale 3-D prestack Kirchhoff depth migration software capable of full-volume imaging has been successfully implemented and applied to a six-million trace (46.9 Gbyte) marine data set from a salt/subsalt play in the Gulf of Mexico. Velocity model building and updates use an image-driven strategy and were performed in a Sun Sparc environment. Images obtained by 3-D prestack migration after three velocity iterations are substantially better focused and reveal drilling targets that were not visible in images obtained from conventional 3-D poststack time migration. Amplitudes are well preserved, so anomalies associated with known reservoirs conform to the petrophysical predictions. Prototype development was on an 8-node Intel iPSC860 computer; the production version was run on an 1824-node Intel Paragon computer. The code has been successfully ported to CRAY (T3D) and Unix workstation (PVM) environments.
Reactor Dosimetry Applications Using RAPTOR-M3G:. a New Parallel 3-D Radiation Transport Code
NASA Astrophysics Data System (ADS)
Longoni, Gianluca; Anderson, Stanwood L.
2009-08-01
The numerical solution of the Linearized Boltzmann Equation (LBE) via the Discrete Ordinates method (SN) requires extensive computational resources for large 3-D neutron and gamma transport applications due to the concurrent discretization of the angular, spatial, and energy domains. This paper will discuss the development RAPTOR-M3G (RApid Parallel Transport Of Radiation - Multiple 3D Geometries), a new 3-D parallel radiation transport code, and its application to the calculation of ex-vessel neutron dosimetry responses in the cavity of a commercial 2-loop Pressurized Water Reactor (PWR). RAPTOR-M3G is based domain decomposition algorithms, where the spatial and angular domains are allocated and processed on multi-processor computer architectures. As compared to traditional single-processor applications, this approach reduces the computational load as well as the memory requirement per processor, yielding an efficient solution methodology for large 3-D problems. Measured neutron dosimetry responses in the reactor cavity air gap will be compared to the RAPTOR-M3G predictions. This paper is organized as follows: Section 1 discusses the RAPTOR-M3G methodology; Section 2 describes the 2-loop PWR model and the numerical results obtained. Section 3 addresses the parallel performance of the code, and Section 4 concludes this paper with final remarks and future work.
NASA Astrophysics Data System (ADS)
Huang, Qinghua; Li, Zhanhui; Wang, Yanbin
2010-12-01
We presented a parallel 3-D staggered grid pseudospectral time domain (PSTD) method for simulating ground-penetrating radar (GPR) wave propagation. We took the staggered grid method to weaken the global effect in PSTD and developed a modified fast Fourier transform (FFT) spatial derivative operator to eliminate the wraparound effect due to the implicit periodical boundary condition in FFT operator. After the above improvements, we achieved the parallel PSTD computation based on an overlap domain decomposition method without any absorbing condition for each subdomain, which can significantly reduce the required grids in each overlap subdomain comparing with other proposed algorithms. We test our parallel technique for some numerical models and obtained consistent results with the analytical ones and/or those of the nonparallel PSTD method. The above numerical tests showed that our parallel PSTD algorithm is effective in simulating 3-D GPR wave propagation, with merits of saving computation time, as well as more flexibility in dealing with complicated models without losing the accuracy. The application of our parallel PSTD method in applied geophysics and paleoseismology based on GPR data confirmed the efficiency of our algorithm and its potential applications in various subdisciplines of solid earth geophysics. This study would also provide a useful parallel PSTD approach to the simulation of other geophysical problems on distributed memory PC cluster.
Massively parallel computation of 3D flow and reactions in chemical vapor deposition reactors
Salinger, A.G.; Shadid, J.N.; Hutchinson, S.A.; Hennigan, G.L.; Devine, K.D.; Moffat, H.K.
1997-12-01
Computer modeling of Chemical Vapor Deposition (CVD) reactors can greatly aid in the understanding, design, and optimization of these complex systems. Modeling is particularly attractive in these systems since the costs of experimentally evaluating many design alternatives can be prohibitively expensive, time consuming, and even dangerous, when working with toxic chemicals like Arsine (AsH{sub 3}): until now, predictive modeling has not been possible for most systems since the behavior is three-dimensional and governed by complex reaction mechanisms. In addition, CVD reactors often exhibit large thermal gradients, large changes in physical properties over regions of the domain, and significant thermal diffusion for gas mixtures with widely varying molecular weights. As a result, significant simplifications in the models have been made which erode the accuracy of the models` predictions. In this paper, the authors will demonstrate how the vast computational resources of massively parallel computers can be exploited to make possible the analysis of models that include coupled fluid flow and detailed chemistry in three-dimensional domains. For the most part, models have either simplified the reaction mechanisms and concentrated on the fluid flow, or have simplified the fluid flow and concentrated on rigorous reactions. An important CVD research thrust has been in detailed modeling of fluid flow and heat transfer in the reactor vessel, treating transport and reaction of chemical species either very simply or as a totally decoupled problem. Using the analogy between heat transfer and mass transfer, and the fact that deposition is often diffusion limited, much can be learned from these calculations; however, the effects of thermal diffusion, the change in physical properties with composition, and the incorporation of surface reaction mechanisms are not included in this model, nor can transitions to three-dimensional flows be detected.
Characterization of a parallel-beam CCD optical-CT apparatus for 3D radiation dosimetry.
Krstajić, Nikola; Doran, Simon J
2007-07-01
3D measurement of optical attenuation is of interest in a variety of fields of biomedical importance, including spectrophotometry, optical projection tomography (OPT) and analysis of 3D radiation dosimeters. Accurate, precise and economical 3D measurements of optical density (OD) are a crucial step in enabling 3D radiation dosimeters to enter wider use in clinics. Polymer gels and Fricke gels, as well as dosimeters not based around gels, have been characterized for 3D dosimetry over the last two decades. A separate problem is the verification of the best readout method. A number of different imaging modalities (magnetic resonance imaging (MRI), optical CT, x-ray CT and ultrasound) have been suggested for the readout of information from 3D dosimeters. To date only MRI and laser-based optical CT have been characterized in detail. This paper describes some initial steps we have taken in establishing charge coupled device (CCD)-based optical CT as a viable alternative to MRI for readout of 3D radiation dosimeters. The main advantage of CCD-based optical CT over traditional laser-based optical CT is a speed increase of at least an order of magnitude, while the simplicity of its architecture would lend itself to cheaper implementation than both MRI and laser-based optical CT if the camera itself were inexpensive enough. Specifically, we study the following aspects of optical metrology, using high quality test targets: (i) calibration and quality of absorbance measurements and the camera requirements for 3D dosimetry; (ii) the modulation transfer function (MTF) of individual projections; (iii) signal-to-noise ratio (SNR) in the projection and reconstruction domains; (iv) distortion in the projection domain, depth-of-field (DOF) and telecentricity. The principal results for our current apparatus are as follows: (i) SNR of optical absorbance in projections is better than 120:1 for uniform phantoms in absorbance range 0.3 to 1.6 (and better than 200:1 for absorbances 1.0 to
Characterization of a parallel-beam CCD optical-CT apparatus for 3D radiation dosimetry
NASA Astrophysics Data System (ADS)
Krstajic, Nikola; Doran, Simon J.
2007-07-01
3D measurement of optical attenuation is of interest in a variety of fields of biomedical importance, including spectrophotometry, optical projection tomography (OPT) and analysis of 3D radiation dosimeters. Accurate, precise and economical 3D measurements of optical density (OD) are a crucial step in enabling 3D radiation dosimeters to enter wider use in clinics. Polymer gels and Fricke gels, as well as dosimeters not based around gels, have been characterized for 3D dosimetry over the last two decades. A separate problem is the verification of the best readout method. A number of different imaging modalities (magnetic resonance imaging (MRI), optical CT, x-ray CT and ultrasound) have been suggested for the readout of information from 3D dosimeters. To date only MRI and laser-based optical CT have been characterized in detail. This paper describes some initial steps we have taken in establishing charge coupled device (CCD)-based optical CT as a viable alternative to MRI for readout of 3D radiation dosimeters. The main advantage of CCD-based optical CT over traditional laser-based optical CT is a speed increase of at least an order of magnitude, while the simplicity of its architecture would lend itself to cheaper implementation than both MRI and laser-based optical CT if the camera itself were inexpensive enough. Specifically, we study the following aspects of optical metrology, using high quality test targets: (i) calibration and quality of absorbance measurements and the camera requirements for 3D dosimetry; (ii) the modulation transfer function (MTF) of individual projections; (iii) signal-to-noise ratio (SNR) in the projection and reconstruction domains; (iv) distortion in the projection domain, depth-of-field (DOF) and telecentricity. The principal results for our current apparatus are as follows: (i) SNR of optical absorbance in projections is better than 120:1 for uniform phantoms in absorbance range 0.3 to 1.6 (and better than 200:1 for absorbances 1.0 to
Borazjani, Iman; Ge, Liang; Le, Trung; Sotiropoulos, Fotis
2013-01-01
We develop an overset-curvilinear immersed boundary (overset-CURVIB) method in a general non-inertial frame of reference to simulate a wide range of challenging biological flow problems. The method incorporates overset-curvilinear grids to efficiently handle multi-connected geometries and increase the resolution locally near immersed boundaries. Complex bodies undergoing arbitrarily large deformations may be embedded within the overset-curvilinear background grid and treated as sharp interfaces using the curvilinear immersed boundary (CURVIB) method (Ge and Sotiropoulos, Journal of Computational Physics, 2007). The incompressible flow equations are formulated in a general non-inertial frame of reference to enhance the overall versatility and efficiency of the numerical approach. Efficient search algorithms to identify areas requiring blanking, donor cells, and interpolation coefficients for constructing the boundary conditions at grid interfaces of the overset grid are developed and implemented using efficient parallel computing communication strategies to transfer information among sub-domains. The governing equations are discretized using a second-order accurate finite-volume approach and integrated in time via an efficient fractional-step method. Various strategies for ensuring globally conservative interpolation at grid interfaces suitable for incompressible flow fractional step methods are implemented and evaluated. The method is verified and validated against experimental data, and its capabilities are demonstrated by simulating the flow past multiple aquatic swimmers and the systolic flow in an anatomic left ventricle with a mechanical heart valve implanted in the aortic position. PMID:23833331
gEMfitter: a highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration.
Hoang, Thai V; Cavin, Xavier; Ritchie, David W
2013-11-01
Fitting high resolution protein structures into low resolution cryo-electron microscopy (cryo-EM) density maps is an important technique for modeling the atomic structures of very large macromolecular assemblies. This article presents "gEMfitter", a highly parallel fast Fourier transform (FFT) EM density fitting program which can exploit the special hardware properties of modern graphics processor units (GPUs) to accelerate both the translational and rotational parts of the correlation search. In particular, by using the GPU's special texture memory hardware to rotate 3D voxel grids, the cost of rotating large 3D density maps is almost completely eliminated. Compared to performing 3D correlations on one core of a contemporary central processor unit (CPU), running gEMfitter on a modern GPU gives up to 26-fold speed-up. Furthermore, using our parallel processing framework, this speed-up increases linearly with the number of CPUs or GPUs used. Thus, it is now possible to use routinely more robust but more expensive 3D correlation techniques. When tested on low resolution experimental cryo-EM data for the GroEL-GroES complex, we demonstrate the satisfactory fitting results that may be achieved by using a locally normalised cross-correlation with a Laplacian pre-filter, while still being up to three orders of magnitude faster than the well-known COLORES program. PMID:24060989
Cotranslational processing mechanisms: towards a dynamic 3D model.
Giglione, Carmela; Fieulaine, Sonia; Meinnel, Thierry
2009-08-01
Recent major advances have been made in understanding how cotranslational events are achieved in the course of protein biosynthesis. Specifically, several studies have shed light into the dynamic process of how nascent chains emerging from the ribosome are supported by protein biogenesis factors to ensure both processing and folding mechanisms. To take into account the awareness that coordination is needed, a new 'concerted model' recently proposed simultaneous action of both processes on the ribosome. In the model, any emerging nascent chain is first encountered by the chaperone trigger factor (TF), which forms an open cradle underneath the ribosomal exit tunnel. This cradle serves as a passive router that channels the nascent chains to the first cotranslational event, the proteolysis event performed by the N-terminal methionine excision machinery. Although fascinating, this model clearly raises more questions than it answers. Does the data used to develop this model stand up to scrutiny and, if not, what are the alternative mechanisms that the data suggest? PMID:19647435
Categorical prototyping: incorporating molecular mechanisms into 3D printing.
Brommer, Dieter B; Giesa, Tristan; Spivak, David I; Buehler, Markus J
2016-01-15
We apply the mathematical framework of category theory to articulate the precise relation between the structure and mechanics of a nanoscale system in a macroscopic domain. We maintain the chosen molecular mechanical properties from the nanoscale to the continuum scale. Therein we demonstrate a procedure to 'protoype a model', as category theory enables us to maintain certain information across disparate fields of study, distinct scales, or physical realizations. This process fits naturally with prototyping, as a prototype is not a complete product but rather a reduction to test a subset of properties. To illustrate this point, we use large-scale multi-material printing to examine the scaling of the elastic modulus of 2D carbon allotropes at the macroscale and validate our printed model using experimental testing. The resulting hand-held materials can be examined more readily, and yield insights beyond those available in the original digital representations. We demonstrate this concept by twisting the material, a test beyond the scope of the original model. The method developed can be extended to other methods of additive manufacturing. PMID:26618369
Categorical prototyping: incorporating molecular mechanisms into 3D printing
NASA Astrophysics Data System (ADS)
Brommer, Dieter B.; Giesa, Tristan; Spivak, David I.; Buehler, Markus J.
2016-01-01
We apply the mathematical framework of category theory to articulate the precise relation between the structure and mechanics of a nanoscale system in a macroscopic domain. We maintain the chosen molecular mechanical properties from the nanoscale to the continuum scale. Therein we demonstrate a procedure to ‘protoype a model’, as category theory enables us to maintain certain information across disparate fields of study, distinct scales, or physical realizations. This process fits naturally with prototyping, as a prototype is not a complete product but rather a reduction to test a subset of properties. To illustrate this point, we use large-scale multi-material printing to examine the scaling of the elastic modulus of 2D carbon allotropes at the macroscale and validate our printed model using experimental testing. The resulting hand-held materials can be examined more readily, and yield insights beyond those available in the original digital representations. We demonstrate this concept by twisting the material, a test beyond the scope of the original model. The method developed can be extended to other methods of additive manufacturing.
Zhao, Hewei; Yue, Yonghai; Guo, Lin; Wu, Juntao; Zhang, Youwei; Li, Xiaodong; Mao, Shengcheng; Han, Xiaodong
2016-07-01
Ceramic/polymer composite equipped with 3D interlocking skeleton (3D IL) is developed through a simple freeze-casting method, exhibiting exceptionally light weight, high strength, toughness, and shock resistance. Long-range crack energy dissipation enabled by 3D interlocking structure is considered as the primary reinforcing mechanism for such superior properties. The smart composite design strategy should hold a place in developing future structural engineering materials. PMID:27135462
Freestanding 3D supramolecular particle bridges: fabrication and mechanical behavior.
Ling, Xing Yi; Phang, In Yee; Schönherr, Holger; Reinhoudt, David N; Vancso, G Julius; Huskens, Jurriaan
2009-06-01
Freestanding particle bridges with controlled composition and macroscopic robustness are demonstrated by the use of supramolecular nanoparticle assembly. Self-assembly of nanoparticles, templating, and supramolecular glue infiltration are combined to form stable and ordered three-dimensional polystyrene particle composites on a polydimethylsiloxane stamp. Freestanding hybrid polystyrene nanoparticle bridges are obtained by transfer printing of the hybrid structures onto topographically patterned substrates via host-guest interactions. The mechanical robustness and rigidity of the particle bridges can be controlled by manipulating the layer-by-layer cycles of supramolecular glues of gold nanoparticles and dendrimers. Atomic force microscopy-based microbending results, in particular the location and force-dependent deflection behavior, confirm that the particle bridge fulfills the classical supported-beam characteristics. As estimated from classical beam theory, the bending moduli of the particle bridges vary between 0.8 and 1.1 GPa, depending on the degree of filling by the supramolecular glues. Failure analysis on the particle structure indicates linear elastic behavior and a plastic deformation upon failure. PMID:19373830
Parallel Adaptive Computation of Blood Flow in a 3D ``Whole'' Body Model
NASA Astrophysics Data System (ADS)
Zhou, M.; Figueroa, C. A.; Taylor, C. A.; Sahni, O.; Jansen, K. E.
2008-11-01
Accurate numerical simulations of vascular trauma require the consideration of a larger portion of the vasculature than previously considered, due to the systemic nature of the human body's response. A patient-specific 3D model composed of 78 connected arterial branches extending from the neck to the lower legs is constructed to effectively represent the entire body. Recently developed outflow boundary conditions that appropriately represent the downstream vasculature bed which is not included in the 3D computational domain are applied at 78 outlets. In this work, the pulsatile blood flow simulations are started on a fairly uniform, unstructured mesh that is subsequently adapted using a solution-based approach to efficiently resolve the flow features. The adapted mesh contains non-uniform, anisotropic elements resulting in resolution that conforms with the physical length scales present in the problem. The effects of the mesh resolution on the flow field are studied, specifically on relevant quantities of pressure, velocity and wall shear stress.
NASA Astrophysics Data System (ADS)
Wang, S.; De Hoop, M. V.; Xia, J.; Li, X.
2011-12-01
We consider the modeling of elastic seismic wave propagation on a rectangular domain via the discretization and solution of the inhomogeneous coupled Helmholtz equation in 3D, by exploiting a parallel multifrontal sparse direct solver equipped with Hierarchically Semi-Separable (HSS) structure to reduce the computational complexity and storage. In particular, we are concerned with solving this equation on a large domain, for a large number of different forcing terms in the context of seismic problems in general, and modeling in particular. We resort to a parsimonious mixed grid finite differences scheme for discretizing the Helmholtz operator and Perfect Matched Layer boundaries, resulting in a non-Hermitian matrix. We make use of a nested dissection based domain decomposition, and introduce an approximate direct solver by developing a parallel HSS matrix compression, factorization, and solution approach. We cast our massive parallelization in the framework of the multifrontal method. The assembly tree is partitioned into local trees and a global tree. The local trees are eliminated independently in each processor, while the global tree is eliminated through massive communication. The solver for the inhomogeneous equation is a parallel hybrid between multifrontal and HSS structure. The computational complexity associated with the factorization is almost linear with the size of the Helmholtz matrix. Our numerical approach can be compared with the spectral element method in 3D seismic applications.
Parallel load balancing strategy for Volume-of-Fluid methods on 3-D unstructured meshes
NASA Astrophysics Data System (ADS)
Jofre, Lluís; Borrell, Ricard; Lehmkuhl, Oriol; Oliva, Assensi
2015-02-01
Volume-of-Fluid (VOF) is one of the methods of choice to reproduce the interface motion in the simulation of multi-fluid flows. One of its main strengths is its accuracy in capturing sharp interface geometries, although requiring for it a number of geometric calculations. Under these circumstances, achieving parallel performance on current supercomputers is a must. The main obstacle for the parallelization is that the computing costs are concentrated only in the discrete elements that lie on the interface between fluids. Consequently, if the interface is not homogeneously distributed throughout the domain, standard domain decomposition (DD) strategies lead to imbalanced workload distributions. In this paper, we present a new parallelization strategy for general unstructured VOF solvers, based on a dynamic load balancing process complementary to the underlying DD. Its parallel efficiency has been analyzed and compared to the DD one using up to 1024 CPU-cores on an Intel SandyBridge based supercomputer. The results obtained on the solution of several artificially generated test cases show a speedup of up to ∼12× with respect to the standard DD, depending on the interface size, the initial distribution and the number of parallel processes engaged. Moreover, the new parallelization strategy presented is of general purpose, therefore, it could be used to parallelize any VOF solver without requiring changes on the coupled flow solver. Finally, note that although designed for the VOF method, our approach could be easily adapted to other interface-capturing methods, such as the Level-Set, which may present similar workload imbalances.
Implementation of a 3D mixing layer code on parallel computers
NASA Technical Reports Server (NTRS)
Roe, K.; Thakur, R.; Dang, T.; Bogucz, E.
1995-01-01
This paper summarizes our progress and experience in the development of a Computational-Fluid-Dynamics code on parallel computers to simulate three-dimensional spatially-developing mixing layers. In this initial study, the three-dimensional time-dependent Euler equations are solved using a finite-volume explicit time-marching algorithm. The code was first programmed in Fortran 77 for sequential computers. The code was then converted for use on parallel computers using the conventional message-passing technique, while we have not been able to compile the code with the present version of HPF compilers.
Focusing optics of a parallel beam CCD optical tomography apparatus for 3D radiation gel dosimetry.
Krstajić, Nikola; Doran, Simon J
2006-04-21
Optical tomography of gel dosimeters is a promising and cost-effective avenue for quality control of radiotherapy treatments such as intensity-modulated radiotherapy (IMRT). Systems based on a laser coupled to a photodiode have so far shown the best results within the context of optical scanning of radiosensitive gels, but are very slow ( approximately 9 min per slice) and poorly suited to measurements that require many slices. Here, we describe a fast, three-dimensional (3D) optical computed tomography (optical-CT) apparatus, based on a broad, collimated beam, obtained from a high power LED and detected by a charged coupled detector (CCD). The main advantages of such a system are (i) an acquisition speed approximately two orders of magnitude higher than a laser-based system when 3D data are required, and (ii) a greater simplicity of design. This paper advances our previous work by introducing a new design of focusing optics, which take information from a suitably positioned focal plane and project an image onto the CCD. An analysis of the ray optics is presented, which explains the roles of telecentricity, focusing, acceptance angle and depth-of-field (DOF) in the formation of projections. A discussion of the approximation involved in measuring the line integrals required for filtered backprojection reconstruction is given. Experimental results demonstrate (i) the effect on projections of changing the position of the focal plane of the apparatus, (ii) how to measure the acceptance angle of the optics, and (iii) the ability of the new scanner to image both absorbing and scattering gel phantoms. The quality of reconstructed images is very promising and suggests that the new apparatus may be useful in a clinical setting for fast and accurate 3D dosimetry. PMID:16585845
Parallel 3-D particle-in-cell modelling of charged ultrarelativistic beam dynamics
NASA Astrophysics Data System (ADS)
Boronina, Marina A.; Vshivkov, Vitaly A.
2015-12-01
> ) in supercolliders. We use the 3-D set of Maxwell's equations for the electromagnetic fields, and the Vlasov equation for the distribution function of the beam particles. The model incorporates automatically the longitudinal effects, which can play a significant role in the cases of super-high densities. We present numerical results for the dynamics of two focused ultrarelativistic beams with a size ratio 10:1:100. The results demonstrate high efficiency of the proposed computational methods and algorithms, which are applicable to a variety of problems in relativistic plasma physics.
Characterization of a parallel beam CCD optical-CT apparatus for 3D radiation dosimetry
NASA Astrophysics Data System (ADS)
Krstajić, Nikola; Doran, Simon J.
2006-12-01
This paper describes the initial steps we have taken in establishing CCD based optical-CT as a viable alternative for 3-D radiation dosimetry. First, we compare the optical density (OD) measurements from a high quality test target and variable neutral density filter (VNDF). A modulation transfer function (MTF) of individual projections is derived for three positions of the sinusoidal test target within the scanning tank. Our CCD is then characterized in terms of its signal-to-noise ratio (SNR). Finally, a sample reconstruction of a scan of a PRESAGETM (registered trademark of Heuris Pharma, NJ, Skillman, USA.) dosimeter is given, demonstrating the capabilities of the apparatus.
Simulations of implosions with a 3D, parallel, unstructured-grid, radiation-hydrodynamics code
Kaiser, T B; Milovich, J L; Prasad, M K; Rathkopf, J; Shestakov, A I
1998-12-28
An unstructured-grid, radiation-hydrodynamics code is used to simulate implosions. Although most of the problems are spherically symmetric, they are run on 3D, unstructured grids in order to test the code's ability to maintain spherical symmetry of the converging waves. Three problems, of increasing complexity, are presented. In the first, a cold, spherical, ideal gas bubble is imploded by an enclosing high pressure source. For the second, we add non-linear heat conduction and drive the implosion with twelve laser beams centered on the vertices of an icosahedron. In the third problem, a NIF capsule is driven with a Planckian radiation source.
3D multi-scale analysis of coupled heat and moisture transport and its parallel implementation
NASA Astrophysics Data System (ADS)
Kruis, Jaroslav
2016-06-01
Parallel implementation of two-scale model of coupled heat and moisture transport is described. The coupled heat and moisture transport is based on the Künzel model. Motivation for the two-scale analysis comes from the requirement to describe distribution of the relative humidity and temperature in historical masonry structures.
NASA Astrophysics Data System (ADS)
Schultz, A.
2010-12-01
3D forward solvers lie at the core of inverse formulations used to image the variation of electrical conductivity within the Earth's interior. This property is associated with variations in temperature, composition, phase, presence of volatiles, and in specific settings, the presence of groundwater, geothermal resources, oil/gas or minerals. The high cost of 3D solutions has been a stumbling block to wider adoption of 3D methods. Parallel algorithms for modeling frequency domain 3D EM problems have not achieved wide scale adoption, with emphasis on fairly coarse grained parallelism using MPI and similar approaches. The communications bandwidth as well as the latency required to send and receive network communication packets is a limiting factor in implementing fine grained parallel strategies, inhibiting wide adoption of these algorithms. Leading Graphics Processor Unit (GPU) companies now produce GPUs with hundreds of GPU processor cores per die. The footprint, in silicon, of the GPU's restricted instruction set is much smaller than the general purpose instruction set required of a CPU. Consequently, the density of processor cores on a GPU can be much greater than on a CPU. GPUs also have local memory, registers and high speed communication with host CPUs, usually through PCIe type interconnects. The extremely low cost and high computational power of GPUs provides the EM geophysics community with an opportunity to achieve fine grained (i.e. massive) parallelization of codes on low cost hardware. The current generation of GPUs (e.g. NVidia Fermi) provides 3 billion transistors per chip die, with nearly 500 processor cores and up to 6 GB of fast (DDR5) GPU memory. This latest generation of GPU supports fast hardware double precision (64 bit) floating point operations of the type required for frequency domain EM forward solutions. Each Fermi GPU board can sustain nearly 1 TFLOP in double precision, and multiple boards can be installed in the host computer system. We
A new method to combine 3D reconstruction volumes for multiple parallel circular cone beam orbits
Baek, Jongduk; Pelc, Norbert J.
2010-01-01
Purpose: This article presents a new reconstruction method for 3D imaging using a multiple 360° circular orbit cone beam CT system, specifically a way to combine 3D volumes reconstructed with each orbit. The main goal is to improve the noise performance in the combined image while avoiding cone beam artifacts. Methods: The cone beam projection data of each orbit are reconstructed using the FDK algorithm. When at least a portion of the total volume can be reconstructed by more than one source, the proposed combination method combines these overlap regions using weighted averaging in frequency space. The local exactness and the noise performance of the combination method were tested with computer simulations of a Defrise phantom, a FORBILD head phantom, and uniform noise in the raw data. Results: A noiseless simulation showed that the local exactness of the reconstructed volume from the source with the smallest tilt angle was preserved in the combined image. A noise simulation demonstrated that the combination method improved the noise performance compared to a single orbit reconstruction. Conclusions: In CT systems which have overlap volumes that can be reconstructed with data from more than one orbit and in which the spatial frequency content of each reconstruction can be calculated, the proposed method offers improved noise performance while keeping the local exactness of data from the source with the smallest tilt angle. PMID:21089770
Simulation of the 3D viscoelastic free surface flow by a parallel corrected particle scheme
NASA Astrophysics Data System (ADS)
Jin-Lian, Ren; Tao, Jiang
2016-02-01
In this work, the behavior of the three-dimensional (3D) jet coiling based on the viscoelastic Oldroyd-B model is investigated by a corrected particle scheme, which is named the smoothed particle hydrodynamics with corrected symmetric kernel gradient and shifting particle technique (SPH_CS_SP) method. The accuracy and stability of SPH_CS_SP method is first tested by solving Poiseuille flow and Taylor-Green flow. Then the capacity for the SPH_CS_SP method to solve the viscoelastic fluid is verified by the polymer flow through a periodic array of cylinders. Moreover, the convergence of the SPH_CS_SP method is also investigated. Finally, the proposed method is further applied to the 3D viscoelastic jet coiling problem, and the influences of macroscopic parameters on the jet coiling are discussed. The numerical results show that the SPH_CS_SP method has higher accuracy and better stability than the traditional SPH method and other corrected SPH method, and can improve the tensile instability. Project supported by the Natural Science Foundation of Jiangsu Province, China (Grant Nos. BK20130436 and BK20150436) and the Natural Science Foundation of the Higher Education Institutions of Jiangsu Province, China (Grant No. 15KJB110025).
Lim, Jong-Min; Bertrand, Nicolas; Valencia, Pedro M.; Rhee, Minsoung; Langer, Robert; Jon, Sangyong; Farokhzad, Omid C.; Karnik, Rohit
2014-01-01
Microfluidic synthesis of nanoparticles (NPs) can enhance the controllability and reproducibility in physicochemical properties of NPs compared to bulk synthesis methods. However, applications of microfluidic synthesis are typically limited to in vitro studies due to low production rates. Herein, we report the parallelization of NP synthesis by 3D hydrodynamic flow focusing (HFF) using a multilayer microfluidic system to enhance the production rate without losing the advantages of reproducibility, controllability, and robustness. Using parallel 3D HFF, polymeric poly(lactide-co-glycolide)-b-polyethyleneglycol (PLGA-PEG) NPs with sizes tunable in the range of 13–150 nm could be synthesized reproducibly with high production rate. As a proof of concept, we used this system to perform in vivo pharmacokinetic and biodistribution study of small (20 nm diameter) PLGA-PEG NPs that are otherwise difficult to synthesize. Microfluidic parallelization thus enables synthesis of NPs with tunable properties with production rates suitable for both in vitro and in vivo studies. PMID:23969105
Large-Scale Parallel Unstructured Mesh Computations for 3D High-Lift Analysis
NASA Technical Reports Server (NTRS)
Mavriplis, D. J.; Pirzadeh, S.
1999-01-01
A complete "geometry to drag-polar" analysis capability for three-dimensional high-lift configurations is described. The approach is based on the use of unstructured meshes in order to enable rapid turnaround for complicated geometries which arise in high-lift configurations. Special attention is devoted to creating a capability for enabling analyses on highly resolved grids. Unstructured meshes of several million vertices are initially generated on a work-station, and subsequently refined on a supercomputer. The flow is solved on these refined meshes on large parallel computers using an unstructured agglomeration multigrid algorithm. Good prediction of lift and drag throughout the range of incidences is demonstrated on a transport take-off configuration using up to 24.7 million grid points. The feasibility of using this approach in a production environment on existing parallel machines is demonstrated, as well as the scalability of the solver on machines using up to 1450 processors.
Large-scale Parallel Unstructured Mesh Computations for 3D High-lift Analysis
NASA Technical Reports Server (NTRS)
Mavriplis, Dimitri J.; Pirzadeh, S.
1999-01-01
A complete "geometry to drag-polar" analysis capability for the three-dimensional high-lift configurations is described. The approach is based on the use of unstructured meshes in order to enable rapid turnaround for complicated geometries that arise in high-lift configurations. Special attention is devoted to creating a capability for enabling analyses on highly resolved grids. Unstructured meshes of several million vertices are initially generated on a work-station, and subsequently refined on a supercomputer. The flow is solved on these refined meshes on large parallel computers using an unstructured agglomeration multigrid algorithm. Good prediction of lift and drag throughout the range of incidences is demonstrated on a transport take-off configuration using up to 24.7 million grid points. The feasibility of using this approach in a production environment on existing parallel machines is demonstrated, as well as the scalability of the solver on machines using up to 1450 processors.
Large-Scale Parallel Unstructured Mesh Computations for 3D High-Lift Analysis
NASA Technical Reports Server (NTRS)
Mavriplis, D. J.; Pirzadeh, S.
1999-01-01
A complete "geometry to drag-polar" analysis capability for three-dimensional high-lift configurations is described. The approach is based on the use of unstructured meshes in order to enable rapid turnaround for complicated geometries which arise in high-lift con gurations. Special attention is devoted to creating a capability for enabling analyses on highly resolved grids. Unstructured meshes of several million vertices are initially generated on a work-station, and subsequently refined on a supercomputer. The flow is solved on these refined meshes on large parallel computers using an unstructured agglomeration multigrid algorithm. Good prediction of lift and drag throughout the range of incidences is demonstrated on a transport take-off configuration using up to 24.7 million grid points. The feasibility of using this approach in a production environment on existing parallel machines is demonstrated, as well as the scalability of the solver on machines using up to 1450 processors.
A parallel dynamic load balancing algorithm for 3-D adaptive unstructured grids
NASA Technical Reports Server (NTRS)
Vidwans, A.; Kallinderis, Y.; Venkatakrishnan, V.
1993-01-01
Adaptive local grid refinement and coarsening results in unequal distribution of workload among the processors of a parallel system. A novel method for balancing the load in cases of dynamically changing tetrahedral grids is developed. The approach employs local exchange of cells among processors in order to redistribute the load equally. An important part of the load balancing algorithm is the method employed by a processor to determine which cells within its subdomain are to be exchanged. Two such methods are presented and compared. The strategy for load balancing is based on the Divide-and-Conquer approach which leads to an efficient parallel algorithm. This method is implemented on a distributed-memory MIMD system.
High-Performance Computation of Distributed-Memory Parallel 3D Voronoi and Delaunay Tessellation
Peterka, Tom; Morozov, Dmitriy; Phillips, Carolyn
2014-11-14
Computing a Voronoi or Delaunay tessellation from a set of points is a core part of the analysis of many simulated and measured datasets: N-body simulations, molecular dynamics codes, and LIDAR point clouds are just a few examples. Such computational geometry methods are common in data analysis and visualization; but as the scale of simulations and observations surpasses billions of particles, the existing serial and shared-memory algorithms no longer suffice. A distributed-memory scalable parallel algorithm is the only feasible approach. The primary contribution of this paper is a new parallel Delaunay and Voronoi tessellation algorithm that automatically determines which neighbor points need to be exchanged among the subdomains of a spatial decomposition. Other contributions include periodic and wall boundary conditions, comparison of our method using two popular serial libraries, and application to numerous science datasets.
Task-parallel implementation of 3D shortest path raytracing for geophysical applications
NASA Astrophysics Data System (ADS)
Giroux, Bernard; Larouche, Benoît
2013-04-01
This paper discusses two variants of the shortest path method and their parallel implementation on a shared-memory system. One variant is designed to perform raytracing in models with stepwise distributions of interval velocity while the other is better suited for continuous velocity models. Both rely on a discretization scheme where primary nodes are located at the corners of cuboid cells and where secondary nodes are found on the edges and sides of the cells. The parallel implementations allow raytracing concurrently for different sources, providing an attractive framework for ray-based tomography. The accuracy and performance of the implementations were measured by comparison with the analytic solution for a layered model and for a vertical gradient model. Mean relative error less than 0.2% was obtained with 5 secondary nodes for the layered model and 9 secondary nodes for the gradient model. Parallel performance depends on the level of discretization refinement, on the number of threads, and on the problem size, with the most determinant variable being the level of discretization refinement (number of secondary nodes). The results indicate that a good trade-off between speed and accuracy is achieved with the number of secondary nodes equal to 5. The programs are written in C++ and rely on the Standard Template Library and OpenMP.
NASA Astrophysics Data System (ADS)
Chen, Zhaoxi; Meng, Xiaohong; Guo, Lianghui; Liu, Guofeng
2012-09-01
The 3D correlation imaging for gravity and gravity gradiometry data provides a rapid approach to the equivalent estimation of objective bodies with different density contrasts in the subsurface. The subsurface is divided into a 3D regular grid, and then a cross correlation between the observed data and the theoretical gravity anomaly due to a point mass source is calculated at each grid node. The resultant correlation coefficients are adopted to describe the equivalent mass distribution in a quantitate probability sense. However, when the size of the survey data is large, it is still computationally expensive. With the advent of the CUDA, GPUs lead to a new path for parallel computing, which have been widely applied in seismic processing, astronomy, molecular dynamics simulation, fluid mechanics and some other fields. We transfer the main time-consuming program of 3D correlation imaging into GPU device, where the program can be executed in a parallel way. The synthetic and real tests have been performed to validate the correctness of our code on NVIDIA GTX 550. The precision evaluation and performance speedup comparison of the CPU and GPU implementations are illustrated with different sizes of gravity data. When the size of grid nodes and observed data sets is 1024×1024×1 and 1024×1024, the speed up can reach to 81.5 for gravity data and 90.7 for gravity vertical gradient data respectively, thus providing the basis for the rapid interpretation of gravity and gravity gradiometry data.
3D parallel-detection microwave tomography for clinical breast imaging
Epstein, N. R.; Meaney, P. M.; Paulsen, K. D.
2014-12-15
A biomedical microwave tomography system with 3D-imaging capabilities has been constructed and translated to the clinic. Updates to the hardware and reconfiguration of the electronic-network layouts in a more compartmentalized construct have streamlined system packaging. Upgrades to the data acquisition and microwave components have increased data-acquisition speeds and improved system performance. By incorporating analog-to-digital boards that accommodate the linear amplification and dynamic-range coverage our system requires, a complete set of data (for a fixed array position at a single frequency) is now acquired in 5.8 s. Replacement of key components (e.g., switches and power dividers) by devices with improved operational bandwidths has enhanced system response over a wider frequency range. High-integrity, low-power signals are routinely measured down to −130 dBm for frequencies ranging from 500 to 2300 MHz. Adequate inter-channel isolation has been maintained, and a dynamic range >110 dB has been achieved for the full operating frequency range (500–2900 MHz). For our primary band of interest, the associated measurement deviations are less than 0.33% and 0.5° for signal amplitude and phase values, respectively. A modified monopole antenna array (composed of two interwoven eight-element sub-arrays), in conjunction with an updated motion-control system capable of independently moving the sub-arrays to various in-plane and cross-plane positions within the illumination chamber, has been configured in the new design for full volumetric data acquisition. Signal-to-noise ratios (SNRs) are more than adequate for all transmit/receive antenna pairs over the full frequency range and for the variety of in-plane and cross-plane configurations. For proximal receivers, in-plane SNRs greater than 80 dB are observed up to 2900 MHz, while cross-plane SNRs greater than 80 dB are seen for 6 cm sub-array spacing (for frequencies up to 1500 MHz). We demonstrate accurate
3D parallel-detection microwave tomography for clinical breast imaging
NASA Astrophysics Data System (ADS)
Epstein, N. R.; Meaney, P. M.; Paulsen, K. D.
2014-12-01
A biomedical microwave tomography system with 3D-imaging capabilities has been constructed and translated to the clinic. Updates to the hardware and reconfiguration of the electronic-network layouts in a more compartmentalized construct have streamlined system packaging. Upgrades to the data acquisition and microwave components have increased data-acquisition speeds and improved system performance. By incorporating analog-to-digital boards that accommodate the linear amplification and dynamic-range coverage our system requires, a complete set of data (for a fixed array position at a single frequency) is now acquired in 5.8 s. Replacement of key components (e.g., switches and power dividers) by devices with improved operational bandwidths has enhanced system response over a wider frequency range. High-integrity, low-power signals are routinely measured down to -130 dBm for frequencies ranging from 500 to 2300 MHz. Adequate inter-channel isolation has been maintained, and a dynamic range >110 dB has been achieved for the full operating frequency range (500-2900 MHz). For our primary band of interest, the associated measurement deviations are less than 0.33% and 0.5° for signal amplitude and phase values, respectively. A modified monopole antenna array (composed of two interwoven eight-element sub-arrays), in conjunction with an updated motion-control system capable of independently moving the sub-arrays to various in-plane and cross-plane positions within the illumination chamber, has been configured in the new design for full volumetric data acquisition. Signal-to-noise ratios (SNRs) are more than adequate for all transmit/receive antenna pairs over the full frequency range and for the variety of in-plane and cross-plane configurations. For proximal receivers, in-plane SNRs greater than 80 dB are observed up to 2900 MHz, while cross-plane SNRs greater than 80 dB are seen for 6 cm sub-array spacing (for frequencies up to 1500 MHz). We demonstrate accurate recovery
3D parallel-detection microwave tomography for clinical breast imaging.
Epstein, N R; Meaney, P M; Paulsen, K D
2014-12-01
A biomedical microwave tomography system with 3D-imaging capabilities has been constructed and translated to the clinic. Updates to the hardware and reconfiguration of the electronic-network layouts in a more compartmentalized construct have streamlined system packaging. Upgrades to the data acquisition and microwave components have increased data-acquisition speeds and improved system performance. By incorporating analog-to-digital boards that accommodate the linear amplification and dynamic-range coverage our system requires, a complete set of data (for a fixed array position at a single frequency) is now acquired in 5.8 s. Replacement of key components (e.g., switches and power dividers) by devices with improved operational bandwidths has enhanced system response over a wider frequency range. High-integrity, low-power signals are routinely measured down to -130 dBm for frequencies ranging from 500 to 2300 MHz. Adequate inter-channel isolation has been maintained, and a dynamic range >110 dB has been achieved for the full operating frequency range (500-2900 MHz). For our primary band of interest, the associated measurement deviations are less than 0.33% and 0.5° for signal amplitude and phase values, respectively. A modified monopole antenna array (composed of two interwoven eight-element sub-arrays), in conjunction with an updated motion-control system capable of independently moving the sub-arrays to various in-plane and cross-plane positions within the illumination chamber, has been configured in the new design for full volumetric data acquisition. Signal-to-noise ratios (SNRs) are more than adequate for all transmit/receive antenna pairs over the full frequency range and for the variety of in-plane and cross-plane configurations. For proximal receivers, in-plane SNRs greater than 80 dB are observed up to 2900 MHz, while cross-plane SNRs greater than 80 dB are seen for 6 cm sub-array spacing (for frequencies up to 1500 MHz). We demonstrate accurate recovery
3D parallel-detection microwave tomography for clinical breast imaging
Meaney, P. M.; Paulsen, K. D.
2014-01-01
A biomedical microwave tomography system with 3D-imaging capabilities has been constructed and translated to the clinic. Updates to the hardware and reconfiguration of the electronic-network layouts in a more compartmentalized construct have streamlined system packaging. Upgrades to the data acquisition and microwave components have increased data-acquisition speeds and improved system performance. By incorporating analog-to-digital boards that accommodate the linear amplification and dynamic-range coverage our system requires, a complete set of data (for a fixed array position at a single frequency) is now acquired in 5.8 s. Replacement of key components (e.g., switches and power dividers) by devices with improved operational bandwidths has enhanced system response over a wider frequency range. High-integrity, low-power signals are routinely measured down to −130 dBm for frequencies ranging from 500 to 2300 MHz. Adequate inter-channel isolation has been maintained, and a dynamic range >110 dB has been achieved for the full operating frequency range (500–2900 MHz). For our primary band of interest, the associated measurement deviations are less than 0.33% and 0.5° for signal amplitude and phase values, respectively. A modified monopole antenna array (composed of two interwoven eight-element sub-arrays), in conjunction with an updated motion-control system capable of independently moving the sub-arrays to various in-plane and cross-plane positions within the illumination chamber, has been configured in the new design for full volumetric data acquisition. Signal-to-noise ratios (SNRs) are more than adequate for all transmit/receive antenna pairs over the full frequency range and for the variety of in-plane and cross-plane configurations. For proximal receivers, in-plane SNRs greater than 80 dB are observed up to 2900 MHz, while cross-plane SNRs greater than 80 dB are seen for 6 cm sub-array spacing (for frequencies up to 1500 MHz). We demonstrate accurate
McGhee, J.M.; Roberts, R.M.; Morel, J.E.
1997-06-01
A spherical harmonics research code (DANTE) has been developed which is compatible with parallel computer architectures. DANTE provides 3-D, multi-material, deterministic, transport capabilities using an arbitrary finite element mesh. The linearized Boltzmann transport equation is solved in a second order self-adjoint form utilizing a Galerkin finite element spatial differencing scheme. The core solver utilizes a preconditioned conjugate gradient algorithm. Other distinguishing features of the code include options for discrete-ordinates and simplified spherical harmonics angular differencing, an exact Marshak boundary treatment for arbitrarily oriented boundary faces, in-line matrix construction techniques to minimize memory consumption, and an effective diffusion based preconditioner for scattering dominated problems. Algorithm efficiency is demonstrated for a massively parallel SIMD architecture (CM-5), and compatibility with MPP multiprocessor platforms or workstation clusters is anticipated.
NASA Astrophysics Data System (ADS)
Awatsuji, Yasuhiro; Xia, Peng; Wang, Yexin; Matoba, Osamu
2016-03-01
Digital holography is a technique of 3D measurement of object. The technique uses an image sensor to record the interference fringe image containing the complex amplitude of object, and numerically reconstructs the complex amplitude by computer. Parallel phase-shifting digital holography is capable of accurate 3D measurement of dynamic object. This is because this technique can reconstruct the complex amplitude of object, on which the undesired images are not superimposed, form a single hologram. The undesired images are the non-diffraction wave and the conjugate image which are associated with holography. In parallel phase-shifting digital holography, a hologram, whose phase of the reference wave is spatially and periodically shifted every other pixel, is recorded to obtain complex amplitude of object by single-shot exposure. The recorded hologram is decomposed into multiple holograms required for phase-shifting digital holography. The complex amplitude of the object is free from the undesired images is reconstructed from the multiple holograms. To validate parallel phase-shifting digital holography, a high-speed parallel phase-shifting digital holography system was constructed. The system consists of a Mach-Zehnder interferometer, a continuous-wave laser, and a high-speed polarization imaging camera. Phase motion picture of dynamic air flow sprayed from a nozzle was recorded at 180,000 frames per second (FPS) have been recorded by the system. Also phase motion picture of dynamic air induced by discharge between two electrodes has been recorded at 1,000,000 FPS, when high voltage was applied between the electrodes.
High-speed 3D imaging using two-wavelength parallel-phase-shift interferometry.
Safrani, Avner; Abdulhalim, Ibrahim
2015-10-15
High-speed three dimensional imaging based on two-wavelength parallel-phase-shift interferometry is presented. The technique is demonstrated using a high-resolution polarization-based Linnik interferometer operating with three high-speed phase-masked CCD cameras and two quasi-monochromatic modulated light sources. The two light sources allow for phase unwrapping the single source wrapped phase so that relatively high step profiles having heights as large as 3.7 μm can be imaged in video rate with ±2 nm accuracy and repeatability. The technique is validated using a certified very large scale integration (VLSI) step standard followed by a demonstration from the semiconductor industry showing an integrated chip with 2.75 μm height copper micro pillars at different packing densities. PMID:26469586
Parallel deconvolution of large 3D images obtained by confocal laser scanning microscopy.
Pawliczek, Piotr; Romanowska-Pawliczek, Anna; Soltys, Zbigniew
2010-03-01
Various deconvolution algorithms are often used for restoration of digital images. Image deconvolution is especially needed for the correction of three-dimensional images obtained by confocal laser scanning microscopy. Such images suffer from distortions, particularly in the Z dimension. As a result, reliable automatic segmentation of these images may be difficult or even impossible. Effective deconvolution algorithms are memory-intensive and time-consuming. In this work, we propose a parallel version of the well-known Richardson-Lucy deconvolution algorithm developed for a system with distributed memory and implemented with the use of Message Passing Interface (MPI). It enables significantly more rapid deconvolution of two-dimensional and three-dimensional images by efficiently splitting the computation across multiple computers. The implementation of this algorithm can be used on professional clusters provided by computing centers as well as on simple networks of ordinary PC machines. PMID:19725070
Parallel Implementation of an Adaptive Scheme for 3D Unstructured Grids on the SP2
NASA Technical Reports Server (NTRS)
Oliker, Leonid; Biswas, Rupak; Strawn, Roger C.
1996-01-01
Dynamic mesh adaption on unstructured grids is a powerful tool for computing unsteady flows that require local grid modifications to efficiently resolve solution features. For this work, we consider an edge-based adaption scheme that has shown good single-processor performance on the C90. We report on our experience parallelizing this code for the SP2. Results show a 47.OX speedup on 64 processors when 10% of the mesh is randomly refined. Performance deteriorates to 7.7X when the same number of edges are refined in a highly-localized region. This is because almost all mesh adaption is confined to a single processor. However, this problem can be remedied by repartitioning the mesh immediately after targeting edges for refinement but before the actual adaption takes place. With this change, the speedup improves dramatically to 43.6X.
Parallel implementation of an adaptive scheme for 3D unstructured grids on the SP2
NASA Technical Reports Server (NTRS)
Strawn, Roger C.; Oliker, Leonid; Biswas, Rupak
1996-01-01
Dynamic mesh adaption on unstructured grids is a powerful tool for computing unsteady flows that require local grid modifications to efficiently resolve solution features. For this work, we consider an edge-based adaption scheme that has shown good single-processor performance on the C90. We report on our experience parallelizing this code for the SP2. Results show a 47.0X speedup on 64 processors when 10 percent of the mesh is randomly refined. Performance deteriorates to 7.7X when the same number of edges are refined in a highly-localized region. This is because almost all the mesh adaption is confined to a single processor. However, this problem can be remedied by repartitioning the mesh immediately after targeting edges for refinement but before the actual adaption takes place. With this change, the speedup improves dramatically to 43.6X.
NASA Astrophysics Data System (ADS)
Li, Dian-Sen; Fang, Dai-Ning; Lu, Zi-Xing; Yang, Zhen-Yu; Jiang, Nan
2010-08-01
In the first part of the work, we have established a new parameterized three-dimensional (3D) finite element model (FEM) which precisely simulated the spatial configuration of the braiding yarns and considered the cross-section deformation as well as the surface contact relationship between the yarns. This paper presents a prediction of the effective elastic properties and the meso-scale mechanical response of 3D braided composites to verify the validation of the FEM. The effects of the braiding parameters on the mechanical properties are investigated in detail. By analyzing the deformation and stress nephogram of the model, a reasonable overall stress field is provided and the results well support the strength prediction. The results indicate it is convenient to predict all the elastic constants of 3D braided composites with different parameters simultaneously using the FEM. Moreover, the FEM can successfully predict the meso-scale mechanical response of 3D braided composites containing periodical structures.
Enhancements, Parallelization and Future Directions of the V3FIT 3-D Equilibrium Reconstruction Code
NASA Astrophysics Data System (ADS)
Cianciosa, M. R.; Hanson, J. D.; Maurer, D. A.; Hartwell, G. J.; Archmiller, M. C.; Ma, X.; Herfindal, J.
2014-10-01
Three-dimensional equilibrium reconstruction is spreading beyond its original application to stellarators. Three-dimensional effects in nominally axisymmetric systems, including quasi-helical states in reversed field pinches and error fields in tokamaks, are becoming increasingly important. V3FIT is a fully three dimensional equilibrium reconstruction code in widespread use throughout the fusion community. The code has recently undergone extensive revision to prepare for the next generation of equilibrium reconstruction problems. The most notable changes are the abstraction of the equilibrium model, the propagation of experimental errors to the reconstructed results, support for multicolor soft x-ray emissivity cameras, and recent efforts to add parallelization for efficient computation on multi-processor system. Work presented will contain discussions on these new capabilities. We will compare probability distributions of reconstructed parameters with results from whole shot reconstructions. We will show benchmarking and profiling results of initial performance improvements through the addition of OpenMP and MPI support. We will discuss future directions of the V3FIT code including steps taken for support of the W-7X stellarator. Work supported by US. Department of Energy Grant No. DEFG-0203-ER-54692B.
A 3D MPI-Parallel GPU-accelerated framework for simulating ocean wave energy converters
NASA Astrophysics Data System (ADS)
Pathak, Ashish; Raessi, Mehdi
2015-11-01
We present an MPI-parallel GPU-accelerated computational framework for studying the interaction between ocean waves and wave energy converters (WECs). The computational framework captures the viscous effects, nonlinear fluid-structure interaction (FSI), and breaking of waves around the structure, which cannot be captured in many potential flow solvers commonly used for WEC simulations. The full Navier-Stokes equations are solved using the two-step projection method, which is accelerated by porting the pressure Poisson equation to GPUs. The FSI is captured using the numerically stable fictitious domain method. A novel three-phase interface reconstruction algorithm is used to resolve three phases in a VOF-PLIC context. A consistent mass and momentum transport approach enables simulations at high density ratios. The accuracy of the overall framework is demonstrated via an array of test cases. Numerical simulations of the interaction between ocean waves and WECs are presented. Funding from the National Science Foundation CBET-1236462 grant is gratefully acknowledged.
NASA Astrophysics Data System (ADS)
Koldan, Jelena; Puzyrev, Vladimir; de la Puente, Josep; Houzeaux, Guillaume; Cela, José María
2014-06-01
We present an elaborate preconditioning scheme for Krylov subspace methods which has been developed to improve the performance and reduce the execution time of parallel node-based finite-element (FE) solvers for 3-D electromagnetic (EM) numerical modelling in exploration geophysics. This new preconditioner is based on algebraic multigrid (AMG) that uses different basic relaxation methods, such as Jacobi, symmetric successive over-relaxation (SSOR) and Gauss-Seidel, as smoothers and the wave front algorithm to create groups, which are used for a coarse-level generation. We have implemented and tested this new preconditioner within our parallel nodal FE solver for 3-D forward problems in EM induction geophysics. We have performed series of experiments for several models with different conductivity structures and characteristics to test the performance of our AMG preconditioning technique when combined with biconjugate gradient stabilized method. The results have shown that, the more challenging the problem is in terms of conductivity contrasts, ratio between the sizes of grid elements and/or frequency, the more benefit is obtained by using this preconditioner. Compared to other preconditioning schemes, such as diagonal, SSOR and truncated approximate inverse, the AMG preconditioner greatly improves the convergence of the iterative solver for all tested models. Also, when it comes to cases in which other preconditioners succeed to converge to a desired precision, AMG is able to considerably reduce the total execution time of the forward-problem code-up to an order of magnitude. Furthermore, the tests have confirmed that our AMG scheme ensures grid-independent rate of convergence, as well as improvement in convergence regardless of how big local mesh refinements are. In addition, AMG is designed to be a black-box preconditioner, which makes it easy to use and combine with different iterative methods. Finally, it has proved to be very practical and efficient in the
NASA Astrophysics Data System (ADS)
Morgan, J. P.; Hasenclever, J.; Shi, C.
2009-12-01
Computational studies of mantle convection face large challenges to obtain fast and accurate solutions for variable viscosity 3d flow. Recently we have been using parallel (MPI-based) MATLAB to more thoroughly explore possible pitfalls and algorithmic improvements to current ‘best-practice’ variable viscosity Stokes and D’Arcy flow solvers. Here we focus on study of finite-element solvers based on a decomposition of the equations for incompressible Stokes flow: Ku + Gp = f and G’u = 0 (K-velocity stiffness matrix, G-discretized gradient operator, G’=transpose(G)-discretized divergence operator) into a single equation for pressure Sp==G’K^-1Gp =G’K^-1f, in which the velocity is also updated as part of each pressure iteration. The outer pressure iteration is solved with preconditioned conjugate gradients (CG) (Maday and Patera, 1989), with a multigrid-preconditioned CG solver for the z=K^-1 (Gq) step of each pressure iteration. One fairly well-known pitfall (Fortin, 1985) is that constant-pressure elements can generate a spurious non-zero flow under a constant body force within non-rectangular geometries. We found a new pitfall when using an iterative method to solve the Kz=y operation in evaluating each G’K^-1Gq product -- even if the residual of the outer pressure equation converges to zero, the discrete divergence of this equation does not correspondingly converge; the error in the incompressibility depends on roughly the square of the tolerance used to solve each Kz=y velocity-like subproblem. Our current best recipe is: (1) Use flexible CG (cf. Notay, 2001) to solve the outer pressure problem. This is analogous to GMRES for a symmetric positive definite problem. It allows use of numerically unsymmetric and/or inexact preconditioners with CG. (2) In this outer-iteration, use an ‘alpha-bar’ technique to find the appropriate magnitude alpha to change the solution in each search direction. This improvement allows a similar iterative tolerance of
3D printed auxetic forms on knitted fabrics for adjustable permeability and mechanical properties
NASA Astrophysics Data System (ADS)
Grimmelsmann, N.; Meissner, H.; Ehrmann, A.
2016-07-01
The 3D printing technology can be applied into manufacturing primary shaping diverse products, from models dealing as examples for future products that will be produced with another technique, to useful objects. Since 3D printing is nowadays significantly slower than other possibilities to manufacture items, such as die casting, it is often used for small parts that are produced in small numbers or for products that cannot be created in another way. Combinations of 3D printing with other objects, adding novel functionalities to them, are thus favourable to a complete primary shaping process. Textile fabrics belong to the objects whose mechanical and other properties can notably be modified by adding 3D printed forms. This article mainly reports on a new possibility to change the permeability of textile fabrics by 3D printing auxetic forms, e.g. for utilising them in textile filters. In addition, auxetic forms 3D printed on knitted fabrics can bring about mechanical properties that are conducive to tensile constructions.
NASA Astrophysics Data System (ADS)
Gainullin, I. K.; Sonkin, M. A.
2015-03-01
A parallelized three-dimensional (3D) time-dependent Schrodinger equation (TDSE) solver for one-electron systems is presented in this paper. The TDSE Solver is based on the finite-difference method (FDM) in Cartesian coordinates and uses a simple and explicit leap-frog numerical scheme. The simplicity of the numerical method provides very efficient parallelization and high performance of calculations using Graphics Processing Units (GPUs). For example, calculation of 106 time-steps on the 1000ṡ1000ṡ1000 numerical grid (109 points) takes only 16 hours on 16 Tesla M2090 GPUs. The TDSE Solver demonstrates scalability (parallel efficiency) close to 100% with some limitations on the problem size. The TDSE Solver is validated by calculation of energy eigenstates of the hydrogen atom (13.55 eV) and affinity level of H- ion (0.75 eV). The comparison with other TDSE solvers shows that a GPU-based TDSE Solver is 3 times faster for the problems of the same size and with the same cost of computational resources. The usage of a non-regular Cartesian grid or problem-specific non-Cartesian coordinates increases this benefit up to 10 times. The TDSE Solver was applied to the calculation of the resonant charge transfer (RCT) in nanosystems, including several related physical problems, such as electron capture during H+-H0 collision and electron tunneling between H- ion and thin metallic island film.
NASA Astrophysics Data System (ADS)
Kim, Jaewook; Ghim, Young-Chul; Nuclear Fusion and Plasma Lab Team
2014-10-01
A BES (beam emission spectroscopy) system and an MIR (Microwave Imaging Reflectometer) system installed in KSTAR measure 2D (radial and poloidal) density fluctuations at two different toroidal locations. This gives a possibility of measuring the parallel correlation length of ion-scale turbulence in KSTAR. Due to lack of measurement points in toroidal direction and shorter separation distance between the diagnostics compared to an expected parallel correlation length, it is necessary to confirm whether a conventional statistical method, i.e., using a cross-correlation function, is valid for measuring the parallel correlation length. For this reason, we generated synthetic 3D density fluctuation data following Gaussian random field in a toroidal coordinate system that mimic real density fluctuation data. We measure the correlation length of the synthetic data by fitting a Gaussian function to the cross-correlation function. We observe that there is disagreement between the measured and actual correlation lengths, and the degree of disagreement is a function of at least, correlation length, correlation time and advection velocity of synthetic data. We identify the cause of disagreement and propose an appropriate method to measure correct correlation length.
NASA Astrophysics Data System (ADS)
Petersson, Anders; Rodgers, Arthur
2010-05-01
conserving, coupling procedure for the elastic wave equation at grid refinement interfaces. When used together with our single grid finite difference scheme, it results in a method which is provably stable, without artificial dissipation, for arbitrary heterogeneous isotropic elastic materials. The new coupling procedure is based on satisfying the summation-by-parts principle across refinement interfaces. From a practical standpoint, an important advantage of the proposed method is the absence of tunable numerical parameters, which seldom are appreciated by application experts. In WPP, the composite grid discretization is combined with a curvilinear grid approach that enables accurate modeling of free surfaces on realistic (non-planar) topography. The overall method satisfies the summation-by-parts principle and is stable under a CFL time step restriction. A feature of great practical importance is that WPP automatically generates the composite grid based on the user provided topography and the depths of the grid refinement interfaces. The WPP code has been verified extensively, for example using the method of manufactured solutions, by solving Lamb's problem, by solving various layer over half- space problems and comparing to semi-analytic (FK) results, and by simulating scenario earthquakes where results from other seismic simulation codes are available. WPP has also been validated against seismographic recordings of moderate earthquakes. WPP performs well on large parallel computers and has been run on up to 32,768 processors using about 26 Billion grid points (78 Billion DOF) and 41,000 time steps. WPP is an open source code that is available under the Gnu general public license.
Finite Element Analysis of Thermo-Mechanical Properties of 3D Braided Composites
NASA Astrophysics Data System (ADS)
Jiang, Li-li; Xu, Guo-dong; Cheng, Su; Lu, Xia-mei; Zeng, Tao
2014-04-01
This paper presents a modified finite element model (FEM) to investigate the thermo-mechanical properties of three-dimensional (3D) braided composite. The effective coefficients of thermal expansion (CTE) and the meso-scale mechanical response of 3D braided composites are predicted. The effects of the braiding angle and fiber volume fraction on the effective CTE are evaluated. The results are compared to the experimental data available in the literature to demonstrate the accuracy and reliability of the present method. The tensile stress distributions of the representative volume element (RVE) are also outlined. It is found that the stress of the braiding yarn has a significant increase with temperature rise; on the other hand, the temperature change has an insignificant effect on the stress of the matrix. In addition, a rapid decrease in the tensile strength of 3D braided composites is observed with the increase in temperature. It is revealed that the thermal conditions have a significant effect on the strength of 3D braided composites. The present method provides an effective tool to predict the stresses of 3D braided composites under thermo-mechanical loading.
Ma, Yingliang; Saetzler, Kurt
2008-01-01
In this paper we describe a novel 3D subdivision strategy to extract the surface of binary image data. This iterative approach generates a series of surface meshes that capture different levels of detail of the underlying structure. At the highest level of detail, the resulting surface mesh generated by our approach uses only about 10% of the triangles in comparison to the marching cube algorithm (MC) even in settings were almost no image noise is present. Our approach also eliminates the so-called "staircase effect" which voxel based algorithms like the MC are likely to show, particularly if non-uniformly sampled images are processed. Finally, we show how the presented algorithm can be parallelized by subdividing 3D image space into rectilinear blocks of subimages. As the algorithm scales very well with an increasing number of processors in a multi-threaded setting, this approach is suited to process large image data sets of several gigabytes. Although the presented work is still computationally more expensive than simple voxel-based algorithms, it produces fewer surface triangles while capturing the same level of detail, is more robust towards image noise and eliminates the above-mentioned "staircase" effect in anisotropic settings. These properties make it particularly useful for biomedical applications, where these conditions are often encountered. PMID:17993710
Untethered hovering flapping flight of a 3D-printed mechanical insect.
Richter, Charles; Lipson, Hod
2011-01-01
This project focuses on developing a flapping-wing hovering insect using 3D-printed wings and mechanical parts. The use of 3D printing technology has greatly expanded the possibilities for wing design, allowing wing shapes to replicate those of real insects or virtually any other shape. It has also reduced the time of a wing design cycle to a matter of minutes. An ornithopter with a mass of 3.89 g has been constructed using the 3D printing technique and has demonstrated an 85-s passively stable untethered hovering flight. This flight exhibits the functional utility of printed materials for flapping-wing experimentation and ornithopter construction and for understanding the mechanical principles underlying insect flight and control. PMID:21370958
Mechanical Modelling of Pultrusion Process: 2D and 3D Numerical Approaches
NASA Astrophysics Data System (ADS)
Baran, Ismet; Hattel, Jesper H.; Akkerman, Remko; Tutum, Cem C.
2015-02-01
The process induced variations such as residual stresses and distortions are a critical issue in pultrusion, since they affect the structural behavior as well as the mechanical properties and geometrical precision of the final product. In order to capture and investigate these variations, a mechanical analysis should be performed. In the present work, the two dimensional (2D) quasi-static plane strain mechanical model for the pultrusion of a thick square profile developed by the authors is further improved using generalized plane strain elements. In addition to that, a more advanced 3D thermo-chemical-mechanical analysis is carried out using 3D quadratic elements which is a novel application for the numerical modelling of the pultrusion process. It is found that the 2D mechanical models give relatively reasonable and accurate stress and displacement evolutions in the transverse direction as compared to the 3D model. Moreover, the generalized plane strain model predicts the longitudinal process induced stresses more similar to the ones calculated in the 3D model as compared with the plane strain model.
3D printed cellular solid outperforms traditional stochastic foam in long-term mechanical response
NASA Astrophysics Data System (ADS)
Maiti, A.; Small, W.; Lewicki, J. P.; Weisgraber, T. H.; Duoss, E. B.; Chinn, S. C.; Pearson, M. A.; Spadaccini, C. M.; Maxwell, R. S.; Wilson, T. S.
2016-04-01
3D printing of polymeric foams by direct-ink-write is a recent technological breakthrough that enables the creation of versatile compressible solids with programmable microstructure, customizable shapes, and tunable mechanical response including negative elastic modulus. However, in many applications the success of these 3D printed materials as a viable replacement for traditional stochastic foams critically depends on their mechanical performance and micro-architectural stability while deployed under long-term mechanical strain. To predict the long-term performance of the two types of foams we employed multi-year-long accelerated aging studies under compressive strain followed by a time-temperature-superposition analysis using a minimum-arc-length-based algorithm. The resulting master curves predict superior long-term performance of the 3D printed foam in terms of two different metrics, i.e., compression set and load retention. To gain deeper understanding, we imaged the microstructure of both foams using X-ray computed tomography, and performed finite-element analysis of the mechanical response within these microstructures. This indicates a wider stress variation in the stochastic foam with points of more extreme local stress as compared to the 3D printed material, which might explain the latter’s improved long-term stability and mechanical performance.
3D printed cellular solid outperforms traditional stochastic foam in long-term mechanical response.
Maiti, A; Small, W; Lewicki, J P; Weisgraber, T H; Duoss, E B; Chinn, S C; Pearson, M A; Spadaccini, C M; Maxwell, R S; Wilson, T S
2016-01-01
3D printing of polymeric foams by direct-ink-write is a recent technological breakthrough that enables the creation of versatile compressible solids with programmable microstructure, customizable shapes, and tunable mechanical response including negative elastic modulus. However, in many applications the success of these 3D printed materials as a viable replacement for traditional stochastic foams critically depends on their mechanical performance and micro-architectural stability while deployed under long-term mechanical strain. To predict the long-term performance of the two types of foams we employed multi-year-long accelerated aging studies under compressive strain followed by a time-temperature-superposition analysis using a minimum-arc-length-based algorithm. The resulting master curves predict superior long-term performance of the 3D printed foam in terms of two different metrics, i.e., compression set and load retention. To gain deeper understanding, we imaged the microstructure of both foams using X-ray computed tomography, and performed finite-element analysis of the mechanical response within these microstructures. This indicates a wider stress variation in the stochastic foam with points of more extreme local stress as compared to the 3D printed material, which might explain the latter's improved long-term stability and mechanical performance. PMID:27117858
3D printed cellular solid outperforms traditional stochastic foam in long-term mechanical response
Maiti, A.; Small, W.; Lewicki, J.; Weisgraber, T. H.; Duoss, E. B.; Chinn, S. C.; Pearson, M. A.; Spadaccini, C. M.; Maxwell, R. S.; Wilson, T. S.
2016-04-27
3D printing of polymeric foams by direct-ink-write is a recent technological breakthrough that enables the creation of versatile compressible solids with programmable microstructure, customizable shapes, and tunable mechanical response including negative elastic modulus. However, in many applications the success of these 3D printed materials as a viable replacement for traditional stochastic foams critically depends on their mechanical performance and micro-architectural stability while deployed under long-term mechanical strain. To predict the long-term performance of the two types of foams we employed multi-year-long accelerated aging studies under compressive strain followed by a time-temperature-superposition analysis using a minimum-arc-length-based algorithm. The resulting master curvesmore » predict superior long-term performance of the 3D printed foam in terms of two different metrics, i.e., compression set and load retention. To gain deeper understanding, we imaged the microstructure of both foams using X-ray computed tomography, and performed finite-element analysis of the mechanical response within these microstructures. As a result, this indicates a wider stress variation in the stochastic foam with points of more extreme local stress as compared to the 3D printed material, which might explain the latter’s improved long-term stability and mechanical performance.« less
3D printed cellular solid outperforms traditional stochastic foam in long-term mechanical response
Maiti, A.; Small, W.; Lewicki, J. P.; Weisgraber, T. H.; Duoss, E. B.; Chinn, S. C.; Pearson, M. A.; Spadaccini, C. M.; Maxwell, R. S.; Wilson, T. S.
2016-01-01
3D printing of polymeric foams by direct-ink-write is a recent technological breakthrough that enables the creation of versatile compressible solids with programmable microstructure, customizable shapes, and tunable mechanical response including negative elastic modulus. However, in many applications the success of these 3D printed materials as a viable replacement for traditional stochastic foams critically depends on their mechanical performance and micro-architectural stability while deployed under long-term mechanical strain. To predict the long-term performance of the two types of foams we employed multi-year-long accelerated aging studies under compressive strain followed by a time-temperature-superposition analysis using a minimum-arc-length-based algorithm. The resulting master curves predict superior long-term performance of the 3D printed foam in terms of two different metrics, i.e., compression set and load retention. To gain deeper understanding, we imaged the microstructure of both foams using X-ray computed tomography, and performed finite-element analysis of the mechanical response within these microstructures. This indicates a wider stress variation in the stochastic foam with points of more extreme local stress as compared to the 3D printed material, which might explain the latter’s improved long-term stability and mechanical performance. PMID:27117858
Effect of tow alignment on the mechanical performance of 3D woven textile composites
NASA Technical Reports Server (NTRS)
Norman, Timothy L.; Allison, Patti; Baldwin, Jack W.; Gracias, Brian K.; Seesdorf, Dave
1993-01-01
Three-dimensional (3D) woven preforms are currently being considered for use as primary structural components. Lack of technology to properly manufacture, characterize and predict mechanical properties, and predict damage mechanisms leading to failure are problems facing designers of textile composite materials. Two material systems with identical specifications but different manufacturing approaches are investigated. One manufacturing approach resulted in an irregular (nonuniform) preform geometry. The other approach yielded the expected preform geometry (uniform). The objectives are to compare the mechanical properties of the uniform and nonuniform angle interlock 3D weave constructions. The effect of adding layers of laminated tape to the outer surfaces of the textile preform is also examined. Damage mechanisms are investigated and test methods are evaluated.
3D entangled fractional squeezing transformation and its quantum mechanical correspondence
NASA Astrophysics Data System (ADS)
Jia, Fang; Xu, Shuang; Deng, Cheng-Zhi; Liu, Cun-Jin; Hu, Li-Yun
2016-06-01
A new type of entangled fractional squeezing transformation (EFrST) has been theoretically proposed for 2D entanglement [ Front. Phys. 10, 100302 (2015)]. In this paper, we shall extend this case to that of 3D entanglement by introducing a type of three-mode entangled state representation, which is not the product of three 1D cases. Using the technique of integration within an ordered product of operators, we derive a compact unitary operator corresponding to the 3D fractional entangling transformation, which is an entangling operator that presents a clear transformation relation. We also verified that the additivity property of the novel 3D EFrST is of a Fourier character by using its quantum mechanical description. As an application of this representation, the EFrST of the three-mode number state is calculated using the quantum description of the EFrST.
Mechanical properties of 2D and 3D braided textile composites
NASA Technical Reports Server (NTRS)
Norman, Timothy L.
1991-01-01
The purpose of this research was to determine the mechanical properties of 2D and 3D braided textile composite materials. Specifically, those designed for tension or shear loading were tested under static loading to failure to investigate the effects of braiding. The overall goal of the work was to provide a structural designer with an idea of how textile composites perform under typical loading conditions. From test results for unnotched tension, it was determined that the 2D is stronger, stiffer, and has higher elongation to failure than the 3D. It was also found that the polyetherether ketone (PEEK) resin system was stronger, stiffer, and had higher elongation at failure than the resin transfer molding (RTM) epoxy. Open hole tension tests showed that PEEK resin is more notch sensitive than RTM epoxy. Of greater significance, it was found that the 3D is less notch sensitive than the 2D. Unnotched compression tests indicated, as did the tension tests, that the 2D is stronger, stiffer, and has higher elongation at failure than the RTM epoxy. The most encouraging results were from compression after impact. The 3D braided composite showed a compression after impact failure stress equal to 92 percent of the unimpacted specimen. The 2D braided composite failed at about 67 percent of the unimpacted specimen. Higher damage tolerance is observed in textiles over conventional composite materials. This is observed in the results, especially in the 3D braided materials.
Delivery mechanisms of 3D geological models - a perspective from the British Geological Survey
NASA Astrophysics Data System (ADS)
Terrington, Ricky; Myers, Antony; Wood, Ben; Arora, Baneet
2013-04-01
the world with its ability to stream high resolution national and world scale datasets seamlessly. All of these tools have some technological and visualisation limitations and not one delivery mechanism is suitable for all. The idea from the BGS when it comes to model delivery mechanisms is to offer as many different 3D data formats and delivery options as possible to cover all user requirements. Most importantly, it is about giving the user what they want and engaging with them to encourage the use of the advanced functionality of some of this software so that a deeper understanding about the subsurface is gained. Sometimes this solution might be a high-tech solution via mobile devices, but at other times a print-out of a contour plot might be what is required. In the end it is the consumer that has to be satisfied with the product they are receiving.
NASA Astrophysics Data System (ADS)
Weiss, K.-P.; Bagrets, N.; Lange, C.; Goldacker, W.; Wohlgemuth, J.
2015-12-01
Insulating materials for use in cryogenic boundary conditions are still limited to a proved selection as Polyamid, Glasfiber reinforced resins, PEEK, Vespel etc. These materials are usually formed to parts by mechanical machining or sometimes by cast methods. Shaping complex geometries in one piece is limited. Innovative 3D printing is now an upcoming revolutionary technology to construct functional parts from a couple of thermoplastic materials as ABS, Nylon and others which possess quite good mechanical stability and allow realizing very complex shapes with very subtle details. Even a wide range of material mixtures is an option and thermal treatments can be used to finish the material structure for higher performance. The use of such materials in cryogenic environment is very attractive but so far poor experience exists. In this paper, first investigations of the thermal conductivity, expansion and mechanical strength are presented for a few selected commercial 3D material samples to evaluate their application prospects in the cryogenic temperature regime.
NASA Astrophysics Data System (ADS)
Zhao, Ruogang; Wang, Weigang; Boudou, Thomas; Chen, Christopher; Reich, Daniel
2013-03-01
Tissue stiffness and cellular contractility are two of the most important biomechanical factors regulating pathological transitions of encapsulated cells, such as the differentiation of fibroblasts into myofibroblasts - a key event contributing to tissue fibrosis. However, a quantitative correlation between tissue stiffness and cellular contraction and myofibroblast differentiation has not yet been established in 3D environments, mainly due to the lack of suitable 3D tissue culture models that allow both tissue remodeling and simultaneous measurement of the cell/tissue mechanics. To address this, we have developed a magnetic microtissue tester system that allows the remodeling of arrays of cell-laden 3D collagen microtissues and the measurement of cell and tissue mechanics using magnetically actuated elastomeric microcantilevers. By measuring the development of cell/tissue mechanical properties and the expression level of α-smooth muscle actin (α-SMA, a marker for myofibroblast differentiation) during a 6 day culture period, we found microtissue stiffness increased by 45% and α-SMA expression increased by 38%, but tissue contraction forces only increased by 10%, indicating that tissue stiffness may be the predominant mechanical factor for regulation of myofibroblast differentiation. This study provides new quantitative insight into the regulatory effect of cell and tissue mechanics on cellular function. Supported in part by NIH grant HL090747
Techniques for Assessing 3-D Cell-Matrix Mechanical Interactions In Vitro and In Vivo
Miron-Mendoza, Miguel; Koppaka, Vindhya; Zhou, Chengxin; Petroll, W. Matthew
2013-01-01
Cellular interactions with extracellular matrices (ECM) through the application of mechanical forces mediate numerous biological processes including developmental morphogenesis, wound healing and cancer metastasis. They also play a key role in the cellular repopulation and/or remodeling of engineered tissues and organs. While 2-D studies can provide important insights into many aspects of cellular mechanobiology, cells reside within 3-D ECMs in vivo, and matrix structure and dimensionality have been shown to impact cell morphology, protein organization and mechanical behavior. Global measurements of cell-induced compaction of 3-D collagen matrices can provide important insights into the regulation of overall cell contractility by various cytokines and signaling pathways. However, to understand how the mechanics of cell spreading, migration, contraction and matrix remodeling are regulated at the molecular level, these processes must also be studied in individual cells. Here we review the evolution and application of techniques for imaging and assessing local cell-matrix mechanical interactions in 3-D culture models, tissue explants and living animals. PMID:23819988
Techniques for assessing 3-D cell-matrix mechanical interactions in vitro and in vivo.
Miron-Mendoza, Miguel; Koppaka, Vindhya; Zhou, Chengxin; Petroll, W Matthew
2013-10-01
Cellular interactions with extracellular matrices (ECM) through the application of mechanical forces mediate numerous biological processes including developmental morphogenesis, wound healing and cancer metastasis. They also play a key role in the cellular repopulation and/or remodeling of engineered tissues and organs. While 2-D studies can provide important insights into many aspects of cellular mechanobiology, cells reside within 3-D ECMs in vivo, and matrix structure and dimensionality have been shown to impact cell morphology, protein organization and mechanical behavior. Global measurements of cell-induced compaction of 3-D collagen matrices can provide important insights into the regulation of overall cell contractility by various cytokines and signaling pathways. However, to understand how the mechanics of cell spreading, migration, contraction and matrix remodeling are regulated at the molecular level, these processes must also be studied in individual cells. Here we review the evolution and application of techniques for imaging and assessing local cell-matrix mechanical interactions in 3-D culture models, tissue explants and living animals. PMID:23819988
Mechanical Performance and Parameter Sensitivity Analysis of 3D Braided Composites Joints
Wu, Yue; Nan, Bo; Chen, Liang
2014-01-01
3D braided composite joints are the important components in CFRP truss, which have significant influence on the reliability and lightweight of structures. To investigate the mechanical performance of 3D braided composite joints, a numerical method based on the microscopic mechanics is put forward, the modeling technologies, including the material constants selection, element type, grid size, and the boundary conditions, are discussed in detail. Secondly, a method for determination of ultimate bearing capacity is established, which can consider the strength failure. Finally, the effect of load parameters, geometric parameters, and process parameters on the ultimate bearing capacity of joints is analyzed by the global sensitivity analysis method. The results show that the main pipe diameter thickness ratio γ, the main pipe diameter D, and the braided angle α are sensitive to the ultimate bearing capacity N. PMID:25121121
Mechanical performance and parameter sensitivity analysis of 3D braided composites joints.
Wu, Yue; Nan, Bo; Chen, Liang
2014-01-01
3D braided composite joints are the important components in CFRP truss, which have significant influence on the reliability and lightweight of structures. To investigate the mechanical performance of 3D braided composite joints, a numerical method based on the microscopic mechanics is put forward, the modeling technologies, including the material constants selection, element type, grid size, and the boundary conditions, are discussed in detail. Secondly, a method for determination of ultimate bearing capacity is established, which can consider the strength failure. Finally, the effect of load parameters, geometric parameters, and process parameters on the ultimate bearing capacity of joints is analyzed by the global sensitivity analysis method. The results show that the main pipe diameter thickness ratio γ, the main pipe diameter D, and the braided angle α are sensitive to the ultimate bearing capacity N. PMID:25121121
NASA Astrophysics Data System (ADS)
Li, L. C.; Tang, C. A.; Li, G.; Wang, S. Y.; Liang, Z. Z.; Zhang, Y. B.
2012-09-01
The failure mechanism of hydraulic fractures in heterogeneous geological materials is an important topic in mining and petroleum engineering. A three-dimensional (3D) finite element model that considers the coupled effects of seepage, damage, and the stress field is introduced. This model is based on a previously developed two-dimensional (2D) version of the model (RFPA2D-Rock Failure Process Analysis). The RFPA3D-Parallel model is developed using a parallel finite element method with a message-passing interface library. The constitutive law of this model considers strength and stiffness degradation, stress-dependent permeability for the pre-peak stage, and deformation-dependent permeability for the post-peak stage. Using this model, 3D modelling of progressive failure and associated fluid flow in rock are conducted and used to investigate the hydro-mechanical response of rock samples at laboratory scale. The responses investigated are the axial stress-axial strain together with permeability evolution and fracture patterns at various stages of loading. Then, the hydraulic fracturing process inside a rock specimen is numerically simulated. Three coupled processes are considered: (1) mechanical deformation of the solid medium induced by the fluid pressure acting on the fracture surfaces and the rock skeleton, (2) fluid flow within the fracture, and (3) propagation of the fracture. The numerically simulated results show that the fractures from a vertical wellbore propagate in the maximum principal stress direction without branching, turning, and twisting in the case of a large difference in the magnitude of the far-field stresses. Otherwise, the fracture initiates in a non-preferred direction and plane then turns and twists during propagation to become aligned with the preferred direction and plane. This pattern of fracturing is common when the rock formation contains multiple layers with different material properties. In addition, local heterogeneity of the rock
3D transrectal ultrasound prostate biopsy using a mechanical imaging and needle-guidance system
NASA Astrophysics Data System (ADS)
Bax, Jeffrey; Cool, Derek; Gardi, Lori; Montreuil, Jacques; Gil, Elena; Bluvol, Jeremy; Knight, Kerry; Smith, David; Romagnoli, Cesare; Fenster, Aaron
2008-03-01
Prostate biopsy procedures are generally limited to 2D transrectal ultrasound (TRUS) imaging for biopsy needle guidance. This limitation results in needle position ambiguity and an insufficient record of biopsy core locations in cases of prostate re-biopsy. We have developed a multi-jointed mechanical device that supports a commercially available TRUS probe with an integrated needle guide for precision prostate biopsy. The device is fixed at the base, allowing the joints to be manually manipulated while fully supporting its weight throughout its full range of motion. Means are provided to track the needle trajectory and display this trajectory on a corresponding TRUS image. This allows the physician to aim the needle-guide at predefined targets within the prostate, providing true 3D navigation. The tracker has been designed for use with several end-fired transducers that can be rotated about the longitudinal axis of the probe to generate 3D images. The tracker reduces the variability associated with conventional hand-held probes, while preserving user familiarity and procedural workflow. In a prostate phantom, biopsy needles were guided to within 2 mm of their targets, and the 3D location of the biopsy core was accurate to within 3 mm. The 3D navigation system is validated in the presence of prostate motion in a preliminary patient study.
Mechanical properties and shape memory effect of 3D-printed PLA-based porous scaffolds.
Senatov, F S; Niaza, K V; Zadorozhnyy, M Yu; Maksimkin, A V; Kaloshkin, S D; Estrin, Y Z
2016-04-01
In the present work polylactide (PLA)/15wt% hydroxyapatite (HA) porous scaffolds with pre-modeled structure were obtained by 3D-printing by fused filament fabrication. Composite filament was obtained by extrusion. Mechanical properties, structural characteristics and shape memory effect (SME) were studied. Direct heating was used for activation of SME. The average pore size and porosity of the scaffolds were 700μm and 30vol%, respectively. Dispersed particles of HA acted as nucleation centers during the ordering of PLA molecular chains and formed an additional rigid fixed phase that reduced molecular mobility, which led to a shift of the onset of recovery stress growth from 53 to 57°C. A more rapid development of stresses was observed for PLA/HA composites with the maximum recovery stress of 3.0MPa at 70°C. Ceramic particles inhibited the growth of cracks during compression-heating-compression cycles when porous PLA/HA 3D-scaffolds recovered their initial shape. Shape recovery at the last cycle was about 96%. SME during heating may have resulted in "self-healing" of scaffold by narrowing the cracks. PLA/HA 3D-scaffolds were found to withstand up to three compression-heating-compression cycles without delamination. It was shown that PLA/15%HA porous scaffolds obtained by 3D-printing with shape recovery of 98% may be used as self-fitting implant for small bone defect replacement owing to SME. PMID:26710259
Micro-structured materials and mechanical cues in 3D collagen gels.
Phillips, James B; Brown, Robert
2011-01-01
Collagen gels provide a versatile and widely used substrate for three-dimensional (3D) cell culture. Here we describe how cell-seeded Type-I collagen gels can be adapted to provide powerful 3D models to support a wide range of research applications where cell/substrate alignment, density, stiffness/compliance, and strain are critical factors. In their fully hydrated form, rectangular collagen gels can be tethered such that endogenous forces generated as resident cells attach to and remodel the fibrillar collagen network can align the substrate in a controllable, predictable, and quantifiable manner. By removing water from collagen gels (plastic compression), their density increases towards that of body tissues, facilitating the engineering of a range of biomimetic constructs with controllable mechanical properties. This dense collagen can be used in combination with other components to achieve a range of functional properties from controlled perfusion, or tensile/compressive strength to new micro-structures. Detailed methodology is provided for the assembly of a range of 3D collagen materials including tethered aligned hydrogels and plastic compressed constructs. A range of techniques for analysing cell behaviour within these models, including microscopy and molecular analyses are described. These systems therefore provide a highly controllable mechanical and chemical micro-environment for investigating a wide range of cellular responses. PMID:21042973
Mechanical Properties of 3-D Printed Cellular Foams with triangular cells
NASA Astrophysics Data System (ADS)
Bunga, Pratap Kumar
In the present work, poly lactic acid (PLA) is used as a model system to investigate the mechanical behavior of 3-D printed foams with triangular cells. Solid PLA tension and compression specimens and foams made of PLA were fabricated using fused deposition 3-D printing technique. The solid PLA tension specimens were characterized for their densities and found to be about 10% lower in density as compared to their bulk counter parts. The triangular foams had a relative density of about 64%. The relationships between the structure of the foams and its deformation behavior under compression along two in-plane directions were characterized. Furthermore, simple finite element models were developed to understand the observed deformation behavior of triangular foams.
Parallel Algebraic Multigrids for Structural mechanics
Brezina, M; Tong, C; Becker, R
2004-05-11
This paper presents the results of a comparison of three parallel algebraic multigrid (AMG) preconditioners for structural mechanics applications. In particular, they are interested in investigating both the scalability and robustness of the preconditioners. Numerical results are given for a range of structural mechanics problems with various degrees of difficulty.
Narayanaswamy, Arunachalam; Dwarakapuram, Saritha; Bjornsson, Christopher S.; Cutler, Barbara M.; Shain, William
2010-01-01
This paper presents robust 3-D algorithms to segment vasculature that is imaged by labeling laminae, rather than the lumenal volume. The signal is weak, sparse, noisy, nonuniform, low-contrast, and exhibits gaps and spectral artifacts, so adaptive thresholding and Hessian filtering based methods are not effective. The structure deviates from a tubular geometry, so tracing algorithms are not effective. We propose a four step approach. The first step detects candidate voxels using a robust hypothesis test based on a model that assumes Poisson noise and locally planar geometry. The second step performs an adaptive region growth to extract weakly labeled and fine vessels while rejecting spectral artifacts. To enable interactive visualization and estimation of features such as statistical confidence, local curvature, local thickness, and local normal, we perform the third step. In the third step, we construct an accurate mesh representation using marching tetrahedra, volume-preserving smoothing, and adaptive decimation algorithms. To enable topological analysis and efficient validation, we describe a method to estimate vessel centerlines using a ray casting and vote accumulation algorithm which forms the final step of our algorithm. Our algorithm lends itself to parallel processing, and yielded an 8× speedup on a graphics processor (GPU). On synthetic data, our meshes had average error per face (EPF) values of (0.1–1.6) voxels per mesh face for peak signal-to-noise ratios from (110–28 dB). Separately, the error from decimating the mesh to less than 1% of its original size, the EPF was less than 1 voxel/face. When validated on real datasets, the average recall and precision values were found to be 94.66% and 94.84%, respectively. PMID:20199906
NASA Astrophysics Data System (ADS)
DeJong, Andrew
Numerical models of fluid-structure interaction have grown in importance due to increasing interest in environmental energy harvesting, airfoil-gust interactions, and bio-inspired formation flying. Powered by increasingly powerful parallel computers, such models seek to explain the fundamental physics behind the complex, unsteady fluid-structure phenomena. To this end, a high-fidelity computational model based on the high-order spectral difference method on 3D unstructured, dynamic meshes has been developed. The spectral difference method constructs continuous solution fields within each element with a Riemann solver to compute the inviscid fluxes at the element interfaces and an averaging mechanism to compute the viscous fluxes. This method has shown promise in the past as a highly accurate, yet sufficiently fast method for solving unsteady viscous compressible flows. The solver is monolithically coupled to the equations of motion of an elastically mounted 3-degree of freedom rigid bluff body undergoing flow-induced lift, drag, and torque. The mesh is deformed using 4 methods: an analytic function, Laplace equation, biharmonic equation, and a bi-elliptic equation with variable diffusivity. This single system of equations -- fluid and structure -- is advanced through time using a 5-stage, 4th-order Runge-Kutta scheme. Message Passing Interface is used to run the coupled system in parallel on up to 240 processors. The solver is validated against previously published numerical and experimental data for an elastically mounted cylinder. The effect of adding an upstream body and inducing wake galloping is observed.
Yap, Choon Hwai; Park, Dae Woo; Dutta, Debaditya; Simon, Marc; Kim, Kang
2014-01-01
Being multilayered and anisotropic, biological tissues such as cardiac and arterial walls are structurally complex, making full assessment and understanding of their mechanical behavior challenging. Current standard mechanical testing uses surface markers to track tissue deformations and does not provide deformation data below the surface. In the study described here, we found that combining mechanical testing with 3-D ultrasound speckle tracking could overcome this limitation. Rat myocardium was tested with a biaxial tester and was concurrently scanned with high-frequency ultrasound in three dimensions. The strain energy function was computed from stresses and strains using an iterative non-linear curve-fitting algorithm. Because the strain energy function consists of terms for the base matrix and for embedded fibers, spatially varying fiber orientation was also computed by curve fitting. Using finite-element simulations, we first validated the accuracy of the non-linear curve-fitting algorithm. Next, we compared experimentally measured rat myocardium strain energy function values with those in the literature and found a matching order of magnitude. Finally, we retained samples after the experiments for fiber orientation quantification using histology and found that the results satisfactorily matched those computed in the experiments. We conclude that 3-D ultrasound speckle tracking can be a useful addition to traditional mechanical testing of biological tissues and may provide the benefit of enabling fiber orientation computation. PMID:25616585
Mechanisms of DNA damage response to targeted irradiation in organotypic 3D skin cultures.
Acheva, Anna; Ghita, Mihaela; Patel, Gaurang; Prise, Kevin M; Schettino, Giuseppe
2014-01-01
DNA damage (caused by direct cellular exposure and bystander signaling) and the complex pathways involved in its repair are critical events underpinning cellular and tissue response following radiation exposures. There are limited data addressing the dynamics of DNA damage induction and repair in the skin particularly in areas not directly exposed. Here we investigate the mechanisms regulating DNA damage, repair, intracellular signalling and their impact on premature differentiation and development of inflammatory-like response in the irradiated and surrounding areas of a 3D organotypic skin model. Following localized low-LET irradiation (225 kVp X-rays), low levels of 53BP1 foci were observed in the 3D model (3.8±0.28 foci/Gy/cell) with foci persisting and increasing in size up to 48 h post irradiation. In contrast, in cell monolayers 14.2±0.6 foci/Gy/cell and biphasic repair kinetics with repair completed before 24 h was observed. These differences are linked to differences in cellular status with variable level of p21 driving apoptotic signalling in 2D and accelerated differentiation in both the directly irradiated and bystander areas of the 3D model. The signalling pathways utilized by irradiated keratinocytes to induce DNA damage in non-exposed areas of the skin involved the NF-κB transcription factor and its downstream target COX-2. PMID:24505255
Effect of HDAC Inhibitors on Corneal Keratocyte Mechanical Phenotypes in 3-D Collagen Matrices
Koppaka, Vindhya; Lakshman, Neema
2015-01-01
Purpose: Histone deacetylase inhibitors (HDAC) have been shown to inhibit the TGFβ-induced myofibroblast transformation of corneal fibroblasts in 2-D culture. However, the effect of HDAC inhibitors on keratocyte spreading, contraction, and matrix remodeling in 3-D culture has not been directly assessed. The goal of this study was to investigate the effects of the HDAC inhibitors Trichostatin A (TSA) and Vorinostat (SAHA) on corneal keratocyte mechanical phenotypes in 3-D culture using defined serum-free culture conditions. Methods: Rabbit corneal keratocytes were plated within standard rat tail type I collagen matrices (2.5 mg/ml) or compressed collagen matrices (~100 mg/ml) and cultured for up to 4 days in serum-free media, PDGF BB, TGFβ1, and either 50 nM TSA, 10 μM SAHA, or vehicle (DMSO). F-actin, α-SM-actin, and collagen fibrils were imaged using confocal microscopy. Cell morphology and global matrix contraction were quantified digitally. The expression of α-SM-actin was assessed using western blotting. Results: Corneal keratocytes in 3-D matrices had a quiescent mechanical phenotype, as indicated by a dendritic morphology, a lack of stress fibers, and minimal cell-induced matrix remodeling. This phenotype was generally maintained following the addition of TSA or SAHA. TGFβ1 induced a contractile phenotype, as indicated by a loss of dendritic cell processes, the development of stress fibers, and significant matrix compaction. In contrast, cells cultured in TGFβ1 plus TSA or SAHA remained dendritic and did not form stress fibers or induce ECM compaction. Western blotting showed that the expression of α-SM actin after treatment with TGFβ1 was inhibited by TSA and SAHA. PDGF BB stimulated the elongation of keratocytes and the extension of dendritic processes within 3-D matrices without inducing stress fiber formation or collagen reorganization. This spreading response was maintained in the presence of TSA or SAHA. Conclusions: Overall, HDAC inhibitors
A Completely 3D Model for the Simulation of Mechanized Tunnel Excavation
NASA Astrophysics Data System (ADS)
Zhao, Kai; Janutolo, Michele; Barla, Giovanni
2012-07-01
For long deep tunnels as currently under construction through the Alps, mechanized excavation using tunnel boring machines (TBMs) contributes significantly to savings in construction time and costs. Questions are, however, posed due to the severe ground conditions which are in cases anticipated or encountered along the main tunnel alignment. A major geological hazard is the squeezing of weak rocks, but also brittle failure can represent a significant problem. For the design of mechanized tunnelling in such conditions, the complex interaction between the rock mass, the tunnel machine, its system components, and the tunnel support need to be analysed in detail and this can be carried out by three-dimensional (3D) models including all these components. However, the state-of-the-art shows that very few fully 3D models for mechanical deep tunnel excavation in rock have been developed so far. A completely three-dimensional simulator of mechanised tunnel excavation is presented in this paper. The TBM of reference is a technologically advanced double shield TBM designed to cope with both conditions. Design analyses with reference to spalling hazard along the Brenner and squeezing along the Lyon-Turin Base Tunnel are discussed.
Mechanical characterization of 2D, 2D stitched, and 3D braided/RTM materials
NASA Technical Reports Server (NTRS)
Deaton, Jerry W.; Kullerd, Susan M.; Portanova, Marc A.
1993-01-01
Braided composite materials have potential for application in aircraft structures. Fuselage frames, floor beams, wing spars, and stiffeners are examples where braided composites could find application if cost effective processing and damage tolerance requirements are met. Another important consideration for braided composites relates to their mechanical properties and how they compare to the properties of composites produced by other textile composite processes being proposed for these applications. Unfortunately, mechanical property data for braided composites do not appear extensively in the literature. Data are presented in this paper on the mechanical characterization of 2D triaxial braid, 2D triaxial braid plus stitching, and 3D (through-the-thickness) braid composite materials. The braided preforms all had the same graphite tow size and the same nominal braid architectures, (+/- 30 deg/0 deg), and were resin transfer molded (RTM) using the same mold for each of two different resin systems. Static data are presented for notched and unnotched tension, notched and unnotched compression, and compression after impact strengths at room temperature. In addition, some static results, after environmental conditioning, are included. Baseline tension and compression fatigue results are also presented, but only for the 3D braided composite material with one of the resin systems.
Microtubule regulation of corneal fibroblast morphology and mechanical activity in 3-D culture
Kim, Areum; Petroll, W. Matthew
2007-01-01
The purpose of this study was to investigate the role of microtubules in regulating corneal fibroblast structure and mechanical behavior using static (3-D) and dynamic (4-D) imaging of both cells and their surrounding matrix. Human corneal fibroblasts transfected to express GFP-zyxin (to label focal adhesions) or GFP-tubulin (to label microtubules) were plated at low density inside 100 μm thick type I collagen matrices. After 24 hours, the effects of nocodazole (to depolymerize microtubules), cytochalasin D (to disrupt f-actin), and/or Y-27632 (to block Rho-kinase) were evaluated using 3-D and 4-D imaging of both cells and ECM. After 24 hours of incubation, cells had well organized microtubules and prominent focal adhesions, and significant cell-induced matrix compaction was observed. Addition of nocodazole induced rapid microtubule disruption which resulted in Rho activation and additional cellular contraction. The matrix was pulled inward by retracting pseudopodial processes, and focal adhesions appeared to mediate this process, when present. Following 24 hour exposure to nocodazole, there was an even greater increase in both the number of stress fibers and the amount of matrix compaction and alignment at the ends of cells. When Rho-kinase was inhibited, disruption of microtubules resulted in retraction of dendritic cell processes, and rapid formation and extension of lamellipodial processes at random locations along the cell body, eventually leading to a convoluted, disorganized cell shape. These data suggest that microtubules modulate both cellular contractility and local collagen matrix reorganization via regulation of Rho/Rho kinase activity. In addition, microtubules appear to play a central role in dynamic regulation of cell spreading mechanics, morphology and polarity in 3-D culture. PMID:17716657
3D Printing Bioceramic Porous Scaffolds with Good Mechanical Property and Cell Affinity
Chang, Chih-Hao; Lin, Chih-Yang; Liu, Fwu-Hsing; Chen, Mark Hung-Chih; Lin, Chun-Pin; Ho, Hong-Nerng; Liao, Yunn-Shiuan
2015-01-01
Artificial bone grafting is widely used in current orthopedic surgery for bone defect problems. Unfortunately, surgeons remain unsatisfied with the current commercially available products. One of the major complaints is that these products cannot provide sufficient mechanical strength to support the human skeletal structure. In this study, we aimed to develop a bone scaffold with better mechanical property and good cell affinity by 3D printing (3DP) techniques. A self-developed 3D printer with laser-aided gelling (LAG) process was used to fabricate bioceramic scaffolds with inter-porous structures. To improve the mechanical property of the bioceramic parts after heating, CaCO3 was added to the silica ceramic slurry. CaCO3 was blended into a homogenous SiO2-sol dispersion at weight ratios varying from 0/100 to 5/95 to 9/91 (w/w). Bi-component CaCO3/SiO2-sol was prepared as a biocomposite for the 3DP scaffold. The well-mixed biocomposite was used to fabricate the bioceramic green part using the LAG method. The varied scaffolds were sintered at different temperatures ranging from 900 to 1500°C, and the mechanical property was subsequently analyzed. The scaffolds showed good property with the composite ratio of 5:95 CaCO3:SiO2 at a sintering temperature of 1300°C. The compressive strength was 47 MPa, and the porosity was 34%. The topography of the sintered 3DP bioceramic scaffold was examined by SEM, EDS and XRD. The silica bioceramic presented no cytotoxicity and good MG-63 osteoblast-like cell affinity, demonstrating good biocompatibility. Therefore, the new silica biocomposite is viable for fabricating 3DP bone bioceramics with improved mechanical property and good cell affinity. PMID:26618362
3D Printing Bioceramic Porous Scaffolds with Good Mechanical Property and Cell Affinity.
Chang, Chih-Hao; Lin, Chih-Yang; Liu, Fwu-Hsing; Chen, Mark Hung-Chih; Lin, Chun-Pin; Ho, Hong-Nerng; Liao, Yunn-Shiuan
2015-01-01
Artificial bone grafting is widely used in current orthopedic surgery for bone defect problems. Unfortunately, surgeons remain unsatisfied with the current commercially available products. One of the major complaints is that these products cannot provide sufficient mechanical strength to support the human skeletal structure. In this study, we aimed to develop a bone scaffold with better mechanical property and good cell affinity by 3D printing (3DP) techniques. A self-developed 3D printer with laser-aided gelling (LAG) process was used to fabricate bioceramic scaffolds with inter-porous structures. To improve the mechanical property of the bioceramic parts after heating, CaCO3 was added to the silica ceramic slurry. CaCO3 was blended into a homogenous SiO2-sol dispersion at weight ratios varying from 0/100 to 5/95 to 9/91 (w/w). Bi-component CaCO3/SiO2-sol was prepared as a biocomposite for the 3DP scaffold. The well-mixed biocomposite was used to fabricate the bioceramic green part using the LAG method. The varied scaffolds were sintered at different temperatures ranging from 900 to 1500°C, and the mechanical property was subsequently analyzed. The scaffolds showed good property with the composite ratio of 5:95 CaCO3:SiO2 at a sintering temperature of 1300°C. The compressive strength was 47 MPa, and the porosity was 34%. The topography of the sintered 3DP bioceramic scaffold was examined by SEM, EDS and XRD. The silica bioceramic presented no cytotoxicity and good MG-63 osteoblast-like cell affinity, demonstrating good biocompatibility. Therefore, the new silica biocomposite is viable for fabricating 3DP bone bioceramics with improved mechanical property and good cell affinity. PMID:26618362
Ott, Lindsey M; Zabel, Taylor A; Walker, Natalie K; Farris, Ashley L; Chakroff, Jason T; Ohst, Devan G; Johnson, Jed K; Gehrke, Steven H; Weatherly, Robert A; Detamore, Michael S
2016-04-01
Tracheal stenosis can become a fatal condition, and current treatments include augmentation of the airway with autologous tissue. A tissue-engineered approach would not require a donor source, while providing an implant that meets both surgeons' and patients' needs. A fibrous, polymeric scaffold organized in gradient bilayers of polycaprolactone (PCL) and poly-lactic-co-glycolic acid (PLGA) with 3D printed structural ring supports, inspired by the native trachea rings, could meet this need. The purpose of the current study was to characterize the tracheal scaffolds with mechanical testing models to determine the design most suitable for maintaining a patent airway. Degradation over 12 weeks revealed that scaffolds with the 3D printed rings had superior properties in tensile and radial compression, with at least a three fold improvement and 8.5-fold improvement, respectively, relative to the other scaffold groups. The ringed scaffolds produced tensile moduli, radial compressive forces, and burst pressures similar to or exceeding physiological forces and native tissue data. Scaffolds with a thicker PCL component had better suture retention and tube flattening recovery properties, with the monolayer of PCL (PCL-only group) exhibiting a 2.3-fold increase in suture retention strength (SRS). Tracheal scaffolds with ring reinforcements have improved mechanical properties, while the fibrous component increased porosity and cell infiltration potential. These scaffolds may be used to treat various trachea defects (patch or circumferential) and have the potential to be employed in other tissue engineering applications. PMID:27097554
A 3D coupled hydro-mechanical granular model for the prediction of hot tearing formation
NASA Astrophysics Data System (ADS)
Sistaninia, M.; Phillion, A. B.; Drezet, J.-M.; Rappaz, M.
2012-07-01
A new 3D coupled hydro-mechanical granular model that simulates hot tearing formation in metallic alloys is presented. The hydro-mechanical model consists of four separate 3D modules. (I) The Solidification Module (SM) is used for generating the initial solid-liquid geometry. Based on a Voronoi tessellation of randomly distributed nucleation centers, this module computes solidification within each polyhedron using a finite element based solute diffusion calculation for each element within the tessellation. (II) The Fluid Flow Module (FFM) calculates the solidification shrinkage and deformation-induced pressure drop within the intergranular liquid. (III) The Semi-solid Deformation Module (SDM) is used to simulate deformation of the granular structure via a combined finite element / discrete element method. In this module, deformation of the solid grains is modeled using an elasto-viscoplastic constitutive law. (IV) The Failure Module (FM) is used to simulate crack initiation and propagation with the fracture criterion estimated from the overpressure required to overcome the capillary forces at the liquid-gas interface. The FFM, SDM, and FM are coupled processes since solid deformation, intergranular flow, and crack initiation are deeply linked together. The granular model predictions have been validated against bulk data measured experimentally and calculated with averaging techniques.
NASA Astrophysics Data System (ADS)
Chen, X.; Yao, L.; Xue, J.; Zhao, D.; Lan, Y.; Qian, X.; Wang, C. X.; Qiu, Y.
2008-12-01
Three-dimensional aramid woven fabrics were treated with atmospheric pressure plasmas, on one side or both sides to determine the plasma penetration depth in the 3D fabrics and the influences on final composite mechanical properties. The properties of the fibers from different layers of the single side treated fabrics, including surface morphology, chemical composition, wettability and adhesion properties were investigated using scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), contact angle measurement and microbond tests. Meanwhile, flexural properties of the composites reinforced with the fabrics untreated and treated on both sides were compared using three-point bending tests. The results showed that the fibers from the outer most surface layer of the fabric had a significant improvement in their surface roughness, chemical bonding, wettability and adhesion properties after plasma treatment; the treatment effect gradually diminished for the fibers in the inner layers. In the third layer, the fiber properties remained approximately the same to those of the control. In addition, three-point bending tests indicated that the 3D aramid composite had an increase of 11% in flexural strength and 12% in flexural modulus after the plasma treatment. These results indicate that composite mechanical properties can be improved by the direct fabric treatment instead of fiber treatment with plasmas if the fabric is less than four layers thick.
NASA Astrophysics Data System (ADS)
Bose, Prasenjit; Eyckmans, Jeroen; Chen, Christopher; Reich, Daniel
The adhesion of cells to the extracellular matrix (ECM) plays a crucial role in a variety of cellular functions. The main building blocks of the ECM are 3D networks of fibrous proteins whose structure and alignments varies with tissue type. However, the impact of ECM alignment on cellular behaviors such as cell adhesion, spreading, extension and mechanics remains poorly understood. We present results on the development of a microtissue-based system that enables control of the structure, orientation, and degree of fibrillar alignment in 3D fibroblast-populated collagen gels. The tissues self-assemble from cell-laden collagen gels placed in micro-fabricated wells containing sets of elastic pillars. The contractile action of the cells leads to controlled alignment of the fibrous collagen, depending on the number and location of the pillars in each well. The pillars are elastic, and are utilized to measure the contractile forces of the microtissues, and by incorporating magnetic material in selected pillars, time-varying forces can be applied to the tissues for dynamic stimulation and measurement of mechanical properties. Results on the effects of varying pillar shape, spacing, location, and stiffness on microtissue organization and contractility will be presented. This work is supported by NSF CMMI-1463011.
MMP Regulation of Corneal Keratocyte Motility and Mechanics in 3-D Collagen Matrices
Zhou, Chengxin; Petroll, W. Matthew
2014-01-01
Previous studies have shown that platelet derived growth factor (PDGF) can stimulate corneal keratocyte spreading and migration within 3-D collagen matrices, without inducing transformation to a contractile, fibroblastic phenotype. The goal of this study was to investigate the role of matrix metalloproteinases (MMPs) in regulating PDGF-induced changes in keratocyte motility and mechanical differentiation. Rabbit corneal keratocytes were isolated and cultured in serum-free media (S-) to maintain their quiescent phenotype. A nested collagen matrix construct was used to assess 3-D cell migration, and a standard collagen matrix model was used to assess cell morphology and cell-mediated matrix contraction. In both cases constructs were cultured in S- supplemented with PDGF, with or without the broad spectrum MMP inhibitors GM6001 or BB-94. After 4 days, f-actin, nuclei and collagen fibrils were imaged using confocal microscopy. To assess sub-cellular mechanical activity (extension and retraction of cell processes), time-lapse DIC imaging was also performed. MT1-MMP expression and MMP-mediated collagen degradation by were also examined. Results demonstrated that neither GM6001 nor BB-94 affected corneal keratocyte viability or proliferation in 3-D culture. PDGF stimulated elongation and migration of corneal keratocytes within type I collagen matrices, without causing a loss of their dendritic morphology or inducing formation of intracellular stress fibers. Treatment with GM6001 and BB-94 inhibited PDGF-induced keratocyte spreading and migration. Relatively low levels of keratocyte-induced matrix contraction were also maintained in PDGF, and the amount of PDGF-induced collagen degradation was similar to that observed in S- controls. The collagen degradation pattern was consistent with membrane-associated MMP activity, and keratocytes showed positive staining for MT1-MMP, albeit weak. Both matrix contraction and collagen degradation were reduced by MMP inhibition. For most
Microdomain heterogeneity in 3D affects the mechanics of neonatal cardiac myocyte contraction.
Curtis, Matthew W; Budyn, Elisa; Desai, Tejal A; Samarel, Allen M; Russell, Brenda
2013-01-01
Cardiac muscle cells are known to adapt to their physical surroundings, optimizing intracellular organization and contractile function for a given culture environment. A previously developed in vitro model system has shown that the inclusion of discrete microscale domains (or microrods) in three dimensions (3D) can alter long-term growth responses of neonatal ventricular myocytes. The aim of this work was to understand how cellular contact with such a domain affects various mechanical changes involved in cardiac muscle cell remodeling. Myocytes were maintained in 3D gels over 5 days in the presence or absence of 100-μm-long microrods, and the effect of this local heterogeneity on cell behavior was analyzed via several imaging techniques. Microrod abutment resulted in approximately twofold increases in the maximum displacement of spontaneously beating myocytes, as based on confocal microscopy scans of the gel xy-plane or the myocyte long axis. In addition, microrods caused significant increases in the proportion of aligned myofibrils (≤20° deviation from long axis) in fixed myocytes. Microrod-related differences in axial contraction could be abrogated by long-term interruption of certain signals of the RhoA-/Rho-associated kinase (ROCK) or protein kinase C (PKC) pathway. Furthermore, microrod-induced increases in myocyte size and protein content were prevented by ROCK inhibition. In all, the data suggest that microdomain heterogeneity in 3D appears to promote the development of axially aligned contractile machinery in muscle cells, an observation that may have relevance to a number of cardiac tissue engineering interventions. PMID:22407215
Quantification of Diaphragm Mechanics in Pompe Disease Using Dynamic 3D MRI
Mogalle, Katja; Perez-Rovira, Adria; Ciet, Pierluigi; Wens, Stephan C. A.; van Doorn, Pieter A.; Tiddens, Harm A. W. M.; van der Ploeg, Ans T.; de Bruijne, Marleen
2016-01-01
Background Diaphragm weakness is the main reason for respiratory dysfunction in patients with Pompe disease, a progressive metabolic myopathy affecting respiratory and limb-girdle muscles. Since respiratory failure is the major cause of death among adult patients, early identification of respiratory muscle involvement is necessary to initiate treatment in time and possibly prevent irreversible damage. In this paper we investigate the suitability of dynamic MR imaging in combination with state-of-the-art image analysis methods to assess respiratory muscle weakness. Methods The proposed methodology relies on image registration and lung surface extraction to quantify lung kinematics during breathing. This allows for the extraction of geometry and motion features of the lung that characterize the independent contribution of the diaphragm and the thoracic muscles to the respiratory cycle. Results Results in 16 3D+t MRI scans (10 Pompe patients and 6 controls) of a slow expiratory maneuver show that kinematic analysis from dynamic 3D images reveals important additional information about diaphragm mechanics and respiratory muscle involvement when compared to conventional pulmonary function tests. Pompe patients with severely reduced pulmonary function showed severe diaphragm weakness presented by minimal motion of the diaphragm. In patients with moderately reduced pulmonary function, cranial displacement of posterior diaphragm parts was reduced and the diaphragm dome was oriented more horizontally at full inspiration compared to healthy controls. Conclusion Dynamic 3D MRI provides data for analyzing the contribution of both diaphragm and thoracic muscles independently. The proposed image analysis method has the potential to detect less severe diaphragm weakness and could thus be used to determine the optimal start of treatment in adult patients with Pompe disease in prospect of increased treatment response. PMID:27391236
NASA Astrophysics Data System (ADS)
Yu, Jhao-Ming; Chen, Liang-Yu; Pan, Min-Cheng; Hsu, Ya-Fen; Pan, Min-Chun
2015-03-01
Diffuse optical imaging (DOI) providing functional information of tissues has drawn great attention for the last two decades. Near infrared (NIR) DOI systems composed of scanning bench, opt-electrical measurement module, system control, and data processing and image reconstruction schemes are developed for the screening and diagnosis of breast tumors. Mostly, the scanning bench belonging to fixed source-and-detector configuration limits computed image resolution to an extent. To cope with the issue, we propose, design and implement a 3D prostrate ring-scanning equipment for NIR DOI with flexible combinations of illumination and detection, and with the function of radial, circular and vertical movement without hard compression of breast tissue like the imaging system using or incorporating with X-ray mammographic bench. Especially, a rotation-sliding-and-moving mechanism was designed for the guidance of source- and detection-channel movement. Following the previous justification for synthesized image reconstruction, in the paper the validation using varied phantoms is further conducted and 3D image reconstruction for their absorption and scattering coefficients is illustrated through the computation of our in-house coded schemes. The source and detection NIR data are acquired to reconstruct the 3D images through the operation of scanning bench in the movement of vertical, radial and circular directions. Rather than the fixed configuration, the addressed screening/diagnosing equipment has the flexibility for optical-channel expansion with a compromise among construction cost, operation time, and spatial resolution of reconstructed μa and μs' images.
Microdomain heterogeneity in 3D affects the mechanics of neonatal cardiac myocyte contraction
Curtis, Matthew W.; Budyn, Elisa; Desai, Tejal A.; Samarel, Allen M.
2012-01-01
Cardiac muscle cells are known to adapt to their physical surroundings, optimizing intracellular organization and contractile function for a given culture environment. A previously developed in vitro model system has shown that the inclusion of discrete microscale domains (or microrods) in three dimensions (3D) can alter long-term growth responses of neonatal ventricular myocytes. The aim of this work was to understand how cellular contact with such a domain affects various mechanical changes involved in cardiac muscle cell remodeling. Myocytes were maintained in 3D gels over 5 days in the presence or absence of 100 – μm-long microrods, and the effect of this local heterogeneity on cell behavior was analyzed via several imaging techniques. Microrod abutment resulted in approximately twofold increases in the maximum displacement of spontaneously beating myocytes, as based on confocal microscopy scans of the gel xy-plane or the myocyte long axis. In addition, microrods caused significant increases in the proportion of aligned myofibrils (≤20° deviation from long axis) in fixed myocytes. Microrod-related differences in axial contraction could be abrogated by long-term interruption of certain signals of the RhoA-/Rho-associated kinase (ROCK) or protein kinase C (PKC) pathway. Furthermore, microrod-induced increases in myocyte size and protein content were prevented by ROCK inhibition. In all, the data suggest that microdomain heterogeneity in 3D appears to promote the development of axially aligned contractile machinery in muscle cells, an observation that may have relevance to a number of cardiac tissue engineering interventions. PMID:22407215
Petroll, W. Matthew; Ma, Lisha; Kim, Areum; Ly, Linda; Vishwanath, Mridula
2009-01-01
The goal of this study was to determine the morphological and sub-cellular mechanical effects of Rac activation on fibroblasts within 3-D collagen matrices. Corneal fibroblasts were plated at low density inside 100 μm thick fibrillar collagen matrices and cultured for 1 to 2 days in serum-free media. Time-lapse imaging was then performed using Nomarski DIC. After an acclimation period, perfusion was switched to media containing PDGF. In some experiments, Y-27632 or blebbistatin were used to inhibit Rho-kinase (ROCK) or myosin II, respectively. PDGF activated Rac and induced cell spreading, which resulted in an increase in cell length, cell area, and the number of pseudopodial processes. Tractional forces were generated by extending pseudopodia, as indicated by centripetal displacement and realignment of collagen fibrils. Interestingly, the pattern of pseudopodial extension and local collagen fibril realignment was highly dependent upon the initial orientation of fibrils at the leading edge. Following ROCK or myosin II inhibition, significant ECM relaxation was observed, but small displacements of collagen fibrils continued to be detected at the tips of pseudopodia. Taken together, the data suggests that during Rac-induced cell spreading within 3-D matrices, there is a shift in the distribution of forces from the center to the periphery of corneal fibroblasts. ROCK mediates the generation of large myosin II-based tractional forces during cell spreading within 3-D collagen matrices, however residual forces can be generated at the tips of extending pseudopodia that are both ROCK and myosin II-independent. PMID:18452153
NASA Astrophysics Data System (ADS)
Duclaux, Guillaume; Huismans, Ritske S.; May, Dave
2015-04-01
How and why do continents break? More than two decades of analogue and 2D plane-strain numerical experiments have shown that despite the origin of the forces driving extension, the geometry of continental rifts falls into three categories - or modes: narrow rift, wide rift, or core complex. The mode of extension itself is strongly influenced by the rheology (and rheological behaviour) of the modelled layered system. In every model, an initial thermal or mechanical heterogeneity, such as a weak seed or a notch, is imposed to help localise the deformation and avoid uniform stretching of the lithosphere by pure shear. While it is widely accepted that structural inheritance is a key parameter for controlling rift localisation - as implied by the Wilson Cycle - modelling the effect of lithospheric heterogeneities on the long-term tectonic evolution of an extending plate in full 3D remains challenging. Recent progress in finite-element methods applied to computational tectonics along with the improved accessibility to high performance computers, now enable to switch from plane strain thermo-mechanical experiments to full 3D high-resolution experiments. Here we investigate the role of mechanical heterogeneities on rift opening, linkage and propagation during extension of a layered lithospheric systems with pTatin3d, a geodynamics modeling package utilising the material-point-method for tracking material composition, combined with a multigrid finite-element method to solve heterogeneous, incompressible visco-plastic Stokes problems. The initial model setup consists in a box of 1200 km horizontally by 250 km deep. It includes a 35 km layer of continental crust, underlaid by 85 km of sub-continental lithospheric mantle, and an asthenospheric mantle. Crust and mantle have visco-plastic rheologies with a pressure dependent yielding, which includes strain weakening, and a temperature, stress, strain-rate-dependent viscosity based on wet quartzite rheology for the crust, and wet
NASA Astrophysics Data System (ADS)
Moradi, Mina; Aghazadeh Mohandesi, Jamshid
2015-11-01
The incorporation of defects in junction area of 1D and 2D carbon nanostructures has a major impact on properties of their 3D structures. In the present study, molecular dynamics simulation is utilized to examine the mechanical behavior of graphene sheet (GS) in carbon nanotube (CNT)-GS junctions. The tensile load was applied along the GS in connection with CNTs of different chiralities. The adaptive intermolecular reactive empirical bond order potential was chosen to model C-C interactions. It provided a reliable model for CNT, GS and their junctions. The results revealed that the connection of CNT to the GS with a hole could improve the mechanical properties of defective GS, which appeared to be independent of CNT type. It was found that the high strength C-C bonds postpone the crack propagation and motivates new crack nucleation. When a hole or CNT placed on the GS, it caused stress concentration, exactly along a line on its side. The lower mechanical properties were consequently associated with crack nucleation and propagation on both sides in a way that cracks encountered each other during the failure; while, the cracks in pristine GS propagate parallel to each other and could not encounter each other.
Mapping dynamic mechanical remodeling in 3D tumor models via particle tracking microrheology
NASA Astrophysics Data System (ADS)
Jones, Dustin P.; Hanna, William; Celli, Jonathan P.
2015-03-01
Particle tracking microrheology (PTM) has recently been employed as a non-destructive way to longitudinally track physical changes in 3D pancreatic tumor co-culture models concomitant with tumor growth and invasion into the extracellular matrix (ECM). While the primary goal of PTM is to quantify local viscoelasticity via the Generalized Stokes-Einstein Relation (GSER), a more simplified way of describing local tissue mechanics lies in the tabulation and subsequent visualization of the spread of probe displacements in a given field of view. Proper analysis of this largely untapped byproduct of standard PTM has the potential to yield valuable insight into the structure and integrity of the ECM. Here, we use clustering algorithms in R to analyze the trajectories of probes in 3D pancreatic tumor/fibroblast co-culture models in an attempt to differentiate between probes that are effectively constrained by the ECM and/or contractile traction forces, and those that exhibit uninhibited mobility in local water-filled pores. We also discuss the potential pitfalls of this method. Accurately and reproducibly quantifying the boundary between these two categories of probe behavior could result in an effective method for measuring the average pore size in a given region of ECM. Such a tool could prove useful for studying stromal depletion, physical impedance to drug delivery, and degradation due to cellular invasion.
McCracken, Joselle M; Badea, Adina; Kandel, Mikhail E; Gladman, A Sydney; Wetzel, David J; Popescu, Gabriel; Lewis, Jennifer A; Nuzzo, Ralph G
2016-05-01
3D hydrogel scaffolds are widely used in cellular microcultures and tissue engineering. Using direct ink writing, microperiodic poly(2-hydroxyethyl-methacrylate) (pHEMA) scaffolds are created that are then printed, cured, and modified by absorbing 30 kDa protein poly-l-lysine (PLL) to render them biocompliant in model NIH/3T3 fibroblast and MC3T3-E1 preosteoblast cell cultures. Spatial light interference microscopy (SLIM) live cell imaging studies are carried out to quantify cellular motilities for each cell type, substrate, and surface treatment of interest. 3D scaffold mechanics is investigated using atomic force microscopy (AFM), while their absorption kinetics are determined by confocal fluorescence microscopy (CFM) for a series of hydrated hydrogel films prepared from prepolymers with different homopolymer-to-monomer (Mr ) ratios. The observations reveal that the inks with higher Mr values yield relatively more open-mesh gels due to a lower degree of entanglement. The biocompatibility of printed hydrogel scaffolds can be controlled by both PLL content and hydrogel mesh properties. PMID:26924676
Parallel Mechanisms for Visual Search in Zebrafish
Proulx, Michael J.; Parker, Matthew O.; Tahir, Yasser; Brennan, Caroline H.
2014-01-01
Parallel visual search mechanisms have been reported previously only in mammals and birds, and not animals lacking an expanded telencephalon such as bees. Here we report the first evidence for parallel visual search in fish using a choice task where the fish had to find a target amongst an increasing number of distractors. Following two-choice discrimination training, zebrafish were presented with the original stimulus within an increasing array of distractor stimuli. We found that zebrafish exhibit no significant change in accuracy and approach latency as the number of distractors increased, providing evidence of parallel processing. This evidence challenges theories of vertebrate neural architecture and the importance of an expanded telencephalon for the evolution of executive function. PMID:25353168
Parallel software support for computational structural mechanics
NASA Technical Reports Server (NTRS)
Jordan, Harry F.
1987-01-01
The application of the parallel programming methodology known as the Force was conducted. Two application issues were addressed. The first involves the efficiency of the implementation and its completeness in terms of satisfying the needs of other researchers implementing parallel algorithms. Support for, and interaction with, other Computational Structural Mechanics (CSM) researchers using the Force was the main issue, but some independent investigation of the Barrier construct, which is extremely important to overall performance, was also undertaken. Another efficiency issue which was addressed was that of relaxing the strong synchronization condition imposed on the self-scheduled parallel DO loop. The Force was extended by the addition of logical conditions to the cases of a parallel case construct and by the inclusion of a self-scheduled version of this construct. The second issue involved applying the Force to the parallelization of finite element codes such as those found in the NICE/SPAR testbed system. One of the more difficult problems encountered is the determination of what information in COMMON blocks is actually used outside of a subroutine and when a subroutine uses a COMMON block merely as scratch storage for internal temporary results.
Xie, G.; Li, J.
1997-05-01
A new 3D electromagnetic modeling and nonlinear inversion algorithm is presented based on global integral and local differential equations decomposition (GILD). The GILD parallel nonlinear inversion algorithm consists of five parts: (1) the domain is decomposed into subdomain SI and subdomain SII; (2) a new global magnetic integral equation in SI and the local magnetic differential equations IN SII will be used together to obtain the magnetic field in the modeling step; (3) the new global magnetic integral Jacobian equation in SI and the local magnetic differential Jacobian equations in SII will be used together to update the electric conductivity and permittivity from the magnetic field data in the inversion step; (4) the subdomain SII can naturally and uniformly be decomposed into 2{sup n} smaller sub-cubic-domains; the sparse matrix in each sub-cubic-domain can be eliminated separately, in parallel; (5) a new parallel multiple hierarchy substructure algorithm will be used to solve the smaller full matrices in SI, in parallel. The applications of the new 3D parallel GILD EM modeling and nonlinear inversion algorithm and software are: (1) to create high resolution controlled-source electric conductivity and permittivity imaging for interpreting electromagnetic field data acquired from cross hole, surface to borehole, surface to surface, single hole, and multiple holes; (2) to create the magnetotelluric high resolution imaging from the surface impedance and field data. The new GILD parallel nonlinear inversion will be a 3D/2.5D powerful imaging tool for the oil geophysical exploration and environmental remediation and monitoring.
NASA Astrophysics Data System (ADS)
Al-Jamal, Khuloud T.; Nerl, Hannah; Müller, Karin H.; Ali-Boucetta, Hanene; Li, Shouping; Haynes, Peter D.; Jinschek, Joerg R.; Prato, Maurizio; Bianco, Alberto; Kostarelos, Kostas; Porter, Alexandra E.
2011-06-01
Carbon nanotubes (CNTs) are being investigated for a variety of biomedical applications. Despite numerous studies, the pathways by which carbon nanotubes enter cells and their subsequent intracellular trafficking and distribution remain poorly determined. Here, we use 3-D electron tomography techniques that offer optimum enhancement of contrast between carbon nanotubes and the plasma membrane to investigate the mechanisms involved in the cellular uptake of shortened, functionalised multi-walled carbon nanotubes (MWNT-NH3+). Both human lung epithelial (A549) cells, that are almost incapable of phagocytosis and primary macrophages, capable of extremely efficient phagocytosis, were used. We observed that MWNT-NH3+ were internalised in both phagocytic and non-phagocytic cells by any one of three mechanisms: (a) individually via membrane wrapping; (b) individually by direct membrane translocation; and (c) in clusters within vesicular compartments. At early time points following intracellular translocation, we noticed accumulation of nanotube material within various intracellular compartments, while a long-term (14-day) study using primary human macrophages revealed that MWNT-NH3+ were able to escape vesicular (phagosome) entrapment by translocating directly into the cytoplasm.Carbon nanotubes (CNTs) are being investigated for a variety of biomedical applications. Despite numerous studies, the pathways by which carbon nanotubes enter cells and their subsequent intracellular trafficking and distribution remain poorly determined. Here, we use 3-D electron tomography techniques that offer optimum enhancement of contrast between carbon nanotubes and the plasma membrane to investigate the mechanisms involved in the cellular uptake of shortened, functionalised multi-walled carbon nanotubes (MWNT-NH3+). Both human lung epithelial (A549) cells, that are almost incapable of phagocytosis and primary macrophages, capable of extremely efficient phagocytosis, were used. We observed
Seal, Sudip K; Perumalla, Kalyan S
2009-01-01
Radio signal strength estimation is essential in many applications, including the design of military radio communications and industrial wireless installations. While classical approaches such as finite difference methods are well-known, new event-based models of radio signal propagation have been recently shown to deliver such estimates faster (via serial execution) than other methods. For scenarios with large or richly-featured geographical volumes, however, parallel processing is required to meet the memory and computation time demands. Here, we present a scalable and efficient parallel execution of a recently-developed event-based radio signal propagation model. We demonstrate its scalability to thousands of processors, with parallel speedups over 1000x. The speed and scale achieved by our parallel execution enable larger scenarios and faster execution than has ever been reported before.
Wave Phase-Sensitive Transformation of 3d-Straining of Mechanical Fields
NASA Astrophysics Data System (ADS)
Smirnov, I. N.; Speranskiy, A. A.
2015-11-01
It is the area of research of oscillatory processes in elastic mechanical systems. Technical result of innovation is creation of spectral set of multidimensional images which reflect time-correlated three-dimensional vector parameters of metrological, and\\or estimated, and\\or design parameters of oscillations in mechanical systems. Reconstructed images of different dimensionality integrated in various combinations depending on their objective function can be used as homeostatic profile or cybernetic image of oscillatory processes in mechanical systems for an objective estimation of current operational conditions in real time. The innovation can be widely used to enhance the efficiency of monitoring and research of oscillation processes in mechanical systems (objects) in construction, mechanical engineering, acoustics, etc. Concept method of vector vibrometry based on application of vector 3D phase- sensitive vibro-transducers permits unique evaluation of real stressed-strained states of power aggregates and loaded constructions and opens fundamental innovation opportunities: conduct of continuous (on-line regime) reliable monitoring of turboagregates of electrical machines, compressor installations, bases, supports, pipe-lines and other objects subjected to damaging effect of vibrations; control of operational safety of technical systems at all the stages of life cycle including design, test production, tuning, testing, operational use, repairs and resource enlargement; creation of vibro-diagnostic systems of authentic non-destructive control of anisotropic characteristics of materials resistance of power aggregates and loaded constructions under outer effects and operational flaws. The described technology is revolutionary, universal and common for all branches of engineering industry and construction building objects.
NASA Astrophysics Data System (ADS)
Sabantina, L.; Kinzel, F.; Ehrmann, A.; Finsterbusch, K.
2015-07-01
The 3D printing belongs to the rapidly emerging technologies which have the chance to revolutionize the way products are created. In the textile industry, several designers have already presented creations of shoes, dresses or other garments which could not be produced with common techniques. 3D printing, however, is still far away from being a usual process in textile and clothing production. The main challenge results from the insufficient mechanical properties, especially the low tensile strength, of pure 3D printed products, prohibiting them from replacing common technologies such as weaving or knitting. Thus, one way to the application of 3D printed forms in garments is combining them with textile fabrics, the latter ensuring the necessary tensile strength. This article reports about different approaches to combine 3D printed polymers with different textile materials and fabrics, showing chances and limits of this technique.
A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution
Gilles, Benjamin; Hamant, Olivier; Boudaoud, Arezki; Traas, Jan; Godin, Christophe
2015-01-01
The link between genetic regulation and the definition of form and size during morphogenesis remains largely an open question in both plant and animal biology. This is partially due to the complexity of the process, involving extensive molecular networks, multiple feedbacks between different scales of organization and physical forces operating at multiple levels. Here we present a conceptual and modeling framework aimed at generating an integrated understanding of morphogenesis in plants. This framework is based on the biophysical properties of plant cells, which are under high internal turgor pressure, and are prevented from bursting because of the presence of a rigid cell wall. To control cell growth, the underlying molecular networks must interfere locally with the elastic and/or plastic extensibility of this cell wall. We present a model in the form of a three dimensional (3D) virtual tissue, where growth depends on the local modulation of wall mechanical properties and turgor pressure. The model shows how forces generated by turgor-pressure can act both cell autonomously and non-cell autonomously to drive growth in different directions. We use simulations to explore lateral organ formation at the shoot apical meristem. Although different scenarios lead to similar shape changes, they are not equivalent and lead to different, testable predictions regarding the mechanical and geometrical properties of the growing lateral organs. Using flower development as an example, we further show how a limited number of gene activities can explain the complex shape changes that accompany organ outgrowth. PMID:25569615
Boudon, Frédéric; Chopard, Jérôme; Ali, Olivier; Gilles, Benjamin; Hamant, Olivier; Boudaoud, Arezki; Traas, Jan; Godin, Christophe
2015-01-01
The link between genetic regulation and the definition of form and size during morphogenesis remains largely an open question in both plant and animal biology. This is partially due to the complexity of the process, involving extensive molecular networks, multiple feedbacks between different scales of organization and physical forces operating at multiple levels. Here we present a conceptual and modeling framework aimed at generating an integrated understanding of morphogenesis in plants. This framework is based on the biophysical properties of plant cells, which are under high internal turgor pressure, and are prevented from bursting because of the presence of a rigid cell wall. To control cell growth, the underlying molecular networks must interfere locally with the elastic and/or plastic extensibility of this cell wall. We present a model in the form of a three dimensional (3D) virtual tissue, where growth depends on the local modulation of wall mechanical properties and turgor pressure. The model shows how forces generated by turgor-pressure can act both cell autonomously and non-cell autonomously to drive growth in different directions. We use simulations to explore lateral organ formation at the shoot apical meristem. Although different scenarios lead to similar shape changes, they are not equivalent and lead to different, testable predictions regarding the mechanical and geometrical properties of the growing lateral organs. Using flower development as an example, we further show how a limited number of gene activities can explain the complex shape changes that accompany organ outgrowth. PMID:25569615
NASA Technical Reports Server (NTRS)
Zhang, Jun; Ge, Lixin; Kouatchou, Jules
2000-01-01
A new fourth order compact difference scheme for the three dimensional convection diffusion equation with variable coefficients is presented. The novelty of this new difference scheme is that it Only requires 15 grid points and that it can be decoupled with two colors. The entire computational grid can be updated in two parallel subsweeps with the Gauss-Seidel type iterative method. This is compared with the known 19 point fourth order compact differenCe scheme which requires four colors to decouple the computational grid. Numerical results, with multigrid methods implemented on a shared memory parallel computer, are presented to compare the 15 point and the 19 point fourth order compact schemes.
Hayes, J C; Norman, M
1999-10-28
This report details an investigation into the efficacy of two approaches to solving the radiation diffusion equation within a radiation hydrodynamic simulation. Because leading-edge scientific computing platforms have evolved from large single-node vector processors to parallel aggregates containing tens to thousands of individual CPU's, the ability of an algorithm to maintain high compute efficiency when distributed over a large array of nodes is critically important. The viability of an algorithm thus hinges upon the tripartite question of numerical accuracy, total time to solution, and parallel efficiency.
A system for high resolution 3D mapping using laser radar and requiring no beam scanning mechanisms
NASA Astrophysics Data System (ADS)
Rademacher, Paul
1988-06-01
The inherently high angular and range resolution capabilities associated with radar systems operating at optical frequencies are at once a blessing and a curse. Standard implementations consist of very narrow field of view optical receivers operating in conjunction with laser transmitters or even narrower illumination beamwidth. While high angular resolution is thus achieved, mechanical scanning is required to gather data over extended fields of view. The many laser pulse transmissions necessary to cover the entire field of view increase the detectability of the system by enemy sensors. A system concept is proposed which, through the use of a single laser transmitter and multiple optical receivers, largely eliminate these deficiencies. Complete 3D data over a broad angular field of view and depth of field can be gathered based upon the reflections from a single transmitted laser pulse. Covert operation is enhanced as a result of the sparse laser transmissions required. The eye safety characteristics of the system are also enhanced. Proprietary coding of optical shutters in each of the multiple optical receivers permits the number of such receivers to be reduced to a very practical few. An alternative configuration of the system reduces the number of receivers required to one, at the expense of increased data acquisition time. The multiple receiver configuration is simply a parallel processing implementation of the single receiver approach. While data rate is reduced by the single receiver configuration, it still greatly exceeds that of scanning systems, and hardware complexity is also reduced significantly.
Mechanisms driving estuarine water quality: A 3D biogeochemical model for informed management
NASA Astrophysics Data System (ADS)
Wild-Allen, Karen; Skerratt, Jenny; Whitehead, Jason; Rizwi, Farhan; Parslow, John
2013-12-01
Estuaries are amongst the most productive marine ecosystems of the world but are also some of the most degraded due to coastal urban development. Sparse sampling of complex interactions between estuarine physics, sediment transport, chemistry, and biology limits understanding of the processes controlling estuarine water quality and confounds active management. We use a 3D coupled hydrodynamic, sediment and biogeochemical model to identify the key mechanisms driving fine-scale fluctuations in water quality in a temperate micro-tidal salt wedge estuary [Derwent Estuary, Tasmania]. Model results are dynamically consistent with relatively sparse monitoring data collected over a seasonal cycle and are considered to be a plausible hypothesis of sub-monitoring scale processes occurring in the estuary. The model shows enhanced mixing of nutrients across the pycnocline downstream of the salt wedge front that supports a persistent phytoplankton bloom. The length and flow regime of the estuary results in nutrient recycling and retention in the estuarine circulation driving a decline in bottom water dissolved oxygen in the mid- and upper-reaches. A budget analysis of modelled nitrogen suggests high levels of denitrification are critical to the maintenance of existing water quality. Active estuarine management focused on the improvement of bottom water dissolved oxygen for ecological health reasons must either concurrently reduce anthropogenic nitrogen loads or be sure to maintain high levels of microbial denitrification for net water quality improvement.
Mechanical properties of aligned carbon nanotube architectures: origin from 3D morphology
NASA Astrophysics Data System (ADS)
Stein, Itai Y.; Wardle, Brian L.
The scale-dependent properties of carbon nanotubes (CNTs) continue to motivate their study for next-generation material architectures. While recent work has shown that aligned CNT arrays can be made on the cm-scale, such systems exhibit properties that are orders of magnitude below those predicted by existing theories. This deviation mainly stems from the rudimentary assumptions made about the CNT morphology: CNTs are either devoid of local curvature (i.e. waviness) or have waviness that is easy to model, e.g. using helices and sine waves. Here, we use a simulation framework comprised of 105 CNTs with realistic 3D stochastic morphologies to elucidate the role morphology plays in the orders of magnitude over-prediction of the effective stiffness of aligned CNT structures. Application to aligned CNT polymer and carbon matrix nanocomposites reveals that the elimination of the torsion deformation mechanism, which dominates the effective compliance of CNT arrays, through CNT interactions with the matrix is responsible for the stiffness enhancement in CNT nanocomposites. This works paves the way to more accurate property prediction of CNT nanocomposites, and further work to predict the transport properties of aligned CNT architectures is planned.
NASA Astrophysics Data System (ADS)
Ren, Xin; Shen, Jianhu; Ghaedizadeh, Arash; Tian, Hongqi; Xie, Yi Min
2015-09-01
Auxetic metamaterials are synthetic materials with microstructures engineered to achieve negative Poisson’s ratios. Auxetic metamaterials are of great interest because of their unusual properties and various potential applications. However, most of the previous research has been focused on auxetic behaviour of elastomers under elastic deformation. Inspired by our recent finding of the loss of auxetic behaviour in metallic auxetic metamaterials, a systematic experimental and numerical investigation has been carried out to explore the mechanism behind this phenomenon. Using an improved methodology of generating buckling-induced auxetic metamaterials, several samples of metallic auxetic metamaterials have been fabricated using a 3D printing technique. The experiments on those samples have revealed the special features of auxetic behaviour for metallic auxetic metamaterials and proved the effectiveness of our structural modification. Parametric studies have been performed through experimentally validated finite element models to explore the auxetic performance of the designed metallic metamaterials. It is found that the auxetic performance can be tuned by the geometry of microstructures, and the strength and stiffness can be tuned by the plasticity of the base material while maintaining the auxetic performance.
NASA Technical Reports Server (NTRS)
Aftosmis, M. J.; Berger, M. J.; Murman, S. M.; Kwak, Dochan (Technical Monitor)
2002-01-01
The proposed paper will present recent extensions in the development of an efficient Euler solver for adaptively-refined Cartesian meshes with embedded boundaries. The paper will focus on extensions of the basic method to include solution adaptation, time-dependent flow simulation, and arbitrary rigid domain motion. The parallel multilevel method makes use of on-the-fly parallel domain decomposition to achieve extremely good scalability on large numbers of processors, and is coupled with an automatic coarse mesh generation algorithm for efficient processing by a multigrid smoother. Numerical results are presented demonstrating parallel speed-ups of up to 435 on 512 processors. Solution-based adaptation may be keyed off truncation error estimates using tau-extrapolation or a variety of feature detection based refinement parameters. The multigrid method is extended to for time-dependent flows through the use of a dual-time approach. The extension to rigid domain motion uses an Arbitrary Lagrangian-Eulerlarian (ALE) formulation, and results will be presented for a variety of two- and three-dimensional example problems with both simple and complex geometry.
Kressler, Bryan; Spincemaille, Pascal; Prince, Martin R; Wang, Yi
2006-09-01
Time-resolved 3D MRI with high spatial and temporal resolution can be achieved using spiral sampling and sliding-window reconstruction. Image reconstruction is computationally intensive because of the need for data regridding, a large number of temporal phases, and multiple RF receiver coils. Inhomogeneity blurring correction for spiral sampling further increases the computational work load by an order of magnitude, hindering the clinical utility of spiral trajectories. In this work the reconstruction time is reduced by a factor of >40 compared to reconstruction using a single processor. This is achieved by using a cluster of 32 commercial off-the-shelf computers, commodity networking hardware, and readily available software. The reconstruction system is demonstrated for time-resolved spiral contrast-enhanced (CE) peripheral MR angiography (MRA), and a reduction of reconstruction time from 80 min to 1.8 min is achieved. PMID:16892189
NASA Astrophysics Data System (ADS)
Fereshtenejad, Sayedalireza; Song, Jae-Joon
2016-06-01
Applications of 3D printing technology become more widespread in many research fields because of its rapid development and valuable capabilities. In rock mechanics and mining engineering, this technology has the potential to become a useful tool that might help implement a number of research studies previously considered impractical. Most commercial 3D printers cannot print prototypes with mechanical properties that match precisely those of natural rock samples. Therefore, some additional enhancements are required for 3D printers to be effectively utilized for rock mechanics applications. In this study, we printed and studied specimens using a powder-based commercial ZPrinter® 450 with ZP® 150 powder and Zb® 63 binder used as raw materials. The specimens printed by this 3D printer exhibited relatively low strength and ductile behavior, implying that it needs further improvements. Hence, we focused on several ways to determine the best combination of printing options and post-processing including the effects of the printing direction, printing layer thickness, binder saturation level, and heating process on the uniaxial compressive strength (UCS) and stress-strain behavior of the printed samples. The suggested procedures have demonstrated their effectiveness by obtaining the printed samples that behave similarly to the natural rocks with low UCS. Although our optimization methods were particularly successful, further improvements are required to expand 3D printer application in the area of rock mechanics.
Three Degree of Freedom Parallel Mechanical Linkage
NASA Technical Reports Server (NTRS)
Adelstein, Bernard D. (Inventor)
1998-01-01
A three degree of freedom parallel mechanism or linkage that couples three degree of freedom translational displacements at an endpoint, such as a handle, a hand grip, or a robot tool, to link rotations about three axes that are fixed with respect to a common base or ground link. The mechanism includes a three degree of freedom spherical linkage formed of two closed loops, and a planar linkage connected to the endpoint. The closed loops are rotatably interconnected, and made of eight rigid links connected by a plurality of single degree of freedom revolute joints. Three of these revolute joints are base joints and are connected to a common ground. such that the axis lines passing through the revolute joints intersect at a common fixed center point K forming the center of a spherical work volume in which the endpoint is capable of moving. 'Me three degrees of freedom correspond to the spatial displacement of the endpoint, for instance. The mechanism provides a new overall spatial kinematic linkage composed of a minimal number of rigid links and rotary joints. The mechanism has improved mechanical stiffness, and conveys mechanical power bidirectionally between the human operator and the electromechanical actuators. It does not require gears, belts. cable, screw or other types of transmission elements, and is useful in applications requiring full backdrivability. Thus, this invention can serve as the mechanical linkage for actively powered devices such as compliant robotic manipulators and force-reflecting hand controllers, and passive devices such as manual input devices for computers and other systems.
Fracture mechanics of propagating 3-D fatigue cracks with parametric dislocations
NASA Astrophysics Data System (ADS)
Takahashi, Akiyuki; Ghoniem, Nasr M.
2013-07-01
Propagation of 3-D fatigue cracks is analyzed using a discrete dislocation representation of the crack opening displacement. Three dimensional cracks are represented with Volterra dislocation loops in equilibrium with the applied external load. The stress intensity factor (SIF) is calculated using the Peach-Koehler (PK) force acting on the crack tip dislocation loop. Loading mode decomposition of the SIF is achieved by selection of Burgers vector components to correspond to each fracture mode in the PK force calculations. The interaction between 3-D cracks and free surfaces is taken into account through application of the superposition principle. A boundary integral solution of an elasticity problem in a finite domain is superposed onto the elastic field solution of the discrete dislocation method in an infinite medium. The numerical accuracy of the SIF is ascertained by comparison with known analytical solution of a 3-D crack problem in pure mode I, and for mixed-mode loading. Finally, fatigue crack growth simulations are performed with the Paris law, showing that 3-D cracks do not propagate in a self-similar shape, but they re-configure as a result of their interaction with external boundaries. A specific numerical example of fatigue crack growth is presented to demonstrate the utility of the developed method for studies of 3-D crack growth during fatigue.
Lee, Howon; Fang, Nicholas X.
2012-01-01
Buckling is a classical topic in mechanics. While buckling has long been studied as one of the major structural failure modes1, it has recently drawn new attention as a unique mechanism for pattern transformation. Nature is full of such examples where a wealth of exotic patterns are formed through mechanical instability2-5. Inspired by this elegant mechanism, many studies have demonstrated creation and transformation of patterns using soft materials such as elastomers and hydrogels6-11. Swelling gels are of particular interest because they can spontaneously trigger mechanical instability to create various patterns without the need of external force6-10. Recently, we have reported demonstration of full control over buckling pattern of micro-scaled tubular gels using projection micro-stereolithography (PμSL), a three-dimensional (3D) manufacturing technology capable of rapidly converting computer generated 3D models into physical objects at high resolution12,13. Here we present a simple method to build up a simplified PμSL system using a commercially available digital data projector to study swelling-induced buckling instability for controlled pattern transformation. A simple desktop 3D printer is built using an off-the-shelf digital data projector and simple optical components such as a convex lens and a mirror14. Cross-sectional images extracted from a 3D solid model is projected on the photosensitive resin surface in sequence, polymerizing liquid resin into a desired 3D solid structure in a layer-by-layer fashion. Even with this simple configuration and easy process, arbitrary 3D objects can be readily fabricated with sub-100 μm resolution. This desktop 3D printer holds potential in the study of soft material mechanics by offering a great opportunity to explore various 3D geometries. We use this system to fabricate tubular shaped hydrogel structure with different dimensions. Fixed on the bottom to the substrate, the tubular gel develops inhomogeneous stress
Lee, Howon; Fang, Nicholas X
2012-01-01
Buckling is a classical topic in mechanics. While buckling has long been studied as one of the major structural failure modes(1), it has recently drawn new attention as a unique mechanism for pattern transformation. Nature is full of such examples where a wealth of exotic patterns are formed through mechanical instability(2-5). Inspired by this elegant mechanism, many studies have demonstrated creation and transformation of patterns using soft materials such as elastomers and hydrogels(6-11). Swelling gels are of particular interest because they can spontaneously trigger mechanical instability to create various patterns without the need of external force(6-10). Recently, we have reported demonstration of full control over buckling pattern of micro-scaled tubular gels using projection micro-stereolithography (PμSL), a three-dimensional (3D) manufacturing technology capable of rapidly converting computer generated 3D models into physical objects at high resolution(12,13). Here we present a simple method to build up a simplified PμSL system using a commercially available digital data projector to study swelling-induced buckling instability for controlled pattern transformation. A simple desktop 3D printer is built using an off-the-shelf digital data projector and simple optical components such as a convex lens and a mirror(14). Cross-sectional images extracted from a 3D solid model is projected on the photosensitive resin surface in sequence, polymerizing liquid resin into a desired 3D solid structure in a layer-by-layer fashion. Even with this simple configuration and easy process, arbitrary 3D objects can be readily fabricated with sub-100 μm resolution. This desktop 3D printer holds potential in the study of soft material mechanics by offering a great opportunity to explore various 3D geometries. We use this system to fabricate tubular shaped hydrogel structure with different dimensions. Fixed on the bottom to the substrate, the tubular gel develops
Lockwood, Sarah Y; Meisel, Jayda E; Monsma, Frederick J; Spence, Dana M
2016-02-01
The process of bringing a drug to market involves many steps, including the preclinical stage, where various properties of the drug candidate molecule are determined. These properties, which include drug absorption, distribution, metabolism, and excretion, are often displayed in a pharmacokinetic (PK) profile. While PK profiles are determined in animal models, in vitro systems that model in vivo processes are available, although each possesses shortcomings. Here, we present a 3D-printed, diffusion-based, and dynamic in vitro PK device. The device contains six flow channels, each with integrated porous membrane-based insert wells. The pores of these membranes enable drugs to freely diffuse back and forth between the flow channels and the inserts, thus enabling both loading and clearance portions of a standard PK curve to be generated. The device is designed to work with 96-well plate technology and consumes single-digit milliliter volumes to generate multiple PK profiles, simultaneously. Generation of PK profiles by use of the device was initially performed with fluorescein as a test molecule. Effects of such parameters as flow rate, loading time, volume in the insert well, and initial concentration of the test molecule were investigated. A prediction model was generated from this data, enabling the user to predict the concentration of the test molecule at any point along the PK profile within a coefficient of variation of ∼ 5%. Depletion of the analyte from the well was characterized and was determined to follow first-order rate kinetics, indicated by statistically equivalent (p > 0.05) depletion half-lives that were independent of the starting concentration. A PK curve for an approved antibiotic, levofloxacin, was generated to show utility beyond the fluorescein test molecule. PMID:26727249
A 3D point-kernel multiple scatter model for parallel-beam SPECT based on a gamma-ray buildup factor
NASA Astrophysics Data System (ADS)
Marinkovic, Predrag; Ilic, Radovan; Spaic, Rajko
2007-09-01
A three-dimensional (3D) point-kernel multiple scatter model for point spread function (PSF) determination in parallel-beam single-photon emission computed tomography (SPECT), based on a dose gamma-ray buildup factor, is proposed. This model embraces nonuniform attenuation in a voxelized object of imaging (patient body) and multiple scattering that is treated as in the point-kernel integration gamma-ray shielding problems. First-order Compton scattering is done by means of the Klein-Nishina formula, but the multiple scattering is accounted for by making use of a dose buildup factor. An asset of the present model is the possibility of generating a complete two-dimensional (2D) PSF that can be used for 3D SPECT reconstruction by means of iterative algorithms. The proposed model is convenient in those situations where more exact techniques are not economical. For the proposed model's testing purpose calculations (for the point source in a nonuniform scattering object for parallel beam collimator geometry), the multiple-order scatter PSF generated by means of the proposed model matched well with those using Monte Carlo (MC) simulations. Discrepancies are observed only at the exponential tails mostly due to the high statistic uncertainty of MC simulations in this area, but not because of the inappropriateness of the model.
Olubamiji, Adeola D; Izadifar, Zohreh; Si, Jennifer L; Cooper, David M L; Eames, B Frank; Chen, Daniel X B
2016-06-01
Three-dimensional (3D)-printed poly(ε)-caprolactone (PCL)-based scaffolds are increasingly being explored for cartilage tissue engineering (CTE) applications. However, ensuring that the mechanical properties of these PCL-based constructs are comparable to that of articular cartilage that they are meant to regenerate is an area that has been under-explored. This paper presents the effects of PCL's molecular weight (MW) and scaffold's pore geometric configurations; strand size (SZ), strand spacing (SS), and strand orientation (SO), on mechanical properties of 3D-printed PCL scaffolds. The results illustrate that MW has significant effect on compressive moduli and yield strength of 3D-printed PCL scaffolds. Specifically, PCL with MW of 45 K was a more feasible choice for fabrication of visco-elastic, flexible and load-bearing PCL scaffolds. Furthermore, pore geometric configurations; SZ, SS, and SO, all significantly affect on tensile moduli of scaffolds. However, only SZ and SS have statistically significant effects on compressive moduli and porosity of these scaffolds. That said, inverse linear relationship was observed between porosity and mechanical properties of 3D-printed PCL scaffolds in Pearson's correlation test. Altogether, this study illustrates that modulating MW of PCL and pore geometrical configurations of the scaffolds enabled design and fabrication of PCL scaffolds with mechanical and biomimetic properties that better mimic mechanical behaviour of human articular cartilage. Thus, the modulated PCL scaffold proposed in this study is a framework that offers great potentials for CTE applications. PMID:27328736
A mechanically driven form of Kirigami as a route to 3D mesostructures in micro/nanomembranes
Zhang, Yihui; Yan, Zheng; Nan, Kewang; Xiao, Dongqing; Liu, Yuhao; Luan, Haiwen; Fu, Haoran; Wang, Xizhu; Yang, Qinglin; Wang, Jiechen; Ren, Wen; Si, Hongzhi; Liu, Fei; Yang, Lihen; Li, Hejun; Wang, Juntong; Guo, Xuelin; Luo, Hongying; Wang, Liang; Huang, Yonggang; Rogers, John A.
2015-01-01
Assembly of 3D micro/nanostructures in advanced functional materials has important implications across broad areas of technology. Existing approaches are compatible, however, only with narrow classes of materials and/or 3D geometries. This paper introduces ideas for a form of Kirigami that allows precise, mechanically driven assembly of 3D mesostructures of diverse materials from 2D micro/nanomembranes with strategically designed geometries and patterns of cuts. Theoretical and experimental studies demonstrate applicability of the methods across length scales from macro to nano, in materials ranging from monocrystalline silicon to plastic, with levels of topographical complexity that significantly exceed those that can be achieved using other approaches. A broad set of examples includes 3D silicon mesostructures and hybrid nanomembrane–nanoribbon systems, including heterogeneous combinations with polymers and metals, with critical dimensions that range from 100 nm to 30 mm. A 3D mechanically tunable optical transmission window provides an application example of this Kirigami process, enabled by theoretically guided design. PMID:26372959
A mechanically driven form of Kirigami as a route to 3D mesostructures in micro/nanomembranes.
Zhang, Yihui; Yan, Zheng; Nan, Kewang; Xiao, Dongqing; Liu, Yuhao; Luan, Haiwen; Fu, Haoran; Wang, Xizhu; Yang, Qinglin; Wang, Jiechen; Ren, Wen; Si, Hongzhi; Liu, Fei; Yang, Lihen; Li, Hejun; Wang, Juntong; Guo, Xuelin; Luo, Hongying; Wang, Liang; Huang, Yonggang; Rogers, John A
2015-09-22
Assembly of 3D micro/nanostructures in advanced functional materials has important implications across broad areas of technology. Existing approaches are compatible, however, only with narrow classes of materials and/or 3D geometries. This paper introduces ideas for a form of Kirigami that allows precise, mechanically driven assembly of 3D mesostructures of diverse materials from 2D micro/nanomembranes with strategically designed geometries and patterns of cuts. Theoretical and experimental studies demonstrate applicability of the methods across length scales from macro to nano, in materials ranging from monocrystalline silicon to plastic, with levels of topographical complexity that significantly exceed those that can be achieved using other approaches. A broad set of examples includes 3D silicon mesostructures and hybrid nanomembrane-nanoribbon systems, including heterogeneous combinations with polymers and metals, with critical dimensions that range from 100 nm to 30 mm. A 3D mechanically tunable optical transmission window provides an application example of this Kirigami process, enabled by theoretically guided design. PMID:26372959
NASA Astrophysics Data System (ADS)
Huang, Zhifeng
2015-09-01
Chirality does naturally exist, and the building blocks of life (e.g. DNA, proteins, peptides and sugars) are usually chiral. Chirality inherently imposes chemical/biological selectivity on functional molecules; hence the discrimination in molecular chirality from an enantiomer to the other mirror image (i.e. enantioselection) has fundamental and application significance. Enantiomers interact with left and right handed circularly polarized light in a different manner with respect to optical extinction; hence, electronic circular dichroism (ECD) has been widely used for enantioselection. However, enantiomers usually have remarkably low ECD intensity, mainly owing to the small electric transition dipole moment induced by molecular sizes compared to the ECD-active wavelength in the UV-visible-near IR region. To enhance ECD magnitude, recently it has being developed 3D chiral nanoplasmonic structures having a helical path, and the dimensions are comparable to the ECD wavelength. However, it is still ambiguous the origin of 3D chiroplasmonics, and there is a lack of studying the interaction of 3D chiroplasmoncs with enantiomers for the application of enantioselection. Herein, we will present a one-step fabrication of 3D silver nanospirals (AgNSs) via low-substrate-temperature glancing angle deposition. AgNSs can be deposited on a wide range of substrates (including transparent and flexible substrates), in an area on the order of cm2. A set of spiral dimensions (such as spiral pitches, number of turns and handedness) have been easily engineered to tune the chiroptic properties, leading to studying the chiroplasmonic principles together with finite element simulation and the LC model. At the end, it will be demonstrated that 3D chiroplasmonics can differentiate molecular chirality of enantiomers with dramatic enhancement in the anisotropy g factor. This study opens a door to sensitively discriminate enantiomer chirality.
Theoretical study on the reaction mechanism of the gas-phase H2/CO2/Ni(3D) system.
Qin, Song; Hu, Changwei; Yang, Huaqing; Su, Zhishan
2005-07-28
The ground-state potential energy surface (PES) in the gas-phase H2/CO2/Ni(3D) system is investigated at the CCSD(T)//B3LYP/6-311+G(2d,2p) levels in order to explore the possible reaction mechanism of the reverse water gas shift reaction catalyzed by Ni(3D). The calculations predict that the C-O bond cleavage of CO2 assisted by co-interacted H2 is prior to the dissociation of the H2, and the most feasible reaction path for Ni(3D) + H2 + CO2 --> Ni(3D) + H2O + CO is endothermic by 12.5 kJ mol(-1) with an energy barrier of 103.9 kJ mol(-1). The rate-determining step for the overall reaction is predicted to be the hydrogen migration with water formation. The promotion effect of H2 on the cleavage of C-O bond in CO2 is also discussed and compared with the analogous reaction of Ni(3D) + CO2 --> NiO + CO, and the difference between triplet and singlet H2/CO2/Ni systems is also discussed. PMID:16833994
Qiang, J.; Leitner, D.; Todd, D.S.; Ryne, R.D.
2005-03-15
The superconducting ECR ion source VENUS serves as the prototype injector ion source for the Rare Isotope Accelerator (RIA) driver linac. The RIA driver linac requires a great variety of high charge state ion beams with up to an order of magnitude higher intensity than currently achievable with conventional ECR ion sources. In order to design the beam line optics of the low energy beam line for the RIA front end for the wide parameter range required for the RIA driver accelerator, reliable simulations of the ion beam extraction from the ECR ion source through the ion mass analyzing system are essential. The RIA low energy beam transport line must be able to transport intense beams (up to 10 mA) of light and heavy ions at 30 keV.For this purpose, LBNL is developing the parallel 3D particle-in-cell code IMPACT to simulate the ion beam transport from the ECR extraction aperture through the analyzing section of the low energy transport system. IMPACT, a parallel, particle-in-cell code, is currently used to model the superconducting RF linac section of RIA and is being modified in order to simulate DC beams from the ECR ion source extraction. By using the high performance of parallel supercomputing we will be able to account consistently for the changing space charge in the extraction region and the analyzing section. A progress report and early results in the modeling of the VENUS source will be presented.
NASA Astrophysics Data System (ADS)
Qiang, J.; Leitner, D.; Todd, D. S.; Ryne, R. D.
2005-03-01
The superconducting ECR ion source VENUS serves as the prototype injector ion source for the Rare Isotope Accelerator (RIA) driver linac. The RIA driver linac requires a great variety of high charge state ion beams with up to an order of magnitude higher intensity than currently achievable with conventional ECR ion sources. In order to design the beam line optics of the low energy beam line for the RIA front end for the wide parameter range required for the RIA driver accelerator, reliable simulations of the ion beam extraction from the ECR ion source through the ion mass analyzing system are essential. The RIA low energy beam transport line must be able to transport intense beams (up to 10 mA) of light and heavy ions at 30 keV. For this purpose, LBNL is developing the parallel 3D particle-in-cell code IMPACT to simulate the ion beam transport from the ECR extraction aperture through the analyzing section of the low energy transport system. IMPACT, a parallel, particle-in-cell code, is currently used to model the superconducting RF linac section of RIA and is being modified in order to simulate DC beams from the ECR ion source extraction. By using the high performance of parallel supercomputing we will be able to account consistently for the changing space charge in the extraction region and the analyzing section. A progress report and early results in the modeling of the VENUS source will be presented.
Farzadi, Arghavan; Solati-Hashjin, Mehran; Asadi-Eydivand, Mitra; Abu Osman, Noor Azuan
2014-01-01
Powder-based inkjet 3D printing method is one of the most attractive solid free form techniques. It involves a sequential layering process through which 3D porous scaffolds can be directly produced from computer-generated models. 3D printed products' quality are controlled by the optimal build parameters. In this study, Calcium Sulfate based powders were used for porous scaffolds fabrication. The printed scaffolds of 0.8 mm pore size, with different layer thickness and printing orientation, were subjected to the depowdering step. The effects of four layer thicknesses and printing orientations, (parallel to X, Y and Z), on the physical and mechanical properties of printed scaffolds were investigated. It was observed that the compressive strength, toughness and Young's modulus of samples with 0.1125 and 0.125 mm layer thickness were more than others. Furthermore, the results of SEM and μCT analyses showed that samples with 0.1125 mm layer thickness printed in X direction have more dimensional accuracy and significantly close to CAD software based designs with predefined pore size, porosity and pore interconnectivity. PMID:25233468
Li, Shengtai; Li, Hui
2012-06-14
the position of the planet, we adopt the corotating frame that allows the planet moving only in radial direction if only one planet is present. This code has been extensively tested on a number of problems. For the earthmass planet with constant aspect ratio h = 0.05, the torque calculated using our code matches quite well with the the 3D linear theory results by Tanaka et al. (2002). The code is fully parallelized via message-passing interface (MPI) and has very high parallel efficiency. Several numerical examples for both fixed planet and moving planet are provided to demonstrate the efficacy of the numerical method and code.
NASA Astrophysics Data System (ADS)
Tramm, John R.; Gunow, Geoffrey; He, Tim; Smith, Kord S.; Forget, Benoit; Siegel, Andrew R.
2016-05-01
In this study we present and analyze a formulation of the 3D Method of Characteristics (MOC) technique applied to the simulation of full core nuclear reactors. Key features of the algorithm include a task-based parallelism model that allows independent MOC tracks to be assigned to threads dynamically, ensuring load balancing, and a wide vectorizable inner loop that takes advantage of modern SIMD computer architectures. The algorithm is implemented in a set of highly optimized proxy applications in order to investigate its performance characteristics on CPU, GPU, and Intel Xeon Phi architectures. Speed, power, and hardware cost efficiencies are compared. Additionally, performance bottlenecks are identified for each architecture in order to determine the prospects for continued scalability of the algorithm on next generation HPC architectures.
NASA Astrophysics Data System (ADS)
Tackley, P. J.
2013-12-01
StagYY is a well-established code for modelling mantle convection in 3D spherical geometry (Tackley, PEPI 2008), incorporating several physical complexities such as compressibility, phase transitions, compositional variations, strongly temperature-dependent, non-linear rheology, tracers to track composition, continents, partial melting and melt migration. It uses a finite volume discretization (primitive variables on a staggered grid) on the yin-yang spherical grid (minimum overlap version). Geometric multigrid is used for simultaneous solution of the Stokes and mass conservation equations. Here, parallelization using MPI is discussed, and performance and scaling of the current StagYY version on up to 4096 cores on grids of up to 768x2304x512x2 cells (1.8 billion, corresponding to 7.2 billion unknowns) is demonstrated. Complexities related to scaling further to 100,000s to millions of cores are discussed together with possible solutions and performance projections.
Mechanisms of clay smear formation in 3D - a field study
NASA Astrophysics Data System (ADS)
Kettermann, Michael; Tronberens, Sebastian; Urai, Janos; Asmus, Sven
2016-04-01
Clay smears in sedimentary basins are important factors defining the sealing properties of faults. However, as clay smears are highly complex 3D structures, processes involved in the formation and deformation of clay smears are not well identified and understood. To enhance the prediction of sealing properties of clay smears extensive studies of these structures are necessary including the 3D information. We present extraordinary outcrop data from an open cast lignite mine (Hambach) in the Lower Rhine Embayment, Germany. The faults formed at a depth of 150 m, and have Shale Gouge Ratios between 0.1 and 0.3. Material in the fault zones is layered, with sheared sand, sheared clay and tectonically mixed sand-clay gouge. We studied the 3D thickness distribution of clay smear from a series of thin-spaced incremental cross-sections and several cross-sections in larger distances along the fault. Additionally, we excavated two large clay smear surfaces. Our observations show that clay smears are strongly affected by R- and R'-shears, mostly at the footwall side of our outcrops. These shears can locally cross and offset clay smears, forming holes. Thinnest parts of the clay smears are often located close to source layer cutoffs. Investigating the 3D thickness of the clay smears shows a heterogeneous distribution, rather than a continuous thinning of the smear with increasing distance to the source layers. We found two types of layered clay smears: one with continuous sheared sand between two clay smears providing vertical pathways for fluid flow, and one which consists of overlapping clay patches separated by sheared sand that provide a tortuous pathway across the clay smear. On smaller scale we identified grain-scale mixing as an important process for the formation of clay smears. Sand can be entrained into the clay smear by mixing from the surrounding host rock as well as due to intense shearing of sand lenses that were incorporated into the smear. This causes clay smears
3D thermo-chemical-mechanical simulation of power ramps with ALCYONE fuel code
NASA Astrophysics Data System (ADS)
Baurens, B.; Sercombe, J.; Riglet-Martial, C.; Desgranges, L.; Trotignon, L.; Maugis, P.
2014-09-01
This paper presents the coupling of the fuel performance code ALCYONE with the thermochemical code ANGE and its application to Iodine-Stress Corrosion Cracking (I-SCC). The coupling is illustrated by a 3D simulation of a power ramp. The release of chemically active gases (CsI(g), Tex(1
Evers, H; Mayer, A; Engelmann, U; Schröter, A; Baur, U; Wolsiffer, K; Meinzer, H P
1998-01-01
This paper describes ongoing research concerning interactive volume visualization coupled with tools for volumetric analysis. To establish an easy to use application, the 3D-visualization has been embedded in a state of the art teleradiology system, where additional functionality is often desired beyond basic image transfer and management. Major clinical requirements for deriving spatial measures are covered by the tools, in order to realize extended diagnosis support and therapy planning. Introducing the general plug-in mechanism this work exemplarily describes the useful extension of an approved application. Interactive visualization was achieved by a hybrid approach taking advantage of both the precise volume visualization based on the Heidelberg Raytracing Model and the graphics acceleration of modern workstations. Several tools for volumetric analysis extend the 3D-viewing. They offer 3D-pointing devices to select locations in the data volume, measure anatomical structures or control segmentation processes. A haptic interface provides a realistic perception while navigating within the 3D-reconstruction. The work is closely related to research work in the field of heart, liver and head surgery. In cooperation with our medical partners the development of tools as presented proceed the integration of image analysis into clinical routine. PMID:10384617
Skorski, Matthew; Esenther, Jake; Ahmed, Zeeshan; Miller, Abigail E.
2016-01-01
To expand the chemical capabilities of 3D printed structures generated from commercial thermoplastic printers, we have produced and printed polymer filaments that contain inorganic nanoparticles. TiO2 was dispersed into acrylonitrile butadiene styrene (ABS) and extruded into filaments with 1.75 mm diameters. We produced filaments with TiO2 compositions of 1%, 5%, and 10% (kg/kg) and printed structures using a commercial 3D printer. Our experiments suggest that ABS undergoes minor degradation in the presence of TiO2 during the different processing steps. The measured mechanical properties (strain and Young’s modulus) for all of the composites are similar to those of structures printed from the pure polymer. TiO2 incorporation at 1% negatively affects the stress at breaking point and the flexural stress. Structures produced from the 5 and 10% nanocomposites display a higher breaking point stress than those printed from the pure polymer. TiO2 within the printed matrix was able to quench the intrinsic fluorescence of the polymer. TiO2 was also able to photocatalyze the degradation of a rhodamine 6G in solution. These experiments display chemical reactivity in nanocomposites that are printed using commercial 3D printers, and we expect that our methodology will help to inform others who seek to incorporate catalytic nanoparticles in 3D printed structures. PMID:27375367
Nonintrusive 3D reconstruction of human bone models to simulate their bio-mechanical response
NASA Astrophysics Data System (ADS)
Alexander, Tsouknidas; Antonis, Lontos; Savvas, Savvakis; Nikolaos, Michailidis
2012-06-01
3D finite element models representing functional parts of the human skeletal system, have been repeatedly introduced over the last years, to simulate biomechanical response of anatomical characteristics or investigate surgical treatment. The reconstruction of geometrically accurate FEM models, poses a significant challenge for engineers and physicians, as recent advances in tissue engineering dictate highly customized implants, while facilitating the production of alloplast materials that are employed to restore, replace or supplement the function of human tissue. The premises of every accurate reconstruction method, is to encapture the precise geometrical characteristics of the examined tissue and thus the selection of a sufficient imaging technique is of the up-most importance. This paper reviews existing and potential applications related to the current state-of-the-art of medical imaging and simulation techniques. The procedures are examined by introducing their concepts; strengths and limitations, while the authors also present part of their recent activities in these areas. [Figure not available: see fulltext.
NASA Astrophysics Data System (ADS)
Pereira, J. P.; Duarte, C. A.; Jiao, X.; Guoy, D.
2009-06-01
This paper presents a study of generalized enrichment functions for 3D curved crack fronts. Two coordinate systems used in the definition of singular curved crack front enrichment functions are analyzed. In the first one, a set of Cartesian coordinate systems defined along the crack front is used. In the second case, the geometry of the crack front is approximated by a set of curvilinear coordinate systems. A description of the computation of derivatives of enrichment functions and curvilinear base vectors is presented. The coordinate systems are automatically defined using geometrical information provided by an explicit representation of the crack surface. A detailed procedure to accurately evaluate the surface normal, conormal and tangent vectors along curvilinear crack fronts in explicit crack surface representations is also presented. An accurate and robust definition of orthonormal vectors along crack fronts is crucial for the proper definition of enrichment functions. Numerical experiments illustrate the accuracy and robustness of the proposed approaches.
Fevotte, F.; Lathuiliere, B.
2013-07-01
The large increase in computing power over the past few years now makes it possible to consider developing 3D full-core heterogeneous deterministic neutron transport solvers for reference calculations. Among all approaches presented in the literature, the method first introduced in [1] seems very promising. It consists in iterating over resolutions of 2D and ID MOC problems by taking advantage of prismatic geometries without introducing approximations of a low order operator such as diffusion. However, before developing a solver with all industrial options at EDF, several points needed to be clarified. In this work, we first prove the convergence of this iterative process, under some assumptions. We then present our high-performance, parallel implementation of this algorithm in the MICADO solver. Benchmarking the solver against the Takeda case shows that the 2D-1D coupling algorithm does not seem to affect the spatial convergence order of the MOC solver. As for performance issues, our study shows that even though the data distribution is suited to the 2D solver part, the efficiency of the ID part is sufficient to ensure a good parallel efficiency of the global algorithm. After this study, the main remaining difficulty implementation-wise is about the memory requirement of a vector used for initialization. An efficient acceleration operator will also need to be developed. (authors)
NASA Astrophysics Data System (ADS)
Krstulović-Opara, Lovre; Surjak, Martin; Vesenjak, Matej; Tonković, Zdenko; Kodvanj, Janoš; Domazet, Željko
2015-11-01
To investigate the applicability of infrared thermography as a tool for acquiring dynamic yielding in metals, a comparison of infrared thermography with three dimensional digital image correlation has been made. Dynamical tension tests and three point bending tests of aluminum alloys have been performed to evaluate results obtained by IR thermography in order to detect capabilities and limits for these two methods. Both approaches detect pastification zone migrations during the yielding process. The results of the tension test and three point bending test proved the validity of the IR approach as a method for evaluating the dynamic yielding process when used on complex structures such as cellular porous materials. The stability of the yielding process in the three point bending test, as contrary to the fluctuation of the plastification front in the tension test, is of great importance for the validation of numerical constitutive models. The research proved strong performance, robustness and reliability of the IR approach when used to evaluate yielding during dynamic loading processes, while the 3D DIC method proved to be superior in the low velocity loading regimes. This research based on two basic tests, proved the conclusions and suggestions presented in our previous research on porous materials where middle wave infrared thermography was applied.
NASA Astrophysics Data System (ADS)
Kai, Zhu; Enyu, Guo; Wenqian, Zhou; Sansan, Shuai; Tao, Jing; Hongliang, Hou; Yanjin, Xu
2015-06-01
Metal-foam materials have been used increasingly in industry for their low-density, high-toughness and high impact resistance properties. Understanding the macro-scale mechanical properties of these materials is essential to evaluate their actual performance and thus to optimize the structures and properties accordingly. Synchrotron radiation X-ray microtomographytechnique is a promising method to study 3D structures at small length scales, which provides high spatial resolution and allows the researchers to observe the change of structures/features in situ without destroying the original objects. In this work, the real 3D structure of closed-cell aluminum foam was obtained by using synchrotron radiation X-ray microtomography. The reconstructed 3D model of the foam was further utilized as input for the subsequent mechanical study to investigate the localized deformation behaviors and evolution process of the foam under longitudinal quasi-static uniaxial compressive loading. By analyzing the simulated results, it is demonstrated that the deformation bands always initiate and propagate along the cell walls which are finally folded upon loading. And the large spherical cells are more susceptible to yielding, as well as to the stress concentration than the cells with other shapes. This finding is consistent with the experimental results.
Parallel solid mechanics codes at Sandia National Laboratories
McGlaun, M.
1994-08-01
Computational physicists at Sandia National Laboratories have moved their production codes to distributed memory parallel computers. The codes include the multi-material CTH Eulerian code, structural mechanics code. This presentation discusses our experiences moving the codes to parallel computers and experiences running the codes. Moving large production codes onto parallel computers require developing parallel algorithms, parallel data bases and parallel support tools. We rewrote the Eulerian CTH code for parallel computers. We were able to move both ALEGRA and PRONTO to parallel computers with only a modest number of modifications. We restructured the restart and graphics data bases to make them parallel and minimize the I/O to the parallel computer. We developed mesh decomposition tools to divide a rectangular or arbitrary connectivity mesh into sub-meshes. The sub-meshes map to processors and minimize the communication between processors. We developed new visualization tools to process the very large, parallel data bases. This presentation also discusses our experiences running these codes on Sandia`s 1840 compute node Intel Paragon, 1024 processor nCUBE and networked workstations. The parallel version of CTH uses the Paragon and nCUBE for production calculations. The ALEGRA and PRONTO codes are moving off networked workstations onto the Paragon and nCUBE massively parallel computers.
NASA Astrophysics Data System (ADS)
Jaya Christiyan, K. G.; Chandrasekhar, U.; Venkateswarlu, K.
2016-02-01
Additive Manufacturing (AM) technologies have been emerged as a fabrication method to obtain engineering components within a short span of time. Desktop 3D printing, also referred as additive layer manufacturing technology is one of the powerful method of rapid prototyping (RP) technique that fabricates three dimensional engineering components. In this method, 3D digital CAD data is converted directly to a product. In the present investigation, ABS + hydrous magnesium silicate composite was considered as the starting material. Mechanical properties of ABS + hydrous magnesium silicate composite material were evaluated. ASTM D638 and ASTM D760 standards were followed for carrying out tensile and flexural tests, respectively. Samples with different layer thickness and printing speed were prepared. Based on the experimental results, it is suggested that low printing speed, and low layer thickness has resulted maximum tensile and flexural strength, as compared to all the other process parameters samples.
Chenot, Jean-Loup; Bay, Francois
2007-04-07
The different stages of metal forming processes often involve - beyond the mechanical deformations processes - other physical coupled problems, such as heat transfer, electromagnetism or metallurgy. The purpose of this paper is to focus on problems involving electromagnetic couplings. After a brief recall on electromagnetic modeling, we shall then focus on induction heating processes and present some results regarding heat transfer, as well as mechanical couplings. A case showing coupling for metallurgic microstructure evolution will conclude this paper.
Electrical conduction mechanisms in PbSe and PbS nano crystals 3D matrix layer
NASA Astrophysics Data System (ADS)
Arbell, Matan; Hechster, Elad; Sarusi, Gabby
2016-02-01
A simulation study and measurements of the electrical conductance in a PbSe and PbS spherical Nano-crystal 3D matrix layer was carried out focusing on its dependences of Nano-crystal size distribution and size gradient along the layer thickness (z-direction). The study suggests a new concept of conductance enhancement by utilizing a size gradient along the layer thickness from mono-layer to the next mono-layer of the Nano-crystals, in order to create a gradient of the energy levels and thus improve directional conductance in this direction. A Monte Carlo simulation of the charge carriers path along the layer thickness of the Nano-crystals 3D matrix using the Miller-Abrahams hopping model was performed. We then compared the conductance characteristics of the gradual size 3D matrix layer to a constant-sized 3D matrix layer that was used as a reference in the simulation. The numerical calculations provided us with insights into the actual conductance mechanism of the PbSe and PbS Nano-crystals 3D matrix and explained the discrepancies in actual conductance and the variability in measured mobilities published in the literature. It is found that the mobility and thus conductance are dependent on a critical electrical field generated between two adjacent nano-crystals. Our model explains the conductance dependents on the: Cathode-Anode distance, the distance between the adjacent nano-crystals in the 3D matrix layer and the size distribution along the current direction. Part of the model (current-voltage dependence) was validated using a current-voltage measurements taken on a constant size normal distribution nano-crystals PbS layer (330nm thick) compared with the predicted I-V curves. It is shown that under a threshold bias, the current is very low, while after above a threshold bias the conductance is significantly increased due to increase of hopping probability. Once reaching the maximum probability the current tend to level-off reaching the maximal conductance
NASA Technical Reports Server (NTRS)
Leventis, Nicholas
2005-01-01
In analogy to supramolecular assemblies, which are pursued because of properties above and beyond those of the individual molecules, self-standing monolithic three-dimensional assemblies of nanoparticles also have unique properties attributed to their structure. For example, ultra low-density 3-D assemblies of silica nanoparticles, known as silica aerogels, are characterized by large internal void space, high surface area and very low thermal conductivity. Aerogels, however, are also extremely fragile materials, limiting their application to a few specialized environments, e.g., in nuclear reactors as Cerenkov radiation detectors, in space (refer to NASA's Stardust Program) and aboard certain planetary vehicles (thermal insulators on Mars Rovers in 1997 and 2004). The fragility problem is traced to well-defined weak points in the aerogel skeletal framework, the interparticle necks. Using the surface functionality of the nanoparticle building blocks as a focal point, we have directed attachment of a conformal polymer coating over the entire framework, rendering all necks wider. Thus, although the bulk density may increase only by 3x, the mesoporosity (pores in the range 2-50 nm) remains unchanged, while the strength of the material increases by up to 300... Having addressed the fragility problem, aerogels are now robust materials, and a variety of applications, ranging from thermal/acoustic insulators to catalyst supports, to platform for sensors, and dielectrics are all within reach. Our approach employs molecular science to manipulate nanoscopic matter for achieving useful macroscopic properties, and in our view it resides at the core of what defines nanotechnology. In that spirit, this technology is expandable in three directions. Thus, we have already crosslinked successfully amine-modified silica, and we anticipate that more rich chemistry will be realized by been creative with the nanoparticle surface modifiers. On the other hand, although we do not expect
NASA Astrophysics Data System (ADS)
Kordy, M.; Wannamaker, P.; Maris, V.; Cherkaev, E.; Hill, G.
2016-01-01
We have developed an algorithm, which we call HexMT, for 3-D simulation and inversion of magnetotelluric (MT) responses using deformable hexahedral finite elements that permit incorporation of topography. Direct solvers parallelized on symmetric multiprocessor (SMP), single-chassis workstations with large RAM are used throughout, including the forward solution, parameter Jacobians and model parameter update. In Part I, the forward simulator and Jacobian calculations are presented. We use first-order edge elements to represent the secondary electric field (E), yielding accuracy O(h) for E and its curl (magnetic field). For very low frequencies or small material admittivities, the E-field requires divergence correction. With the help of Hodge decomposition, the correction may be applied in one step after the forward solution is calculated. This allows accurate E-field solutions in dielectric air. The system matrix factorization and source vector solutions are computed using the MKL PARDISO library, which shows good scalability through 24 processor cores. The factorized matrix is used to calculate the forward response as well as the Jacobians of electromagnetic (EM) field and MT responses using the reciprocity theorem. Comparison with other codes demonstrates accuracy of our forward calculations. We consider a popular conductive/resistive double brick structure, several synthetic topographic models and the natural topography of Mount Erebus in Antarctica. In particular, the ability of finite elements to represent smooth topographic slopes permits accurate simulation of refraction of EM waves normal to the slopes at high frequencies. Run-time tests of the parallelized algorithm indicate that for meshes as large as 176 × 176 × 70 elements, MT forward responses and Jacobians can be calculated in ˜1.5 hr per frequency. Together with an efficient inversion parameter step described in Part II, MT inversion problems of 200-300 stations are computable with total run times
NASA Astrophysics Data System (ADS)
He, Shan; Zhang, Linxi; Liu, Ying; Rafailovich, Miriam; Garcia Center for Polymers at Engineered Interfaces Team
In this study, engineered electrospun scaffolds with fibers oriented with designed curvature in three dimensions (3D) including the looped structure were developed based on the principle of electrostatic repulsion. Here we illustrate that 3D electrospun recycled polystyrene fibers could closely mimic the unique architectures of multi-direction and multi-layer nano-spiderweb. In contrast to virgin PS, the recycled PS (Dart Styrofoam) are known to contain zinc stearate which acts as a surfactant resulting in higher electrical charge and larger fiber curvature, hence, lower modulus. The surfactant, which is known to decrease the surface tension, may have also been effective at decreasing the confinement of the PS, where chain stretching was shown to occur, in response to the high surface tension at the air interface. Three dimensional flexible architecture with complex structures are shown to be necessary in order to block the motion of Cimex lectularius. Here we show how an engineered electrospun network of surfactant modified polymer fibers with calculated dimensions can be used to immobilize the insects. The mechanical response of the fibers has to be specifically tailored so that it is elastically deformed, without fracturing or flowing. Carefully controlling and tailoring the electrospinning parameters we can now utilize architected 3D nanofiber to create an environmental-friendly Cimex immobilization device which can lead to annihilation solution for all the other harmful insects.
Yao, Qingqiang; Wei, Bo; Guo, Yang; Jin, Chengzhe; Du, Xiaotao; Yan, Chao; Yan, Junwei; Hu, Wenhao; Xu, Yan; Zhou, Zhi; Wang, Yijin; Wang, Liming
2015-01-01
The study aims to investigate the techniques of design and construction of CT 3D reconstructional data-based polycaprolactone (PCL)-hydroxyapatite (HA) scaffold. Femoral and lumbar spinal specimens of eight male New Zealand white rabbits were performed CT and laser scanning data-based 3D printing scaffold processing using PCL-HA powder. Each group was performed eight scaffolds. The CAD-based 3D printed porous cylindrical stents were 16 piece × 3 groups, including the orthogonal scaffold, the Pozi-hole scaffold and the triangular hole scaffold. The gross forms, fiber scaffold diameters and porosities of the scaffolds were measured, and the mechanical testing was performed towards eight pieces of the three kinds of cylindrical scaffolds, respectively. The loading force, deformation, maximum-affordable pressure and deformation value were recorded. The pore-connection rate of each scaffold was 100 % within each group, there was no significant difference in the gross parameters and micro-structural parameters of each scaffold when compared with the design values (P > 0.05). There was no significant difference in the loading force, deformation and deformation value under the maximum-affordable pressure of the three different cylinder scaffolds when the load was above 320 N. The combination of CT and CAD reverse technology could accomplish the design and manufacturing of complex bone tissue engineering scaffolds, with no significant difference in the impacts of the microstructures towards the physical properties of different porous scaffolds under large load. PMID:25596860
Development of a Mechanically Tuneable 3D Scaffold for Vascular Reconstruction
Rodriguez, Maritza; Juran, Cassandra; McClendon, Mark; Eyadiel, Cyril; McFetridge, Peter
2012-01-01
Material compliance has been shown to be a predictor of vascular graft patency and as such is a critical parameter when designing new materials. While ex vivo derived materials have been clinically successful in a number of applications their mechanical properties are a direct function of the original vessel and are not easily controllable. These investigations describe an approach to modulate the mechanical properties of an ex vivo derived scaffold by machining variable (discrete) wall thicknesses to control compliance. Human umbilical arteries (HUA) were machine-lathed directly from the umbilical cord at wall thicknesses of 250, 500, 750, and 1000 μm then decellularized using 1 % sodium dodecyl sulfate (SDS). Compliance over physiological pressures, increased from 3.08±1.84% to 11.47±4.11% as direct function of each discrete vessel diameter. Radial stress strain analysis revealed primary and secondary failure points attributed to the discrete layers within the anisotropic scaffold. Maximum strength and suture retention were shown to increase with increasing wall thickness, by contrast stress failure decreased with increasing thickness due to increasing proportions of the mechanically weaker amorphous Wharton’s jelly (WJ). Reseeded smooth muscle cells were shown to adhere, proliferate, and migrate from the scaffold surface showing the potential of the HUA as a mechanically ‘tunable’ material with applications as an acellular implant or as a tissue engineered construct. PMID:22826192
Development of a mechanically tuneable 3D scaffold for vascular reconstruction.
Rodriguez, Maritza; Juran, Cassandra; McClendon, Mark; Eyadiel, Cyril; McFetridge, Peter S
2012-12-01
Material compliance has been shown to be a predictor of vascular graft patency and as such is a critical parameter when designing new materials. Although ex vivo derived materials have been clinically successful in a number of applications their mechanical properties are a direct function of the original vessel and are not easily controllable. These investigations describe an approach to modulate the mechanical properties of an ex vivo derived scaffold by machining variable (discrete) wall thicknesses to control compliance. Human umbilical arteries (HUAs) were machine lathed directly from the umbilical cord at wall thicknesses of 250, 500, 750, and 1000 μm then decellularized using 1% sodium dodecyl sulfate. Compliance over physiological pressures, increased from 3.08 ± 1.84% to 11.47 ± 4.11% as direct function of each discrete vessel diameter. Radial stress strain analysis revealed primary and secondary failure points attributed to the discrete layers within the anisotropic scaffold. Maximum strength and suture retention were shown to increase with increasing wall thickness, by contrast stress failure decreased with increasing thickness due to increasing proportions of the mechanically weaker amorphous Wharton's jelly. Reseeded smooth muscle cells were shown to adhere, proliferate, and migrate from the scaffold surface showing the potential of the HUA as a mechanically "tunable" material with applications as an acellular implant or as a tissue engineered construct. © 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 100A:3189-3196, 2012. PMID:22826192
NASA Astrophysics Data System (ADS)
Santasusana, Miquel; Irazábal, Joaquín; Oñate, Eugenio; Carbonell, Josep Maria
2016-07-01
In this work, we present a new methodology for the treatment of the contact interaction between rigid boundaries and spherical discrete elements (DE). Rigid body parts are present in most of large-scale simulations. The surfaces of the rigid parts are commonly meshed with a finite element-like (FE) discretization. The contact detection and calculation between those DE and the discretized boundaries is not straightforward and has been addressed by different approaches. The algorithm presented in this paper considers the contact of the DEs with the geometric primitives of a FE mesh, i.e. facet, edge or vertex. To do so, the original hierarchical method presented by Horner et al. (J Eng Mech 127(10):1027-1032, 2001) is extended with a new insight leading to a robust, fast and accurate 3D contact algorithm which is fully parallelizable. The implementation of the method has been developed in order to deal ideally with triangles and quadrilaterals. If the boundaries are discretized with another type of geometries, the method can be easily extended to higher order planar convex polyhedra. A detailed description of the procedure followed to treat a wide range of cases is presented. The description of the developed algorithm and its validation is verified with several practical examples. The parallelization capabilities and the obtained performance are presented with the study of an industrial application example.
NASA Astrophysics Data System (ADS)
Santasusana, Miquel; Irazábal, Joaquín; Oñate, Eugenio; Carbonell, Josep Maria
2016-04-01
In this work, we present a new methodology for the treatment of the contact interaction between rigid boundaries and spherical discrete elements (DE). Rigid body parts are present in most of large-scale simulations. The surfaces of the rigid parts are commonly meshed with a finite element-like (FE) discretization. The contact detection and calculation between those DE and the discretized boundaries is not straightforward and has been addressed by different approaches. The algorithm presented in this paper considers the contact of the DEs with the geometric primitives of a FE mesh, i.e. facet, edge or vertex. To do so, the original hierarchical method presented by Horner et al. (J Eng Mech 127(10):1027-1032, 2001) is extended with a new insight leading to a robust, fast and accurate 3D contact algorithm which is fully parallelizable. The implementation of the method has been developed in order to deal ideally with triangles and quadrilaterals. If the boundaries are discretized with another type of geometries, the method can be easily extended to higher order planar convex polyhedra. A detailed description of the procedure followed to treat a wide range of cases is presented. The description of the developed algorithm and its validation is verified with several practical examples. The parallelization capabilities and the obtained performance are presented with the study of an industrial application example.
Hypercluster - Parallel processing for computational mechanics
NASA Technical Reports Server (NTRS)
Blech, Richard A.
1988-01-01
An account is given of the development status, performance capabilities and implications for further development of NASA-Lewis' testbed 'hypercluster' parallel computer network, in which multiple processors communicate through a shared memory. Processors have local as well as shared memory; the hypercluster is expanded in the same manner as the hypercube, with processor clusters replacing the normal single processor node. The NASA-Lewis machine has three nodes with a vector personality and one node with a scalar personality. Each of the vector nodes uses four board-level vector processors, while the scalar node uses four general-purpose microcomputer boards.
A fully 3D atomistic quantum mechanical study on random dopant induced effects in 25nm MOSFETs
Wang, Lin-Wang; Jiang, Xiang-Wei; Deng, Hui-Xiong; Luo, Jun-Wei; Li, Shu-Shen; Wang, Lin-Wang; Xia, Jian-Bai
2008-07-11
We present a fully 3D atomistic quantum mechanical simulation for nanometered MOSFET using a coupled Schroedinger equation and Poisson equation approach. Empirical pseudopotential is used to represent the single particle Hamiltonian and linear combination of bulk band (LCBB) method is used to solve the million atom Schroedinger's equation. We studied gate threshold fluctuations and threshold lowering due to the discrete dopant configurations. We compared our results with semiclassical simulation results. We found quantum mechanical effects increase the threshold fluctuation while decreases the threshold lowering. The increase of threshold fluctuation is in agreement with previous study based on approximated density gradient approach to represent the quantum mechanical effect. However, the decrease in threshold lowering is in contrast with the previous density gradient calculations.
Predicting mechanical competence of trabecular bone using 3D tensor-scale-based parameters
NASA Astrophysics Data System (ADS)
Saha, Punam K.; Wald, Michael J.; Radin, Alex; Wehrli, Felix W.
2005-04-01
Trabecular bone (TB) consists of a network of interconnected struts and plates occurring near the joints of long bones and in the axial skeleton. In response to mechanical stresses it remodels such that trabeculae are aligned with the major stress lines, thus leading to a highly anisotropic network. Beside bone volume fraction, anisotropy and topological indices are known to be strong predictor of the TB mechanical competence. In osteoporosis, the most common bone disorder, the remodeling balance is perturbed due to increased resorption, resulting in net bone loss accompanied by architectural deterioration, leading to fragile bone and increased fracture risk. In vertebral osteoporosis, preferential loss of transverse trabeculae leads to increased anisotropy and change in topology, hence exact measurements of these parameters are of paramount interest. Current in vivo imaging yields voxel size comparable to TB thickness, thus resulting in inherently fuzzy representations. The commonly used methods for anisotropy require binarization which is difficult to achieve in the limited spatial resolution regime where the intensity histogram is mono-modal. Here, we present a new tensor scale (t-scale) based TB architectural measures that (1) obviates binarization, and (2) yields localized measures. We evaluate the performance of this method on micro-CT images of vertebral bone and test the hypothesis that the method, along with BMD and other structural parameters, allows prediction of TB"s mechanical competence. Toward this goal, we estimate Young"s modulus (YM) of (13mm)3 vertebral TB samples under uniaxial loading and examine linear correlation of different t-scale parameters computed via micro-CT imaging .
3D dislocation dynamics: stress-strain behavior and hardening mechanisms in FCC and BCC metals
Hirth, J P; Rhee, M; Zhib, H M; de la Rubia, T D
1999-02-19
A dislocation dynamics (DD) model for plastic deformation, connecting the macroscopic mechanical properties to basic physical laws governing dislocation mobility and related interaction mechanisms, has been under development. In this model there is a set of critical reactions that determine the overall results of the simulations, such as the stress-strain curve. These reactions are, annihilation, formation of jogs, junctions, and dipoles, and cross-slip. In this paper we discuss these reactions and the manner in which they influence the simulated stress- strain behavior in fcc and bcc metals. In particular, we examine the formation (zipping) and strength of dipoles and junctions, and effect of jogs, using the dislocation dynamics model. We show that the strengths (unzipping) of these reactions for various configurations can be determined by direct evaluation of the elastic interactions. Next, we investigate the phenomenon of hardening in metals subjected to cascade damage dislocations. The microstructure investigated consists of small dislocation loops decorating the mobile dislocations. Preliminary results reveal that these loops act as hardening agents, trapping the dislocations and resulting in increased hardening.
Xu, Fan; Zhao, Ruogang; Liu, Alan S; Metz, Tristin; Shi, Yu; Bose, Prasenjit; Reich, Daniel H
2015-06-01
This paper describes an approach to actuate magnetically arrays of microtissue constructs for long-term mechanical conditioning and subsequent biomechanical measurements. Each construct consists of cell/matrix material self-assembled around a pair of flexible poly(dimethylsiloxane) (PDMS) pillars. The deflection of the pillars reports the tissues' contractility. Magnetic stretching of individual microtissues via magnetic microspheres mounted on the cantilevers has been used to elucidate the tissues' elastic modulus and response to varying mechanical boundary conditions. This paper describes the fabrication of arrays of micromagnetic structures that can transduce an externally applied uniform magnetic field to actuate simultaneously multiple microtissues. These structures are fabricated on silicon-nitride coated Si wafers and contain electrodeposited Ni bars. Through-etched holes provide optical and culture media access when the devices are mounted on the PDMS microtissue scaffold devices. Both static and AC forces (up to 20 μN on each microtissue) at physiological frequencies are readily generated in external fields of 40 mT. Operation of the magnetic arrays was demonstrated via measurements of elastic modulus and dynamic stiffening in response to AC actuation of fibroblast populated collagen microtissues. PMID:25959132
A 3-D constrained mixture model for mechanically mediated vascular growth and remodeling
Wan, William; Hansen, Laura
2010-01-01
In contrast to the widely applied approach to model soft tissue remodeling employing the concept of volumetric growth, microstructurally motivated models are capable of capturing many of the underlying mechanisms of growth and remodeling; i.e., the production, removal, and remodeling of individual constituents at different rates and to different extents. A 3-dimensional constrained mixture computational framework has been developed for vascular growth and remodeling, considering new, microstructurally motivated kinematics and constitutive equations and new stress and muscle activation mediated evolution equations. Our computational results for alterations in flow and pressure, using reasonable physiological values for rates of constituent growth and turnover, concur with findings in the literature. For example, for flow-induced remodeling, our simulations predict that, although the wall shear stress is restored completely, the circumferential stress is not restored employing realistic physiological rate parameters. Also, our simulations predict different levels of thickening on inner versus outer wall locations, as shown in numerous reports of pressure-induced remodeling. Whereas the simulations are meant to be illustrative, they serve to highlight the experimental data currently lacking to fully quantify mechanically mediated adaptations in the vasculature. PMID:20039091
A microfabricated magnetic actuation device for mechanical conditioning of arrays of 3D microtissues
Xu, Fan; Zhao, Ruogang; Liu, Alan S.; Metz, Tristin; Shi, Yu; Bose, Prasenjit; Reich, Daniel H.
2015-01-01
This paper describes an approach to actuate magnetically arrays of microtissue constructs for long-term mechanical conditioning and subsequent biomechanical measurements. Each construct consists of cell/matrix material self-assembled around a pair of flexible poly(dimethylsiloxane) (PDMS) pillars. The deflection of the pillars reports the tissues’ contractility. Magnetic stretching of individual microtissues via magnetic microspheres mounted on the cantilevers has been used to elucidate the tissues’ elastic modulus and response to varying mechanical boundary conditions. This paper describes the fabrication of arrays of micromagnetic structures that can transduce an externally applied uniform magnetic field to actuate simultaneously multiple microtissues. These structures are fabricated on silicon-nitride coated Si wafers and contain electrodeposited Ni bars. Through-etched holes provide optical and culture media access when the devices are mounted on the PDMS microtissue scaffold devices. Both static and AC forces (up to 20 μN on each microtissue) at physiological frequencies are readily generated in external fields of 40 mT. Operation of the magnetic arrays was demonstrated via measurements of elastic modulus and dynamic stiffening in response to AC actuation of fibroblast populated collagen microtissues. PMID:25959132
NASA Astrophysics Data System (ADS)
Miccio, L.; Memmolo, P.; Merola, F.; Fusco, S.; Netti, P. A.; Ferraro, P.
2014-03-01
A method for 3D tracking has been developed exploiting Digital Holography features in Microscopy (DHM). In the framework of self-consistent platform for manipulation and measurement of biological specimen we use DHM for quantitative and completely label free analysis of samples with low amplitude contrast. Tracking capability extend the potentiality of DHM allowing to monitor the motion of appropriate probes and correlate it with sample properties. Complete 3D tracking has been obtained for the probes avoiding the amplitude refocusing in traditional tracking processes. Moreover, in biology and biomedical research fields one of the main topic is the understanding of morphology and mechanics of cells and microorganisms. Biological samples present low amplitude contrast that limits the information that can be retrieved through optical bright-field microscope measurements. The main effect on light propagating in such objects is in phase. This is known as phase-retardation or phase-shift. DHM is an innovative and alternative approach in microscopy, it's a good candidate for no-invasive and complete specimen analysis because its main characteristic is the possibility to discern between intensity and phase information performing quantitative mapping of the Optical Path Length. In this paper, the flexibility of DH is employed to analyze cell mechanics of unstained cells subjected to appropriate stimuli. DHM is used to measure all the parameters useful to understand the deformations induced by external and controlled stresses on in-vitro cells. Our configuration allows 3D tracking of micro-particles and, simultaneously, furnish quantitative phase-contrast maps. Experimental results are presented and discussed for in vitro cells.
Simulation of semi-explicit mechanisms of SOA formation from glyoxal in a 3-D model
NASA Astrophysics Data System (ADS)
Knote, C.; Hodzic, A.; Jimenez, J. L.; Volkamer, R.; Orlando, J. J.; Baidar, S.; Brioude, J.; Fast, J.; Gentner, D. R.; Goldstein, A. H.; Hayes, P. L.; Knighton, W. B.; Oetjen, H.; Setyan, A.; Stark, H.; Thalman, R.; Tyndall, G.; Washenfelder, R.; Waxman, E.; Zhang, Q.
2013-10-01
New pathways to form secondary organic aerosols (SOA) have been postulated recently. Glyoxal, the smallest dicarbonyl, is one of the proposed precursors. It has both anthropogenic and biogenic sources, and readily partitions into the aqueous-phase of cloud droplets and deliquesced aerosols where it undergoes both reversible and irreversible chemistry. In this work we extend the regional scale chemistry transport model WRF-Chem to include a detailed gas-phase chemistry of glyoxal formation as well as a state-of-the-science module describing its partitioning and reactions in the aqueous-phase of aerosols. A comparison of several proposed mechanisms is performed to quantify the relative importance of different formation pathways and their regional variability. The CARES/CalNex campaigns over California in summer 2010 are used as case studies to evaluate the model against observations. In all simulations the LA basin was found to be the hotspot for SOA formation from glyoxal, which contributes between 1% and 15% of the model SOA depending on the mechanism used. Our results indicate that a mechanism based only on a simple uptake coefficient, as frequently employed in global modeling studies, leads to higher SOA contributions from glyoxal compared to a more detailed description that considers aerosol phase state and chemical composition. In the more detailed simulations, surface uptake is found to be the main contributor to SOA mass compared to a volume process and reversible formation. We find that contribution of the latter is limited by the availability of glyoxal in aerosol water, which is in turn controlled by an increase in the Henry's law constant depending on salt concentrations ("salting-in"). A kinetic limitation in this increase prevents substantial partitioning of glyoxal into aerosol water at high salt concentrations. If this limitation is removed, volume pathways contribute >20% of glyoxal SOA mass, and the total mass formed (5.8% of total SOA in the LA
Role of Mechanical Cues in Cell Differentiation and Proliferation: A 3D Numerical Model
Mousavi, Seyed Jamaleddin; Hamdy Doweidar, Mohamed
2015-01-01
Cell differentiation, proliferation and migration are essential processes in tissue regeneration. Experimental evidence confirms that cell differentiation or proliferation can be regulated according to the extracellular matrix stiffness. For instance, mesenchymal stem cells (MSCs) can differentiate to neuroblast, chondrocyte or osteoblast within matrices mimicking the stiffness of their native substrate. However, the precise mechanisms by which the substrate stiffness governs cell differentiation or proliferation are not well known. Therefore, a mechano-sensing computational model is here developed to elucidate how substrate stiffness regulates cell differentiation and/or proliferation during cell migration. In agreement with experimental observations, it is assumed that internal deformation of the cell (a mechanical signal) together with the cell maturation state directly coordinates cell differentiation and/or proliferation. Our findings indicate that MSC differentiation to neurogenic, chondrogenic or osteogenic lineage specifications occurs within soft (0.1-1 kPa), intermediate (20-25 kPa) or hard (30-45 kPa) substrates, respectively. These results are consistent with well-known experimental observations. Remarkably, when a MSC differentiate to a compatible phenotype, the average net traction force depends on the substrate stiffness in such a way that it might increase in intermediate and hard substrates but it would reduce in a soft matrix. However, in all cases the average net traction force considerably increases at the instant of cell proliferation because of cell-cell interaction. Moreover cell differentiation and proliferation accelerate with increasing substrate stiffness due to the decrease in the cell maturation time. Thus, the model provides insights to explain the hypothesis that substrate stiffness plays a key role in regulating cell fate during mechanotaxis. PMID:25933372
A Massively Parallel Solver for the Mechanical Harmonic Analysis of Accelerator Cavities
O. Kononenko
2015-02-17
ACE3P is a 3D massively parallel simulation suite that developed at SLAC National Accelerator Laboratory that can perform coupled electromagnetic, thermal and mechanical study. Effectively utilizing supercomputer resources, ACE3P has become a key simulation tool for particle accelerator R and D. A new frequency domain solver to perform mechanical harmonic response analysis of accelerator components is developed within the existing parallel framework. This solver is designed to determine the frequency response of the mechanical system to external harmonic excitations for time-efficient accurate analysis of the large-scale problems. Coupled with the ACE3P electromagnetic modules, this capability complements a set of multi-physics tools for a comprehensive study of microphonics in superconducting accelerating cavities in order to understand the RF response and feedback requirements for the operational reliability of a particle accelerator. (auth)
Davidson, Joshua R; Appuhamillage, Gayan A; Thompson, Christina M; Voit, Walter; Smaldone, Ronald A
2016-07-01
A design paradigm is demonstrated that enables new functional 3D printed materials made by fused filament fabrication (FFF) utilizing a thermally reversible dynamic covalent Diels-Alder reaction to dramatically improve both strength and toughness via self-healing mechanisms. To achieve this, we used as a mending agent a partially cross-linked terpolymer consisting of furan-maleimide Diels-Alder (fmDA) adducts that exhibit reversibility at temperatures typically used for FFF printing. When this mending agent is blended with commercially available polylactic acid (PLA) and printed, the resulting materials demonstrate an increase in the interfilament adhesion strength along the z-axis of up to 130%, with ultimate tensile strength increasing from 10 MPa in neat PLA to 24 MPa in fmDA-enhanced PLA. Toughness in the z-axis aligned prints increases by up to 460% from 0.05 MJ/m(3) for unmodified PLA to 0.28 MJ/m(3) for the remendable PLA. Importantly, it is demonstrated that a thermally reversible cross-linking paradigm based on the furan-maleimide Diels-Alder (fmDA) reaction can be more broadly applied to engineer property enhancements and remending abilities to a host of other 3D printable materials with superior mechanical properties. PMID:27299858
LDRD final report: Automated planning and programming of assembly of fully 3D mechanisms
Kaufman, S.G.; Wilson, R.H.; Jones, R.E.; Calton, T.L.; Ames, A.L.
1996-11-01
This report describes the results of assembly planning research under the LDRD. The assembly planning problem is that of finding a sequence of assembly operations, starting from individual parts, that will result in complete assembly of a device specified as a CAD model. The automated assembly programming problem is that of automatically producing a robot program that will carry out a given assembly sequence. Given solutions to both of these problems, it is possible to automatically program a robot to assemble a mechanical device given as a CAD data file. This report describes the current state of our solutions to both of these problems, and a software system called Archimedes 2 we have constructed to automate these solutions. Because Archimedes 2 can input CAD data in several standard formats, we have been able to test it on a number of industrial assembly models more complex than any before attempted by automated assembly planning systems, some having over 100 parts. A complete path from a CAD model to an automatically generated robot program for assembling the device represented by the CAD model has also been demonstrated.
NASA Astrophysics Data System (ADS)
Lee, Min-Gu; Baeg, Seung-Ho; Lee, Ki-Min; Lee, Hae-Seok; Baeg, Moon-Hong; Park, Jong-Ok; Kim, Hong-Ki
2011-06-01
The purpose of this research is to develop a new 3D LIDAR sensor, named KIDAR-B25, for measuring 3D image information with high range accuracy, high speed and compact size. To measure a distance to the target object, we developed a range measurement unit, which is implemented by the direct Time-Of-Flight (TOF) method using TDC chip, a pulsed laser transmitter as an illumination source (pulse width: 10 ns, wavelength: 905 nm, repetition rate: 30kHz, peak power: 20W), and an Si APD receiver, which has high sensitivity and wide bandwidth. Also, we devised a horizontal and vertical scanning mechanism, climbing in a spiral and coupled with the laser optical path. Besides, control electronics such as the motor controller, the signal processing unit, the power distributor and so on, are developed and integrated in a compact assembly. The key point of the 3D LIDAR design proposed in this paper is to use the compact scanning mechanism, which is coupled with optical module horizontally and vertically. This KIDAR-B25 has the same beam propagation axis for emitting pulse laser and receiving reflected one with no optical interference each other. The scanning performance of the KIDAR-B25 has proven with the stable operation up to 20Hz (vertical), 40Hz (horizontal) and the time is about 1.7s to reach the maximum speed. The range of vertical plane can be available up to +/-10 degree FOV (Field Of View) with a 0.25 degree angular resolution. The whole horizontal plane (360 degree) can be also available with 0.125 degree angular resolution. Since the KIDAR-B25 sensor has been planned and developed to be used in mobile robots for navigation, we conducted an outdoor test for evaluating its performance. The experimental results show that the captured 3D imaging data can be usefully applicable to the navigation of the robot for detecting and avoiding the moving objects with real time.
Hanada, Yasutaka; Sugioka, Koji; Shihira-Ishikawa, Ikuko; Kawano, Hiroyuki; Miyawaki, Atsushi; Midorikawa, Katsumi
2011-06-21
Phormidium, a genus of filamentous cyanobacteria, forms endosymbiotic associations with seedling roots that accelerate the growth of the vegetable seedlings. Understanding the gliding mechanism of Phormidium will facilitate improved formation of this association and increased vegetable production. To observe the gliding movements, we fabricated various microfluidic chips termed nanoaquariums using a femtosecond (fs) laser. Direct fs laser writing, followed by annealing and successive wet etching in dilute hydrofluoric acid solution, can easily produce three-dimensional (3D) microfluidics with different structures embedded in a photostructurable glass. Using the fs laser, optical waveguides and filters were integrated with the microfluidic structures in the microchips, allowing the gliding mechanism to be more easily clarified. Using this apparatus, we found that CO(2) secreted from the seedling root attracts Phormidium in the presence of light, and determined the light intensity and specific wavelength necessary for gliding. PMID:21562650
Chang, Gregory; Deniz, Cem; Honig, Stephen; Rajapakse, Chamith S.; Egol, Kenneth; Regatte, Ravinder R.; Brown, Ryan
2013-01-01
Purpose High-resolution imaging of deeper anatomy such as the hip is challenging due to low signal-to-noise ratio (SNR), necessitating long scan times. Multi-element coils can increase SNR and reduce scan time through parallel imaging (PI). We assessed the feasibility of using a 26-element receive coil setup to perform 3 T MRI of proximal femur microarchitecture without and with PI. Materials and Methods This study had institutional review board approval. We scanned thirteen subjects on a 3 T scanner using 26 receive-elements and a 3-D FLASH sequence without and with PI (acceleration factors (AF) 2, 3, 4). We assessed SNR, depiction of individual trabeculae, PI performance (1/g-factor), and image quality with PI (1=non-visualization to 5=excellent). Results SNR maps demonstrate higher SNR for the 26-element setup compared to a 12-element setup for hip MRI. Without PI, individual proximal femur trabeculae were well-depicted, including microarchitectural deterioration in osteoporotic subjects. With PI, 1/g values for the 26-element/12-element receive-setup were 0.71/0.45, 0.56/0.25, and 0.44/0.08 at AF2, AF3, and AF4, respectively. Image quality was: AF1, excellent (4.8±0.4); AF2, good (4.2±1.0); AF3, average (3.3±1.0); AF4, non-visualization (1.4±0.9). Conclusion A 26-element receive-setup permits 3 T MRI of proximal femur microarchitecture with good image quality up to PI AF2. PMID:24711013
Particle Acceleration in 3D Magnetic Reconnection
NASA Astrophysics Data System (ADS)
Dahlin, J.; Drake, J. F.; Swisdak, M.
2015-12-01
Magnetic reconnection is an important driver of energetic particles in phenomena such as magnetospheric storms and solar flares. Using kinetic particle-in-cell (PIC) simulations, we show that the stochastic magnetic field structure which develops during 3D reconnection plays a vital role in particle acceleration and transport. In a 2D system, electrons are trapped in magnetic islands which limits their energy gain. In a 3D system, however, the stochastic magnetic field enables the energetic electrons to access volume-filling acceleration regions and therefore gain energy much more efficiently than in the 2D system. We also examine the relative roles of two important acceleration drivers: parallel electric fields and a Fermi mechanism associated with reflection of charged particles from contracting field lines. We find that parallel electric fields are most important for accelerating low energy particles, whereas Fermi reflection dominates energetic particle production. We also find that proton energization is reduced in the 3D system.
NASA Astrophysics Data System (ADS)
Sweeney, Charles; Lackey, Blake; Saed, Mohammad; Green, Micah
Three-dimensional (3D) printed parts produced by fused-filament fabrication of a thermoplastic polymer have become increasingly popular at both the commercial and consumer level. The mechanical integrity of these rapid-prototyped parts however, is severely limited by the interfillament bond strength between adjacent extruded layers. In this report we propose for the first time a method for welding thermoplastic interfaces of 3D printed parts using the extreme heating response of carbon nanotubes (CNTs) to microwave energy. To achieve this, we developed a coaxial printer filament with a pure polylactide (PLA) core and a CNT composite sheath. This produces parts with a thin electrically percolating network of CNTs at the interfaces between adjacent extruded layers. These interfaces are then welded together upon microwave irradiation at 2.45GHz. Our patent-pending method has been shown to increase the tensile toughness by 1000% and tensile strength by 35%. We investigated the dielectric properties of the PLA/CNT composites at microwave frequencies and performed in-situ microwave thermometry using a forward-looking infrared (FLIR) camera to characterize the heating response of the PLA/CNT composites upon microwave irradiation.
NASA Astrophysics Data System (ADS)
Koster, Kay; Stouthamer, Esther; Cohen, Kim; Stafleu, Jan; Busschers, Freek; Middelkoop, Hans
2016-04-01
Peat is abundantly present within the Holocene coastal-deltaic sequence of the Netherlands, where it is alternating with clastic fluvial, estuarine and lagoonal deposits. The areas that are rich in peat are vulnerable to land subsidence, resulting from consolidation and oxidation, due to loading by overlying deposits, infrastructure and buildings, as well as excessive artificial drainage. The physical properties of the peat are very heterogeneous, with variable clastic admixture up to 80% of its mass and rapid decrease in porosity with increasing effective stress. Mapping the spatial distribution of the peat properties is essential for identifying areas most susceptible to future land subsidence, as mineral content determines volume loss by oxidation, and porosity influences the rate of consolidation. Here we present the outline of a study focusing on mapping mechanical peat properties in relation to density and amount of admixed clastic constituents of Holocene peat layers (in 3D). In this study we use a staged approach: 1) Identifying soil mechanical properties in two large datasets that are managed by Utrecht University and the Geological Survey. 2) Determining relations between these properties and palaeogeographical development of the area by evaluating these properties against known geological concepts such as distance to clastic source (river, estuary etc.). 3) Implementing the obtained relations in GeoTOP, which is a 3D geological subsurface model of the Netherlands developed by the Geological Survey. The model will be used, among others, to assess the susceptibility of different areas to peat related land subsidence and load bearing capacity of the subsurface. So far, our analysis has focused stage 1, by establishing empirical relations between mechanical peat properties in ~70 paired (piezometer) cone penetration tests and continuously cored boreholes with LOI measurements. Results show strong correlations between net cone resistance (qn), excess pore
Baino, Francesco; Ferraris, Monica; Bretcanu, Oana; Verné, Enrica; Vitale-Brovarone, Chiara
2013-03-01
Fabrication of 3-D highly porous, bioactive, and mechanically competent scaffolds represents a significant challenge of bone tissue engineering. In this work, Bioglass®-derived glass-ceramic scaffolds actually fulfilling this complex set of requirements were successfully produced through the sponge replication method. Scaffold processing parameters and sintering treatment were carefully designed in order to obtain final porous bodies with pore content (porosity above 70 %vol), trabecular architecture and mechanical properties (compressive strength up to 3 MPa) analogous to those of the cancellous bone. Influence of the Bioglass® particles size on the structural and mechanical features of the sintered scaffolds was considered and discussed. Relationship between porosity and mechanical strength was investigated and modeled. Three-dimensional architecture, porosity, mechanical strength and in vitro bioactivity of the optimized Bioglass®-derived scaffolds were also compared to those of CEL2-based glass-ceramic scaffolds (CEL2 is an experimental bioactive glass originally developed by the authors at Politecnico di Torino) fabricated by the same processing technique, in an attempt at understanding the role of different bioactive glass composition on the major features of scaffolds prepared by the same method. PMID:22207602
NASA Astrophysics Data System (ADS)
Magri, Fabien; Tillner, Elena; Kempka, Thomas; Wang, Wenqing; Watanabe, Norihiro; Zimmermann, Günter
2013-04-01
CO2 storage in deep saline aquifers is one of the strategies used to reduce greenhouse gas emissions into the atmosphere. However, pressure buildup due to the CO2 injection process and subsequent pressure dissipation alter the recent stress field in and around the reservoir. These stress changes may lead to ground uplift, rock fracturing or fault reactivation. In order to study these phenomena by numerical simulations, flow and mechanical equations have to be solved together, requiring a hydro-mechanical coupling. In the present study, a prospective CO2 storage site located in the Northeast German Basin serves as 3D geological framework for a numerical evaluation of deformations and in situ stress changes induced by CO2 injection into the Middle Bunter sandstone. For that purpose, two open-source simulators are coupled: TOUGH2 (Pruess et al., 1999) is applied to calculate reservoir pore pressures which are subsequently transferred into the hydro-geomechanical simulator OpenGeoSys (Wang et al., 2009) to solve the hydro-mechanical equations. A scenario analysis was undertaken to evaluate the mechanical effects of CO2 injection on the reservoir and caprock stability. The results show that under specific assumptions the vertical movement of the top reservoir is negligible. Furthermore, the changes in the recent stress field predicted by geomechanical modeling are limited to the surrounding of the injection well and not significant enough to endanger the mechanical stability of the reservoir and caprock considering the geological boundary conditions of the study area and the proposed injection scheme The presented study demonstrates the hydro-mechanical effects of CO2 storage in a well-constrained 3D geological regional-scale model based on the characterization of residual rocks, and can therefore be representative for CO2 storage in the Northeast German Basin. References Pruess, K., C.M. Oldenburg, and G. Moridis, "TOUGH2 User's Guide, Version 2.0", Lawrence Berkeley
A parallel finite element scheme for thermo-hydro-mechanical (THM) coupled problems in porous media
NASA Astrophysics Data System (ADS)
Wang, Wenqing; Kosakowski, Georg; Kolditz, Olaf
2009-08-01
Many applied problems in geoscience require knowledge about complex interactions between multiple physical and chemical processes in the sub-surface. As a direct experimental investigation is often not possible, numerical simulation is a common approach. The numerical analysis of coupled thermo-hydro-mechanical (THM) problems is computationally very expensive, and therefore the applicability of existing codes is still limited to simplified problems. In this paper we present a novel implementation of a parallel finite element method (FEM) for the numerical analysis of coupled THM problems in porous media. The computational task of the FEM is partitioned into sub-tasks by a priori domain decomposition. The sub-tasks are assigned to the CPU nodes concurrently. Parallelization is achieved by simultaneously establishing the sub-domain mesh topology, synchronously assembling linear equation systems in sub-domains and obtaining the overall solution with a sub-domain linear solver (parallel BiCGStab method with Jacobi pre-conditioner). The present parallelization method is implemented in an object-oriented way using MPI for inter-processor communication. The parallel code was successfully tested with a 2-D example from the international DECOVALEX benchmarking project. The achieved speed-up for a 3-D extension of the test example on different computers demonstrates the advantage of the present parallel scheme.
Studies on formation mechanism of 3D Cu2O nanospheres through self-assembly of 0D nanodots
NASA Astrophysics Data System (ADS)
Zhang, Lun; Yu, Bing; Ying, Pengzhan; Wu, Ling; Chen, Shanliang; Wang, Jieru; Gu, Xiuquan; Zhou, Rui; Ni, Zhonghai
2015-08-01
Cu2O crystals with different morphologies (solid and porous) and sizes (from 25 to 282 nm) were synthesized controllably through a facile solvothermal route. The growth mechanism was investigated by SEM and TEM with varying the concentration of poly (vinylpyrrolidone) (PVP, K30), CH3COO- (Ac-) and NO3- acid ions in the precursor solution. The self-assembly of three types of Cu2O nano-structures was observed through a general route of zero-dimensional (0D) → 2D → 3D. When Cu(Ac)2ṡH2O was used as the copper sources, 0D Cu2O nanodots with size of 2-7 nm were firstly assembled to 2D quasi-spherical and bookmark-like structures via Oriented attachment (OA), and then converted into 3D hierarchical Cu2O nanoclusters (a few tens of nm) and porous sub-microspheres with an average size of 282 nm, respectively. While Cu(NO3)2ṡ3H2O was used instead of Cu(Ac)2ṡH2O, the similar assembly process occurred leading to the formation of Cu2O porous nanospheres of 40-140 nm which exhibit better adsorption ability toward methyl orange compared with activated carbon. In addition, we also investigated the dependence of Cu2O crystals on the concentration of acid ions (Ac- and NO3-). Compared with Ac-, the size and morphology of the obtained products were less dependent on the concentration of NO3- acid ions. This study might provide a new insight into the growth mechanism of Cu2O based micro- or nanostructures.
Kinematic analysis of a flexible six-DOF parallel mechanism.
Jing, Feng-Shui; Tan, Min; Hou, Zeng-Guang; Liang, Zi-Ze; Wang, Yun-Kuan; Gupta, Madan M; Nikiforuk, Peter N
2006-04-01
In this paper, a new type of six-degrees of freedom (DOF) flexible parallel mechanism (FPM) is presented. This type of parallel mechanism possesses several favorable properties: (1) its number of DOFs is independent of the number of serial chains which make up the mechanism; (2) it has no kinematical singularities; (3) it is designed to move on rails, and therefore its workspace is much larger than that of a conventional parallel manipulator; and (4) without changing the number of DOFs and the kinematics of the mechanisms, the number of the serial chains can be reconfigured according to the needs of the tasks. These properties make the mechanism very preferable in practice, especially for such tasks as joining huge ship blocks, in which the manipulated objects vary dramatically both in weights and dimensions. Furthermore, the mechanism can be used as either a fully actuated system or an underactuated system. In the fully actuated case, the mechanism has six DOF motion capabilities and manipulation capabilities. However, in the underactuated case, the mechanism still has six DOF motion capabilities, but it has only five DOF manipulation capabilities. In this paper, both the inverse and forward kinematics are studied and expressed in a closed form. The workspace and singularity analysis of the mechanism are also presented. An example is presented to illustrate how to calculate the kinematics of the mechanism in both fully-actuated and underactuated cases. Finally, an application of such a mechanism to manufacturing industry is introduced. PMID:16602597
NASA Astrophysics Data System (ADS)
Barnhart, Donald H.; Chan, Victor S. S.; Halliwell, Neil A.; Coupland, Jeremy M.
1999-10-01
This paper reports the use of a new holographic measurement system in the study of 3D surface displacements. Although equally applicable to fluid and solid mechanics, the aim of this report is to demonstrate the system's use in quantitative surface displacement measurements with a classical cantilever experiment, using a continuous-wave diode-pumped YAG laser system. The reported results exhibit an accuracy corresponding to other interferometric systems, but with a much larger displacement range. The measurement system employs a novel optical image shifting method to eliminate the problem of directional ambiguity. In addition, the reported system uses 3D complex correlation rather than 2D real correlation, thereby offering a direct method for measuring 3D displacement in 3D space. FInally, with the novel use of an optical fiber to probe the recorded holographic image space, it is found to be a simple matter to directly obtain 3D displacement measurements at precisely known surface locations.
NASA Astrophysics Data System (ADS)
Otto, Christopher; Kempka, Thomas; Kapusta, Krzysztof; Stańczyk, Krzysztof
2016-04-01
Underground coal gasification (UCG) has the potential to increase the world-wide coal reserves by utilization of coal deposits not mineable by conventional methods. The UCG process involves combusting coal in situ to produce a high-calorific synthesis gas, which can be applied for electricity generation or chemical feedstock production. Apart from its high economic potentials, UCG may induce site-specific environmental impacts such as fault reactivation, induced seismicity and ground subsidence, potentially inducing groundwater pollution. Changes overburden hydraulic conductivity resulting from thermo-mechanical effects may introduce migration pathways for UCG contaminants. Due to the financial efforts associated with UCG field trials, numerical modeling has been an important methodology to study coupled processes considering UCG performance. Almost all previous UCG studies applied 1D or 2D models for that purpose, that do not allow to predict the performance of a commercial-scale UCG operation. Considering our previous findings, demonstrating that far-field models can be run at a higher computational efficiency by using temperature-independent thermo-mechanical parameters, representative coupled simulations based on complex 3D regional-scale models were employed in the present study. For that purpose, a coupled thermo-mechanical 3D model has been developed to investigate the environmental impacts of UCG based on a regional-scale of the Polish Wieczorek mine located in the Upper Silesian Coal Basin. The model size is 10 km × 10 km × 5 km with ten dipping lithological layers, a double fault and 25 UCG reactors. Six different numerical simulation scenarios were investigated, considering the transpressive stress regime present in that part of the Upper Silesian Coal Basin. Our simulation results demonstrate that the minimum distance between the UCG reactors is about the six-fold of the coal seam thickness to avoid hydraulic communication between the single UCG
Modeling of Nonlinear Mechanical Behavior for 3D Needled C/C-SiC Composites Under Tensile Load
NASA Astrophysics Data System (ADS)
Xie, Junbo; Fang, Guodong; Chen, Zhen; Liang, Jun
2016-04-01
This paper established a macroscopic constitutive model to describe the nonlinear stress-strain behavior of 3D needled C/C-SiC composites under tensile load. Extensive on- and off-axis tensile tests were performed to investigate the macroscopic mechanical behavior and damage characteristics of the composites. The nonlinear mechanical behavior of the material was mainly induced by matrix tensile cracking and fiber/matrix debonding. Permanent deformations and secant modulus degradation were observed in cyclic loading-unloading tests. The nonlinear stress-strain relationship of the material could be described macroscopically by plasticity deformation and stiffness degradation. In the proposed model, we employed a plasticity theory with associated plastic flow rule to describe the evolution of plastic strains. A novel damage variable was also introduced to characterize the stiffness degradation of the material. The damage evolution law was derived from the statistical distribution of material strength. Parameters of the proposed model can be determined from off-axis tensile tests. Stress-strain curves predicted by this model showed reasonable agreement with experimental results.
Modeling of Nonlinear Mechanical Behavior for 3D Needled C/C-SiC Composites Under Tensile Load
NASA Astrophysics Data System (ADS)
Xie, Junbo; Fang, Guodong; Chen, Zhen; Liang, Jun
2016-08-01
This paper established a macroscopic constitutive model to describe the nonlinear stress-strain behavior of 3D needled C/C-SiC composites under tensile load. Extensive on- and off-axis tensile tests were performed to investigate the macroscopic mechanical behavior and damage characteristics of the composites. The nonlinear mechanical behavior of the material was mainly induced by matrix tensile cracking and fiber/matrix debonding. Permanent deformations and secant modulus degradation were observed in cyclic loading-unloading tests. The nonlinear stress-strain relationship of the material could be described macroscopically by plasticity deformation and stiffness degradation. In the proposed model, we employed a plasticity theory with associated plastic flow rule to describe the evolution of plastic strains. A novel damage variable was also introduced to characterize the stiffness degradation of the material. The damage evolution law was derived from the statistical distribution of material strength. Parameters of the proposed model can be determined from off-axis tensile tests. Stress-strain curves predicted by this model showed reasonable agreement with experimental results.
Li, Zhengdong; Zou, Donghua; Zhang, Jianhua; Shao, Yu; Huang, Ping; Chen, Yijiu
2015-10-01
We report a craniocerebral trauma case in which a man sustained severe skull fractures and cerebral contusions and it demanded elucidating the injury mechanism of being formed by strike or tumble. However, the initial features of skull fractures were mostly lost when the forensic pathologists involved in the case 5 months later because of injury healing and craniocerebral surgery. Therefore, we aimed to reconstruct the original skull fracture features by utilizing the digital reconstruction technologies in terms of CT (computed tomography) scanning, 3D (3-dimentional) reconstruction, and virtual surgical tools. The original fracture skull was assembled by using Mimics 13.0 based on the CT slices of postoperative head and the removed craniotomy skull flaps, which revealed fracture features of focal and overall skull deformation. Based on the assembly skull model and the contrecoup cerebral contusions, we conclude that the man suffered a tumble after being drunk and the serious craniocerebral trauma occurred. The case demonstrated that the digital reconstruction technologies can serve as effective approaches for forensic investigation in case of survived craniocerebral trauma patients without direct evidences interpreting the original trauma patterns, which could potentially be helpful in exploring the injury mechanisms. PMID:26232886
Hsu, Christina M. L.; Palmeri, Mark L.; Segars, W. Paul; Veress, Alexander I.; Dobbins, James T.
2011-01-01
Purpose: The authors previously introduced a methodology to generate a realistic three-dimensional (3D), high-resolution, computer-simulated breast phantom based on empirical data. One of the key components of such a phantom is that it provides a means to produce a realistic simulation of clinical breast compression. In the current study, they have evaluated a finite element (FE) model of compression and have demonstrated the effect of a variety of mechanical properties on the model using a dense mesh generated from empirical breast data. While several groups have demonstrated an effective compression simulation with lower density finite element meshes, the presented study offers a mesh density that is able to model the morphology of the inner breast structures more realistically than lower density meshes. This approach may prove beneficial for multimodality breast imaging research, since it provides a high level of anatomical detail throughout the simulation study. Methods: In this paper, the authors describe methods to improve the high-resolution performance of a FE compression model. In order to create the compressible breast phantom, dedicated breast CT data was segmented and a mesh was generated with 4-noded tetrahedral elements. Using an explicit FE solver to simulate breast compression, several properties were analyzed to evaluate their effect on the compression model including: mesh density, element type, density, and stiffness of various tissue types, friction between the skin and the compression plates, and breast density. Following compression, a simulated projection was generated to demonstrate the ability of the compressible breast phantom to produce realistic simulated mammographic images. Results: Small alterations in the properties of the breast model can change the final distribution of the tissue under compression by more than 1 cm; which ultimately results in different representations of the breast model in the simulated images. The model
Nole, Michael; Daigle, Hugh; Mohanty, Kishore; Cook, Ann; Hillman, Jess
2015-12-15
. Therefore, it is likely that additional mechanisms are at play, notably bound water activity reduction in clays. Three-dimensionality allows for inclusion of lithologic heterogeneities, which focus fluid flow and subsequently allow for heterogeneity in the methane migration mechanisms that dominate in marine sediments at a local scale. Incorporating recently acquired 3D seismic data from Walker Ridge to inform the lithologic structure of our modeled reservoir, we show that even with deep adjective sourcing of methane along highly permeable pathways, local hydrate accumulations can be sourced either by diffusive or advective methane flux; advectively-sourced hydrates accumulate evenly in highly permeable strata, while diffusively-sourced hydrates are characterized by thin strata-bound intervals with high clay-sand pore size contrasts.
Wang, Yanli; Xu, Hanbing; ERDMAN III, DONALD L; Starbuck, J Michael; Simunovic, Srdjan
2011-01-01
Characterization of the material mechanical behavior at sub-Hopkinson regime (0.1 to 1000 s{sup -1}) is very challenging due to instrumentation limitations and the complexity of data analysis involved in dynamic loading. In this study, AZ31 magnesium alloy sheet specimens are tested using a custom designed servo-hydraulic machine in tension at nominal strain rates up to 1000 s{sup -1}. In order to resolve strain measurement artifacts, the specimen displacement is measured using 3D Digital Image correlation instead from actuator motion. The total strain is measured up to {approx} 30%, which is far beyond the measurable range of electric resistance strain gages. Stresses are calculated based on the elastic strains in the tab of a standard dog-bone shaped specimen. Using this technique, the stresses measured for strain rates of 100 s{sup -1} and lower show little or no noise comparing to load cell signals. When the strain rates are higher than 250 s{sup -1}, the noises and oscillations in the stress measurements are significantly decreased from {approx} 250 to 50 MPa. Overall, it is found that there are no significant differences in the elongation, although the material exhibits slight work hardening when the strain rate is increased from 1 to 100 s{sup -1}.
NASA Technical Reports Server (NTRS)
Wang, John T.; Pineda, Evan J.; Ranatunga, Vipul; Smeltzer, Stanley S.
2015-01-01
A simple continuum damage mechanics (CDM) based 3D progressive damage analysis (PDA) tool for laminated composites was developed and implemented as a user defined material subroutine to link with a commercially available explicit finite element code. This PDA tool uses linear lamina properties from standard tests, predicts damage initiation with an easy-to-implement Hashin-Rotem failure criteria, and in the damage evolution phase, evaluates the degradation of material properties based on the crack band theory and traction-separation cohesive laws. It follows Matzenmiller et al.'s formulation to incorporate the degrading material properties into the damaged stiffness matrix. Since nonlinear shear and matrix stress-strain relations are not implemented, correction factors are used for slowing the reduction of the damaged shear stiffness terms to reflect the effect of these nonlinearities on the laminate strength predictions. This CDM based PDA tool is implemented as a user defined material (VUMAT) to link with the Abaqus/Explicit code. Strength predictions obtained, using this VUMAT, are correlated with test data for a set of notched specimens under tension and compression loads.
NASA Astrophysics Data System (ADS)
Chen, Lin; Gerya, Taras V.
2016-04-01
Preexisting lateral variations in crustal thickness and lithospheric thermal state are documented for the formation of some orogenic plateaux. Here we use high-resolution 3-D thermo-mechanical simulations to investigate the influence of preexisting lateral lithospheric strength heterogeneity on the growth of orogenic plateau. The modeling results illustrate an episodic scenario for plateau growth: (1) an early rapid growth stage, characterized by rapid surface uplift and intensive crustal buckling and thickening; (2) an outward spreading stage, characterized by significant lateral expansion of the plateau edges; and (3) a mature stage, characterized by the development of the intracrustal partial melting and subduction of the surrounding lithosphere under the plateau. Sensitivity analyses indicate that lateral variation in crustal thickness favors outward spreading of orogenic plateau, while lateral variation in geothermal gradient favors crustal buckling. The model in absence of lateral strength heterogeneity leads to progressive migration of orogenic belt. Our models show that the plateau's lower crust is largely coupled with underlying lithospheric mantle and does not flow into the surrounding lithospheres, casting doubt on the lower crust flow model. We suggest that the Himalayan-Tibetan orogenic system can be best understood within the framework that the proto-southern Asian margin was fairly weak prior to the India-Asia collision to steer the formation of a large hot orogenic plateau there.
Neal, Devin; Sakar, Mahmut Selman; Bashir, Rashid; Chan, Vincent; Asada, Haruhiko Harry
2015-06-01
In this study, we present a quantitative approach to construct effective 3D muscle tissues through shape optimization and load impedance matching with electrical and optical stimulation. We have constructed long, thin, fascicle-like skeletal muscle tissue and optimized its form factor through mechanical characterization. A new apparatus was designed and built, which allowed us to measure force-displacement characteristics with diverse load stiffnesses. We have found that (1) there is an optimal form factor that maximizes the muscle stress, (2) the energy transmitted to the load can be maximized with matched load stiffness, and (3) optical stimulation using channelrhodopsin2 in the muscle tissue can generate a twitch force as large as its electrical counterpart for well-developed muscle tissue. Using our tissue construct method, we found that an optimal initial diameter of 500 μm outperformed tissues using 250 μm by more than 60% and tissues using 760 μm by 105%. Using optimal load stiffness, our tissues have generated 12 pJ of energy per twitch at a peak generated stress of 1.28 kPa. Additionally, the difference in optically stimulated twitch performance versus electrically stimulated is a function of how well the overall tissue performs, with average or better performing strips having less than 10% difference. The unique mechanical characterization method used is generalizable to diverse load conditions and will be used to match load impedance to muscle tissue impedance for a wide variety of applications. PMID:25714129
NASA Astrophysics Data System (ADS)
Komatsu, Y.; Kobayashi, T.; Fujii, T.
2015-12-01
The stratigraphy of the Miyazaki-oki forearc basin along the Southwest Japan Arc comprises the early Miocene to early Pleistocene Miyazaki Group and the Hyuganada Group. These groups comprise sediments (up to 5000 m) deposited in deep marine to shallow marine environments. Based on characteristics of well data outside seismic exploration area and stratigraphy of land areas, the Miyazaki Group was divided into four seismic units and the Hyuganada Group was divided into two seismic units. In this area, bottom-simulating reflectors (BSRs) have been widely observed and considered as representing lower boundaries of methane-hydrate-bearing deposits. However, the gas hydrate accumulation mechanism for this area is not yet well understood. We show the relation between sandy sediment distribution identified from the 3D seismic geomorphological analysis and methane hydrate occurrence to identify the accumulation mechanism. A submarine fan system was subdivided into four seismic facies: Submarine canyon complexes; Leveed channel complexes; Submarine fan complexes; Mass transport complexes (MTD). Depositional systems of target layers are characterized by a transition from submarine fan deposits (Miyazaki Group) to channel-levee deposits and MTD (Hyuganada Group). This transition of depositional environments is strongly influenced by global tectonics since early Miocene in the Southwest Japan Arc. A part of channel-fill located around structural wing and middle fan deposits above the BSR is inferred as sediments intercalated with sandy layers. We consider that these deposits contain methane hydrate because the sandy sediment distribution approximately coincides with a high-velocity zone as an indicator of gas hydrate. The comparison of the areal extent of the seismic facies and the mapped structural configuration, suggest that the gas hydrate accumulation represent combination structural-stratigraphic trap.
NASA Astrophysics Data System (ADS)
Bavusi, M.; Dumoulin, J.; Loperte, A.; Rizzo, E.; Soldovieri, F.
2012-04-01
, a zero setting acquisition was carried out before perturbing the plate. Described experience demonstrates the GPR is a reliable technique for the: • foundation soil characterization and monitoring • Reinforced structural elements monitoring • asphalt/reinforced concrete characterization and monitoring • detection of water infiltration, structural elements, defects • evaluation of restoration intervention. In fact, the GPR technique was able to investigate the layers beyond the asphalt and provides a spatial resolution complying with the needs of the technical problem at hand by use of different antennas. Moreover noticeable performances of this technique can be further improved by implementing 3D processing and MT inversion procedures in order to increase the amount of information by the survey [2]. Acknowledgements. The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under Grant Agreement n. 225663 Joint Call FP7-ICT-SEC-2007-1 [1] Lapenna, V.; Cuomo, V.; Rizzo, E.; Fiore, S.; Troisi, S.; Straface, S. (2006). A new Large Lab-scale Facility for Hydro-Geophysical Experiments: Hydrogeosite. American Geophysical Union, Fall Meeting 2006, abstract #H31B-1422 [2] Bavusi M., Soldovieri F., Di Napoli R., Loperte A., Di Cesare A., Ponzo F.C and Lapenna V. (2011). Ground penetrating radar and microwave tomography 3D applications for the deck evaluation of the Musmeci bridge in Potenza, Italy. J. Geophys. Eng. 8 S33 doi:10.1088/1742-2132/8/3/S04
A parallel sparse algorithm targeting arterial fluid mechanics computations
NASA Astrophysics Data System (ADS)
Manguoglu, Murat; Takizawa, Kenji; Sameh, Ahmed H.; Tezduyar, Tayfun E.
2011-09-01
Iterative solution of large sparse nonsymmetric linear equation systems is one of the numerical challenges in arterial fluid-structure interaction computations. This is because the fluid mechanics parts of the fluid + structure block of the equation system that needs to be solved at every nonlinear iteration of each time step corresponds to incompressible flow, the computational domains include slender parts, and accurate wall shear stress calculations require boundary layer mesh refinement near the arterial walls. We propose a hybrid parallel sparse algorithm, domain-decomposing parallel solver (DDPS), to address this challenge. As the test case, we use a fluid mechanics equation system generated by starting with an arterial shape and flow field coming from an FSI computation and performing two time steps of fluid mechanics computation with a prescribed arterial shape change, also coming from the FSI computation. We show how the DDPS algorithm performs in solving the equation system and demonstrate the scalability of the algorithm.
Applications of parallel global optimization to mechanics problems
NASA Astrophysics Data System (ADS)
Schutte, Jaco Francois
Global optimization of complex engineering problems, with a high number of variables and local minima, requires sophisticated algorithms with global search capabilities and high computational efficiency. With the growing availability of parallel processing, it makes sense to address these requirements by increasing the parallelism in optimization strategies. This study proposes three methods of concurrent processing. The first method entails exploiting the structure of population-based global algorithms such as the stochastic Particle Swarm Optimization (PSO) algorithm and the Genetic Algorithm (GA). As a demonstration of how such an algorithm may be adapted for concurrent processing we modify and apply the PSO to several mechanical optimization problems on a parallel processing machine. Desirable PSO algorithm features such as insensitivity to design variable scaling and modest sensitivity to algorithm parameters are demonstrated. A second approach to parallelism and improving algorithm efficiency is by utilizing multiple optimizations. With this method a budget of fitness evaluations is distributed among several independent sub-optimizations in place of a single extended optimization. Under certain conditions this strategy obtains a higher combined probability of converging to the global optimum than a single optimization which utilizes the full budget of fitness evaluations. The third and final method of parallelism addressed in this study is the use of quasiseparable decomposition, which is applied to decompose loosely coupled problems. This yields several sub-problems of lesser dimensionality which may be concurrently optimized with reduced effort.
NASA Astrophysics Data System (ADS)
Yang, Jianfeng; Kaus, Boris
2016-04-01
The mechanism of intraplate deformation remains incompletely understood by plate tectonics theory. The India-Asia collision zone is the largest present-day example of continental collision, which makes it an ideal location to study the processes of continental deformation. Existing models of lithospheric deformation are typically quasi two-dimensional and often assume that the lithosphere is a thin viscous sheet, which deforms homogeneously as a result of the collision, or flows above a partially molten lower crust, which explains the exhumation of Himalayan units and lateral spreading of Tibetan plateau. An opposing view is that most deformation localize in shear zones separating less deformed blocks, requiring the lithosphere to have an elasto-plastic rather than a viscous rheology. In order to distinguish which model best fits the observations we develop a 3-D visco-elasto-plastic model, which can model both distributed and highly localized deformation. In our preliminary result, most of the large-scale strike-slips faults including Altyn-Tagh fault, Xianshuihe fault, Red-River fault, Sagaing fault and Jiali fault can be simulated. The topography is consistent with observations that flat plateau in central Tibet and steep, abrupt margins adjacent to Sichuan basin, and gradual topography in southeast Tibet. These models suggest that the localized large-scale strike-slip faults accommodate the continental deformation. These results show the importance of a weak lower crust and topographic effects, as well as the effect of rheology and temperature structure of the lithosphere on the deformation patterns.
Bammer, Roland; Hope, Thomas A.; Aksoy, Murat; Alley, Marcus T.
2012-01-01
Exact knowledge of blood flow characteristics in the major cerebral vessels is of great relevance for diagnosing cerebrovascular abnormalities. This involves the assessment of hemodynamically critical areas as well as the derivation of biomechanical parameters such as wall shear stress and pressure gradients. A time-resolved, 3D phase-contrast (PC) MRI method using parallel imaging was implemented to measure blood flow in three dimensions at multiple instances over the cardiac cycle. The 4D velocity data obtained from 14 healthy volunteers were used to investigate dynamic blood flow with the use of multiplanar reformatting, 3D streamlines, and 4D particle tracing. In addition, the effects of magnetic field strength, parallel imaging, and temporal resolution on the data were investigated in a comparative evaluation at 1.5T and 3T using three different parallel imaging reduction factors and three different temporal resolutions in eight of the 14 subjects. Studies were consistently performed faster at 3T than at 1.5T because of better parallel imaging performance. A high temporal resolution (65 ms) was required to follow dynamic processes in the intracranial vessels. The 4D flow measurements provided a high degree of vascular conspicuity. Time-resolved streamline analysis provided features that have not been reported previously for the intracranial vasculature. PMID:17195166
NASA Astrophysics Data System (ADS)
Barnhart, Donald H.; Chan, Victor S. S.; Halliwell, Neil A.; Coupland, Jeremy M.
1999-10-01
This paper introduces a new approach to 3D displacement and velocity measurements that unifies the disciplines of holographic interferometry and holographic particle image velocimetry (HPIV). Equally applicable to fluid and solid mechanics, the overall system enables quantitative displacement measurements between two holographically recorded events from either particle or surface scattering sites, working with both pulsed and continuous-wave laser systems. The resulting measurements exhibit an accuracy corresponding to interferometric system, but with a dynamic range found with PIV systems. Most importantly, this paper introduces the novel use of an optical fiber to specify the measurement points, remove optical aberrations of windows, and eliminate directional ambiguity. An optical fiber is used to probe the recorded holographic image space at each 3D measurement point in order to extract the 3D displacement vectors. This fiber system also employs a novel optical image shifting method to eliminate the problem of directional ambiguity. In addition, the reported system uses 3D complex optical correlation rather than 2D real digital correlation. It is therefore a simple matter to directly obtain 3D displacement and velocity measurements at precisely known 3D locations in the object space. By correlating both the amplitude and phase information in the holographic image, this system can measure spatial distributions of displacements even when the presence of severe aberrations preclude the detection of sharp images.
NASA Astrophysics Data System (ADS)
Koptev, Alexander; Burov, Evgueni; Gerya, Taras
2014-05-01
We conducted high-resolution 3D thermo-mechanical numerical modeling experiments to explore evolution and styles of plume-activated rifting in presence of preexisting far-field tectonic stress/strain field and tectonic heritage (in form of cratonic blocks embedded in «normal lithosphere»). The experiments demonstrate strong dependence of rifting style on preexisting far-field tectonic stress/strain field and initial thermo-rheological profile, as well as on the tectonic heritage. The models with homogeneous lithosphere demonstrate strongly non-linear impact of far-field extension rates on timing of break-up processes. Experiments with relatively fast far-field extension (6 mm/y) show intensive normal fault localization in crust and uppermost mantle above the zones of plume-head emplacement some 15-20 Myrs after the onset of the experiment. When plume head material reaches the bottom of the continental crust (at ~25 Myrs), the latter is rapidly ruptured (<1 Myrs) and several steady oceanic floor spreading centers develop. Slower (3 mm/y) far-field velocities result in disproportionally longer break-up time (from 60 to 70 Myrs depending on initial isoterm at the crust bottom). Although in all experiments with homogeneous lithosphere spreading centers have similar orientation perpendicular to the direction of far-field extension, their number and spatial location are different for different extension rates and thermo-rheological structures of the lithosphere. On the contrary, in case of normal lithosphere containing embedded cratonic block, spreading zones develop symmetrically, embracing cratonic micro-plate along its long sides. Presence of cratonic blocks leads to splitting of the plume head onto initially nearly symmetrical parts, each of which flows towards beneath the craton borders. This craton-controlled distribution of plume material causes the crustal strain localization and uprise of plume material along the craton boundaries. Though there is a net
Probabilistic structural mechanics research for parallel processing computers
NASA Technical Reports Server (NTRS)
Sues, Robert H.; Chen, Heh-Chyun; Twisdale, Lawrence A.; Martin, William R.
1991-01-01
Aerospace structures and spacecraft are a complex assemblage of structural components that are subjected to a variety of complex, cyclic, and transient loading conditions. Significant modeling uncertainties are present in these structures, in addition to the inherent randomness of material properties and loads. To properly account for these uncertainties in evaluating and assessing the reliability of these components and structures, probabilistic structural mechanics (PSM) procedures must be used. Much research has focused on basic theory development and the development of approximate analytic solution methods in random vibrations and structural reliability. Practical application of PSM methods was hampered by their computationally intense nature. Solution of PSM problems requires repeated analyses of structures that are often large, and exhibit nonlinear and/or dynamic response behavior. These methods are all inherently parallel and ideally suited to implementation on parallel processing computers. New hardware architectures and innovative control software and solution methodologies are needed to make solution of large scale PSM problems practical.
Wedged AFM-cantilevers for parallel plate cell mechanics.
Stewart, Martin P; Hodel, Adrian W; Spielhofer, Andreas; Cattin, Cedric J; Müller, Daniel J; Helenius, Jonne
2013-04-01
The combination of atomic force microscopy (AFM) and optical microscopy has gained popularity for mechanical analysis of living cells. In particular, recent AFM-based assays featuring tipless cantilevers and whole-cell deformation have yielded insights into cellular function, structure, and dynamics. However, in these assays the standard ≈10° tilt of the cantilever prevents uniaxial loading, which complicates assessment of cellular geometry and can cause cell sliding or loss of loosely adherent cells. Here, we describe an approach to modify tipless cantilevers with wedges and, thereby, achieve proper parallel plate mechanics. We provide guidance on material selection, the wedge production process, property and geometry assessment, and the calibration of wedged cantilevers. Furthermore, we demonstrate their ability to simplify the assessment of cell shape, prevent lateral displacement of round cells during compression, and improve the assessment of cell mechanical properties. PMID:23473778
Argos: A novel 3-DoF parallel wrist mechanism
Vischer, P.; Clavel, R.
2000-01-01
This article presents a novel parallel spherical mechanism called argos with three rotational degrees of freedom. Design aspects of the first prototype built of the Argos mechanism are discussed. The direct kinematic problem is solved, leading always to four nonsingular configurations of the end effector for a given set of joint angles. The inverse-kinematic problem yields two possible configurations for each of the three pantographs for a given orientation of the end effector. Potential applications of the Argos mechanism are robot wrists, orientable machine tool beds, joy sticks, surgical manipulators, and orientable units for optical components. Another pantograph based new structure named PantoScope having two rotational DoF is also briefly introduced.
NASA Astrophysics Data System (ADS)
Boutelier, D. A.; Cruden, A. R.
2013-12-01
The general sequence of tectonic events leading to the formation of collisional mountain belts includes closure of an ocean basin through oceanic subduction, subduction of a continental margin and deformation of the lithosphere. Laboratory experiments reproducing this fundamental chain of events investigate the three-dimensional and thermo-mechanical mechanics of the associated processes. Experiments reveal that this basic scenario can be considerably modified at the beginning of continental subduction. The buoyancy of the subducted passive margin causes a strong horizontal compression in the plates, which can lead to the formation of new thrusts in the magmatic arc or back-arc spreading center if the collision was preceded by oceanic subduction in the tensile regime. Several complex scenarios can develop, depending on the polarity of the new thrusts. If the new thrust in the arc or back-arc has the same polarity as the main subduction zone, the entire area located between the trench and the new thrust can be subducted, leaving little evidence of its former existence in the geological record. This process also modifies the thermal and mechanical regime of the subducted lithosphere, resulting in lower temperatures in the subducted crust thereby allowing deeper subduction. If the polarity of the new thrust is opposite to that of the existing subduction zone, the two slabs collide at depth, with the new slab generally cutting through the pre-existing slab. The distribution of convergence across several thrusts necessarily leads to a reduction of the convergence rate on the pre-existing subduction thrust. This leads to a reduction of the viscous coupling supporting the subducted lithosphere, causing an increase in downdip tension in the slab, and a rapid decrease of the slab strength due to temperature increase, eventually leading to slab break-off. Finally, the deformation caused by the subduction of the buoyant continental crust is fundamentally three
NASA Astrophysics Data System (ADS)
Zheng, Xiang; Yang, Chao; Cai, Xiao-Chuan; Keyes, David
2015-03-01
We present a numerical algorithm for simulating the spinodal decomposition described by the three dimensional Cahn-Hilliard-Cook (CHC) equation, which is a fourth-order stochastic partial differential equation with a noise term. The equation is discretized in space and time based on a fully implicit, cell-centered finite difference scheme, with an adaptive time-stepping strategy designed to accelerate the progress to equilibrium. At each time step, a parallel Newton-Krylov-Schwarz algorithm is used to solve the nonlinear system. We discuss various numerical and computational challenges associated with the method. The numerical scheme is validated by a comparison with an explicit scheme of high accuracy (and unreasonably high cost). We present steady state solutions of the CHC equation in two and three dimensions. The effect of the thermal fluctuation on the spinodal decomposition process is studied. We show that the existence of the thermal fluctuation accelerates the spinodal decomposition process and that the final steady morphology is sensitive to the stochastic noise. We also show the evolution of the energies and statistical moments. In terms of the parallel performance, it is found that the implicit domain decomposition approach scales well on supercomputers with a large number of processors.
Zheng, Xiang; Yang, Chao; Cai, Xiao-Chuan; Keyes, David
2015-03-15
We present a numerical algorithm for simulating the spinodal decomposition described by the three dimensional Cahn–Hilliard–Cook (CHC) equation, which is a fourth-order stochastic partial differential equation with a noise term. The equation is discretized in space and time based on a fully implicit, cell-centered finite difference scheme, with an adaptive time-stepping strategy designed to accelerate the progress to equilibrium. At each time step, a parallel Newton–Krylov–Schwarz algorithm is used to solve the nonlinear system. We discuss various numerical and computational challenges associated with the method. The numerical scheme is validated by a comparison with an explicit scheme of high accuracy (and unreasonably high cost). We present steady state solutions of the CHC equation in two and three dimensions. The effect of the thermal fluctuation on the spinodal decomposition process is studied. We show that the existence of the thermal fluctuation accelerates the spinodal decomposition process and that the final steady morphology is sensitive to the stochastic noise. We also show the evolution of the energies and statistical moments. In terms of the parallel performance, it is found that the implicit domain decomposition approach scales well on supercomputers with a large number of processors.
NASA Astrophysics Data System (ADS)
Sadeghi Neshat, Hamid; Bax, Jeffery; Barker, Kevin; Gardi, Lori; Chedalavada, Jason; Kakani, Nirmal; Fenster, Aaron
2014-03-01
Image-guided percutaneous ablation is the standard treatment for focal liver tumors deemed inoperable and is commonly used to maintain eligibility for patients on transplant waitlists. Radiofrequency (RFA), microwave (MWA) and cryoablation technologies are all delivered via one or a number of needle-shaped probes inserted directly into the tumor. Planning is mostly based on contrast CT/MRI. While intra-procedural CT is commonly used to confirm the intended probe placement, 2D ultrasound (US) remains the main, and in some centers the only imaging modality used for needle guidance. Corresponding intraoperative 2D US with planning and other intra-procedural imaging modalities is essential for accurate needle placement. However, identification of matching features of interest among these images is often challenging given the limited field-of-view (FOV) and low quality of 2D US images. We have developed a passive tracking arm with a motorized scan-head and software tools to improve guiding capabilities of conventional US by large FOV 3D US scans that provides more anatomical landmarks that can facilitate registration of US with both planning and intra-procedural images. The tracker arm is used to scan the whole liver with a high geometrical accuracy that facilitates multi-modality landmark based image registration. Software tools are provided to assist with the segmentation of the ablation probes and tumors, find the 2D view that best shows the probe(s) from a 3D US image, and to identify the corresponding image from planning CT scans. In this paper, evaluation results from laboratory testing and a phase 1 clinical trial for planning and guiding RFA and MWA procedures using the developed system will be presented. Early clinical results show a comparable performance to intra-procedural CT that suggests 3D US as a cost-effective alternative with no side-effects in centers where CT is not available.
Zeinali, Soheila; Çetin, Barbaros; Oliaei, Samad Nadimi Bavil; Karpat, Yiğit
2015-07-01
Microfluidics is the combination of micro/nano fabrication techniques with fluid flow at microscale to pursue powerful techniques in controlling and manipulating chemical and biological processes. Sorting and separation of bio-particles are highly considered in diagnostics and biological analyses. Dielectrophoresis (DEP) has offered unique advantages for microfluidic devices. In DEP devices, asymmetric pair of planar electrodes could be employed to generate non-uniform electric fields. In DEP applications, facing 3D sidewall electrodes is considered to be one of the key solutions to increase device throughput due to the generated homogeneous electric fields along the height of microchannels. Despite the advantages, fabrication of 3D vertical electrodes requires a considerable challenge. In this study, two alternative fabrication techniques have been proposed for the fabrication of a microfluidic device with 3D sidewall electrodes. In the first method, both the mold and the electrodes are fabricated using high precision machining. In the second method, the mold with tilted sidewalls is fabricated using high precision machining and the electrodes are deposited on the sidewall using sputtering together with a shadow mask fabricated by electric discharge machining. Both fabrication processes are assessed as highly repeatable and robust. Moreover, the two methods are found to be complementary with respect to the channel height. Only the manipulation of particles with negative-DEP is demonstrated in the experiments, and the throughput values up to 105 particles / min is reached in a continuous flow. The experimental results are compared with the simulation results and the limitations on the fabrication techniques are also discussed. PMID:25808433
NASA Astrophysics Data System (ADS)
Kettermann, Michael; Thronberens, Sebastian; Juarez, Oscar; Lajos Urai, Janos; Ziegler, Martin; Asmus, Sven; Kruger, Ulrich
2016-05-01
Clay smears in normal faults can form seals for hydrocarbons and groundwater, and their prediction in the subsurface is an important problem in applied and basic geoscience. However, neither their complex 3-D structure, nor their processes of formation or destruction are well understood, and outcrop studies to date are mainly 2-D. We present a 3-D study of an excavated normal fault with clay smear, together with both source layers, in unlithified sand and clay of the Hambach open-cast lignite mine in Germany. The faults formed at a depth of 150 m, and have shale gouge ratios between 0.1 and 0.3. The fault zones are layered, with sheared sand, sheared clay and tectonically mixed sand-clay gouge. The thickness of clay smears in two excavated fault zones of 1.8 and 3.8 m2 is approximately log-normal, with values between 5 mm and 5 cm, without holes. The 3-D thickness distribution is heterogeneous. We show that clay smears are strongly affected by R and R' shears, mostly at the footwall side. These shears can locally cross and offset clay smears, forming holes in the clay smear, while thinning of the clay smear by shearing in the fault core is less important. The thinnest parts of the clay smears are often located close to source layer cut-offs. Locally, the clay smear consists of overlapping patches of sheared clay, separated by sheared sand. More commonly, it is one amalgamated zone of sheared sand and clay. A microscopic study of fault-zone samples shows that grain-scale mixing can lead to thickening of the low permeability smears, which may lead to resealing of holes.
NASA Astrophysics Data System (ADS)
Xiu, Ziyang; Deng, Zongquan; Wang, Xiaofeng; Wu, Gaohui
A dense and uniform Sip/LG5 composite were fabricated by squeeze casting technology, and high temperature diffusion treatment was adapted to the composite. Microstructure observation indicated that Si transformed from irregular particles to 3D-structure. Fine dispersive precipitates Si were also observed on Si-Al interface and within Al matrix, smoothing and improving the interface. Based on the microstructure observation, three transformation stages were designated: melting, dissolution and precipitation, solidification. Thermodynamics and kinetics of the transformation can be explained by Gibbs-Thomson effect.
NIF Ignition Target 3D Point Design
Jones, O; Marinak, M; Milovich, J; Callahan, D
2008-11-05
We have developed an input file for running 3D NIF hohlraums that is optimized such that it can be run in 1-2 days on parallel computers. We have incorporated increasing levels of automation into the 3D input file: (1) Configuration controlled input files; (2) Common file for 2D and 3D, different types of capsules (symcap, etc.); and (3) Can obtain target dimensions, laser pulse, and diagnostics settings automatically from NIF Campaign Management Tool. Using 3D Hydra calculations to investigate different problems: (1) Intrinsic 3D asymmetry; (2) Tolerance to nonideal 3D effects (e.g. laser power balance, pointing errors); and (3) Synthetic diagnostics.
NASA Astrophysics Data System (ADS)
Gillespie, K. M.; Speirs, D. C.; Ronald, K.; McConville, S. L.; Phelps, A. D. R.; Bingham, R.; Cross, A. W.; Robertson, C. W.; Whyte, C. G.; He, W.; Vorgul, I.; Cairns, R. A.; Kellett, B. J.
2008-12-01
Auroral Kilometric Radiation (AKR), occurs naturally in the polar regions of the Earth's magnetosphere where electrons are accelerated by electric fields into the increasing planetary magnetic dipole. Here conservation of the magnetic moment converts axial to rotational momentum forming a horseshoe distribution in velocity phase space. This distribution is unstable to cyclotron emission with radiation emitted in the X-mode. In a scaled laboratory reproduction of this process, a 75-85 keV electron beam of 5-40 A was magnetically compressed by a system of solenoids and emissions were observed for cyclotron frequencies of 4.42 GHz and 11.7 GHz resonating with near cut-off TE0,1 and TE0,3 modes, respectively. Here we compare these measurements with numerical predictions from the 3D PiC code KARAT. The 3D simulations accurately predicted the radiation modes and frequencies produced by the experiment. The predicted conversion efficiency between electron kinetic and wave field energy of around 1% is close to the experimental measurements and broadly consistent with quasi-linear theoretical analysis and geophysical observations.
Qiang, J.; Leitner, D.; Todd, D.
2005-05-16
The driver linac of the proposed Rare Isotope Accelerator (RIA) requires a great variety of high intensity, high charge state ion beams. In order to design and to optimize the low energy beamline optics of the RIA front end,we have developed a new parallel three-dimensional model to simulate the low energy, multi-species ion beam formation and transport from the ECR ion source extraction region to the focal plane of the analyzing magnet. A multisection overlapped computational domain has been used to break the original transport system into a number of each subsystem, macro-particle tracking is used to obtain the charge density distribution in this subdomain. The three-dimensional Poisson equation is solved within the subdomain and particle tracking is repeated until the solution converges. Two new Poisson solvers based on a combination of the spectral method and the multigrid method have been developed to solve the Poisson equation in cylindrical coordinates for the beam extraction region and in the Frenet-Serret coordinates for the bending magnet region. Some test examples and initial applications will also be presented.
NASA Astrophysics Data System (ADS)
Sobolev, S. V.; Tympel, J.; Ratschbacher, L.
2015-12-01
The Pamir-Hindu Kush orogenic belt is the result of the indentation of the western corner of the India plate into Eurasia. It has accommodated the highest strain over the shortest meridional distance of the India-Eurasia collision zone. Recent high-resolution seismic tomographic and receiver function studies confirm the presence of a south-dipping continental lithosphere, which has been traced to the depth of more than 200-300 km beneath the northern Pamir (Pamir slab). Balanced cross-section document crustal shortening associated with the corresponding frontal thrust system of a few tens of km, which is much less than the expected (>200-300 km) for intra-continental subduction zone, based on the seismically imaged length of the Pamir slab. Another unique feature of Pamir is the presence of large gneiss domes with the exhumation reaching a depth of 30-40 km.We employ the finite-element thermomechanical modelling technique SLIM3D to simulate the evolution of the Pamir orogeny during the last 25 Myr. The technique is using advanced non-linear elasto-visco-plastic rheology with parameters based on laboratory experiments. Our 3D model extends 1100 km N-S, 800 km E-W, and 300 km deep, and replicates indentation of the western half of India promontory into Eurasia. The moving modelling-window technique allows focusing at the most extensively deforming domains, and a 3D model setup and boundary conditions allow lateral material flow to the west, i.e. perpendicular to the direction of tectonic shortening.The model replicates major features of the lithospheric structure and geological history. For instance, we demonstrate that large part of the roll back of the Pamir slab may be caused by the delamination of the mantle lithosphere together with the lower crust, rather than classical intra-continental subduction involving thrust-imbrication of the uppermost crust. The resulting shortening at the Pamir frontal thrust system appears to be lower than 50 km in accord with
NASA Astrophysics Data System (ADS)
Hicks, Stephen; Rietbrock, Andreas
2015-04-01
The earthquake rupture process is extremely heterogeneous. For subduction zone earthquakes in particular, it is vital to understand how structural variations in the overriding plate and downgoing slab may control slip style. The large-scale 3-D geometry of subduction plate boundaries is rapidly becoming well understood (e.g. Hayes et al., 2012); however, the nature of slip style along any finer-scale structures remains elusive. Regional earthquake moment tensor (RMT) inversion can shed light on faulting mechanisms. However, many traditional regional moment tensor inversions use simplified (1-D) Earth models (e.g. Agurto et al., 2012; Hayes et al., 2013) that only use the lowest frequency parts of the waveform, which may mask source complexity. As a result, we may have to take care when making small-scale interpretations about the causative fault and its slip style. This situation is compounded further by strong lateral variations in subsurface geology, as well as poor station coverage for recording offshore subduction earthquakes. A formal assessment of the resolving capability of RMT inversions in subduction zones is challenging and the application of 3-D waveform simulation techniques in highly heterogeneous media is needed. We generate 3-D waveform simulations of aftershocks from a large earthquake that struck Chile in 2010. The Mw 8.8 Maule earthquake is the sixth largest earthquake ever recorded. Following the earthquake, there was an international deployment of seismic stations in the rupture area, making this one of the best observed aftershock sequences to date. We therefore have a unique opportunity to compare recorded waveforms with simulated waveforms for many earthquakes, shedding light on the effect of 3-D heterogeneity on source imaging. We perform forward simulations using the spectral element wave propagation code, SPEFEM3D (e.g. Komatitsch et al., 2010) for a set of moderate-sized aftershocks (Mw 4.0-5.5). A detailed knowledge of velocity structure
Final Report: Migration Mechanisms for Large-scale Parallel Applications
Jason Nieh
2009-10-30
Process migration is the ability to transfer a process from one machine to another. It is a useful facility in distributed computing environments, especially as computing devices become more pervasive and Internet access becomes more ubiquitous. The potential benefits of process migration, among others, are fault resilience by migrating processes off of faulty hosts, data access locality by migrating processes closer to the data, better system response time by migrating processes closer to users, dynamic load balancing by migrating processes to less loaded hosts, and improved service availability and administration by migrating processes before host maintenance so that applications can continue to run with minimal downtime. Although process migration provides substantial potential benefits and many approaches have been considered, achieving transparent process migration functionality has been difficult in practice. To address this problem, our work has designed, implemented, and evaluated new and powerful transparent process checkpoint-restart and migration mechanisms for desktop, server, and parallel applications that operate across heterogeneous cluster and mobile computing environments. A key aspect of this work has been to introduce lightweight operating system virtualization to provide processes with private, virtual namespaces that decouple and isolate processes from dependencies on the host operating system instance. This decoupling enables processes to be transparently checkpointed and migrated without modifying, recompiling, or relinking applications or the operating system. Building on this lightweight operating system virtualization approach, we have developed novel technologies that enable (1) coordinated, consistent checkpoint-restart and migration of multiple processes, (2) fast checkpointing of process and file system state to enable restart of multiple parallel execution environments and time travel, (3) process migration across heterogeneous
NASA Astrophysics Data System (ADS)
Lipatov, A. S.; Cooper, J. F.; Sittler, E. C.; Hartle, R. E.; Sarantos, M.
2013-12-01
The hybrid kinetic model used here supports comprehensive simulation of the interaction between different spatial and energetic elements of the moon-solar wind-magnetosphere of the Earth system. This involves variable upstream magnetic field and solar wind plasma, including energetic ions, electrons, and neutral atoms. This capability is critical to improved interpretation of existing measurements for surface and atmospheric composition from previous missions and planning future missions. Recently, MAP-PAGE-IMA (Plasma energy Angle and Composition Experiment, and Ion Mass Analyzer) onboard Japanese lunar orbiter SELENE (KAGUYA) detected Moon originating ions at 100 km altitude. Ion species of H+, He++, He+, C+, O+, Na+, K+, and Ar+ were definitively identified. The first portion of our modeling devotes to a study of the H+, H2+, He+, Na+ pickup ion dynamics in cases of flow with a oblique and quasi-parallel magnetic field. In the second series of modeling we also take into account collisions between ions and the surface of the moon and further sputtering of fragments from the surface of the moon. The ion reflection at the lunar surface is also responsible for wave activity in the upstream flow. The solar wind parameters are chosen from ARTEMIS observations. The hybrid kinetic model allows us to take into account the finite gyroradius effects of pickup ions and to estimate correctly the ions velocity distribution and the fluxes along the magnetic field. Modeling shows the asymmetric Mach cone, pickup and reflected ion tails, and presents another type of lunar-solar wind interaction. Our simulation may be also important for the study of the interaction between the solar wind and very weak comets, Mercury and Pluto.
NASA Astrophysics Data System (ADS)
Peng, Yuncheng; Wang, Yao; Deng, Yuan
2016-08-01
With the ever increasing level of performance of energy conversion micro-devices, such as thin-film solar cells and thermoelectric micro-generators or coolers, their reliability and stability still remain a challenge. The high electrical and mechanical stability of an electrode is two of the critical factors that affect the long-term life of devices. Here we show that these factors can be achieved by constructing a 3D porous network of nanostructures in copper film using facile magnetron sputtering technology without any templates. The constructed 3D porous network of nanostructures in Cu film provides not only the advantages of light weight, prominently high conductivity, and large elastic deformation, but also the ability to absorb stress, preventing crack propagation, which is crucial for electrodes to maintain stable electrical and mechanical properties under working conditions. The nanopores inside the 3D network are capable of unrestrained deformation under applied stress resulting in strong elastic recovery. This work puts forward a feasible solution for manufacturing electrodes with excellent electrical and mechanical properties for micro-energy devices.
2009-01-01
Background Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Results Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. Conclusion DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods. PMID:19912625
NASA Technical Reports Server (NTRS)
Asenov, Asen; Brown, A. R.; Slavcheva, G.; Davies, J. H.
2000-01-01
When MOSFETs are scaled to deep submicron dimensions the discreteness and randomness of the dopant charges in the channel region introduces significant fluctuations in the device characteristics. This effect, predicted 20 year ago, has been confirmed experimentally and in simulation studies. The impact of the fluctuations on the functionality, yield, and reliability of the corresponding systems shifts the paradigm of the numerical device simulation. It becomes insufficient to simulate only one device representing one macroscopical design in a continuous charge approximation. An ensemble of macroscopically identical but microscopically different devices has to be characterized by simulation of statistically significant samples. The aims of the numerical simulations shift from predicting the characteristics of a single device with continuous doping towards estimating the mean values and the standard deviations of basic design parameters such as threshold voltage, subthreshold slope, transconductance, drive current, etc. for the whole ensemble of 'atomistically' different devices in the system. It has to be pointed out that even the mean values obtained from 'atomistic' simulations are not identical to the values obtained from continuous doping simulations. In this paper we present a hierarchical approach to the 'atomistic' simulation of aggressively scaled decanano MOSFETs. A full scale 3D drift-diffusion'atomostic' simulation approach is first described and used for verification of the more economical, but also more restricted, options. To reduce the processor time and memory requirements at high drain voltage we have developed a self-consistent option based on a thin slab solution of the current continuity equation only in the channel region. This is coupled to the Poisson's equation solution in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison with the full self-consistent solution. At low drain
Parallel mechanisms suppress cochlear bone remodeling to protect hearing.
Jáuregui, Emmanuel J; Akil, Omar; Acevedo, Claire; Hall-Glenn, Faith; Tsai, Betty S; Bale, Hrishikesh A; Liebenberg, Ellen; Humphrey, Mary Beth; Ritchie, Robert O; Lustig, Lawrence R; Alliston, Tamara
2016-08-01
Bone remodeling, a combination of bone resorption and formation, requires precise regulation of cellular and molecular signaling to maintain proper bone quality. Whereas osteoblasts deposit and osteoclasts resorb bone matrix, osteocytes both dynamically resorb and replace perilacunar bone matrix. Osteocytes secrete proteases like matrix metalloproteinase-13 (MMP13) to maintain the material quality of bone matrix through perilacunar remodeling (PLR). Deregulated bone remodeling impairs bone quality and can compromise hearing since the auditory transduction mechanism is within bone. Understanding the mechanisms regulating cochlear bone provides unique ways to assess bone quality independent of other aspects that contribute to bone mechanical behavior. Cochlear bone is singular in its regulation of remodeling by expressing high levels of osteoprotegerin. Since cochlear bone expresses a key PLR enzyme, MMP13, we examined whether cochlear bone relies on, or is protected from, osteocyte-mediated PLR to maintain hearing and bone quality using a mouse model lacking MMP13 (MMP13(-/-)). We investigated the canalicular network, collagen organization, lacunar volume via micro-computed tomography, and dynamic histomorphometry. Despite finding defects in these hallmarks of PLR in MMP13(-/-) long bones, cochlear bone revealed no differences in these markers, nor hearing loss as measured by auditory brainstem response (ABR) or distortion product oto-acoustic emissions (DPOAEs), between wild type and MMP13(-/-) mice. Dynamic histomorphometry revealed abundant PLR by tibial osteocytes, but near absence in cochlear bone. Cochlear suppression of PLR corresponds to repression of several key PLR genes in the cochlea relative to long bones. These data suggest that cochlear bone uniquely maintains bone quality and hearing independent of MMP13-mediated osteocytic PLR. Furthermore, the cochlea employs parallel mechanisms to inhibit remodeling by osteoclasts and osteoblasts, and by
Schleich, Jean-Marc; Dillenseger, Jean-Louis; Houyel, Lucile; Almange, Claude; Anderson, Robert H
2009-01-01
Learning embryology remains difficult, since it requires understanding of many complex phenomena. The temporal evolution of developmental events has classically been illustrated using cartoons, which create difficulty in linking spatial and temporal aspects, such correlation being the keystone of descriptive embryology. We synthesized the bibliographic data from recent studies of atrial septal development. On the basis of this synthesis, consensus on the stages of atrial septation as seen in the human heart has been reached by a group of experts in cardiac embryology and pediatric cardiology. This has permitted the preparation of three-dimensional (3D) computer graphic objects for the anatomical components involved in the different stages of normal human atrial septation. We have provided a virtual guide to the process of normal atrial septation, the animation providing an appreciation of the temporal and morphologic events necessary to separate the systemic and pulmonary venous returns. We have shown that our animations of normal human atrial septation increase significantly the teaching of the complex developmental processes involved, and provide a new dynamic for the process of learning. PMID:19363807
Wang, Yaxing; Tao, Zetian; Yin, Xuemiao; Shu, Jie; Chen, Lanhua; Sheng, Daopeng; Chai, Zhifang; Albrecht-Schmitt, Thomas E; Wang, Shuao
2015-10-19
The preparation of proton-conducting materials that are functional and stable at intermediate temperatures (393-573 K) is a focal point of fuel cell development. The purely inorganic material, HNd(IO3)4, which possesses a dense 3D framework structure, can reach a maximum of 4.6 × 10(-4) S·cm(-1) at 353 K and 95% relative humidity and exhibit a high conductivity of 8.0 × 10(-5) S·cm(-1) from 373 to 553 K under the flow of wet N2. HNd(IO3)4 exhibits a variety of improvements including high thermal stability, low solubility in water, and resistance to reducing atmosphere. The proton conductivity in such a wide temperature range originates from the intrinsic liberated protons in the structure and the resulting 1D hydrogen-bonding network confirmed by bond valence sum calculation and solid-state NMR analysis. Moreover, two different activation energies are observed in different temperature regions (0.23 eV below 373 K and 0.026 eV from 373 to 553 K), indicating that two types of proton motion are responsible for proton diffusion, as further domenstrated by temperature-dependent open-circuit voltage hysteresis in a tested fuel cell assembly as well as variable-temperature and double quantum filtered solid-state NMR measurements. PMID:26444097
NASA Astrophysics Data System (ADS)
Thiemeyer, Nicolas; Zulauf, Gernold; Mertineit, Michael; Linckens, Jolien; Pusch, Maximilian; Hammer, Jörg
2016-04-01
The Permian Knäuel- and Streifensalz formations (z2HS1 and z2HS2) are main constituents of the Gorleben salt dome (Northern Germany) and show different amounts and distributions of anhydrite. The reconstruction of 3D halite grain shape ellipsoids reveals small grain size (3.4 ± 0.6 mm) and heterogeneous grain shapes in both formations, the latter attributed to the polyphase deformation of the rock salt during diapirism. The halite microfabrics of both formations indicate that strain-induced grain boundary migration was active during deformation. Crystal plastic deformation of halite is further documented by lattice bending, subgrain formation and minor subgrain rotation. Evidence for pressure solution of halite has not been found, but cannot be excluded because of the small grain size, the lack of LPO and the low differential stress (1.1-1.3 MPa) as deduced from subgrain-size piezometry. Anhydrite has been deformed in the brittle-ductile regime by solution precipitation creep, minor dislocation creep and brittle boudinage. No continuous anhydrite layers are preserved, and halite has acted as a sealing matrix embedding the disrupted anhydrite fragments prohibiting any potential migration pathways for fluids. Thus, anhydrite should not have a negative effect on the barrier properties of the Gorleben rock salts investigated in this study.
Miki, Motohiro; Katayama, Kazuhiko
2012-01-01
Norwalk virus (NoV) is responsible for most outbreaks of non-bacterial gastroenteritis. NoV is genetically diverse and show antigenically variable. Recently, we produced a monoclonal antibody called 5B-18 that reacts broadly with NoV genogroup II (GII). We suspected the 5B-18 binds to a conformational epitope on 3D structure of virion. X-ray crystallography showed us that 5B-18 binds to NoV at the P domain, which protrudes from the capsid surface of the virion. However, there seems to be no space that would allow the IgG to approach the virion. To solve this problem, we used cryo-electron microscopy to examine NoV GII virus-like particles (VLPs). The P domain rises up higher in NoV GII than in NoV GI, and it seems to form an outer layer around the virion. Finally, using in silico modeling we found the 5B-18 Fab arms and NoV P region are quite flexible, so that 5B-18 can bind the NoV virion from bottom of P domain. This study demonstrates the shortcomings of studying biological phenomenon by only one technique. Each method has limitations. Multiple methods and modeling in silico are the keys to solving structural problems. PMID:23133439
NASA Astrophysics Data System (ADS)
Ba, Ningning; Zhu, Lianjie; Li, Hongbin; Zhang, Guangzhi; Li, Jianfa; Sun, Jingfeng
2016-03-01
3-dimensional (3D) rod-like CuO with nanowire hierarchical structure has been synthesized successfully by a facile ultrasound assisted method combined with thermal conversion, using rouaite Cu2(OH)3NO3 as the precursor. The product was characterized by XRD, SEM, TEM, HRTEM and FT-IR spectrum. Its optical properties were studied by means of UV-Vis diffuse reflectance absorption spectroscopy and photoluminescence (PL) spectrum. Series of control experiments have been performed to explore influencing factors to the product morphologies and a possible formation mechanism has been proposed. The results show that each CuO rod assembled by tens of nanowires is 200-300 nm in diameter and about 1000 nm in length. Each nanowire contains many interconnected nanoparticles with sizes of about 15 nm. Particularly, ultrasound processing was found beneficial to the formation of the 3D rod-like CuO with nanowire hierarchical structure.
NASA Astrophysics Data System (ADS)
Pletinckx, D.
2011-09-01
The current 3D hype creates a lot of interest in 3D. People go to 3D movies, but are we ready to use 3D in our homes, in our offices, in our communication? Are we ready to deliver real 3D to a general public and use interactive 3D in a meaningful way to enjoy, learn, communicate? The CARARE project is realising this for the moment in the domain of monuments and archaeology, so that real 3D of archaeological sites and European monuments will be available to the general public by 2012. There are several aspects to this endeavour. First of all is the technical aspect of flawlessly delivering 3D content over all platforms and operating systems, without installing software. We have currently a working solution in PDF, but HTML5 will probably be the future. Secondly, there is still little knowledge on how to create 3D learning objects, 3D tourist information or 3D scholarly communication. We are still in a prototype phase when it comes to integrate 3D objects in physical or virtual museums. Nevertheless, Europeana has a tremendous potential as a multi-facetted virtual museum. Finally, 3D has a large potential to act as a hub of information, linking to related 2D imagery, texts, video, sound. We describe how to create such rich, explorable 3D objects that can be used intuitively by the generic Europeana user and what metadata is needed to support the semantic linking.
Ho, Thach-Vu; Iwata, Junichi; Ho, Hoang Anh; Grimes, Weston C; Park, Shery; Sanchez-Lara, Pedro A; Chai, Yang
2015-04-15
Growth factor signaling regulates tissue-tissue interactions to control organogenesis and tissue homeostasis. Specifically, transforming growth factor beta (TGFβ) signaling plays a crucial role in the development of cranial neural crest (CNC) cell-derived bone, and loss of Tgfbr2 in CNC cells results in craniofacial skeletal malformations. Our recent studies indicate that non-canonical TGFβ signaling is activated whereas canonical TGFβ signaling is compromised in the absence of Tgfbr2 (in Tgfbr2(fl/fl);Wnt1-Cre mice). A haploinsufficiency of Tgfbr1 (aka Alk5) (Tgfbr2(fl/fl);Wnt1-Cre;Alk5(fl/+)) largely rescues craniofacial deformities in Tgfbr2 mutant mice by reducing ectopic non-canonical TGFβ signaling. However, the relative involvement of canonical and non-canonical TGFβ signaling in regulating specific craniofacial bone formation remains unclear. We compared the size and volume of CNC-derived craniofacial bones (frontal bone, premaxilla, maxilla, palatine bone, and mandible) from E18.5 control, Tgfbr2(fl/fl);Wnt1-Cre, and Tgfbr2(fl/fl);Wnt1-Cre;Alk5(fl/+)mice. By analyzing three dimensional (3D) micro-computed tomography (microCT) images, we found that different craniofacial bones were restored to different degrees in Tgfbr2(fl/fl);Wnt1-Cre;Alk5(fl/+) mice. Our study provides comprehensive information on anatomical landmarks and the size and volume of each craniofacial bone, as well as insights into the extent that canonical and non-canonical TGFβ signaling cascades contribute to the formation of each CNC-derived bone. Our data will serve as an important resource for developmental biologists who are interested in craniofacial morphogenesis. PMID:25722190
Evaluation of resolution of flexure parallel mechanisms for ultraprecision manipulation
NASA Astrophysics Data System (ADS)
Pham, Huy-Hoang; Chen, I.-Ming
2004-09-01
A method for evaluating the resolution of ultraprecision manipulation systems based on the flexure parallel mechanism (FPM) is presented. The resolution of the open-loop system is theoretically determined by the resolution transmission from the actuated joints to the end-effector and the resolution of actuators. The method studies the definition of the resolution indicators that includes the global resolution transmission scale and the uniformity of resolution over the entire workspace of the flexure mechanism. The computational algorithm for the defined resolution indicators is established based on the sampling method. For illustration, the evaluation method is employed to gauge the resolution performance of a two-degree-of-freedom and a three-degree-of-freedom (3-DOF) planar FPM. To demonstrate its application for optimal design, we use this method for the development of a 3-DOF spatial translational FPM. An experiment is carried out to determine the resolution and the repeatability of the developed FPM and verify the proposed evaluation method. The result shows that the method is suitable for the design of FPM for any desired resolution.
Chen, J.; Alpan, F. A.; Fischer, G.A.; Fero, A.H.
2011-07-01
Traditional two-dimensional (2D)/one-dimensional (1D) SYNTHESIS methodology has been widely used to calculate fast neutron (>1.0 MeV) fluence exposure to reactor pressure vessel in the belt-line region. However, it is expected that this methodology cannot provide accurate fast neutron fluence calculation at elevations far above or below the active core region. A three-dimensional (3D) parallel discrete ordinates calculation for ex-vessel neutron dosimetry on a Westinghouse 4-Loop XL Pressurized Water Reactor has been done. It shows good agreement between the calculated results and measured results. Furthermore, the results show very different fast neutron flux values at some of the former plate locations and elevations above and below an active core than those calculated by a 2D/1D SYNTHESIS method. This indicates that for certain irregular reactor internal structures, where the fast neutron flux has a very strong local effect, it is required to use a 3D transport method to calculate accurate fast neutron exposure. (authors)
NASA Astrophysics Data System (ADS)
Yanagisawa, Takatoshi; Yamagishi, Yasuko; Hamano, Yozo; Stegman, Dave R.; Suetsugu, Daisuke; Bina, Craig; Inoue, Toru; Wiens, Douglas; Jellinek, Mark
2010-11-01
Seismic tomography reveals the natural mode of convection in the Earth is whole mantle with subducted slabs clearly seen as continuous features into the lower mantle. However, simultaneously existing alongside these deep slabs are stagnant slabs which are, if only temporarily, trapped in the upper mantle. Previous numerical models of mantle convection have observed a range of behavior for slabs in the transition zone depending on viscosity stratification and mineral phase transitions, but typically only exhibit flat-lying slabs when mantle convection is layered or trench migration is imposed. We use 3-D spherical models of mantle convection which range up to Earth-like conditions in Rayleigh number to systematically investigate three effects on mantle dynamics: (1) the mineral phase transitions, (2) a strongly temperature-dependent viscosity with plastic yielding at shallow depth, and (3) a viscosity increase in the lower mantle. First a regime diagram is constructed for isoviscous models over a wide range of Rayleigh number and Clapeyron slope for which the convective mode is determined. It agrees very well with previous results from 2-D simulations by Christensen and Yuen (1985), suggesting present-day Earth is in the intermittent convection mode rather than layered or strictly whole mantle. Two calculations at Earth-like conditions (Ra and RaH = 2 í 107 and 5 í 108, respectively) which include effects (2) and (3) are produced with and without the effect of the mineral phase transitions. The first calculation (without the phase transition) successfully produces plate-like behavior with a long wavelength structure and surface heat flow similar to Earth's value. While the observed convective flow pattern in the lower mantle is broader compared to isoviscous models, it basically shows the behavior of whole mantle convection, and does not exhibit any slab flattening at the viscosity increase at 660 km depth. The second calculation which includes the phase
NASA Astrophysics Data System (ADS)
Shemelya, Corey M.; Rivera, Armando; Perez, Angel Torrado; Rocha, Carmen; Liang, Min; Yu, Xiaoju; Kief, Craig; Alexander, David; Stegeman, James; Xin, Hao; Wicker, Ryan B.; MacDonald, Eric; Roberson, David A.
2015-08-01
Material-extrusion three-dimensional (3D) printing has recently attracted much interest because of its process flexibility, rapid response to design alterations, and ability to create structures "on-the-go". For this reason, 3D printing has possible applications in rapid creation of space-based devices, for example cube satellites (CubeSat). This work focused on fabrication and characterization of tungsten-doped polycarbonate polymer matrix composites specifically designed for x-ray radiation-shielding applications. The polycarbonate-tungsten polymer composite obtained intentionally utilizes low loading levels to provide x-ray shielding while limiting effects on other properties of the material, for example weight, electromagnetic functionality, and mechanical strength. The fabrication process, from tungsten functionalization to filament extrusion and material characterization, is described, including printability, determination of x-ray attenuation, tensile strength, impact resistance, and gigahertz permittivity, and failure analysis. The proposed materials are uniquely advantageous when implemented in 3D printed structures, because even a small volume fraction of tungsten has been shown to substantially alter the properties of the resulting composite.
Schmitt, Boris; Li, Tieyan; Kutty, Shelby; Khasheei, Alireza; Schmitt, Katharina R L; Anderson, Robert H; Lunkenheimer, Paul P; Berger, Felix; Kühne, Titus; Peters, Björn
2015-07-01
Beta-blockers contribute to treatment of heart failure. Their mechanism of action, however, is incompletely understood. Gradients in beta-blocker sensitivity of helically aligned cardiomyocytes compared with counteracting transversely intruding cardiomyocytes seem crucial. We hypothesize that selective blockade of transversely intruding cardiomyocytes by low-dose beta-blockade unloads ventricular performance. Cardiac magnetic resonance imaging (MRI) 3D tagging delivers parameters of myocardial performance. We studied 13 healthy volunteers by MRI 3D tagging during escalated intravenous administration of esmolol. The circumferential, longitudinal, and radial myocardial shortening was determined for each dose. The curves were analyzed for peak value, time-to-peak, upslope, and area-under-the-curve. At low doses, from 5 to 25 μg·kg(-1)·min(-1), peak contraction increased while time-to-peak decreased yielding a steeper upslope. Combining the values revealed a left shift of the curves at low doses compared with baseline without esmolol. At doses of 50 to 150 μg·kg(-1)·min(-1), a right shift with flattening occurred. In healthy volunteers we found more pronounced myocardial shortening at low compared with clinical dosage of beta-blockers. In patients with ventricular hypertrophy and higher prevalence of transversely intruding cardiomyocytes selective low-dose beta-blockade could be even more effective. MRI 3D tagging could help to determine optimal individual beta-blocker dosing avoiding undesirable side effects. PMID:25888512
Ginex, Tiziana; Muñoz-Muriedas, Jordi; Herrero, Enric; Gibert, Enric; Cozzini, Pietro; Luque, F J
2016-05-15
Since the development of structure-activity relationships about 50 years ago, 3D-QSAR methods belong to the most refined ligand-based in silico techniques for prediction of biological data using physicochemical molecular fields. In this scenario, this study reports the development and validation of quantum mechanical (QM)-based hydrophobic descriptors derived from the parametrized MST continuum solvation model to be used in 3D-QSAR studies within the framework of the Hydrophobic Pharmacophore (HyPhar) method. To this end, five sets of compounds reported in the literature (dopamine D2/D4 antagonists, antifungal 2-aryl-4-chromanones, and inhibitors of GSK-3, cruzain and thermolysin) have been revisited. The results derived from the QM/MST-based hydrophobic descriptors have been compared with previous CoMFA and CoMSIA studies, and examined in light of the available X-ray crystallographic structures of the targets. The analysis reveals that the combination of electrostatic and nonelectrostatic components of the octanol/water partition coefficient yields pharmacophoric models fully comparable with the predictive potential of standard 3D-QSAR techniques. Moreover, the graphical representation of the hydrophobic maps provides a direct linkage with the pattern of interactions found in crystallographic structures. Overall, the introduction of the QM/MST-based descriptors, which could be easily adapted to other continuum solvation formalisms, paves the way to novel computational strategies for disclosing structure-activity relationships in drug design. © 2016 Wiley Periodicals, Inc. PMID:26813046
Peters, Andreas S; Brunner, Georg; Krieg, Thomas; Eckes, Beate
2015-03-01
Many tissues are constantly exposed to mechanical stress, e.g. shear stress in vascular endothelium, compression forces in cartilage or tensile strain in the skin. Dermal fibroblasts can differentiate into contractile myofibroblasts in a process requiring the presence of TGFβ1 in addition to mechanical load. We aimed at investigating the effect of cyclic mechanical strain on dermal fibroblasts grown in a three-dimensional environment. Therefore, murine dermal fibroblasts were cultured in collagen gels and subjected to cyclic tension at a frequency of 0.1 Hz (6 cycles/min) with a maximal increase in surface area of 10 % for 24 h. This treatment resulted in a significant increase in active TGFβ1 levels, leaving the amount of total TGFβ1 unaffected. TGFβ1 activation led to pSMAD2-mediated transcriptional elevation of downstream mediators, such as CTGF, and an auto-induction of TGFβ1, respectively. PMID:25348252
NASA Astrophysics Data System (ADS)
Wilson, M.; Wheeler, W.
2002-12-01
Current understanding of the processes and pathways by which magma travels from its mantle source, through the crust to the Earth's surface is limited by the lack of continuously exposed sections through "fossil" magmatic systems. We report results from a 50 x 30 km 3-D seismic reflection survey of part of the Voring rifted continental margin of Norway which provide the first detailed images of an entire crustal magmatic plumbing system, from a Moho-level magma chamber, through complexes of sills and dykes in the mid to upper crust, to lavas and vent fields extruded at the early Tertiary paleosurface. The Voring margin of Norway formed during a period of Late Cretaceous to early Tertiary (Eocene) continental break-up when Greenland rifted away from Eurasia, resulting in the opening the NE Atlantic Ocean. Rifting was accompanied by widespread magmatic activity, inferred to be related to the impingement of the Iceland mantle plume on the base of the continental lithosphere. Regionally, magma migration occurred in at least two pulses: 62-59 Ma (main initial phase) and 57-54 Ma (continental break-up phase). Wide-angle seismic experiments indicate the presence of a laccolith-like "high-velocity body" (HVB) in the lower crust beneath most of the outer Voring Basin with P-wave velocities (Vp 7.1-7.4 km/s) characteristic of basaltic igneous rocks, overlying typical mantle rocks with Vp of over 8 km/s. The HVB locally reaches 8 km thickness and at break-up (54 Ma) measured 300 km x 500 km - corresponding to a volume of 450,000 cubic km of basaltic magma. It is interpreted as a magmatic underplate formed over a period of several million years as rising basaltic magmas ponded at the Moho at their level of neutral buoyancy. A laterally extensive sill complex (1000 m thick) occurs at the interface between thinned crystalline basement and the overlying Mesozoic sedimentary sequence. This is interpreted as one of the main intra-crustal magma storage reservoirs and is the most
Meyer-Hermann, Michael
2008-01-01
Mathematical methods in Biology are of increasing relevance for understanding the control and the dynamics of biological systems with medical relevance. In particular, agent-based methods turn more and more important because of fast increasing computational power which makes even large systems accessible. An overview of different mathematical methods used in Theoretical Biology is provided and a novel agent-based method for cell mechanics based on Delaunay-triangulations and Voronoi-tessellations is explained in more detail: The Delaunay-Object-Dynamics method. It is claimed that the model combines physically realistic cell mechanics with a reasonable computational load. The power of the approach is illustrated with two examples, avascular tumor growth and genesis of lymphoid tissue in a cell-flow equilibrium. PMID:18023735
Effects of SiO2 and ZnO doping on mechanical and biological properties of 3D printed TCP scaffolds
Fielding, Gary A.; Bandyopadhyay, Amit; Bose, Susmita
2011-01-01
Objectives To evaluate the effects of SiO2 (0.5 wt %) and ZnO (0.25 wt %) dopants on the mechanical and biological properties of tricalcium phosphate (TCP) scaffolds with three dimensionally (3D) interconnected pores. Methods Scaffolds were created with a commercial 3D printer. Post sintering phase analysis was determined by x-ray diffraction. Surface morphology of the scaffolds was examined by field emission electron microscopy. Mechanical strength was evaluated with a screw driven universal testing machine. MTT assay was used for cellular proliferation characteristics and cellular morphology was examined by field emission electron microscopy. Results Addition of dopants into TCP increased the average density of pure TCP from 90.8 ± 0.8% to 94.1 ± 1.6% and retarded the β to α phase transformation at high sintering temperatures, which resulted in up to 2.5 fold increase in compressive strength. In vitro cell-materials interaction studies, carried out using hFOB cells, confirmed that the addition of SiO2 and ZnO to the scaffolds facilitates faster cell proliferation when compared to pure TCP scaffolds. Significance Addition of SiO2 and ZnO dopants to the TCP scaffolds showed increased mechanical strength as well as increased cellular proliferation. PMID:22047943
Kim, Areum; Zhou, Chengxin; Lakshman, Neema; Petroll, W. Matthew
2012-01-01
Corneal keratocyte migration can impact both corneal clarity and refractive outcome following injury or refractive surgery. In this study, we investigated how culture conditions, ECM properties, and Rho kinase activity regulate the mechanics of keratocyte migration, using a nested collagen matrix model. Time-lapse imaging demonstrated that both serum and PDGF stimulate keratocyte migration into the outer matrix. Although the velocity of cell migration was similar, cells in serum were bipolar and induced significant matrix deformation during migration, whereas PDGF induced extension of branching dendritic processes with smaller, more localized force generation. These differences in cell-induced matrix reorganization were verified with a global matrix contraction assay and confocal reflection imaging, using both bovine and rat tail collagen. When constructs were detached from the substrate to lower the effective stiffness, migration was significantly reduced in serum; but was unchanged in PDGF. These differences in migration mechanics were mediated, in part, by Rho kinase. Overall, corneal keratocytes can effectively migrate through collagen matrices using varying degrees of cellular force generation. Low-contractility migration may facilitate keratocyte repopulation of the stroma following surgery or injury, without altering the structural and mechanical properties that are critical to maintaining corneal transparency. PMID:22233682
Harischandra, Nalin; Cabelguen, Jean-Marie; Ekeberg, Örjan
2010-01-01
Computer simulation has been used to investigate several aspects of locomotion in salamanders. Here we introduce a three-dimensional forward dynamics mechanical model of a salamander, with physically realistic weight and size parameters. Movements of the four limbs and of the trunk and tail are generated by sets of linearly modeled skeletal muscles. In this study, activation of these muscles were driven by prescribed neural output patterns. The model was successfully used to mimic locomotion on level ground and in water. We compare the walking gait where a wave of activity in the axial muscles travels between the girdles, with the trotting gait in simulations using the musculo-mechanical model. In a separate experiment, the model is used to compare different strategies for turning while stepping; either by bending the trunk or by using side-stepping in the front legs. We found that for turning, the use of side-stepping alone or in combination with trunk bending, was more effective than the use of trunk bending alone. We conclude that the musculo-mechanical model described here together with a proper neural controller is useful for neuro-physiological experiments in silico. PMID:21206530
3d-3d correspondence revisited
NASA Astrophysics Data System (ADS)
Chung, Hee-Joong; Dimofte, Tudor; Gukov, Sergei; Sułkowski, Piotr
2016-04-01
In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d {N}=2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. We also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.
NASA Astrophysics Data System (ADS)
Impens, David
The study is designed to provide a robust understanding of the mechanical characteristic of a 3D printed part for selected post processing conditions. The `green' printed parts are generally very brittle and porous, therefore, infiltrates are introduced to alter the mechanical characteristics, which will introduce new opportunities for this technology. Exploratory testing is performed to shape the choices for post processing with the infiltrates. Specimen geometry, specific for tensile, compression and flexural testing were rendered in CAD software and printed on the Z-printer 450 (Zp150 powder / Zb59 binder) with three different build orientations (horizontal/ angled /vertical). Results show that infiltrates can significantly improve the mechanical characteristics and material-infiltrate performance varies per build orientation. It is now understood that this material does not react similar to other materials and cannot be easily predicted. Additional physical testing should be performed and this complete test set should be conducted for new infiltrates.
NASA Astrophysics Data System (ADS)
Kish, Mollie K.
The Marcellus shale is one of the most developed unconventional shale gas reservoirs in the world with a calculated 84.5 trillion cubic feet in proved natural gas reserves in Pennsylvania and West Virginia. To better exploit this resource all geological aspects of the Marcellus shale are being studied. In this study, mechanical stratigraphy and interpreted seismic fracture zones within the Marcellus shale are examined. These geologic criteria are assessed for potential to impact gas production by analyzing the gas production of fourteen horizontal Marcellus shale wells within and around the study area. Mechanical stratigraphy is evaluated from the top of the Tully limestone to the base of the Onondaga limestone to assess vertical heterogeneity of brittleness within and around the Marcellus shale. Brittleness estimations are derived from petrophysical well logs including bulk density, shear velocity and compressional velocity. Mineralogy assessment is completed using Schlumberger's SpectroLithRTM gamma ray spectroscopy mineralogy logs. Elastic moduli including Young's modulus, Poisson's ratio and Lame's parameters are assessed in terms of brittleness and total organic content to develop constraints for areas of high brittleness and high total organic content. The constraints developed at the study well are compared to studies at four other unconventional shale gas sites. The results suggest that mechanical properties are variable and site dependent. Conclusive ranges for Poisson's ratio and Young's modulus constraints for areas of high brittleness and high total organic cannot be developed for an entire shale play but may be useful in local analyses. Seismic discontinuities were extracted from two three dimensional seismic surveys using a post-stack processing workflow that included Ant-Tracking. They are interpreted to be associated with small faults and fracture zones. The relationship between the number of seismic discontinuities intersecting horizontal wells in
Shuai, Cijun; Peng, Shuping
2014-01-01
A scaffold for bone tissue engineering should have highly interconnected porous structure, appropriate mechanical and biological properties. In this work, we fabricated well-interconnected porous β-tricalcium phosphate (β-TCP) scaffolds via selective laser sintering (SLS). We found that the mechanical and biological properties of the scaffolds were improved by doping of zinc oxide (ZnO). Our data showed that the fracture toughness increased from 1.09 to 1.40 MPam1/2, and the compressive strength increased from 3.01 to 17.89 MPa when the content of ZnO increased from 0 to 2.5 wt%. It is hypothesized that the increase of ZnO would lead to a reduction in grain size and an increase in density of the strut. However, the fracture toughness and compressive strength decreased with further increasing of ZnO content, which may be due to the sharp increase in grain size. The biocompatibility of the scaffolds was investigated by analyzing the adhesion and the morphology of human osteoblast-like MG-63 cells cultured on the surfaces of the scaffolds. The scaffolds exhibited better and better ability to support cell attachment and proliferation when the content of ZnO increased from 0 to 2.5 wt%. Moreover, a bone like apatite layer formed on the surfaces of the scaffolds after incubation in simulated body fluid (SBF), indicating an ability of osteoinduction and osteoconduction. In summary, interconnected porous β-TCP scaffolds doped with ZnO were successfully fabricated and revealed good mechanical and biological properties, which may be used for bone repair and replacement potentially. PMID:24498185
Marcé-Nogué, Jordi; Fortuny, Josep; De Esteban-Trivigno, Soledad; Sánchez, Montserrat; Gil, Lluís; Galobart, Àngel
2015-01-01
For the first time in vertebrate palaeontology, the potential of joining Finite Element Analysis (FEA) and Parametrical Analysis (PA) is used to shed new light on two different cranial parameters from the orbits to evaluate their biomechanical role and evolutionary patterns. The early tetrapod group of Stereospondyls, one of the largest groups of Temnospondyls is used as a case study because its orbits position and size vary hugely within the members of this group. An adult skull of Edingerella madagascariensis was analysed using two different cases of boundary and loading conditions in order to quantify stress and deformation response under a bilateral bite and during skull raising. Firstly, the variation of the original geometry of its orbits was introduced in the models producing new FEA results, allowing the exploration of the ecomorphology, feeding strategy and evolutionary patterns of these top predators. Secondly, the quantitative results were analysed in order to check if the orbit size and position were correlated with different stress patterns. These results revealed that in most of the cases the stress distribution is not affected by changes in the size and position of the orbit. This finding supports the high mechanical plasticity of this group during the Triassic period. The absence of mechanical constraints regarding the orbit probably promoted the ecomorphological diversity acknowledged for this group, as well as its ecological niche differentiation in the terrestrial Triassic ecosystems in clades as lydekkerinids, trematosaurs, capitosaurs or metoposaurs. PMID:26107295
Marcé-Nogué, Jordi; Fortuny, Josep; De Esteban-Trivigno, Soledad; Sánchez, Montserrat; Gil, Lluís; Galobart, Àngel
2015-01-01
For the first time in vertebrate palaeontology, the potential of joining Finite Element Analysis (FEA) and Parametrical Analysis (PA) is used to shed new light on two different cranial parameters from the orbits to evaluate their biomechanical role and evolutionary patterns. The early tetrapod group of Stereospondyls, one of the largest groups of Temnospondyls is used as a case study because its orbits position and size vary hugely within the members of this group. An adult skull of Edingerella madagascariensis was analysed using two different cases of boundary and loading conditions in order to quantify stress and deformation response under a bilateral bite and during skull raising. Firstly, the variation of the original geometry of its orbits was introduced in the models producing new FEA results, allowing the exploration of the ecomorphology, feeding strategy and evolutionary patterns of these top predators. Secondly, the quantitative results were analysed in order to check if the orbit size and position were correlated with different stress patterns. These results revealed that in most of the cases the stress distribution is not affected by changes in the size and position of the orbit. This finding supports the high mechanical plasticity of this group during the Triassic period. The absence of mechanical constraints regarding the orbit probably promoted the ecomorphological diversity acknowledged for this group, as well as its ecological niche differentiation in the terrestrial Triassic ecosystems in clades as lydekkerinids, trematosaurs, capitosaurs or metoposaurs. PMID:26107295
Simulation of semi-explicit mechanisms of SOA formation from glyoxal in aerosol in a 3-D model
NASA Astrophysics Data System (ADS)
Knote, C.; Hodzic, A.; Jimenez, J. L.; Volkamer, R.; Orlando, J. J.; Baidar, S.; Brioude, J.; Fast, J.; Gentner, D. R.; Goldstein, A. H.; Hayes, P. L.; Knighton, W. B.; Oetjen, H.; Setyan, A.; Stark, H.; Thalman, R.; Tyndall, G.; Washenfelder, R.; Waxman, E.; Zhang, Q.
2014-06-01
New pathways to form secondary organic aerosol (SOA) have been postulated recently. Glyoxal, the smallest dicarbonyl, is one of the proposed precursors. It has both anthropogenic and biogenic sources, and readily partitions into the aqueous phase of cloud droplets and deliquesced particles where it undergoes both reversible and irreversible chemistry. In this work we extend the regional scale chemistry transport model WRF-Chem to include detailed gas-phase chemistry of glyoxal formation as well as a state-of-the-science module describing its partitioning and reactions in the aerosol aqueous-phase. A comparison of several proposed mechanisms is performed to quantify the relative importance of different formation pathways and their regional variability. The CARES/CalNex campaigns over California in summer 2010 are used as case studies to evaluate the model against observations. A month-long simulation over the continental United States (US) enables us to extend our results to the continental scale. In all simulations over California, the Los Angeles (LA) basin was found to be the hot spot for SOA formation from glyoxal, which contributes between 1% and 15% of the model SOA depending on the mechanism used. Our results indicate that a mechanism based only on a reactive (surface limited) uptake coefficient leads to higher SOA yields from glyoxal compared to a more detailed description that considers aerosol phase state and chemical composition. In the more detailed simulations, surface uptake is found to give the highest SOA mass yields compared to a volume process and reversible formation. We find that the yields of the latter are limited by the availability of glyoxal in aerosol water, which is in turn controlled by an increase in the Henry's law constant depending on salt concentrations ("salting-in"). A time dependence in this increase prevents substantial partitioning of glyoxal into aerosol water at high salt concentrations. If this limitation is removed, volume
NASA Astrophysics Data System (ADS)
Strijker, Geertje; Beekman, Fred; Bertotti, Giovanni; Luthi, Stefan M.
2013-05-01
Stress distributions and deformation patterns in a medium with a pre-existing fracture set are analyzed as a function of the remote compressive stress orientation (σH) using finite element models with increasingly complex fracture configurations. Slip along the fractures causes deformation localization at the tips as wing cracks or shear zones. The deformation intensity is proportional to the amount of slip, attaining a peak value for α = 45° (α: angle between the fracture strike and σH) and slip is linearly proportional with fracture length. Wing cracks develop for high deformation intensities for 30° < α < 60°, whereas primary plastic shear zones develop for low deformation intensities. Additionally, two types of secondary shear zones develop for α < 30° and α > 60°, with constant angles of 135° and - 60° with σH, respectively. Mechanical interaction between fractures in a fracture zone, quantified as change in slip compared to an isolated fracture, decreases with increasing fracture separation. Fracture underlap elongates the fracture length and therefore increases the amount of slip, while fracture overlap exhibits the opposite effect. Fracture slip decreases with an increasing amount of directly adjacent fractures. Mechanical interaction becomes negligible for fracture configurations with spacing-to-length and spacing-to-overlap ratios exceeding 0.5 and that in this case fractures are decoupled. Independent of the pre-existing fracture configuration, the development of a secondary systematic fracture set driven by a remote stress rotation is dominated by σH; development of wing cracks or shear zones is restricted to the fracture tips. Blocks with tapered geometries are present in models with a variable fracture strike, where the maximum principal stress (σ1, applying the geological convention that compressive stresses are positive) trajectories consistently deviate from σH; the presence of two systematic σ1 trajectory orientations suggests
Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control.
Bizarro, Jonathan; Charron, Christophe; Boulon, Séverine; Westman, Belinda; Pradet-Balade, Bérengère; Vandermoere, Franck; Chagot, Marie-Eve; Hallais, Marie; Ahmad, Yasmeen; Leonhardt, Heinrich; Lamond, Angus; Manival, Xavier; Branlant, Christiane; Charpentier, Bruno; Verheggen, Céline; Bertrand, Edouard
2014-11-24
In vitro, assembly of box C/D small nucleolar ribonucleoproteins (snoRNPs) involves the sequential recruitment of core proteins to snoRNAs. In vivo, however, assembly factors are required (NUFIP, BCD1, and the HSP90-R2TP complex), and it is unknown whether a similar sequential scheme applies. In this paper, we describe systematic quantitative stable isotope labeling by amino acids in cell culture proteomic experiments and the crystal structure of the core protein Snu13p/15.5K bound to a fragment of the assembly factor Rsa1p/NUFIP. This revealed several unexpected features: (a) the existence of a protein-only pre-snoRNP complex containing five assembly factors and two core proteins, 15.5K and Nop58; (b) the characterization of ZNHIT3, which is present in the protein-only complex but gets released upon binding to C/D snoRNAs; (c) the dynamics of the R2TP complex, which appears to load/unload RuvBL AAA(+) adenosine triphosphatase from pre-snoRNPs; and (d) a potential mechanism for preventing premature activation of snoRNP catalytic activity. These data provide a framework for understanding the assembly of box C/D snoRNPs. PMID:25404746
NASA Astrophysics Data System (ADS)
Meulien Ohlmann, Odile
2013-02-01
Today the industry offers a chain of 3D products. Learning to "read" and to "create in 3D" becomes an issue of education of primary importance. 25 years professional experience in France, the United States and Germany, Odile Meulien set up a personal method of initiation to 3D creation that entails the spatial/temporal experience of the holographic visual. She will present some different tools and techniques used for this learning, their advantages and disadvantages, programs and issues of educational policies, constraints and expectations related to the development of new techniques for 3D imaging. Although the creation of display holograms is very much reduced compared to the creation of the 90ies, the holographic concept is spreading in all scientific, social, and artistic activities of our present time. She will also raise many questions: What means 3D? Is it communication? Is it perception? How the seeing and none seeing is interferes? What else has to be taken in consideration to communicate in 3D? How to handle the non visible relations of moving objects with subjects? Does this transform our model of exchange with others? What kind of interaction this has with our everyday life? Then come more practical questions: How to learn creating 3D visualization, to learn 3D grammar, 3D language, 3D thinking? What for? At what level? In which matter? for whom?
NASA Astrophysics Data System (ADS)
Weicht, Derek
The Marcellus Shale is a Devonian age black shale formed during the Acadian Orogeny along the eastern margin of North America. The Middle Devonian Marcellus Shale is an unconventional shale-gas reservoir that has been a major target of seismic exploration and gas extraction using hydraulic fracturing and horizontal drilling. This study focuses on analyses of seismic response, mechanical, and petrophysical properties of the Marcellus Shale and surrounding strata in Taylor County, West Virginia. Spectral blueing was performed on the post stack migration seismic volume to enhance the resolution. The resolution of the volume was increased from 61 feet to 47 feet, which improved the detail observed in the seismic response and provided additional insights in the interpretation of the Marcellus and bounding intervals. The isochore map created from the modified Marcellus picks shows greater variability in the thickness of the Marcellus, with an overall trend of thickening to the east. Within the thicker part of the Marcellus, a second negative reflection event appeared that was not obvious in the post stack migration. This event was interpreted to be part of the Lower Marcellus Shale. Lambda-rho and Mu-rho parameters were calculated using compressional and shear wave vibrations and density obtained from the well logs. When combined with the Young's modulus and Poisson's ratio, these cross-plots are indicative of favorable brittle and total organic carbon (TOC) rich zones that highlight potential drilling targets in the Marcellus. TOC was estimated using the Schmoker and Passey methods, and provide very similar estimates within the Marcellus Shale. Specifically note that the Middle and Lower Marcellus are generally the more TOC rich and productive Marcellus zones.
Parallel computation using boundary elements in solid mechanics
NASA Technical Reports Server (NTRS)
Chien, L. S.; Sun, C. T.
1990-01-01
The inherent parallelism of the boundary element method is shown. The boundary element is formulated by assuming the linear variation of displacements and tractions within a line element. Moreover, MACSYMA symbolic program is employed to obtain the analytical results for influence coefficients. Three computational components are parallelized in this method to show the speedup and efficiency in computation. The global coefficient matrix is first formed concurrently. Then, the parallel Gaussian elimination solution scheme is applied to solve the resulting system of equations. Finally, and more importantly, the domain solutions of a given boundary value problem are calculated simultaneously. The linear speedups and high efficiencies are shown for solving a demonstrated problem on Sequent Symmetry S81 parallel computing system.
NASA Technical Reports Server (NTRS)
Lipatov, A. S.; Farrell, W. M.; Cooper, J. F.; Sittler, E. C., Jr.; Hartle, R. E.
2015-01-01
The interactions between the solar wind and Moon-sized objects are determined by a set of the solar wind parameters and plasma environment of the space objects. The orientation of upstream magnetic field is one of the key factors which determines the formation and structure of bow shock wave/Mach cone or Alfven wing near the obstacle. The study of effects of the direction of the upstream magnetic field on lunar-like plasma environment is the main subject of our investigation in this paper. Photoionization, electron-impact ionization and charge exchange are included in our hybrid model. The computational model includes the self-consistent dynamics of the light (hydrogen (+), helium (+)) and heavy (sodium (+)) pickup ions. The lunar interior is considered as a weakly conducting body. Our previous 2013 lunar work, as reported in this journal, found formation of a triple structure of the Mach cone near the Moon in the case of perpendicular upstream magnetic field. Further advances in modeling now reveal the presence of strong wave activity in the upstream solar wind and plasma wake in the cases of quasiparallel and parallel upstream magnetic fields. However, little wave activity is found for the opposite case with a perpendicular upstream magnetic field. The modeling does not show a formation of the Mach cone in the case of theta(Sub B,U) approximately equal to 0 degrees.
Type synthesis for 4-DOF parallel press mechanism using GF set theory
NASA Astrophysics Data System (ADS)
He, Jun; Gao, Feng; Meng, Xiangdun; Guo, Weizhong
2015-07-01
Parallel mechanisms is used in the large capacity servo press to avoid the over-constraint of the traditional redundant actuation. Currently, the researches mainly focus on the performance analysis for some specific parallel press mechanisms. However, the type synthesis and evaluation of parallel press mechanisms is seldom studied, especially for the four degrees of freedom(DOF) press mechanisms. The type synthesis of 4-DOF parallel press mechanisms is carried out based on the generalized function(GF) set theory. Five design criteria of 4-DOF parallel press mechanisms are firstly proposed. The general procedure of type synthesis of parallel press mechanisms is obtained, which includes number synthesis, symmetrical synthesis of constraint GF sets, decomposition of motion GF sets and design of limbs. Nine combinations of constraint GF sets of 4-DOF parallel press mechanisms, ten combinations of GF sets of active limbs, and eleven combinations of GF sets of passive limbs are synthesized. Thirty-eight kinds of press mechanisms are presented and then different structures of kinematic limbs are designed. Finally, the geometrical constraint complexity( GCC), kinematic pair complexity( KPC), and type complexity( TC) are proposed to evaluate the press types and the optimal press type is achieved. The general methodologies of type synthesis and evaluation for parallel press mechanism are suggested.
YouDash3D: exploring stereoscopic 3D gaming for 3D movie theaters
NASA Astrophysics Data System (ADS)
Schild, Jonas; Seele, Sven; Masuch, Maic
2012-03-01
Along with the success of the digitally revived stereoscopic cinema, events beyond 3D movies become attractive for movie theater operators, i.e. interactive 3D games. In this paper, we present a case that explores possible challenges and solutions for interactive 3D games to be played by a movie theater audience. We analyze the setting and showcase current issues related to lighting and interaction. Our second focus is to provide gameplay mechanics that make special use of stereoscopy, especially depth-based game design. Based on these results, we present YouDash3D, a game prototype that explores public stereoscopic gameplay in a reduced kiosk setup. It features live 3D HD video stream of a professional stereo camera rig rendered in a real-time game scene. We use the effect to place the stereoscopic effigies of players into the digital game. The game showcases how stereoscopic vision can provide for a novel depth-based game mechanic. Projected trigger zones and distributed clusters of the audience video allow for easy adaptation to larger audiences and 3D movie theater gaming.
Volumetric 3D Display System with Static Screen
NASA Technical Reports Server (NTRS)
Geng, Jason
2011-01-01
approaches, so there is no image jitter, and has an inherent parallel mechanism for 3D voxel addressing. High spatial resolution is possible with a full color display being easy to implement. The system is low-cost and low-maintenance.
Li, Jiao Jiao; Tian, Yue Li; Zhai, Hong Lin; Lv, Min; Zhang, Xiao Yun
2016-08-01
DYRK1A is characterized by the early development and regulation of neuronal proliferation, and its over expression gives rise to neurological abnormalities. As the promising DYRK1A inhibitors, the binding mechanism between DYRK1A and pyrido[2,3-d]pyrimidines derivatives at molecular level are still veiled. In this article, it was achieved to get the structural insights into pyrido[2,3-d]pyrimidines derivatives as DYRK1A inhibitors by means of comprehensive computational approaches involving molecular docking, molecular dynamics simulation, free energy calculation, and energy decomposition analysis. The calculated energy values were highly consistent with the experimental activities. Based on the individual energy terms analysis, the van der Waals interaction was the major leading force in the DYRK1A-ligand interaction. Lys188 was the important residue that formed the hydrogen bond, which improved the inhibitory activity. Furthermore, four novel inhibitors with higher predicted activity were designed based on the obtained findings and confirmed by molecular simulations. Our study is expected to provide significant drug design strategy for the development of more promising DYRK1A inhibitors. Proteins 2016; 84:1108-1123. © 2016 Wiley Periodicals, Inc. PMID:27119584
ERIC Educational Resources Information Center
Hastings, S. K.
2002-01-01
Discusses 3 D imaging as it relates to digital representations in virtual library collections. Highlights include X-ray computed tomography (X-ray CT); the National Science Foundation (NSF) Digital Library Initiatives; output peripherals; image retrieval systems, including metadata; and applications of 3 D imaging for libraries and museums. (LRW)
PMESH: A parallel mesh generator
Hardin, D.D.
1994-10-21
The Parallel Mesh Generation (PMESH) Project is a joint LDRD effort by A Division and Engineering to develop a unique mesh generation system that can construct large calculational meshes (of up to 10{sup 9} elements) on massively parallel computers. Such a capability will remove a critical roadblock to unleashing the power of massively parallel processors (MPPs) for physical analysis. PMESH will support a variety of LLNL 3-D physics codes in the areas of electromagnetics, structural mechanics, thermal analysis, and hydrodynamics.
Chulya, A.; Gyekenyesi, J.Z.; Gyekenyesi, J.P.
1992-08-01
Nicalon silicon carbide 3D yarn with silicon carbide matrix composites made through a chemical vapor infiltration (CVI) process were investigated under tensile and flexural loading at 23, 1200 and 1550 C in air. The effectiveness of a chemical vapor deposition (CVD) SiC surface coating was also evaluated in severe oxidizing environment. Acoustic emission sensors and in situ optical microscopy were used at room temperature to monitor the failure mechanisms. It is shown that the level of tensile stress at which nonlinear behavior begins is not drastically reduced at 1200 and 1550 C when composites were protected by a SiC surface coating. Extensive fiber pull-out was observed only in the 1550 C specimen. Similar behaviors were also found in flexural specimens. 14 refs.
Parvizi, Mojtaba; Bolhuis-Versteeg, Lydia A M; Poot, André A; Harmsen, Martin C
2016-07-01
Occluding artery disease causes a high demand for bioartificial replacement vessels. We investigated the combined use of biodegradable and creep-free poly (1,3-trimethylene carbonate) (PTMC) with smooth muscle cells (SMC) derived by biochemical or mechanical stimulation of adipose tissue-derived stromal cells (ASC) to engineer bioartificial arteries. Biochemical induction of cultured ASC to SMC was done with TGF-β1 for 7d. Phenotype and function were assessed by qRT-PCR, immunodetection and collagen contraction assays. The influence of mechanical stimulation on non-differentiated and pre-differentiated ASC, loaded in porous tubular PTMC scaffolds, was assessed after culturing under pulsatile flow for 14d. Assays included qRT-PCR, production of extracellular matrix and scanning electron microscopy. ASC adhesion and TGF-β1-driven differentiation to contractile SMC on PTMC did not differ from tissue culture polystyrene controls. Mesenchymal and SMC markers were increased compared to controls. Interestingly, pre-differentiated ASC had only marginal higher contractility than controls. Moreover, in 3D PTMC scaffolds, mechanical stimulation yielded well-aligned ASC-derived SMC which deposited ECM. Under the same conditions, pre-differentiated ASC-derived SMC maintained their SMC phenotype. Our results show that mechanical stimulation can replace TGF-β1 pre-stimulation to generate SMC from ASC and that pre-differentiated ASC keep their SMC phenotype with increased expression of SMC markers. PMID:26989865
NASA Astrophysics Data System (ADS)
Li, Shouzhong; Yu, Jingjun; Zong, Guanghua
2012-11-01
In synthesis of flexure mechanism, parallel arrangement is paid more attention due to its advantages, such as compact structure and higher stiffness. Researchers have derived many parallel flexure mechanisms, but seldom discuss which kind of flexure mechanism can be realized via fully parallel arrangement. The realizable conditions proposed in current work are complicated to engineering applications. To solve two problems on how to judge whether a flexure mechanism can be realized via fully parallel arrangement and how to realize those flexure mechanisms which cannot be realized via fully parallel arrangement, the algebraic condition is derived to judge whether a freedom space is parallel realizable after introducing the definition of parallel realizable and some propositions, and the condition is there exist 6- n independent line constraints in constraint space reciprocal to dimensional freedom space. Then the realizable constraint spaces reciprocal to freedom spaces with 1-3 dimensions are provided. As a result, not all freedom spaces are parallel realizable. For freedom spaces that are not parallel realizable, the criterion of decomposing DOF is proposed to achieve all motion patterns via parallel or hybrid arrangement, that is a high dimensional freedom space can be realized via combining several low dimensional freedom spaces which are parallel realizable. Specific decomposing strategies for 4 and 5 DOF are provided and a complete flowchart is presented to guide designing flexure mechanisms, particularly those which are not parallel realizable. As case studies, synthesis processes of two helical and 3T1R motions are provided to illustrate the proposed approach. The proposed method provides a feasible approach to realize all motion patterns.
NASA Astrophysics Data System (ADS)
Dima, M.; Farisato, G.; Bergomi, M.; Viotto, V.; Magrin, D.; Greggio, D.; Farinato, J.; Marafatto, L.; Ragazzoni, R.; Piazza, D.
2014-08-01
In the last few years 3D printing is getting more and more popular and used in many fields going from manufacturing to industrial design, architecture, medical support and aerospace. 3D printing is an evolution of bi-dimensional printing, which allows to obtain a solid object from a 3D model, realized with a 3D modelling software. The final product is obtained using an additive process, in which successive layers of material are laid down one over the other. A 3D printer allows to realize, in a simple way, very complex shapes, which would be quite difficult to be produced with dedicated conventional facilities. Thanks to the fact that the 3D printing is obtained superposing one layer to the others, it doesn't need any particular work flow and it is sufficient to simply draw the model and send it to print. Many different kinds of 3D printers exist based on the technology and material used for layer deposition. A common material used by the toner is ABS plastics, which is a light and rigid thermoplastic polymer, whose peculiar mechanical properties make it diffusely used in several fields, like pipes production and cars interiors manufacturing. I used this technology to create a 1:1 scale model of the telescope which is the hardware core of the space small mission CHEOPS (CHaracterising ExOPlanets Satellite) by ESA, which aims to characterize EXOplanets via transits observations. The telescope has a Ritchey-Chrétien configuration with a 30cm aperture and the launch is foreseen in 2017. In this paper, I present the different phases for the realization of such a model, focusing onto pros and cons of this kind of technology. For example, because of the finite printable volume (10×10×12 inches in the x, y and z directions respectively), it has been necessary to split the largest parts of the instrument in smaller components to be then reassembled and post-processed. A further issue is the resolution of the printed material, which is expressed in terms of layers
Opportunities in computational mechanics: Advances in parallel computing
Lesar, R.A.
1999-02-01
In this paper, the authors will discuss recent advances in computing power and the prospects for using these new capabilities for studying plasticity and failure. They will first review the new capabilities made available with parallel computing. They will discuss how these machines perform and how well their architecture might work on materials issues. Finally, they will give some estimates on the size of problems possible using these computers.
Parallel algorithms and archtectures for computational structural mechanics
NASA Technical Reports Server (NTRS)
Patrick, Merrell; Ma, Shing; Mahajan, Umesh
1989-01-01
The determination of the fundamental (lowest) natural vibration frequencies and associated mode shapes is a key step used to uncover and correct potential failures or problem areas in most complex structures. However, the computation time taken by finite element codes to evaluate these natural frequencies is significant, often the most computationally intensive part of structural analysis calculations. There is continuing need to reduce this computation time. This study addresses this need by developing methods for parallel computation.
NASA Astrophysics Data System (ADS)
Greenwood, J.; Rucker, D.; Levitt, M.; Yang, X.; Lagmanson, M.
2007-12-01
High Resolution Resistivity data is currently used by hydroGEOPHYSICS, Inc to detect and characterize the distribution of suspected contaminant plumes beneath leaking tanks and disposal sites within the U.S. Department of Energy Hanford Site, in Eastern Washington State. The success of the characterization effort has led to resistivity data acquisition in extremely large survey areas exceeding 0.6 km2 and containing over 6,000 electrodes. Optimal data processing results are achieved by utilizing 105 data points within a single finite difference or finite element model domain. The large number of measurements and electrodes and high resolution of the modeling domain requires a model mesh of over 106 nodes. Existing commercially available resistivity inversion software could not support the domain size due to software and hardware limitations. hydroGEOPHYSICS, Inc teamed with Advanced Geosciences, Inc to advance the existing EarthImager3D inversion software to allow for parallel-processing and large memory support under a 64 bit operating system. The basis for the selection of EarthImager3D is demonstrated with a series of verification tests and benchmark comparisons using synthetic test models, field scale experiments and 6 months of intensive modeling using an array of multi-processor servers. The results of benchmark testing show equivalence to other industry standard inversion codes that perform the same function on significantly smaller domain models. hydroGEOPHYSICS, Inc included the use of 214 steel-cased monitoring wells as "long electrodes", 6000 surface electrodes and 8 buried point source electrodes. Advanced Geosciences, Inc. implemented a long electrode modeling function to support the Hanford Site well casing data. This utility is unique to commercial resistivity inversion software, and was evaluated through a series of laboratory and field scale tests using engineered subsurface plumes. The Hanford site is an ideal proving ground for these methods due
Au, Anthony K; Huynh, Wilson; Horowitz, Lisa F; Folch, Albert
2016-03-14
The advent of soft lithography allowed for an unprecedented expansion in the field of microfluidics. However, the vast majority of PDMS microfluidic devices are still made with extensive manual labor, are tethered to bulky control systems, and have cumbersome user interfaces, which all render commercialization difficult. On the other hand, 3D printing has begun to embrace the range of sizes and materials that appeal to the developers of microfluidic devices. Prior to fabrication, a design is digitally built as a detailed 3D CAD file. The design can be assembled in modules by remotely collaborating teams, and its mechanical and fluidic behavior can be simulated using finite-element modeling. As structures are created by adding materials without the need for etching or dissolution, processing is environmentally friendly and economically efficient. We predict that in the next few years, 3D printing will replace most PDMS and plastic molding techniques in academia. PMID:26854878
Adeniran, Ismail; MacIver, David H.; Garratt, Clifford J.; Ye, Jianqiao; Hancox, Jules C.; Zhang, Henggui
2015-01-01
Aims Atrial stunning, a loss of atrial mechanical contraction, can occur following a successful cardioversion. It is hypothesized that persistent atrial fibrillation-induced electrical remodeling (AFER) on atrial electrophysiology may be responsible for such impaired atrial mechanics. This simulation study aimed to investigate the effects of AFER on atrial electro-mechanics. Methods and Results A 3D electromechanical model of the human atria was developed to investigate the effects of AFER on atrial electro-mechanics. Simulations were carried out in 3 conditions for 4 states: (i) the control condition, representing the normal tissue (state 1) and the tissue 2–3 months after cardioversion (state 2) when the atrial tissue recovers its electrophysiological properties after completion of reverse electrophysiological remodelling; (ii) AFER-SR condition for AF-remodeled tissue with normal sinus rhythm (SR) (state 3); and (iii) AFER-AF condition for AF-remodeled tissue with re-entrant excitation waves (state 4). Our results indicate that at the cellular level, AFER (states 3 & 4) abbreviated action potentials and reduced the Ca2+ content in the sarcoplasmic reticulum, resulting in a reduced amplitude of the intracellular Ca2+ transient leading to decreased cell active force and cell shortening as compared to the control condition (states 1 & 2). Consequently at the whole organ level, atrial contraction in AFER-SR condition (state 3) was dramatically reduced. In the AFER-AF condition (state 4) atrial contraction was almost abolished. Conclusions This study provides novel insights into understanding atrial electro-mechanics illustrating that AFER impairs atrial contraction due to reduced intracellular Ca2+ transients. PMID:26606047
Crandall, K.R.
1987-08-01
TRACE 3-D is an interactive beam-dynamics program that calculates the envelopes of a bunched beam, including linear space-charge forces, through a user-defined transport system. TRACE 3-D provides an immediate graphics display of the envelopes and the phase-space ellipses and allows nine types of beam-matching options. This report describes the beam-dynamics calculations and gives detailed instruction for using the code. Several examples are described in detail.
Crashworthiness simulations with DYNA3D
Schauer, D.A.; Hoover, C.G.; Kay, G.J.; Lee, A.S.; De Groot, A.J.
1996-04-01
Current progress in parallel algorithm research and applications in vehicle crash simulation is described for the explicit, finite element algorithms in DYNA3D. Problem partitioning methods and parallel algorithms for contact at material interfaces are the two challenging algorithm research problems that are addressed. Two prototype parallel contact algorithms have been developed for treating the cases of local and arbitrary contact. Demonstration problems for local contact are crashworthiness simulations with 222 locally defined contact surfaces and a vehicle/barrier collision modeled with arbitrary contact. A simulation of crash tests conducted for a vehicle impacting a U-channel small sign post embedded in soil has been run on both the serial and parallel versions of DYNA3D. A significant reduction in computational time has been observed when running these problems on the parallel version. However, to achieve maximum efficiency, complex problems must be appropriately partitioned, especially when contact dominates the computation.
Valonen, P.K.; Moutos, F.T.; Kusanagi, A.; Moretti, M.; Diekman, B.O.; Welter, J.F.; Caplan, A.I.; Guilak, F.
2009-01-01
Three-dimensionally woven poly(ε-caprolactone)(PCL) scaffolds were combined with adult human mesenchymal stem cells (hMSC) to engineer mechanically functional cartilage constructs in vitro. The specific objectives were to: (i) produce PCL scaffolds with cartilage-like mechanical properties, (ii) demonstrate that hMSCs formed cartilage after 21-days of culture on PCL scaffolds, and (iii) study effects of scaffold structure (loosely vs. tightly woven), culture vessel (static dish vs. oscillating bioreactor), and medium composition (chondrogenic additives with or without serum). Aggregate moduli of 21-day constructs approached normal articular cartilage for tightly woven PCL cultured in bioreactors, were lower for tightly woven PCL cultured statically, and lowest for loosely woven PCL cultured statically (p<0.05). Construct DNA, total collagen, and glyocosaminoglycans (GAG) increased in a manner dependent on time, culture vessel, and medium composition. Chondrogenesis was verified histologically by rounded cells within a hyaline-like matrix that immunostained for collagen type II but not type I. Bioreactors yielded constructs with higher collagen content (p<0.05) and more homogenous matrix than static controls. Chondrogenic additives yielded constructs with higher GAG (p<0.05) and earlier expression of collagen II mRNA if serum was not present in medium. These results show feasibility of functional cartilage tissue engineering from hMSC and 3D woven PCL scaffolds. PMID:20034665
NASA Astrophysics Data System (ADS)
Zhang, Chao; Xu, Xiwu; Chen, Kang
2013-10-01
As new lightweight textile material, 3D five directional and full five directional braided composites (5DBC and F5DBC) have tremendous potential applications in the aerospace industry. Before they are used in primary loading-bearing structures, a rational characterization of their mechanical properties is essential. In this paper, three types of unit-cell models corresponding to the interior, surface and corner regions of 5DBC and F5DBC are proposed. By introducing the reasonable boundary conditions, the effective stiffness properties of these two materials are predicted and compared by the three unit-cells models. The detailed mechanical response characteristic of the three unit-cell models is presented and analyzed in various loading cases. Numerical results show good agreement with experiment data, thus validates the proposed simulation method. Moreover, a parametric study is carried out for analyzing the effects of braiding angle and fiber volume fraction on the elastic properties of 5DBC and F5DBC. The obtained results can help designers to optimize the braided composite structures.
NASA Astrophysics Data System (ADS)
Jian, Xiaoxia; Wu, ChuanSong; Zhang, Guokai; Chen, Ji
2015-11-01
A 3D model is developed to perform numerical investigation on the coupled interaction mechanism of the plasma arc, weld pool and keyhole in plasma arc welding. By considering the traveling of the plasma arc along the welding direction, unified governing equations are solved in the whole domain including the torch, plasma arc, keyhole, weld pool and workpiece, which involves different physical mechanisms in different zones. The local thermodynamic equilibrium-diffusion approximation is used to treat the interface between the plasma arc and weld pool, and the volume-of-fluid method is used to track the evolution of the keyhole wall. The interaction effects between the plasma arc, keyhole and weld pool as well as the heat, mass and pressure transport phenomena in the whole welding domain are quantitatively simulated. It is found that when the torch is moving along the joint line, the axis of the keyhole channel tilts backward, and the envelope of molten metal surrounding the keyhole wall inside the weld pool is unsymmetrical relative to the keyhole channel. The plasma arc welding tests are conducted, and the predicted keyhole dimensions and the fusion zone shape are in agreement with the experimentally measured results.
Tarafder, Solaiman; Dernell, William S; Bandyopadhyay, Amit; Bose, Susmita
2015-04-01
The presence of interconnected macro pores allows guided tissue regeneration in tissue engineering scaffolds. However, highly porous scaffolds suffer from having poor mechanical strength. Previously, we showed that microwave sintering could successfully be used to improve mechanical strength of macro porous tricalcium phosphate (TCP) scaffolds. This study reports the presence of SrO and MgO as dopants in TCP scaffolds improves mechanical and in vivo biological performance. We have used direct three dimensional printing (3DP) technology for scaffold fabrication. These 3DP scaffolds possessed multiscale porosity, that is, 3D interconnected designed macro pores along with intrinsic micro pores. A significant increase in mechanical strength, between 37 and 41%, was achieved due to SrO and MgO doping in TCP as compared with pure TCP. Maximum compressive strengths of 9.38 ± 1.86 MPa and 12.01 ± 1.56 MPa were achieved by conventional and microwave sintering, respectively, for SrO-MgO-doped 3DP scaffolds with 500 μm designed pores. Histomorphological and histomorphometric analysis revealed a significantly higher osteoid, bone and haversian canal formation induced by the presence of SrO and MgO dopants in 3DP TCP as compared with pure TCP scaffolds when tested in rabbit femoral condyle defect model. Increased osteon and thus enhanced network of blood vessel formation, and osteocalcin expression were observed in the doped TCP scaffolds. Our results show that these 3DP SrO-MgO-doped TCP scaffolds have the potential for early wound healing through accelerated osteogenesis and vasculogenesis. PMID:25045131
Similar Genetic Mechanisms Underlie the Parallel Evolution of Floral Phenotypes
Zhang, Wenheng; Kramer, Elena M.; Davis, Charles C.
2012-01-01
The repeated origin of similar phenotypes is invaluable for studying the underlying genetics of adaptive traits; molecular evidence, however, is lacking for most examples of such similarity. The floral morphology of neotropical Malpighiaceae is distinctive and highly conserved, especially with regard to symmetry, and is thought to result from specialization on oil-bee pollinators. We recently demonstrated that CYCLOIDEA2–like genes (CYC2A and CYC2B) are associated with the development of the stereotypical floral zygomorphy that is critical to this plant–pollinator mutualism. Here, we build on this developmental framework to characterize floral symmetry in three clades of Malpighiaceae that have independently lost their oil bee association and experienced parallel shifts in their floral morphology, especially in regard to symmetry. We show that in each case these species exhibit a loss of CYC2B function, and a strikingly similar shift in the expression of CYC2A that is coincident with their shift in floral symmetry. These results indicate that similar floral phenotypes in this large angiosperm clade have evolved via parallel genetic changes from an otherwise highly conserved developmental program. PMID:22558314
[Real time 3D echocardiography].
Bauer, F; Shiota, T; Thomas, J D
2001-07-01
Three-dimensional representation of the heart is an old concern. Usually, 3D reconstruction of the cardiac mass is made by successive acquisition of 2D sections, the spatial localisation and orientation of which require complex guiding systems. More recently, the concept of volumetric acquisition has been introduced. A matricial emitter-receiver probe complex with parallel data processing provides instantaneous of a pyramidal 64 degrees x 64 degrees volume. The image is restituted in real time and is composed of 3 planes (planes B and C) which can be displaced in all spatial directions at any time during acquisition. The flexibility of this system of acquisition allows volume and mass measurement with greater accuracy and reproducibility, limiting inter-observer variability. Free navigation of the planes of investigation allows reconstruction for qualitative and quantitative analysis of valvular heart disease and other pathologies. Although real time 3D echocardiography is ready for clinical usage, some improvements are still necessary to improve its conviviality. Then real time 3D echocardiography could be the essential tool for understanding, diagnosis and management of patients. PMID:11494630
[Real time 3D echocardiography
NASA Technical Reports Server (NTRS)
Bauer, F.; Shiota, T.; Thomas, J. D.
2001-01-01
Three-dimensional representation of the heart is an old concern. Usually, 3D reconstruction of the cardiac mass is made by successive acquisition of 2D sections, the spatial localisation and orientation of which require complex guiding systems. More recently, the concept of volumetric acquisition has been introduced. A matricial emitter-receiver probe complex with parallel data processing provides instantaneous of a pyramidal 64 degrees x 64 degrees volume. The image is restituted in real time and is composed of 3 planes (planes B and C) which can be displaced in all spatial directions at any time during acquisition. The flexibility of this system of acquisition allows volume and mass measurement with greater accuracy and reproducibility, limiting inter-observer variability. Free navigation of the planes of investigation allows reconstruction for qualitative and quantitative analysis of valvular heart disease and other pathologies. Although real time 3D echocardiography is ready for clinical usage, some improvements are still necessary to improve its conviviality. Then real time 3D echocardiography could be the essential tool for understanding, diagnosis and management of patients.
Parallel Adaptive Multi-Mechanics Simulations using Diablo
Parsons, D; Solberg, J
2004-12-03
Coupled multi-mechanics simulations (such as thermal-stress and fluidstructure interaction problems) are of substantial interest to engineering analysts. In addition, adaptive mesh refinement techniques present an attractive alternative to current mesh generation procedures and provide quantitative error bounds that can be used for model verification. This paper discusses spatially adaptive multi-mechanics implicit simulations using the Diablo computer code. (U)
NASA Astrophysics Data System (ADS)
Oldham, Mark
2015-01-01
Radiochromic materials exhibit a colour change when exposed to ionising radiation. Radiochromic film has been used for clinical dosimetry for many years and increasingly so recently, as films of higher sensitivities have become available. The two principle advantages of radiochromic dosimetry include greater tissue equivalence (radiologically) and the lack of requirement for development of the colour change. In a radiochromic material, the colour change arises direct from ionising interactions affecting dye molecules, without requiring any latent chemical, optical or thermal development, with important implications for increased accuracy and convenience. It is only relatively recently however, that 3D radiochromic dosimetry has become possible. In this article we review recent developments and the current state-of-the-art of 3D radiochromic dosimetry, and the potential for a more comprehensive solution for the verification of complex radiation therapy treatments, and 3D dose measurement in general.
NASA Astrophysics Data System (ADS)
Iliesiu, Luca; Kos, Filip; Poland, David; Pufu, Silviu S.; Simmons-Duffin, David; Yacoby, Ran
2016-03-01
We study the conformal bootstrap for a 4-point function of fermions < ψψψψ> in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ × ψ OPE, and also on the central charge C T . We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N . We also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.
Conceptual design of a hybrid parallel mechanism for mask exchanging of TMT
NASA Astrophysics Data System (ADS)
Wang, Jianping; Zhou, Hongfei; Li, Kexuan; Zhou, Zengxiang; Zhai, Chao
2015-10-01
Mask exchange system is an important part of the Multi-Object Broadband Imaging Echellette (MOBIE) on the Thirty Meter Telescope (TMT). To solve the problem of stiffness changing with the gravity vector of the mask exchange system in the MOBIE, the hybrid parallel mechanism design method was introduced into the whole research. By using the characteristics of high stiffness and precision of parallel structure, combined with large moving range of serial structure, a conceptual design of a hybrid parallel mask exchange system based on 3-RPS parallel mechanism was presented. According to the position requirements of the MOBIE, the SolidWorks structure model of the hybrid parallel mask exchange robot was established and the appropriate installation position without interfering with the related components and light path in the MOBIE of TMT was analyzed. Simulation results in SolidWorks suggested that 3-RPS parallel platform had good stiffness property in different gravity vector directions. Furthermore, through the research of the mechanism theory, the inverse kinematics solution of the 3-RPS parallel platform was calculated and the mathematical relationship between the attitude angle of moving platform and the angle of ball-hinges on the moving platform was established, in order to analyze the attitude adjustment ability of the hybrid parallel mask exchange robot. The proposed conceptual design has some guiding significance for the design of mask exchange system of the MOBIE on TMT.
NASA Astrophysics Data System (ADS)
Chan, Victor S. S.; Barnhart, Donald H.; Halliwell, Neil A.; Coupland, Jeremy M.
1999-10-01
A new holographic technique has been developed to measure displacement in solid and fluid mechanics. The method uses double exposure holograms of large numerical aperture to record the light scattered from a solid surface or seeding particles that are assumed to follow the fluid motion. Analysis of the resulting hologram is performed in a piece- wise fashion through spatial correlation of the field that passes through a sampling aperture placed in the real image. In this way it is possible to map 3D displacement of an irregular surface or map the movement of seeding throughout an extended volume of fluid. This paper discusses the cancellation of gross aberrations using a phase conjugate holographic optical element to generate a converging reference wave. Seeded flow or solid surfaces recorded with this reference wave geometry can be reconstructed efficiently using a fiber-optic probe. In addition to aberration cancelling the technique allows a method of image shifting to be introduced thus resolving the direction of the flow or surface displacement.
Fortuny, Josep; Marcé-Nogué, Jordi; Heiss, Egon; Sanchez, Montserrat; Gil, Lluis; Galobart, Àngel
2015-01-01
Biting is an integral feature of the feeding mechanism for aquatic and terrestrial salamanders to capture, fix or immobilize elusive or struggling prey. However, little information is available on how it works and the functional implications of this biting system in amphibians although such approaches might be essential to understand feeding systems performed by early tetrapods. Herein, the skull biomechanics of the Chinese giant salamander, Andrias davidianus is investigated using 3D finite element analysis. The results reveal that the prey contact position is crucial for the structural performance of the skull, which is probably related to the lack of a bony bridge between the posterior end of the maxilla and the anterior quadrato-squamosal region. Giant salamanders perform asymmetrical strikes. These strikes are unusual and specialized behavior but might indeed be beneficial in such sit-and-wait or ambush-predators to capture laterally approaching prey. However, once captured by an asymmetrical strike, large, elusive and struggling prey have to be brought to the anterior jaw region to be subdued by a strong bite. Given their basal position within extant salamanders and their “conservative” morphology, cryptobranchids may be useful models to reconstruct the feeding ecology and biomechanics of different members of early tetrapods and amphibians, with similar osteological and myological constraints. PMID:25853557
Whirley, R.G.; Engelmann, B.E.
1993-11-01
This report is the User Manual for the 1993 version of DYNA3D, and also serves as a User Guide. DYNA3D is a nonlinear, explicit, finite element code for analyzing the transient dynamic response of three-dimensional solids and structures. The code is fully vectorized and is available on several computer platforms. DYNA3D includes solid, shell, beam, and truss elements to allow maximum flexibility in modeling physical problems. Many material models are available to represent a wide range of material behavior, including elasticity, plasticity, composites, thermal effects, and rate dependence. In addition, DYNA3D has a sophisticated contact interface capability, including frictional sliding and single surface contact. Rigid materials provide added modeling flexibility. A material model driver with interactive graphics display is incorporated into DYNA3D to permit accurate modeling of complex material response based on experimental data. Along with the DYNA3D Example Problem Manual, this document provides the information necessary to apply DYNA3D to solve a wide range of engineering analysis problems.
Wireless Rover Meets 3D Design and Product Development
ERIC Educational Resources Information Center
Deal, Walter F., III; Hsiung, Steve C.
2016-01-01
Today there are a number of 3D printing technologies that are low cost and within the budgets of middle and high school programs. Educational technology companies offer a variety of 3D printing technologies and parallel curriculum materials to enable technology and engineering teachers to easily add 3D learning activities to their programs.…
Li, Wenqiang; Gao, Shiyong; Li, Lin; Jiao, Shujie; Li, Hongtao; Wang, Jinzhong; Yu, Qingjiang; Zhang, Yong; Wang, Dongbo; Zhao, Liancheng
2016-07-01
Self-assembly of two-dimensional (2D) nanosheets and one-dimensional (1D) nanorods into three-dimensional (3D) double-sided comb-like ZnO nanostructures has been successfully performed via a simple one-step hydrothermal method on Si and ITO substrates. It is found that the thickness of the ZnO seeds plays a vital role in the formation of 3D double-sided comb-like ZnO. PMID:27279279
NASA Astrophysics Data System (ADS)
Rodrigo Rodríguez Cardozo, Félix; Hjörleifsdóttir, Vala
2015-04-01
One important ingredient in the study of the complex active tectonics in Mexico is the analysis of earthquake focal mechanisms, or the seismic moment tensor. They can be determined trough the calculation of Green functions and subsequent inversion for moment-tensor parameters. However, this calculation is gets progressively more difficult as the magnitude of the earthquakes decreases. Large earthquakes excite waves of longer periods that interact weakly with laterally heterogeneities in the crust. For these earthquakes, using 1D velocity models to compute the Greens fucntions works well. The opposite occurs for smaller and intermediate sized events, where the relatively shorter periods excited interact strongly with lateral heterogeneities in the crust and upper mantle and requires more specific or regional 3D models. In this study, we calculate Greens functions for earthquakes in Mexico using a laterally heterogeneous seismic wave speed model, comprised of mantle model S362ANI (Kustowski et al 2008) and crustal model CRUST 2.0 (Bassin et al 1990). Subsequently, we invert the observed seismograms for the seismic moment tensor using a method developed by Liu et al (2004) an implemented by Óscar de La Vega (2014) for earthquakes in Mexico. By following a brute force approach, in which we include all observed Rayleigh and Love waves of the Mexican National Seismic Network (Servicio Sismológico Naciona, SSN), we obtain reliable focal mechanisms for events that excite a considerable amount of low frequency waves (Mw > 4.8). However, we are not able to consistently estimate focal mechanisms for smaller events using this method, due to high noise levels in many of the records. Excluding the noisy records, or noisy parts of the records manually, requires interactive edition of the data, using an efficient tool for the editing. Therefore, we developed a graphical user interface (GUI), based on python and the python library ObsPy, that allows the edition of observed and
Biomimetic shoulder complex based on 3-PSS/S spherical parallel mechanism
NASA Astrophysics Data System (ADS)
Hou, Yulei; Hu, Xinzhe; Zeng, Daxing; Zhou, Yulin
2015-01-01
The application of the parallel mechanism is still limited in the humanoid robot fields, and the existing parallel humanoid robot joint has not yet been reflected the characteristics of the parallel mechanism completely, also failed to solve the problem, such as small workspace, effectively. From the structural and functional bionic point of view, a three degrees of freedom(DOFs) spherical parallel mechanism for the shoulder complex of the humanoid robot is presented. According to the structure and kinetic characteristics analysis of the human shoulder complex, 3-PSS/S(P for prismatic pair, S for spherical pair) is chosen as the original configuration for the shouder complex. Using genetic algorithm, the optimization of the 3-PSS/S spherical parallel mechanism is performed, and the orientation workspace of the prototype mechanism is enlarged obviously. Combining the practical structure characteristics of the human shouder complex, an offset output mode, which means the output rod of the mechanism turn to any direction at the point a certain distance from the rotation center of the mechanism, is put forward, which provide possibility for the consistent of the workspace of the mechanism and the actual motion space of the human body shoulder joint. The relationship of the attitude angles between different coordinate system is derived, which establishs the foundation for the motion descriptions under different conditions and control development. The 3-PSS/S spherical parallel mechanism is proposed for the shoulder complex, and the consistence of the workspace of the mechanism and the human shoulder complex is realized by the stuctural parameter optimization and the offset output design.
NASA Astrophysics Data System (ADS)
Lollino, Piernicola; Fazio, Nunzio Luciano; Vennari, Carmela; Parise, Mario
2015-04-01
In December 2013 a large landslide occurred along a clay slope located at the south-western outskirts of the Montescaglioso village (Basilicata, Southern Italy) as a consequence of intense and prolonged rainfalls that presumably caused a significant increment of the pore water pressures in the slope. The slope is formed of stiff clays belonging to the formation of the Subappennine Blue Clays, which are over-consolidated and characterized by medium plasticity. According to aerial photos dating back to 1950s, the slope was already affected by previous landslide processes, so that the examined landslide process can be classified as an occasional reactivation according to the well-known classification of Cruden & Varnes (1996). Also, during the last decades several man-made actions in the area resulted in strong changes in the original water surface network that could have played some role in the slope reactivation. Based on displacement data, obtained from a monitoring system installed few days after the phenomenon, and still in function, at present the landslide does not show relevant signs of activity. Preliminary 2-D and 3-D finite element analyses have been carried out to investigate the factors that controlled the mechanism of reactivation of the landslide. The numerical model has been setup based on the available topographical, geological and geomorphological information, the geotechnical properties of the involved soils and the information concerning the piezometric regime in the slope. The results indicate that the mobilized shear strength of the clays ranges between the typical post-peak and residual values for this type of material and confirmed that the strong increment of the pore water pressures in the slope induced by the exceptional rainfalls occurred in the previous days can be identified as the main triggering factor of the reactivation.
Rtimi, Sami; Sanjines, Rosendo; Pulgarin, Cesar; Kiwi, John
2016-01-13
The first evidence for Cu-Ag (50%/50%) nanoparticulate hybrid coatings is presented leading to a complete and almost instantaneous bacterial inactivation in the dark (≤5 min). Dark bacterial inactivation times on Cu-Ag (50%/50%) were observed to coincide with the times required by actinic light irradiation. This provides the evidence that the bimetal Cu-Ag driven inactivation predominates over a CuO/Cu2O and Ag2O oxides inducing a semiconductor driven behavior. Cu- or Ag-coated polyurethane (PU) catheters led to bacterial inactivation needing about ∼30 min. The accelerated bacterial inactivation by Cu-Ag coated on 3D catheters sputtered was investigated in a detailed way. The release of Cu/Ag ions during bacterial inactivation was followed by inductively coupled plasma mass-spectrometry (ICP-MS) and the amount of Cu and Ag-ions released were below the cytotoxicity levels permitted by the sanitary regulations. By stereomicroscopy the amount of live/dead cells were followed during the bacterial inactivation time. By Fourier transform infrared spectroscopy (FTIR), the systematic shift of the -(CH2) band stretching of the outer lipo-polysaccharide bilayer (LPS) was followed to monitor the changes leading to cell lysis. A hydrophobic to hydrophilic transformation of the Cu-Ag PU catheter surface under light was observed within 30 min followed concomitantly to a longer back transformation to the hydrophobic initial state in the dark. Physical insight is provided for the superior performance of Cu-Ag films compared to Cu or Ag films in view of the drastic acceleration of the bacterial inactivation observed on bimetal Cu-Ag films coating PU catheters. A mechanism of bacterial inactivation is suggested that is consistent with the findings reported in this study. PMID:26699928
NASA Astrophysics Data System (ADS)
Iizuka, Keigo
2008-02-01
In order to circumvent the fact that only one observer can view the image from a stereoscopic microscope, an attachment was devised for displaying the 3D microscopic image on a large LCD monitor for viewing by multiple observers in real time. The principle of operation, design, fabrication, and performance are presented, along with tolerance measurements relating to the properties of the cellophane half-wave plate used in the design.
Belenkov, E. A. Ali-Pasha, V. A.
2011-01-15
The structure of clusters of some new carbon 3D-graphite phases have been calculated using the molecular-mechanics methods. It is established that 3D-graphite polytypes {alpha}{sub 1,1}, {alpha}{sub 1,3}, {alpha}{sub 1,5}, {alpha}{sub 2,1}, {alpha}{sub 2,3}, {alpha}{sub 3,1}, {beta}{sub 1,2}, {beta}{sub 1,4}, {beta}{sub 1,6}, {beta}{sub 2,1}, and {beta}{sub 3,2} consist of sp{sup 2}-hybridized atoms, have hexagonal unit cells, and differ in regards to the structure of layers and order of their alternation. A possible way to experimentally synthesize new carbon phases is proposed: the polymerization and carbonization of hydrocarbon molecules.
Static & Dynamic Response of 3D Solids
1996-07-15
NIKE3D is a large deformations 3D finite element code used to obtain the resulting displacements and stresses from multi-body static and dynamic structural thermo-mechanics problems with sliding interfaces. Many nonlinear and temperature dependent constitutive models are available.
Introduction to 3D Graphics through Excel
ERIC Educational Resources Information Center
Benacka, Jan
2013-01-01
The article presents a method of explaining the principles of 3D graphics through making a revolvable and sizable orthographic parallel projection of cuboid in Excel. No programming is used. The method was tried in fourteen 90 minute lessons with 181 participants, which were Informatics teachers, undergraduates of Applied Informatics and gymnasium…
Hou, Yongchao; Zhao, Yang
2015-01-01
A novel 3-PUU parallel robot was put forward, on which kinematic analysis was conducted to obtain its inverse kinematics solution, and on this basis, the limitations of the sliding pair and the Hooke joint on the workspace were analyzed. Moreover, the workspace was solved through the three dimensional limit search method, and then optimization analysis was performed on the workspace of this parallel robot, which laid the foundations for the configuration design and further analysis of the parallel mechanism, with the result indicated that this type of robot was equipped with promising application prospect. In addition that, the workspace after optimization can meet more requirements of patients. PMID:26628930
Hou, Yongchao; Zhao, Yang
2015-01-01
A novel 3-PUU parallel robot was put forward, on which kinematic analysis was conducted to obtain its inverse kinematics solution, and on this basis, the limitations of the sliding pair and the Hooke joint on the workspace were analyzed. Moreover, the workspace was solved through the three dimensional limit search method, and then optimization analysis was performed on the workspace of this parallel robot, which laid the foundations for the configuration design and further analysis of the parallel mechanism, with the result indicated that this type of robot was equipped with promising application prospect. In addition that, the workspace after optimization can meet more requirements of patients. PMID:26628930
NAFLD and Increased Aortic Stiffness: Parallel or Common Physiopathological Mechanisms?
Villela-Nogueira, Cristiane A.; Leite, Nathalie C.; Cardoso, Claudia R. L.; Salles, Gil F.
2016-01-01
Non-alcoholic fatty liver disease (NAFLD) has become the leading cause of chronic liver diseases worldwide. Liver inflammation and fibrosis related to NAFLD contribute to disease progression and increasing liver-related mortality and morbidity. Increasing data suggest that NAFLD may be linked to atherosclerotic vascular disease independent of other established cardiovascular risk factors. Central arterial stiffness has been recognized as a measure of cumulative cardiovascular risk marker load, and the measure of carotid-femoral pulse wave velocity (cf-PWV) is regarded as the gold standard assessment of aortic stiffness. It has been shown that increased aortic stiffness predicts cardiovascular morbidity and mortality in several clinical settings, including type 2 diabetes mellitus, a well-known condition associated with advanced stages of NAFLD. Furthermore, recently-published studies reported a strong association between NAFLD and increased arterial stiffness, suggesting a possible link in the pathogenesis of atherosclerosis and NAFLD. We sought to review the published data on the associations between NAFLD and aortic stiffness, in order to better understand the interplay between these two conditions and identify possible common physiopathological mechanisms. PMID:27104526
Understanding B-→X (3823 )K- via rescattering mechanism and predicting B-→ηc 2(1D2)/ψ3(3D3)K-
NASA Astrophysics Data System (ADS)
Xu, Hao; Liu, Xiang; Matsuki, Takayuki
2016-08-01
We study the observed B-→X (3823 )K- decay via the rescattering mechanism and show that this branching ratio is well reproduced by this mechanism. We further extend this theoretical framework to investigate the decays of B-→ηc 2(1D2)/ψ3(3D3)K- , where the ηc 2(1D2) and the ψ3(3D3) are D -wave charmonium partners of the X (3823 ). Our results show that the branching ratios, B-→ηc 2(1D2)K- and B-→ψ3(3D3)K- , are of the order of 10-5, which can be accessible at LHCb, Belle and forthcoming BelleII.
NASA Astrophysics Data System (ADS)
Jiang, Yao; Li, Tie-Min; Wang, Li-Ping
2015-09-01
This paper investigates the stiffness modeling of compliant parallel mechanism (CPM) based on the matrix method. First, the general compliance matrix of a serial flexure chain is derived. The stiffness modeling of CPMs is next discussed in detail, considering the relative positions of the applied load and the selected displacement output point. The derived stiffness models have simple and explicit forms, and the input, output, and coupling stiffness matrices of the CPM can easily be obtained. The proposed analytical model is applied to the stiffness modeling and performance analysis of an XY parallel compliant stage with input and output decoupling characteristics. Then, the key geometrical parameters of the stage are optimized to obtain the minimum input decoupling degree. Finally, a prototype of the compliant stage is developed and its input axial stiffness, coupling characteristics, positioning resolution, and circular contouring performance are tested. The results demonstrate the excellent performance of the compliant stage and verify the effectiveness of the proposed theoretical model. The general stiffness models provided in this paper will be helpful for performance analysis, especially in determining coupling characteristics, and the structure optimization of the CPM.
NASA Astrophysics Data System (ADS)
Kostrzewski, Andrew A.; Aye, Tin M.; Kim, Dai Hyun; Esterkin, Vladimir; Savant, Gajendra D.
1998-09-01
Physical Optics Corporation has developed an advanced 3-D virtual reality system for use with simulation tools for training technical and military personnel. This system avoids such drawbacks of other virtual reality (VR) systems as eye fatigue, headaches, and alignment for each viewer, all of which are due to the need to wear special VR goggles. The new system is based on direct viewing of an interactive environment. This innovative holographic multiplexed screen technology makes it unnecessary for the viewer to wear special goggles.
NASA Technical Reports Server (NTRS)
1992-01-01
Ames Research Center research into virtual reality led to the development of the Convolvotron, a high speed digital audio processing system that delivers three-dimensional sound over headphones. It consists of a two-card set designed for use with a personal computer. The Convolvotron's primary application is presentation of 3D audio signals over headphones. Four independent sound sources are filtered with large time-varying filters that compensate for motion. The perceived location of the sound remains constant. Possible applications are in air traffic control towers or airplane cockpits, hearing and perception research and virtual reality development.
NASA Astrophysics Data System (ADS)
Utembe, S. R.; Cooke, M. C.; Archibald, A. T.; Shallcross, D. E.; Derwent, R. G.; Jenkin, M. E.
2011-03-01
A secondary organic aerosol (SOA) code, coupled to the reduced Common Representative Intermediates chemical mechanism (CRI v2-R5), has been used in the global 3-D chemistry-transport model, STOCHEM, to simulate the global distribution of organic aerosol (OA) mass loadings. The SOA code represents the gas-to-aerosol partitioning of products formed over several generations of oxidation of a variety of organic precursors emitted from anthropogenic, biogenic and biomass burning sources. The model also includes emissions of primary organic aerosol (POA), based on the AeroCom inventory and the Global Fire Emissions database (GFED). The calculated burdens for POA, 0.89 Tg, and SOA, 0.23 Tg, are well within the range of values that have been reported in previous modelling studies. The calculated SOA annual in-situ production of 22.5 Tg yr -1 also falls within the 8-110 Tg yr -1 range calculated by other models, but is somewhat lower than observationally-constrained top-down estimates which have been reported recently. The oxidation of biogenic precursors is found to account for about 90% of the global SOA burden, and this makes a substantial contribution to the highest annual mean surface OA concentrations (up to 8 μg m -3), which are simulated in tropical forested regions. Comparison of the simulated OA mass loadings with surface observations from a variety of locations indicate a good description of the OA distribution, but with an average underestimation of about a factor of 3. Sustained formation of SOA into the free troposphere is simulated, with important contributions from second and third-generation products of terpene oxidation in the upper troposphere. Comparison of the simulated OA mass loadings with vertical profiles from the ACE-Asia campaign indicates a very good description of the relative variation of OA with altitude, but with consistent underestimation of about a factor of 5. Although the absolute magnitude of the global source strength is underestimated
Simulation of Current Generation in a 3-D Plasma Model
NASA Astrophysics Data System (ADS)
Tsung, F. S.; Dawson, J. M.
1996-11-01
In the advanced tokamak regime, transport phenomena can account for a signficant fraction of the toroidal current, possibly over that driven directly by the ohmic heating electric fields. Bootstrap theory accounts for contributions of the collisional modification of banana orbits on the toroidal currents. In our previous simulations in 21/2-D, currents were spontaneously generated in both the cylindrical and the toroidal geometries, contrary to neoclassical predictions. In these calculations, it was believed that the driving mechanism is the preferential loss of particles whose initial velocity is opposite to that of the plasma current. We are extending these simulations to three dimensions. A parallel 3-D electromagnetic PIC code running on the IBM SP2, with a localized field-solver has been developed to investigate the effects of perturbations parallel to the field lines, and direct comparisons has been made between the 21/2-D and 3-D simulations and we have found good agreements between the 2 1/2-D calculations and the 3-D results. We will present our new results at the meeting. Research partially supported by NSF and DOE.
Cevidanes, Lucia; Tucker, Scott; Styner, Martin; Kim, Hyungmin; Chapuis, Jonas; Reyes, Mauricio; Proffit, William; Turvey, Timothy; Jaskolka, Michael
2009-01-01
This paper discusses the development of methods for computer-aided jaw surgery. Computer-aided jaw surgery allows us to incorporate the high level of precision necessary for transferring virtual plans into the operating room. We also present a complete computer-aided surgery (CAS) system developed in close collaboration with surgeons. Surgery planning and simulation include construction of 3D surface models from Cone-beam CT (CBCT), dynamic cephalometry, semi-automatic mirroring, interactive cutting of bone and bony segment repositioning. A virtual setup can be used to manufacture positioning splints for intra-operative guidance. The system provides further intra-operative assistance with the help of a computer display showing jaw positions and 3D positioning guides updated in real-time during the surgical procedure. The CAS system aids in dealing with complex cases with benefits for the patient, with surgical practice, and for orthodontic finishing. Advanced software tools for diagnosis and treatment planning allow preparation of detailed operative plans, osteotomy repositioning, bone reconstructions, surgical resident training and assessing the difficulties of the surgical procedures prior to the surgery. CAS has the potential to make the elaboration of the surgical plan a more flexible process, increase the level of detail and accuracy of the plan, yield higher operative precision and control, and enhance documentation of cases. Supported by NIDCR DE017727, and DE018962 PMID:20816308
NASA Astrophysics Data System (ADS)
Wu, Lixin
2004-05-01
3D geoscience modeling system (3D GMS) embodied with topological relations is of extreme importance for Geosciences. This paper presents a universal 3D model, generalized tri-prism (GTP) for 3D GMS and real-3D GIS, which is a modification and improvement of former presented analogous tri-prism (ATP) model and is the common model of pyramid model, tetrahedron model and tri-prism (TP) model. The GTP model takes the divergent drill holes, rather than triangulation network after interpolation or vertical parallel drill holes after projection transformation, as its direct data source. Hence, the reliability and quality of the 3D model is maximatily ensured. The GTP component is comprised of six primitives as node, TIN-edge, side-edge, TIN-face, side-face and GTP. Besides, three intermediary diagonal lines in each GTP component are temporary applied for spatial operations. Six groups of topological relations between the six primitives are carefully designed for geo-spatial inquiry and geo-spatial analysis. The mechanisms of chipping, dynamic updating and local refining operations of so constructed 3D geological model are introduced. A real-3D software platform, GeoMo 3D@, developed with VC ++, OPGL and SQL server, demonstrates most of the 3D geo-spatial operations including clipping, separating, uncovering and geo-fence diagram generating based on an actual 3D geological model of a coal mine, Tangshan, P.R. China.
Insect stereopsis demonstrated using a 3D insect cinema
Nityananda, Vivek; Tarawneh, Ghaith; Rosner, Ronny; Nicolas, Judith; Crichton, Stuart; Read, Jenny
2016-01-01
Stereopsis - 3D vision – has become widely used as a model of perception. However, all our knowledge of possible underlying mechanisms comes almost exclusively from vertebrates. While stereopsis has been demonstrated for one invertebrate, the praying mantis, a lack of techniques to probe invertebrate stereopsis has prevented any further progress for three decades. We therefore developed a stereoscopic display system for insects, using miniature 3D glasses to present separate images to each eye, and tested our ability to deliver stereoscopic illusions to praying mantises. We find that while filtering by circular polarization failed due to excessive crosstalk, “anaglyph” filtering by spectral content clearly succeeded in giving the mantis the illusion of 3D depth. We thus definitively demonstrate stereopsis in mantises and also demonstrate that the anaglyph technique can be effectively used to deliver virtual 3D stimuli to insects. This method opens up broad avenues of research into the parallel evolution of stereoscopic computations and possible new algorithms for depth perception. PMID:26740144
3-D Dynamic Behavior of Generalized Polar Wind
NASA Astrophysics Data System (ADS)
Barakat, A. R.; Schunk, R. W.; Demars, H. G.
2003-12-01
The dynamic behavior of the high-latitude plasma during a representative geomagnetic storm is investigated using a 3-D macroscopic particle-in-cell (mac-PIC) model. In this study, we simulate the behavior of a large number ( ˜100 to 1000) of plasma-filled geomagnetic flux tubes. Each flux tube extends from 1200 km to several Earth radii, includes ˜106 simulation particles, and is followed for ˜12 hours. The lower boundary conditions of the model are provided by a 3-D fluid-like model that extends down to 100 km. Several physical mechanisms are included such as wave-particle interactions, ion-ion collisions, low-altitude ion energization, and magnetospheric particles. The computing-intensive nature of the model requires the utilization of parallel programming techniques. We use a cluster of five nodes, with two (1.6 GHz) processors each, that is available at Utah State University, with the intention of transferring the code to a bigger facility in the future. A 3-D picture is assembled from the temporal evolution of the individual flux tubes by keeping track of their locations. This 3-D picture facilitates comparison with observations, such as radar and satellite measurements. The model and its preliminary results are presented.
Insect stereopsis demonstrated using a 3D insect cinema.
Nityananda, Vivek; Tarawneh, Ghaith; Rosner, Ronny; Nicolas, Judith; Crichton, Stuart; Read, Jenny
2016-01-01
Stereopsis - 3D vision - has become widely used as a model of perception. However, all our knowledge of possible underlying mechanisms comes almost exclusively from vertebrates. While stereopsis has been demonstrated for one invertebrate, the praying mantis, a lack of techniques to probe invertebrate stereopsis has prevented any further progress for three decades. We therefore developed a stereoscopic display system for insects, using miniature 3D glasses to present separate images to each eye, and tested our ability to deliver stereoscopic illusions to praying mantises. We find that while filtering by circular polarization failed due to excessive crosstalk, "anaglyph" filtering by spectral content clearly succeeded in giving the mantis the illusion of 3D depth. We thus definitively demonstrate stereopsis in mantises and also demonstrate that the anaglyph technique can be effectively used to deliver virtual 3D stimuli to insects. This method opens up broad avenues of research into the parallel evolution of stereoscopic computations and possible new algorithms for depth perception. PMID:26740144
NASA Astrophysics Data System (ADS)
Gil, José J.; San José, Ignacio
2010-11-01
From our previous definition of the indices of polarimetric purity for 3D light beams [J.J. Gil, J.M. Correas, P.A. Melero and C. Ferreira, Monogr. Semin. Mat. G. de Galdeano 31, 161 (2004)], an analysis of their geometric and physical interpretation is presented. It is found that, in agreement with previous results, the first parameter is a measure of the degree of polarization, whereas the second parameter (called the degree of directionality) is a measure of the mean angular aperture of the direction of propagation of the corresponding light beam. This pair of invariant, non-dimensional, indices of polarimetric purity contains complete information about the polarimetric purity of a light beam. The overall degree of polarimetric purity is obtained as a weighted quadratic average of the degree of polarization and the degree of directionality.
Caspi, S.; Helm, M.; Laslett, L.J.
1991-03-30
We have developed an harmonic representation for the three dimensional field components within the windings of accelerator magnets. The form by which the field is presented is suitable for interfacing with other codes that make use of the 3D field components (particle tracking and stability). The field components can be calculated with high precision and reduced cup time at any location (r,{theta},z) inside the magnet bore. The same conductor geometry which is used to simulate line currents is also used in CAD with modifications more readily available. It is our hope that the format used here for magnetic fields can be used not only as a means of delivering fields but also as a way by which beam dynamics can suggest correction to the conductor geometry. 5 refs., 70 figs.
NASA Technical Reports Server (NTRS)
2004-01-01
The Mars Exploration Rover Spirit took this 3-D navigation camera mosaic of the crater called 'Bonneville' after driving approximately 13 meters (42.7 feet) to get a better vantage point. Spirit's current position is close enough to the edge to see the interior of the crater, but high enough and far enough back to get a view of all of the walls. Because scientists and rover controllers are so pleased with this location, they will stay here for at least two more martian days, or sols, to take high resolution panoramic camera images of 'Bonneville' in its entirety. Just above the far crater rim, on the left side, is the rover's heatshield, which is visible as a tiny reflective speck.
McCracken, Joselle M; Badea, Adina; Kandel, Mikhail E; Gladman, A Sydney; Wetzel, David J; Popescu, Gabriel; Lewis, Jennifer A; Nuzzo, Ralph G
2016-05-01
R. Nuzzo and co-workers show on page 1025 how compositional differences in hydrogels are used to tune their cellular compliance by controlling their polymer mesh properties and subsequent uptake of the protein poly-l-lysine (green spheres in circled inset). The cover image shows pyramid micro-scaffolds prepared using direct ink writing (DIW) that differentially direct fibroblast and preosteoblast growth in 3D, depending on cell motility and surface treatment. PMID:27166616
Puso, M; Maker, B N; Ferencz, R M; Hallquist, J O
2000-03-24
This report provides the NIKE3D user's manual update summary for changes made from version 3.0.0 April 24, 1995 to version 3.3.6 March 24,2000. The updates are excerpted directly from the code printed output file (hence the Courier font and formatting), are presented in chronological order and delineated by NIKE3D version number. NIKE3D is a fully implicit three-dimensional finite element code for analyzing the finite strain static and dynamic response of inelastic solids, shells, and beams. Spatial discretization is achieved by the use of 8-node solid elements, 2-node truss and beam elements, and 4-node membrane and shell elements. Thirty constitutive models are available for representing a wide range of elastic, plastic, viscous, and thermally dependent material behavior. Contact-impact algorithms permit gaps, frictional sliding, and mesh discontinuities along material interfaces. Several nonlinear solution strategies are available, including Full-, Modified-, and Quasi-Newton methods. The resulting system of simultaneous linear equations is either solved iteratively by an element-by-element method, or directly by a direct factorization method.
3D ultrafast ultrasound imaging in vivo
NASA Astrophysics Data System (ADS)
Provost, Jean; Papadacci, Clement; Esteban Arango, Juan; Imbault, Marion; Fink, Mathias; Gennisson, Jean-Luc; Tanter, Mickael; Pernot, Mathieu
2014-10-01
Very high frame rate ultrasound imaging has recently allowed for the extension of the applications of echography to new fields of study such as the functional imaging of the brain, cardiac electrophysiology, and the quantitative imaging of the intrinsic mechanical properties of tumors, to name a few, non-invasively and in real time. In this study, we present the first implementation of Ultrafast Ultrasound Imaging in 3D based on the use of either diverging or plane waves emanating from a sparse virtual array located behind the probe. It achieves high contrast and resolution while maintaining imaging rates of thousands of volumes per second. A customized portable ultrasound system was developed to sample 1024 independent channels and to drive a 32 × 32 matrix-array probe. Its ability to track in 3D transient phenomena occurring in the millisecond range within a single ultrafast acquisition was demonstrated for 3D Shear-Wave Imaging, 3D Ultrafast Doppler Imaging, and, finally, 3D Ultrafast combined Tissue and Flow Doppler Imaging. The propagation of shear waves was tracked in a phantom and used to characterize its stiffness. 3D Ultrafast Doppler was used to obtain 3D maps of Pulsed Doppler, Color Doppler, and Power Doppler quantities in a single acquisition and revealed, at thousands of volumes per second, the complex 3D flow patterns occurring in the ventricles of the human heart during an entire cardiac cycle, as well as the 3D in vivo interaction of blood flow and wall motion during the pulse wave in the carotid at the bifurcation. This study demonstrates the potential of 3D Ultrafast Ultrasound Imaging for the 3D mapping of stiffness, tissue motion, and flow in humans in vivo and promises new clinical applications of ultrasound with reduced intra—and inter-observer variability.
Gait analysis of a radial symmetrical hexapod robot based on parallel mechanisms
NASA Astrophysics Data System (ADS)
Xu, Kun; Ding, Xilun
2014-09-01
Most gait studies of multi-legged robots in past neglected the dexterity of robot body and the relationship between stride length and body height. This paper investigates the performance of a radial symmetrical hexapod robot based on the dexterity of parallel mechanism. Assuming the constraints between the supporting feet and the ground with hinges, the supporting legs and the hexapod body are taken as a parallel mechanism, and each swing leg is regarded as a serial manipulator. The hexapod robot can be considered as a series of hybrid serial-parallel mechanisms while walking on the ground. Locomotion performance can be got by analyzing these equivalent mechanisms. The kinematics of the whole robotic system is established, and the influence of foothold position on the workspace of robot body is analyzed. A new method to calculate the stride length of multi-legged robots is proposed by analyzing the relationship between the workspaces of two adjacent equivalent parallel mechanisms in one gait cycle. Referring to service region and service sphere, weight service sphere and weight service region are put forward to evaluate the dexterity of robot body. The dexterity of single point in workspace and the dexterity distribution in vertical and horizontal projection plane are demonstrated. Simulation shows when the foothold offset goes up to 174 mm, the dexterity of robot body achieves its maximum value 0.1644 in mixed gait. The proposed methods based on parallel mechanisms can be used to calculate the stride length and the dexterity of multi-legged robot, and provide new approach to determine the stride length, body height, footholds in gait planning of multi-legged robot.
Parallel Magnetic Flow Electromagnet for Movable Coil Control-rod Driving Mechanism
Jige, Zhang
2006-07-01
The parallel magnetic flow electromagnet can effectively relax the saturation, which easily takes place in the single magnetic flow electromagnet, and accordingly can improve the drive capacity of the movable coil electromagnet drive mechanism for a mobile reactor control rod. (authors)
Dynamic analysis and control of lightweight manipulators with flexible parallel link mechanisms
NASA Technical Reports Server (NTRS)
Lee, Jeh Won
1991-01-01
The flexible parallel link mechanism is designed for increased rigidity to sustain the buckling when it carries a heavy payload. Compared to a one link flexible manipulator, a two link flexible manipulator, especially the flexible parallel mechanism, has more complicated characteristics in dynamics and control. The objective of this research is the theoretical analysis and the experimental verification of dynamics and control of a two link flexible manipulator with a flexible parallel link mechanism. Nonlinear equations of motion of the lightweight manipulator are derived by the Lagrangian method in symbolic form to better understand the structure of the dynamic model. A manipulator with a flexible parallel link mechanism is a constrained dynamic system whose equations are sensitive to numerical integration error. This constrained system is solved using singular value decomposition of the constraint Jacobian matrix. The discrepancies between the analytical model and the experiment are explained using a simplified and a detailed finite element model. The step response of the analytical model and the TREETOPS model match each other well. The nonlinear dynamics is studied using a sinusoidal excitation. The actuator dynamic effect on a flexible robot was investigated. The effects are explained by the root loci and the Bode plot theoretically and experimentally. For the base performance for the advanced control scheme, a simple decoupled feedback scheme is applied.
A simple method for producing freestanding 3D microstructures by integrated photomask micromolding
NASA Astrophysics Data System (ADS)
Li, Hui
2015-12-01
Freestanding three-dimensional (3D) microstructures are widely used in micro-electro-mechanical system (MEMS) applications or can function as microdevices themselves. However, microfabrication methods for freestanding 3D microstructures have limitations in shape, size, cost, and mass production, etc. In this work, integrated photomask micromolding is demonstrated, which uses a portable UV light source and chrome glass micromolding to fabricate 3D microstructures without alignment. Specifically, a chrome layer on one side of the glass micromold shields the excess filling SU-8 photoresist from UV exposure and only the SU-8 photoresist in mold cavities is crosslinked. The 3D microstructures produced using this method have very high dimensional accuracy and the profile error is approximately 1.5%. This method can be used with features of virtually any size and shape and can be integrated into highly-parallel micromolding processes and has potential for MEMS applications.
NASA Technical Reports Server (NTRS)
1997-01-01
Many prominent rocks near the Sagan Memorial Station are featured in this image, taken in stereo by the Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. Wedge is at lower left; Shark, Half-Dome, and Pumpkin are at center. Flat Top, about four inches high, is at lower right. The horizon in the distance is one to two kilometers away.
Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.
Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right
NASA Technical Reports Server (NTRS)
2004-01-01
This 3-D, microscopic imager mosaic of a target area on a rock called 'Diamond Jenness' was taken after NASA's Mars Exploration Rover Opportunity ground into the surface with its rock abrasion tool for a second time.
Opportunity has bored nearly a dozen holes into the inner walls of 'Endurance Crater.' On sols 177 and 178 (July 23 and July 24, 2004), the rover worked double-duty on Diamond Jenness. Surface debris and the bumpy shape of the rock resulted in a shallow and irregular hole, only about 2 millimeters (0.08 inch) deep. The final depth was not enough to remove all the bumps and leave a neat hole with a smooth floor. This extremely shallow depression was then examined by the rover's alpha particle X-ray spectrometer.
On Sol 178, Opportunity's 'robotic rodent' dined on Diamond Jenness once again, grinding almost an additional 5 millimeters (about 0.2 inch). The rover then applied its Moessbauer spectrometer to the deepened hole. This double dose of Diamond Jenness enabled the science team to examine the rock at varying layers. Results from those grindings are currently being analyzed.
The image mosaic is about 6 centimeters (2.4 inches) across.
A 3D radiative transfer framework. VI. PHOENIX/3D example applications
NASA Astrophysics Data System (ADS)
Hauschildt, P. H.; Baron, E.
2010-01-01
Aims: We demonstrate the application of our 3D radiative transfer framework in the model atmosphere code PHOENIX for a number of spectrum synthesis calculations for very different conditions. Methods: The 3DRT framework discussed in the previous papers of this series was added to our general-purpose model atmosphere code PHOENIX/1D and an extended 3D version PHOENIX/3D was created. The PHOENIX/3D code is parallelized via the MPI library using a hierarchical domain decomposition and displays very good strong scaling. Results: We present the results of several test cases for widely different atmosphere conditions and compare the 3D calculations with equivalent 1D models to assess the internal accuracy of the 3D modeling. In addition, we show the results for a number of parameterized 3D structures. Conclusions: With presently available computational resources it is possible to solve the full 3D radiative transfer (including scattering) problem with the same micro-physics as included in 1D modeling.
Schwartz, Michael P.; Rogers, Robert E.; Singh, Samir P.; Lee, Justin Y.; Loveland, Samuel G.; Koepsel, Justin T.; Witze, Eric S.; Montanez-Sauri, Sara I.; Sung, Kyung E.; Tokuda, Emi Y.; Sharma, Yasha; Everhart, Lydia M.; Nguyen, Eric H.; Zaman, Muhammad H.; Beebe, David J.; Ahn, Natalie G.; Murphy, William L.; Anseth, Kristi S.
2013-01-01
Here, we describe an engineering approach to quantitatively compare migration, morphologies, and adhesion for tumorigenic human fibrosarcoma cells (HT-1080s) and primary human dermal fibroblasts (hDFs) with the aim of identifying distinguishing properties of the transformed phenotype. Relative adhesiveness was quantified using self-assembled monolayer (SAM) arrays and proteolytic 3-dimensional (3D) migration was investigated using matrix metalloproteinase (MMP)-degradable poly(ethylene glycol) (PEG) hydrogels (“synthetic extracellular matrix” or “synthetic ECM”). In synthetic ECM, hDFs were characterized by vinculin-containing features on the tips of protrusions, multipolar morphologies, and organized actomyosin filaments. In contrast, HT-1080s were characterized by diffuse vinculin expression, pronounced β1-integrin on the tips of protrusions, a cortically-organized F-actin cytoskeleton, and quantitatively more rounded morphologies, decreased adhesiveness, and increased directional motility compared to hDFs. Further, HT-1080s were characterized by contractility-dependent motility, pronounced blebbing, and cortical contraction waves or constriction rings, while quantified 3D motility was similar in matrices with a wide range of biochemical and biophysical properties (including collagen) despite substantial morphological changes. While HT-1080s were distinct from hDFs for each of the 2D and 3D properties investigated, several features were similar to WM239a melanoma cells, including rounded, proteolytic migration modes, cortical F-actin organization, and prominent uropod-like structures enriched with β1-integrin, F-actin, and melanoma cell adhesion molecule (MCAM/CD146/MUC18). Importantly, many of the features observed for HT-1080s were analogous to cellular changes induced by transformation, including cell rounding, a disorganized F-actin cytoskeleton, altered organization of focal adhesion proteins, and a weakly adherent phenotype. Based on our results
2015-04-23
A new type of graphene aerogel will make for better energy storage, sensors, nanoelectronics, catalysis and separations. Lawrence Livermore National Laboratory researchers have made graphene aerogel microlattices with an engineered architecture via a 3D printing technique known as direct ink writing. The research appears in the April 22 edition of the journal, Nature Communications. The 3D printed graphene aerogels have high surface area, excellent electrical conductivity, are lightweight, have mechanical stiffness and exhibit supercompressibility (up to 90 percent compressive strain). In addition, the 3D printed graphene aerogel microlattices show an order of magnitude improvement over bulk graphene materials and much better mass transport.
The slider motion error analysis by positive solution method in parallel mechanism
NASA Astrophysics Data System (ADS)
Ma, Xiaoqing; Zhang, Lisong; Zhu, Liang; Yang, Wenguo; Hu, Penghao
2016-01-01
Motion error of slider plays key role in 3-PUU parallel coordinates measuring machine (CMM) performance and influence the CMM accuracy, which attracts lots of experts eyes in the world, Generally, the analysis method is based on the view of space 6-DOF. Here, a new analysis method is provided. First, the structure relation of slider and guideway can be abstracted as a 4-bar parallel mechanism. So, the sliders can be considered as moving platform in parallel kinematic mechanism PKM. Its motion error analysis is also transferred to moving platform position analysis in PKM. Then, after establishing the positive and negative solutions, some existed theory and technology for PKM can be applied to analyze slider straightness motion error and angular motion error simultaneously. Thirdly, some experiments by autocollimator are carried out to capture the original error data about guideway its own error, the data can be described as straightness error function by fitting curvilinear equation. Finally, the Straightness error of two guideways are considered as the variation of rod length in parallel mechanism, the slider's straightness error and angular error can be obtained by putting data into the established model. The calculated result is generally consistent with experiment result. The idea will be beneficial on accuracy calibration and error correction of 3-PUU CMM and also provides a new thought to analyze kinematic error of guideway in precision machine tool and precision instrument.
3D Ultrafast Ultrasound Imaging In Vivo
Provost, Jean; Papadacci, Clement; Arango, Juan Esteban; Imbault, Marion; Gennisson, Jean-Luc; Tanter, Mickael; Pernot, Mathieu
2014-01-01
Very high frame rate ultrasound imaging has recently allowed for the extension of the applications of echography to new fields of study such as the functional imaging of the brain, cardiac electrophysiology, and the quantitative real-time imaging of the intrinsic mechanical properties of tumors, to name a few, non-invasively and in real time. In this study, we present the first implementation of Ultrafast Ultrasound Imaging in three dimensions based on the use of either diverging or plane waves emanating from a sparse virtual array located behind the probe. It achieves high contrast and resolution while maintaining imaging rates of thousands of volumes per second. A customized portable ultrasound system was developed to sample 1024 independent channels and to drive a 32×32 matrix-array probe. Its capability to track in 3D transient phenomena occurring in the millisecond range within a single ultrafast acquisition was demonstrated for 3-D Shear-Wave Imaging, 3-D Ultrafast Doppler Imaging and finally 3D Ultrafast combined Tissue and Flow Doppler. The propagation of shear waves was tracked in a phantom and used to characterize its stiffness. 3-D Ultrafast Doppler was used to obtain 3-D maps of Pulsed Doppler, Color Doppler, and Power Doppler quantities in a single acquisition and revealed, for the first time, the complex 3-D flow patterns occurring in the ventricles of the human heart during an entire cardiac cycle, and the 3-D in vivo interaction of blood flow and wall motion during the pulse wave in the carotid at the bifurcation. This study demonstrates the potential of 3-D Ultrafast Ultrasound Imaging for the 3-D real-time mapping of stiffness, tissue motion, and flow in humans in vivo and promises new clinical applications of ultrasound with reduced intra- and inter-observer variability. PMID:25207828
The psychology of the 3D experience
NASA Astrophysics Data System (ADS)
Janicke, Sophie H.; Ellis, Andrew
2013-03-01
With 3D televisions expected to reach 50% home saturation as early as 2016, understanding the psychological mechanisms underlying the user response to 3D technology is critical for content providers, educators and academics. Unfortunately, research examining the effects of 3D technology has not kept pace with the technology's rapid adoption, resulting in large-scale use of a technology about which very little is actually known. Recognizing this need for new research, we conducted a series of studies measuring and comparing many of the variables and processes underlying both 2D and 3D media experiences. In our first study, we found narratives within primetime dramas had the power to shift viewer attitudes in both 2D and 3D settings. However, we found no difference in persuasive power between 2D and 3D content. We contend this lack of effect was the result of poor conversion quality and the unique demands of 3D production. In our second study, we found 3D technology significantly increased enjoyment when viewing sports content, yet offered no added enjoyment when viewing a movie trailer. The enhanced enjoyment of the sports content was shown to be the result of heightened emotional arousal and attention in the 3D condition. We believe the lack of effect found for the movie trailer may be genre-related. In our final study, we found 3D technology significantly enhanced enjoyment of two video games from different genres. The added enjoyment was found to be the result of an increased sense of presence.
Crack interaction with 3-D dislocation loops
NASA Astrophysics Data System (ADS)
Gao, Huajian
CRACKS in a solid often interact with other crystal defects such as dislocation loops. The interaction effects are of 3-D character yet their analytical treatment has been mostly limited to the 2-D regime due to mathematical complications. This paper shows that distribution of the stress intensity factors along a crack front due to arbitrary dislocation loops may be expressed as simple line integrals along the loop contours. The method of analysis is based on the 3-D Bueckner-Rice weight function theory for elastic crack analysis. Our results have significantly simplified the calculations for 3-D dislocation loops produced in the plastic processes at the crack front due to highly concentrated crack tip stress fields. Examples for crack-tip 3-D loops and 2-D straight dislocations emerging from the crack tip are given to demonstrate applications of the derived formulae. The results are consistent with some previous analytical solutions existing in the literature. As further applications we also analyse straight dislocations that are parallel or perpendicular to the crack plane but are not parallel to the crack front.
NASA Technical Reports Server (NTRS)
Frumkin, Michael; Yan, Jerry
1999-01-01
We present an HPF (High Performance Fortran) implementation of ARC3D code along with the profiling and performance data on SGI Origin 2000. Advantages and limitations of HPF as a parallel programming language for CFD applications are discussed. For achieving good performance results we used the data distributions optimized for implementation of implicit and explicit operators of the solver and boundary conditions. We compare the results with MPI and directive based implementations.
Static balancing of spherical 3-DoF parallel mechanisms and manipulators
Gosselin, C.M.
1999-08-01
The static balancing of spherical three-degree-of-freedom (DoF) parallel mechanisms and manipulators is addressed in this paper. Static balancing is defined here as the set of conditions on mechanism dimensional and inertial parameters which, when satisfied, ensure that the weight of the links does not produce any torque (or force) at the actuators for any configuration of the mechanism, under static conditions. First, the static balancing of a single body mounted on a spherical joint is studied. It is shown that it is possible to balance such a mechanism with springs, and that complete balancing can be achieved even with a single spring. Geometric conditions for the location of the spring attachments are given. Then, the results are applied to the balancing of the two types of 3-DoF spherical parallel mechanisms. The first mechanism is a 9R manipulator, while the second one is referred to as the 3-6-6 spherical mechanism. For each of these mechanisms, the balancing conditions are first derived for systems in which no springs are used. Then, conditions for the balancing using springs are obtained. Static balancing leads to considerable reduction in the actuator torques (or forces), which in turn allows the use of less powerful actuators and therefore leads to more efficient designs. Hence, the balancing conditions derived here are of great interest in a context of design.
A 3-d modular gripper design tool
Brown, R.G.; Brost, R.C.
1997-02-01
Modular fixturing kits are sets of components used for flexible, rapid construction of fixtures. A modular vise is a parallel-jaw vise, each jaw of which is a modular fixture plate with a regular grid of precisely positioned holes. To fixture a part, one places pins in some of the holes so that when the vise is closed, the part is reliably located and completely constrained. The modular vise concept can be adapted easily to the design of modular parallel-jaw grippers for robots. By attaching a grid-plate to each jaw of a parallel-jaw gripper, one gains the ability to easily construct high-quality grasps for a wide variety of parts from a standard set of hardware. Wallack and Canny developed an algorithm for planning planar grasp configurations for the modular vise. In this paper, the authors expand this work to produce a 3-d fixture/gripper design tool. They describe several analyses they have added to the planar algorithm, including a 3-d grasp quality metric based on force information, 3-d geometric loading analysis, and inter-gripper interference analysis. Finally, the authors describe two applications of their code. One of these is an internal application at Sandia, while the other shows a potential use of the code for designing part of an agile assembly line.
NASA Astrophysics Data System (ADS)
Vora, Aditya M.
2009-03-01
In the present article, we report the screening-dependent study of the superconducting state parameters (SSPs), viz. electron-phonon coupling strength λ, Coulomb pseudopotential μ*, transition temperature TC, isotope effect exponent α, and effective interaction strength N0V of 3d-band transition metals binary alloys superconductors have been made extensively in the present work using a model potential formalism and employing the pseudo-alloy-atom (PAA) model for the first time. Five local field correction functions proposed by Hartree (H), Taylor (T), Ichimaru-Utsumi (IU), Farid et al. (F) and Sarkar et al. (S) are used in the present investigation to study the screening influence on the aforesaid properties. The present results of the SSPs obtained from H-screening are found in qualitative agreement with the available experimental data wherever exist.
Lei, Meng; Feng, Huayun; Wang, Cheng; Li, Hailing; Shi, Jingmiao; Wang, Jia; Liu, Zhaogang; Chen, Shanshan; Hu, Shihe; Zhu, Yongqiang
2016-06-01
Proteasome had been clinically validated as an effective target for the treatment of cancers. Up to now, many structurally diverse proteasome inhibitors were discovered. And two of them were launched to treat multiple myeloma (MM) and mantle cell lymphoma (MCL). Based on our previous biological results of dipeptidyl boronic acid proteasome inhibitors, robust 3D-QSAR models were developed and structure-activity relationship (SAR) was summarized. Several structurally novel compounds were designed based on the theoretical models and finally synthesized. Biological results showed that compound 12e was as active as the standard bortezomib in enzymatic and cellular activities. In vivo pharmacokinetic profiles suggested compound 12e showed a long half-life, which indicated that it could be administered intravenously. Cell cycle analysis indicated that compound 12e inhibited cell cycle progression at the G2M stage. PMID:27117691
Swallow, Kevin
2008-10-14
This report documents the results of a project undertaken to develop an ultra-high-accuracy measurement capability, which is necessary to address a rising trend toward miniaturized mechanical products exhibiting dramatically reduced product tolerances. A significant improvement in measurement capability is therefore required to insure that a 4:1 ratio can be maintained between product tolerances and measurement uncertainty.
NASA Astrophysics Data System (ADS)
Hou, Yulei; Li, Zhisen; Wang, Yi; Zhang, Wenwen; Zeng, Daxing; Zhou, Yulin
2016-06-01
The structure design for high ratio of carrying capacity to deadweight is one of the challenges for the bionic mechanism, while the problem concerning high carrying capacity has not yet be solved for the existing shoulder complex. A new type biomimetic shoulder complex, which adopts 3-PSS/S(P for prismatic pair, S for spherical pair) spherical parallel mechanism (SPM), is proposed. The static equilibrium equations of each component are established by using the vector method and the equations for constrain forces with certain load are solved. Then the constrain force on the middle limb and that on the side limbs are compared in order to verify the unloading performance of the mechanism. In addition, the prototype mechanism of the shoulder complex is developed, and the force feedback experiment is conducted to verify the static analysis, which indicates that the middle limb suffers most of the external force and the effect of mechanics unloading is achieved. The 3-PSS/S spherical parallel mechanism is presented for the shoulder complex, and the realization of mechanics unloading is benefit for the improvement of the carrying capacity of the shoulder complex.
Mechanical Study of Superconducting Parallel-Bar Deflecting/Crabbing Cavities
H. Park, J.R. Delayen, S.U. De Silva
2011-07-01
The superconducting parallel-bar deflecting/crabbing cavities have improved properties compared to conventional cavity structures. It is currently being considered for number of applications. The mechanical design analysis is performed on two designs of the 499 MHz parallel-bar deflecting cavity for the Jefferson Lab 12 GeV upgrade. The main purpose of the mechanical study is to examine the structural stability of the cavities under the operating conditions in the accelerators. The study results will suggest the need for additional structural strengthening. Also the study results will help to develop a concept of the tuning method. If the cavity is to be installed in the accelerator it should satisfy a certain design parameters due to the safety requirements (for example, pressure system requirements) which are much severe condition than the actual operating condition.
NASA Technical Reports Server (NTRS)
Lee, Jeh Won
1990-01-01
The objective is the theoretical analysis and the experimental verification of dynamics and control of a two link flexible manipulator with a flexible parallel link mechanism. Nonlinear equations of motion of the lightweight manipulator are derived by the Lagrangian method in symbolic form to better understand the structure of the dynamic model. The resulting equation of motion have a structure which is useful to reduce the number of terms calculated, to check correctness, or to extend the model to higher order. A manipulator with a flexible parallel link mechanism is a constrained dynamic system whose equations are sensitive to numerical integration error. This constrained system is solved using singular value decomposition of the constraint Jacobian matrix. Elastic motion is expressed by the assumed mode method. Mode shape functions of each link are chosen using the load interfaced component mode synthesis. The discrepancies between the analytical model and the experiment are explained using a simplified and a detailed finite element model.
NASA Technical Reports Server (NTRS)
1997-01-01
Yogi, a rock taller than rover Sojourner, is the subject of this image, taken in stereo by the deployed Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. The soil in the foreground has been the location of multiple soil mechanics experiments performed by Sojourner's cleated wheels. Pathfinder scientists were able to control the force inflicted on the soil beneath the rover's wheels, giving them insight into the soil's mechanical properties. The soil mechanics experiments were conducted after this image was taken.
Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.
Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right
Xu, Feng; Hu, Xiao-fang; Qu, Hong-yan; Kang, Dan; Xiao, Ti-qiao
2014-01-01
To investigate the local micro-/nanoscale region in a large scale sample, an image reconstruction method for nanometer computed tomography (nano-CT) was proposed in this paper. In the algorithm, wavelets were used to localize the filtered-backprojection (FBP) algorithm because of its space-frequency localization property. After the implementation of the algorithm, two simulation local reconstruction experiments were performed to confirm its effectiveness. Three evaluation criteria were used in the experiments to judge the quality of the reconstructed images. The experimental results showed that the algorithm proposed in this paper performed best because (1) the quality of its results had improved 20%–30% compared to the results of FBP and 10%–30% compared to the results of another wavelet algorithm; (2) the new algorithm was stable under different circumstances. Besides, an actual reconstruction experiment was performed using real projection data that had been collected in a CT experiment. Two-dimensional (2D) and three-dimensional (3D) images of the sample were reconstructed. The microstructure of the sample could be clearly observed in the reconstructed images. Since much attention has been directed towards the nano-CT technique to investigate the microstructure of materials, this new wavelet-based local tomography algorithm could be considered as a meaningful effort. PMID:24723829
Liu, Musang; Zheng, Nan; Li, Dongmei; Zheng, Hailin; Zhang, Lili; Ge, Hu; Liu, Weida
2016-05-01
Mutations of CYP51A protein (Cytochrome P450 14-α Sterol demethylase) play a central role in the azole resistance of Aspergillus fumigatus The available structural models of CYP51A protein ofA. fumigatus are built based on that of Homo sapiens and that of Mycobacterium tuberculosis, of which the amino acid homology is only 38% and 29% compared with CYP51A protein ofA. fumigatus, respectively. In the present study, we constructed a new 3D structural model ofA. fumigatus CYP51A protein based on a recently resolved crystal structure of the homologous protein in the fungus S. cerevisiae, which shares 50% amino acid homology with A. fumigatus CYP51A protein. Three azole molecules, itraconazole, voriconazole, and posaconazole, were docked to the wild-type and the mutant A. fumigatus CYP51A protein models, respectively, to illustrate the impact of cyp51A mutations to azole-resistance. We found the mutations that occurred at L98, M220, and Y431 positions would decrease the binding affinity of azoles to the CYP51A protein and therefore would reduce their inhibitory effects. Additionally, the mutations of L98 and G432 would reduce the stability of the protein, which might lead to conformational change of its binding pocket and eventually the resistance to azoles. PMID:26768370
Dong, Bo; Xu, Feng; Hu, Xiao-fang; Qu, Hong-yan; Kang, Dan; Xiao, Ti-qiao
2014-01-01
To investigate the local micro-/nanoscale region in a large scale sample, an image reconstruction method for nanometer computed tomography (nano-CT) was proposed in this paper. In the algorithm, wavelets were used to localize the filtered-backprojection (FBP) algorithm because of its space-frequency localization property. After the implementation of the algorithm, two simulation local reconstruction experiments were performed to confirm its effectiveness. Three evaluation criteria were used in the experiments to judge the quality of the reconstructed images. The experimental results showed that the algorithm proposed in this paper performed best because (1) the quality of its results had improved 20%-30% compared to the results of FBP and 10%-30% compared to the results of another wavelet algorithm; (2) the new algorithm was stable under different circumstances. Besides, an actual reconstruction experiment was performed using real projection data that had been collected in a CT experiment. Two-dimensional (2D) and three-dimensional (3D) images of the sample were reconstructed. The microstructure of the sample could be clearly observed in the reconstructed images. Since much attention has been directed towards the nano-CT technique to investigate the microstructure of materials, this new wavelet-based local tomography algorithm could be considered as a meaningful effort. PMID:24723829
The FORCE: A portable parallel programming language supporting computational structural mechanics
NASA Technical Reports Server (NTRS)
Jordan, Harry F.; Benten, Muhammad S.; Brehm, Juergen; Ramanan, Aruna
1989-01-01
This project supports the conversion of codes in Computational Structural Mechanics (CSM) to a parallel form which will efficiently exploit the computational power available from multiprocessors. The work is a part of a comprehensive, FORTRAN-based system to form a basis for a parallel version of the NICE/SPAR combination which will form the CSM Testbed. The software is macro-based and rests on the force methodology developed by the principal investigator in connection with an early scientific multiprocessor. Machine independence is an important characteristic of the system so that retargeting it to the Flex/32, or any other multiprocessor on which NICE/SPAR might be imnplemented, is well supported. The principal investigator has experience in producing parallel software for both full and sparse systems of linear equations using the force macros. Other researchers have used the Force in finite element programs. It has been possible to rapidly develop software which performs at maximum efficiency on a multiprocessor. The inherent machine independence of the system also means that the parallelization will not be limited to a specific multiprocessor.
NASA Astrophysics Data System (ADS)
Mediavilla, Evencio; Arribas, Santiago; Roth, Martin; Cepa-Nogué, Jordi; Sánchez, Francisco
2011-09-01
Preface; Acknowledgements; 1. Introductory review and technical approaches Martin M. Roth; 2. Observational procedures and data reduction James E. H. Turner; 3. 3D Spectroscopy instrumentation M. A. Bershady; 4. Analysis of 3D data Pierre Ferruit; 5. Science motivation for IFS and galactic studies F. Eisenhauer; 6. Extragalactic studies and future IFS science Luis Colina; 7. Tutorials: how to handle 3D spectroscopy data Sebastian F. Sánchez, Begona García-Lorenzo and Arlette Pécontal-Rousset.
3D Elevation Program—Virtual USA in 3D
Lukas, Vicki; Stoker, J.M.
2016-01-01
The U.S. Geological Survey (USGS) 3D Elevation Program (3DEP) uses a laser system called ‘lidar’ (light detection and ranging) to create a virtual reality map of the Nation that is very accurate. 3D maps have many uses with new uses being discovered all the time.
Fernandez, M; House, M; Jambawalikar, S; Zork, N; Vink, J; Wapner, R; Myers, K
2016-01-01
Preterm birth is a strong contributor to perinatal mortality, and preterm infants that survive are at risk for long-term morbidities. During most of pregnancy, appropriate mechanical function of the cervix is required to maintain the developing fetus in utero. Premature cervical softening and subsequent cervical shortening are hypothesized to cause preterm birth. Presently, there is a lack of understanding of the structural and material factors that influence the mechanical function of the cervix during pregnancy. In this study we build finite element models of the pregnant uterus, cervix, and fetal membrane based on magnetic resonance imagining data in order to examine the mechanical function of the cervix under the physiologic loading conditions of pregnancy. We calculate the mechanical loading state of the cervix for two pregnant patients: 22 weeks gestational age with a normal cervical length and 28 weeks with a short cervix. We investigate the influence of (1) anatomical geometry, (2) cervical material properties, and (3) fetal membrane material properties, including its adhesion properties, on the mechanical loading state of the cervix under physiologically relevant intrauterine pressures. Our study demonstrates that membrane-uterus interaction, cervical material modeling, and membrane mechanical properties are factors that must be deliberately and carefully handled in order to construct a high quality mechanical simulation of pregnancy. PMID:25970655
The Digital Space Shuttle, 3D Graphics, and Knowledge Management
NASA Technical Reports Server (NTRS)
Gomez, Julian E.; Keller, Paul J.
2003-01-01
The Digital Shuttle is a knowledge management project that seeks to define symbiotic relationships between 3D graphics and formal knowledge representations (ontologies). 3D graphics provides geometric and visual content, in 2D and 3D CAD forms, and the capability to display systems knowledge. Because the data is so heterogeneous, and the interrelated data structures are complex, 3D graphics combined with ontologies provides mechanisms for navigating the data and visualizing relationships.
Gadjanski, Ivana; Yodmuang, Supansa; Spiller, Kara; Bhumiratana, Sarindr
2013-01-01
Formation of tissue-engineered cartilage is greatly enhanced by mechanical stimulation. However, direct mechanical stimulation is not always a suitable method, and the utilization of mechanisms underlying mechanotransduction might allow for a highly effective and less aggressive alternate means of stimulation. In particular, the purinergic, adenosine 5′-triphosphate (ATP)-mediated signaling pathway is strongly implicated in mechanotransduction within the articular cartilage. We investigated the effects of transient and continuous exogenous ATP supplementation on mechanical properties of cartilaginous constructs engineered using bovine chondrocytes and human mesenchymal stem cells (hMSCs) encapsulated in an agarose hydrogel. For both cell types, we have observed significant increases in equilibrium and dynamic compressive moduli after transient ATP treatment applied in the fourth week of cultivation. Continuous ATP treatment over 4 weeks of culture only slightly improved the mechanical properties of the constructs, without major changes in the total glycosaminoglycan (GAG) and collagen content. Structure–function analyses showed that transiently ATP-treated constructs, and in particular those based on hMSCs, had the highest level of correlation between compositional and mechanical properties. Transiently treated groups showed intense staining of the territorial matrix for GAGs and collagen type II. These results indicate that transient ATP treatment can improve functional mechanical properties of cartilaginous constructs based on chondrogenic cells and agarose hydrogels, possibly by improving the structural organization of the bulk phase and territorial extracellular matrix (ECM), that is, by increasing correlation slopes between the content of the ECM components (GAG, collagen) and mechanical properties of the construct. PMID:23651296
Awad, Ibrahim; Ladani, Leila
2015-12-01
Carbon nanotube (CNT)/copper (Cu) composite material is proposed to replace Cu-based through-silicon vias (TSVs) in micro-electronic packages. The proposed material is believed to offer extraordinary mechanical and electrical properties and the presence of CNTs in Cu is believed to overcome issues associated with miniaturization of Cu interconnects, such as electromigration. This study introduces a multi-scale modeling of the proposed TSV in order to evaluate its mechanical integrity under mechanical and thermo-mechanical loading conditions. Molecular dynamics (MD) simulation was used to determine CNT/Cu interface adhesion properties. A cohesive zone model (CZM) was found to be most appropriate to model the interface adhesion, and CZM parameters at the nanoscale were determined using MD simulation. CZM parameters were then used in the finite element analysis in order to understand the mechanical and thermo-mechanical behavior of composite TSV at micro-scale. From the results, CNT/Cu separation does not take place prior to plastic deformation of Cu in bending, and separation does not take place when standard thermal cycling is applied. Further investigation is recommended in order to alleviate the increased plastic deformation in Cu at the CNT/Cu interface in both loading conditions. PMID:26559788
NASA Astrophysics Data System (ADS)
Awad, Ibrahim; Ladani, Leila
2015-12-01
Carbon nanotube (CNT)/copper (Cu) composite material is proposed to replace Cu-based through-silicon vias (TSVs) in micro-electronic packages. The proposed material is believed to offer extraordinary mechanical and electrical properties and the presence of CNTs in Cu is believed to overcome issues associated with miniaturization of Cu interconnects, such as electromigration. This study introduces a multi-scale modeling of the proposed TSV in order to evaluate its mechanical integrity under mechanical and thermo-mechanical loading conditions. Molecular dynamics (MD) simulation was used to determine CNT/Cu interface adhesion properties. A cohesive zone model (CZM) was found to be most appropriate to model the interface adhesion, and CZM parameters at the nanoscale were determined using MD simulation. CZM parameters were then used in the finite element analysis in order to understand the mechanical and thermo-mechanical behavior of composite TSV at micro-scale. From the results, CNT/Cu separation does not take place prior to plastic deformation of Cu in bending, and separation does not take place when standard thermal cycling is applied. Further investigation is recommended in order to alleviate the increased plastic deformation in Cu at the CNT/Cu interface in both loading conditions.
NASA Astrophysics Data System (ADS)
Li, Shihua; Liu, Yanmin; Cui, Hongliu; Niu, Yunzhan; Zhao, Yanzhi
2016-03-01
Although it is common to eliminate the singularity of parallel mechanism by adding the branched chain with actuation redundancy, there is no theory and method for the configuration synthesis of the branched chain with actuation redundancy in parallel mechanism. Branched chains with actuation redundancy are synthesized for eliminating interior singularity of 3-translational and 1- rotational(3T1R) parallel mechanisms. Guided by the discriminance method of hybrid screw group according to Grassmann line geometry, all the possibilities are listed for the occurrence of interior singularities in 3T1R parallel mechanism. Based on the linear relevance of screw system and the principles of eliminating parallel mechanism singularity with actuation redundancy, different types of branched chains with actuation redundancy are synthesized systematically to indicate the layout and the number of the branched chainsinterior with actuation redundancy. A general method is proposed for the configuration synthesis of the branched chains with actuation redundancy of the redundant parallel mechanism, and it builds a solid foundation for the subsequent performance optimization of the redundant actuation parallel mechanism.
MT3D was first developed by Chunmiao Zheng in 1990 at S.S. Papadopulos & Associates, Inc. with partial support from the U.S. Environmental Protection Agency (USEPA). Starting in 1990, MT3D was released as a pubic domain code from the USEPA. Commercial versions with enhanced capab...
NASA Technical Reports Server (NTRS)
1977-01-01
A market study of a proposed version of a 3-D eyetracker for initial use at NASA's Ames Research Center was made. The commercialization potential of a simplified, less expensive 3-D eyetracker was ascertained. Primary focus on present and potential users of eyetrackers, as well as present and potential manufacturers has provided an effective means of analyzing the prospects for commercialization.
2013-10-01
Earth3D is a computer code designed to allow fast calculation of seismic rays and travel times through a 3D model of the Earth. LLNL is using this for earthquake location and global tomography efforts and such codes are of great interest to the Earth Science community.
[3-D ultrasound in gastroenterology].
Zoller, W G; Liess, H
1994-06-01
Three-dimensional (3D) sonography represents a development of noninvasive diagnostic imaging by real-time two-dimensional (2D) sonography. The use of transparent rotating scans, comparable to a block of glass, generates a 3D effect. The objective of the present study was to optimate 3D presentation of abdominal findings. Additional investigations were made with a new volumetric program to determine the volume of selected findings of the liver. The results were compared with the estimated volumes of 2D sonography and 2D computer tomography (CT). For the processing of 3D images, typical parameter constellations were found for the different findings, which facilitated processing of 3D images. In more than 75% of the cases examined we found an optimal 3D presentation of sonographic findings with respect to the evaluation criteria developed by us for the 3D imaging of processed data. Great differences were found for the estimated volumes of the findings of the liver concerning the three different techniques applied. 3D ultrasound represents a valuable method to judge morphological appearance in abdominal findings. The possibility of volumetric measurements enlarges its potential diagnostic significance. Further clinical investigations are necessary to find out if definite differentiation between benign and malign findings is possible. PMID:7919882
2013-10-30
This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.
None
2014-02-26
This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.
Hoover, C G; DeGroot, A J; Sherwood, R J
2000-06-01
ParaDyn is a parallel version of the DYNA3D computer program, a three-dimensional explicit finite-element program for analyzing the dynamic response of solids and structures. The ParaDyn program has been used as a production tool for over three years for analyzing problems which range in size from a few tens of thousands of elements to between one-million and ten-million elements. ParaDyn runs on parallel computers provided by the Department of Energy Accelerated Strategic Computing Initiative (ASCI) and the Department of Defense High Performance Computing and Modernization Program. Preprocessing and post-processing software utilities and tools are designed to facilitate the generation of partitioned domains for processors on a massively parallel computer and the visualization of both resultant data and boundary data generated in a parallel simulation. This manual provides a brief overview of the parallel implementation; describes techniques for running the ParaDyn program, tools and utilities; and provides examples of parallel simulations.
NASA Astrophysics Data System (ADS)
Walsh, J. R.
2004-02-01
The Euro3D RTN is an EU funded Research Training Network to foster the exploitation of 3D spectroscopy in Europe. 3D spectroscopy is a general term for spectroscopy of an area of the sky and derives its name from its two spatial + one spectral dimensions. There are an increasing number of instruments which use integral field devices to achieve spectroscopy of an area of the sky, either using lens arrays, optical fibres or image slicers, to pack spectra of multiple pixels on the sky (``spaxels'') onto a 2D detector. On account of the large volume of data and the special methods required to reduce and analyse 3D data, there are only a few centres of expertise and these are mostly involved with instrument developments. There is a perceived lack of expertise in 3D spectroscopy spread though the astronomical community and its use in the armoury of the observational astronomer is viewed as being highly specialised. For precisely this reason the Euro3D RTN was proposed to train young researchers in this area and develop user tools to widen the experience with this particular type of data in Europe. The Euro3D RTN is coordinated by Martin M. Roth (Astrophysikalisches Institut Potsdam) and has been running since July 2002. The first Euro3D science conference was held in Cambridge, UK from 22 to 23 May 2003. The main emphasis of the conference was, in keeping with the RTN, to expose the work of the young post-docs who are funded by the RTN. In addition the team members from the eleven European institutes involved in Euro3D also presented instrumental and observational developments. The conference was organized by Andy Bunker and held at the Institute of Astronomy. There were over thirty participants and 26 talks covered the whole range of application of 3D techniques. The science ranged from Galactic planetary nebulae and globular clusters to kinematics of nearby galaxies out to objects at high redshift. Several talks were devoted to reporting recent observations with newly
NASA Technical Reports Server (NTRS)
Walatka, Pamela P.; Buning, Pieter G.; Pierce, Larry; Elson, Patricia A.
1990-01-01
PLOT3D is a computer graphics program designed to visualize the grids and solutions of computational fluid dynamics. Seventy-four functions are available. Versions are available for many systems. PLOT3D can handle multiple grids with a million or more grid points, and can produce varieties of model renderings, such as wireframe or flat shaded. Output from PLOT3D can be used in animation programs. The first part of this manual is a tutorial that takes the reader, keystroke by keystroke, through a PLOT3D session. The second part of the manual contains reference chapters, including the helpfile, data file formats, advice on changing PLOT3D, and sample command files.
Dawood, A; Marti Marti, B; Sauret-Jackson, V; Darwood, A
2015-12-01
3D printing has been hailed as a disruptive technology which will change manufacturing. Used in aerospace, defence, art and design, 3D printing is becoming a subject of great interest in surgery. The technology has a particular resonance with dentistry, and with advances in 3D imaging and modelling technologies such as cone beam computed tomography and intraoral scanning, and with the relatively long history of the use of CAD CAM technologies in dentistry, it will become of increasing importance. Uses of 3D printing include the production of drill guides for dental implants, the production of physical models for prosthodontics, orthodontics and surgery, the manufacture of dental, craniomaxillofacial and orthopaedic implants, and the fabrication of copings and frameworks for implant and dental restorations. This paper reviews the types of 3D printing technologies available and their various applications in dentistry and in maxillofacial surgery. PMID:26657435
NASA Astrophysics Data System (ADS)
Vilán Vilán, José Antonio; Aguado Agelet, Fernando; López Estévez, Miguel; González Muiño, Alberto
2015-02-01
The aim of this article is to announce the results for the antenna deployment mechanism on the Cubesat [1,4] Xatcobeo picosatellite which launched on 13th February, 2012 from the Kourou space port aboard the new VEGA rocket. It was also launched as part of Humsat-D on 21st November, 2013 aboard Dnepr. The main feature of the device is its extremely light weight, achieved by using polymeric materials and additive manufacturing. Analysis was not only made of detailed characteristics but also of the advantages of using this combination, its validity after almost two years of perfect operation in orbit on Xatcobeo, and its latest operational success on Humsat-D. The results show that it deployed as expected in orbit and that it continues to operate correctly on both missions, not only in terms of the deployment mechanism but also the materials used. The analysis focuses on the mechanism's operational reliability and long useful lifetime.
F3D Image Processing and Analysis for Many - and Multi-core Platforms
2014-10-01
F3D is written in OpenCL, so it achieve[sic] platform-portable parallelism on modern mutli-core CPUs and many-core GPUs. The interface and mechanims to access F3D core are written in Java as a plugin for Fiji/ImageJ to deliver several key image-processing algorithms necessary to remove artifacts from micro-tomography data. The algorithms consist of data parallel aware filters that can efficiently utilizes[sic] resources and can work on out of core datasets and scale efficiently across multiple accelerators. Optimizing for data parallel filters, streaming out of core datasets, and efficient resource and memory and data managements over complex execution sequence of filters greatly expedites any scientific workflow with image processing requirements. F3D performs several different types of 3D image processing operations, such as non-linear filtering using bilateral filtering and/or median filtering and/or morphological operators (MM). F3D gray-level MM operators are one-pass constant time methods that can perform morphological transformations with a line-structuring element oriented in discrete directions. Additionally, MM operators can be applied to gray-scale images, and consist of two parts: (a) a reference shape or structuring element, which is translated over the image, and (b) a mechanism, or operation, that defines the comparisons to be performed between the image and the structuring element. This tool provides a critical component within many complex pipelines such as those for performing automated segmentation of image stacks. F3D is also called a "descendent" of Quant-CT, another software we developed in the past. These two modules are to be integrated in a next version. Further details were reported in: D.M. Ushizima, T. Perciano, H. Krishnan, B. Loring, H. Bale, D. Parkinson, and J. Sethian. Structure recognition from high-resolution images of ceramic composites. IEEE International Conference on Big Data, October 2014.
PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITH TURB3D)
NASA Technical Reports Server (NTRS)
Buning, P.
1994-01-01
PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into
PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITHOUT TURB3D)
NASA Technical Reports Server (NTRS)
Buning, P.
1994-01-01
PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into
Real time 3D scanner: investigations and results
NASA Astrophysics Data System (ADS)
Nouri, Taoufik; Pflug, Leopold
1993-12-01
This article presents a concept of reconstruction of 3-D objects using non-invasive and touch loss techniques. The principle of this method is to display parallel interference optical fringes on an object and then to record the object under two angles of view. According to an appropriated treatment one reconstructs the 3-D object even when the object has no symmetrical plan. The 3-D surface data is available immediately in digital form for computer- visualization and for analysis software tools. The optical set-up for recording the 3-D object, the 3-D data extraction and treatment, as well as the reconstruction of the 3-D object are reported and commented on. This application is dedicated for reconstructive/cosmetic surgery, CAD, animation and research purposes.
Kinematics Analysis of the Parallel Mechanism with Vertically Fixed Linear Actuators
NASA Astrophysics Data System (ADS)
Masuda, Takanori; Fujiwara, Motoyoshi; Arai, Tatsuo
A 6 degrees of freedom parallel mechanism actuated by vertically fixed linear actuators was developed for heavy material handling and machining. The mechanism allows easy trajectory generation, since the vertical arrangement of the linear actuators simplifies the caluculation of its inverse kinematics. This paper presents inverse kinematics and Jacobian matirix solutions. Way to avoid component interference, which is divided into three types, is proposed. The combination of design parameters is decided by comparing the characteristics of area of movement, resolution and velocity. The working space is then shown. The singularity is analyzed by evaluating determinants of the Jacobian matrix. Lengthening the connecting rods and limiting the range of the end effector rotational angles are effective in avoiding the singular configurations as well as interference. Finally, the developed prototype mechanism is introduced, and its application to tool positioning and machining is described.
3-D Volume Rendering of Sand Specimen
NASA Technical Reports Server (NTRS)
2004-01-01
Computed tomography (CT) images of resin-impregnated Mechanics of Granular Materials (MGM) specimens are assembled to provide 3-D volume renderings of density patterns formed by dislocation under the external loading stress profile applied during the experiments. Experiments flown on STS-79 and STS-89. Principal Investigator: Dr. Stein Sture
Development and qualification of a mechanical-optical interface for parallel optics links
NASA Astrophysics Data System (ADS)
Chuang, S.; Schoellner, D.; Ugolini, A.; Wakjira, J.; Wolf, G.
2015-03-01
As parallel optics applications continue to expand, there remains a need for an effective coupling interface between the board-level active components and the passive components of the network. While mid-board level photonic turn connectors are available, coupling interfaces are generally not available outside of proprietary solutions. Development of a general mechanical-optical coupling interface opens the door for broader parallel optics implementation. An interface for use between the optical transmitter and the photonic turn connector is introduced. The interface is a monolithic injection molded component with an array of collimating lenses to couple efficiently with common VCSEL/PD designs. The component has precise epoxy control features to manage epoxy bond-line thickness and strength. Suitable UV and thermal epoxies have been qualified for effective die bond placement of the component in the VCSEL/PD environment. Environmental and mechanical performance of the component to industry-standard qualification requirements are reviewed, and tensile force testing and durability results validate the mechanical characteristics of the interface.
Stanton, M M; Samitier, J; Sánchez, S
2015-08-01
Three-dimensional (3D) bioprinting has recently emerged as an extension of 3D material printing, by using biocompatible or cellular components to build structures in an additive, layer-by-layer methodology for encapsulation and culture of cells. These 3D systems allow for cell culture in a suspension for formation of highly organized tissue or controlled spatial orientation of cell environments. The in vitro 3D cellular environments simulate the complexity of an in vivo environment and natural extracellular matrices (ECM). This paper will focus on bioprinting utilizing hydrogels as 3D scaffolds. Hydrogels are advantageous for cell culture as they are highly permeable to cell culture media, nutrients, and waste products generated during metabolic cell processes. They have the ability to be fabricated in customized shapes with various material properties with dimensions at the micron scale. 3D hydrogels are a reliable method for biocompatible 3D printing and have applications in tissue engineering, drug screening, and organ on a chip models. PMID:26066320
Unassisted 3D camera calibration
NASA Astrophysics Data System (ADS)
Atanassov, Kalin; Ramachandra, Vikas; Nash, James; Goma, Sergio R.
2012-03-01
With the rapid growth of 3D technology, 3D image capture has become a critical part of the 3D feature set on mobile phones. 3D image quality is affected by the scene geometry as well as on-the-device processing. An automatic 3D system usually assumes known camera poses accomplished by factory calibration using a special chart. In real life settings, pose parameters estimated by factory calibration can be negatively impacted by movements of the lens barrel due to shaking, focusing, or camera drop. If any of these factors displaces the optical axes of either or both cameras, vertical disparity might exceed the maximum tolerable margin and the 3D user may experience eye strain or headaches. To make 3D capture more practical, one needs to consider unassisted (on arbitrary scenes) calibration. In this paper, we propose an algorithm that relies on detection and matching of keypoints between left and right images. Frames containing erroneous matches, along with frames with insufficiently rich keypoint constellations, are detected and discarded. Roll, pitch yaw , and scale differences between left and right frames are then estimated. The algorithm performance is evaluated in terms of the remaining vertical disparity as compared to the maximum tolerable vertical disparity.
Honda, Wataru; Harada, Shingo; Ishida, Shohei; Arie, Takayuki; Akita, Seiji; Takei, Kuniharu
2015-08-26
A vertically integrated inorganic-based flexible complementary metal-oxide-semiconductor (CMOS) inverter with a temperature sensor with a high inverter gain of ≈50 and a low power consumption of <7 nW mm(-1) is demonstrated using a layer-by-layer assembly process. In addition, the negligible influence of the mechanical flexibility on the performance of the CMOS inverter and the temperature dependence of the CMOS inverter characteristics are discussed. PMID:26177598
Alama-Bermejo, Gema; Bron, James Emmanuel; Raga, Juan Antonio; Holzer, Astrid Sibylle
2012-01-01
Free, amoeboid movement of organisms within media as well as substrate-dependent cellular crawling processes of cells and organisms require an actin cytoskeleton. This system is also involved in the cytokinetic processes of all eukaryotic cells. Myxozoan parasites are known for the disease they cause in economical important fishes. Usually, their pathology is related to rapid proliferation in the host. However, the sequences of their development are still poorly understood, especially with regard to pre-sporogonic proliferation mechanisms. The present work employs light microscopy (LM), electron microscopy (SEM, TEM) and confocal laser scanning microscopy (CLSM) in combination with specific stains (Nile Red, DAPI, Phalloidin), to study the three-dimensional morphology, motility, ultrastructure and cellular composition of Ceratomyxa puntazzi, a myxozoan inhabiting the bile of the sharpsnout seabream. Our results demonstrate the occurrence of two C. puntazzi developmental cycles in the bile, i.e. pre-sporogonic proliferation including frequent budding as well as sporogony, resulting in the formation of durable spore stages and we provide unique details on the ultrastructure and the developmental sequence of bile inhabiting myxozoans. The present study describes, for the first time, the cellular components and mechanisms involved in the motility of myxozoan proliferative stages, and reveals how the same elements are implicated in the processes of budding and cytokinesis in the Myxozoa. We demonstrate that F-actin rich cytoskeletal elements polarize at one end of the parasites and in the filopodia which are rapidly de novo created and re-absorbed, thus facilitating unidirectional parasite motility in the bile. We furthermore discover the myxozoan mechanism of budding as an active, polarization process of cytokinesis, which is independent from a contractile ring and thus differs from the mechanism, generally observed in eurkaryotic cells. We hereby demonstrate that CLSM
Arena3D: visualization of biological networks in 3D
Pavlopoulos, Georgios A; O'Donoghue, Seán I; Satagopam, Venkata P; Soldatos, Theodoros G; Pafilis, Evangelos; Schneider, Reinhard
2008-01-01
Background Complexity is a key problem when visualizing biological networks; as the number of entities increases, most graphical views become incomprehensible. Our goal is to enable many thousands of entities to be visualized meaningfully and with high performance. Results We present a new visualization tool, Arena3D, which introduces a new concept of staggered layers in 3D space. Related data – such as proteins, chemicals, or pathways – can be grouped onto separate layers and arranged via layout algorithms, such as Fruchterman-Reingold, distance geometry, and a novel hierarchical layout. Data on a layer can be clustered via k-means, affinity propagation, Markov clustering, neighbor joining, tree clustering, or UPGMA ('unweighted pair-group method with arithmetic mean'). A simple input format defines the name and URL for each node, and defines connections or similarity scores between pairs of nodes. The use of Arena3D is illustrated with datasets related to Huntington's disease. Conclusion Arena3D is a user friendly visualization tool that is able to visualize biological or any other network in 3D space. It is free for academic use and runs on any platform. It can be downloaded or lunched directly from . Java3D library and Java 1.5 need to be pre-installed for the software to run. PMID:19040715
NASA Astrophysics Data System (ADS)
Dhakal, Binod
The intermetallic NiTi-based alloys are known as Shape Memory material. They exhibit unique ability to remember a shape after large deformation. They are desirable in various engineering applications, such as actuators, biomedical devices, vibration damping, etc, as they can absorb and dissipate mechanical/thermal energies by undergoing a reversible hysteretic shape change under the applied mechanical/thermal cyclic loadings. This reflects the effect of micro-structural changes occurring during phase transformation between Austenite(A) and Martensite(M), as well as differently-oriented M-variants. As typically utilized in applications, a particular shape memory alloy (SMA) device or component operates under a large number of thermo-mechanical cycles, hence, the importance of accounting for the cyclic behavior characteristics in modeling and characterization of these systems. A detailed study of the multi-mechanism-based, comprehensive, thus complex modeling framework (by Saleeb et al) and the determination of its material parameters responsible for the physical significance of the shape memory effect are made. This formulation utilizes multiple, inelastic mechanisms to regulate the partitioning of energy dissipation and storage governing the evolutionary thermo-mechanical behavior. Equipped with the understanding of the physical significance of the model parameters and utilizing the SMA modeling strategy effectively, a comprehensive characterization of the evolutionary, cyclic response of the complex real SMA, known as 55NiTi (Ni49.9Ti50.1) is carried out. The detailed comparisons between the SMA model and experimental results provided the necessary validation of the modeling capabilities of the framework to calibrate the complex alloys like 55NiTi. In addition, the details of interplays between the internal mechanisms to describe the material behavior within all the important response characteristic regions provides a convenient means to compliment the theoretical
NASA Astrophysics Data System (ADS)
Otis, Collin; Ferrero, Pietro; Candler, Graham; Givi, Peyman
2013-11-01
The scalar filtered mass density function (SFMDF) methodology is implemented into the computer code US3D. This is an unstructured Eulerian finite volume hydrodynamic solver and has proven very effective for simulation of compressible turbulent flows. The resulting SFMDF-US3D code is employed for large eddy simulation (LES) on unstructured meshes. Simulations are conducted of subsonic and supersonic flows under non-reacting and reacting conditions. The consistency and the accuracy of the simulated results are assessed along with appraisal of the overall performance of the methodology. The SFMDF-US3D is now capable of simulating high speed flows in complex configurations.
Hong, Sungmin; Sycks, Dalton; Chan, Hon Fai; Lin, Shaoting; Lopez, Gabriel P; Guilak, Farshid; Leong, Kam W; Zhao, Xuanhe
2015-07-15
X. Zhao and co-workers develop on page 4035 a new biocompatible hydrogel system that is extremely tough and stretchable and can be 3D printed into complex structures, such as the multilayer mesh shown. Cells encapsulated in the tough and printable hydrogel maintain high viability. 3D-printed structures of the tough hydrogel can sustain high mechanical loads and deformations. PMID:26172844
Flynn, Cormac; Taberner, Andrew; Nielsen, Poul
2011-02-01
The complex mechanical properties of skin have been the subject of much study in recent years. Several experimental methods developed to measure the mechanical properties of skin in vivo, such as suction or torsion, are unable to measure skin's anisotropic characteristics. An experiment characterising the mechanical properties of in vivo human skin using a novel force-sensitive micro-robot is presented. The micro-robot applied in-plane deformations to the anterior forearm and the posterior upper arm. The behaviour of the skin in each area is highly nonlinear, anisotropic, and viscoelastic. The response of the upper arm skin is very dependent on the orientation of the arm. A finite element model consisting of an Ogden strain energy function and quasi-linear viscoelasticity was developed to simulate the experiments. An orthogonal initial stress field, representing the in vivo skin tension, was used as an additional model parameter. The model simulated the experiments accurately with an error-of-fit of 17.5% for the anterior lower forearm area, 6.5% for the anterior upper forearm and 9.3% for the posterior upper arm. The maximum in vivo tension in each area determined by the model was 6.2 Nm(-1) in the anterior lower forearm, 11.4 Nm(-1) in anterior upper forearm and 5.6 Nm(-1) in the posterior upper arm. The results also show that a finite element model with a neo-Hookean strain energy function cannot simulate the experiments with the same accuracy. PMID:20429025
NASA Astrophysics Data System (ADS)
Barnhart, D. H.; Chan, V. S. S.; Halliwell, N. A.; Coupland, J. M.
2002-08-01
This paper reports on a new form of holographic metrology that enables displacement measurement in both fluid and solid mechanics simultaneously. In such instances, existing holographic methods for displacement measurement would require the application of multiple techniques in a hybrid fashion. Known as object-conjugate reconstruction (OCR), our new approach unifies the disciplines of holographic velocimetry and holographic interferometry. Using complex correlation processing, it provides a sub-wavelength resolution for all three components of displacement and enables automated data extraction at selected points throughout a volume in space.
Fratev, Filip; Benfenati, Emilio
2005-01-01
A combination between 3D-QSAR and molecular mechanics (MM)-docking study was used as a tool to detail and model the mechanism of action of 46 antifungal azoles. Two methods of alignment of the ligands were performed: (i) alignment of the main skeleton without substituents and (ii) alignment of a defined substructure. The best model is characterized by q(2) with the values of 0.70 for yeastlike (yeast), 0.66 for filamentous fungi, and 0.70 for the selectivity against filamentous fungi. 3D-QSAR regression maps derived from six models were used to identify the regions responsible for the differences in the compounds activity against yeast and filamentous fungi. The binding energy of the important substructures (Local Binding Energy-LBE) and its standard deviation were calculated in order to demonstrate quantitatively the contribution of substituents reflecting the diversity of the antifungal activity. The comparisons of these results with the same regions of the contour maps indicated a good correspondence between the 3D-QSAR and MM (LBE) approaches allowing association between the maps and the participating residues in the active sites of P450DM of C. albicans and A. fumigatus. The pi-pi interactions of two or more aromatic groups of the ligands with Phe228 and Tyr132 prove to be most important for the differences in activity against C. albicans. In A. fumigatus there was a better occupation of the inner central I-spiral in the areas around the heme. For the activity against A. fumigatus the pi-pi interactions of aromatic groups of the compounds with Phe509, Phe228, and Tyr132 are significant for the activity. PMID:15921453
Visual inertia of rotating 3-D objects.
Jiang, Y; Pantle, A J; Mark, L S
1998-02-01
Five experiments were designed to determine whether a rotating, transparent 3-D cloud of dots (simulated sphere) could influence the perceived direction of rotation of a subsequent sphere. Experiment 1 established conditions under which the direction of rotation of a virtual sphere was perceived unambiguously. When a near-far luminance difference and perspective depth cues were present, observers consistently saw the sphere rotate in the intended direction. In Experiment 2, a near-far luminance difference was used to create an unambiguous rotation sequence that was followed by a directionally ambiguous rotation sequence that lacked both the near-far luminance cue and the perspective cue. Observers consistently saw the second sequence as rotating in the same direction as the first, indicating the presence of 3-D visual inertia. Experiment 3 showed that 3-D visual inertia was sufficiently powerful to bias the perceived direction of a rotation sequence made unambiguous by a near-far luminance cue. Experiment 5 showed that 3-D visual inertia could be obtained using an occlusion depth cue to create an unambiguous inertia-inducing sequence. Finally, Experiments 2, 4, and 5 all revealed a fast-decay phase of inertia that lasted for approximately 800 msec, followed by an asymptotic phase that lasted for periods as long as 1,600 msec. The implications of these findings are examined with respect to motion mechanisms of 3-D visual inertia. PMID:9529911
Chilcoat, S.R. Hildebrand, S.T.
1995-12-31
Travel time computation in inhomogeneous media is essential for pre-stack Kirchhoff imaging in areas such as the sub-salt province in the Gulf of Mexico. The 2D algorithm published by Vinje, et al, has been extended to 3D to compute wavefronts in complicated inhomogeneous media. The 3D wavefront construction algorithm provides many advantages over conventional ray tracing and other methods of computing travel times in 3D. The algorithm dynamically maintains a reasonably consistent ray density without making a priori guesses at the number of rays to shoot. The determination of caustics in 3D is a straight forward geometric procedure. The wavefront algorithm also enables the computation of multi-valued travel time surfaces.
NASA Astrophysics Data System (ADS)
Yang, Xu; Zhang, Yong; Yang, Chenghua; Xu, Lu; Wang, Qiang; Zhao, Yuan
2016-06-01
Conventional three dimensional (3D) ghost imaging measures range of target based on pulse fight time measurement method. Due to the limit of data acquisition system sampling rate, range resolution of the conventional 3D ghost imaging is usually low. In order to take off the effect of sampling rate to range resolution of 3D ghost imaging, a heterodyne 3D ghost imaging (HGI) system is presented in this study. The source of HGI is a continuous wave laser instead of pulse laser. Temporal correlation and spatial correlation of light are both utilized to obtain the range image of target. Through theory analysis and numerical simulations, it is demonstrated that HGI can obtain high range resolution image with low sampling rate.
3D Numerical simulations of oblique subduction
NASA Astrophysics Data System (ADS)
Malatesta, C.; Gerya, T.; Scambelluri, M.; Crispini, L.; Federico, L.; Capponi, G.
2012-04-01
In the past 2D numerical studies (e.g. Gerya et al., 2002; Gorczyk et al., 2007; Malatesta et al., 2012) provided evidence that during intraoceanic subduction a serpentinite channel forms above the downgoing plate. This channel forms as a result of hydration of the mantle wedge by uprising slab-fluids. Rocks buried at high depths are finally exhumed within this buoyant low-viscosity medium. Convergence rate in these 2D models was described by a trench-normal component of velocity. Several present and past subduction zones worldwide are however driven by oblique convergence between the plates, where trench-normal motion of the subducting slab is coupled with trench-parallel displacement of the plates. Can the exhumation mechanism and the exhumation rates of high-pressure rocks be affected by the shear component of subduction? And how uprise of these rocks can vary along the plate margin? We tried to address these questions performing 3D numerical models that simulate an intraoceanic oblique subduction. The models are based on thermo-mechanical equations that are solved with finite differences method and marker-in-cell techniques combined with multigrid approach (Gerya, 2010). In most of the models a narrow oceanic basin (500 km-wide) surrounded by continental margins is depicted. The basin is floored by either layered or heterogeneous oceanic lithosphere with gabbro as discrete bodies in serpentinized peridotite and a basaltic layer on the top. A weak zone in the mantle is prescribed to control the location of subduction initiation and therefore the plate margins geometry. Finally, addition of a third dimension in the simulations allowed us to test the role of different plate margin geometries on oblique subduction dynamics. In particular in each model we modified the dip angle of the weak zone and its "lateral" geometry (e.g. continuous, segmented). We consider "continuous" weak zones either parallel or increasingly moving away from the continental margins
3D Tissue-Engineered Model of Ewing Sarcoma
Lamhamedi-Cherradi, Salah-Eddine; Santoro, Marco; Ramammoorthy, Vandhana; Menegaz, Brian A.; Bartholomeusz, Geoffrey; Iles, Lakesla R.; Amin, Hesham M.; Livingston, Andrew J.; Mikos, Antonios G.; Ludwig, Joseph A.
2015-01-01
Despite longstanding reliance upon monolayer culture for studying cancer cells, and numerous advantages from both a practical and experimental standpoint, a growing body of evidence suggests more complex three-dimensional (3D) models are necessary to properly mimic many of the critical hallmarks associated with the oncogenesis, maintenance and spread of Ewing sarcoma (ES), the second most common pediatric bone tumor. And as clinicians increasingly turn to biologically-targeted therapies that exert their effects not only on the tumor cells themselves, but also on the surrounding extracellular matrix, it is especially important that preclinical models evolve in parallel to reliably measure antineoplastic effects and possible mechanisms of de novo and acquired drug resistance. Herein, we highlight a number of innovative methods used to fabricate biomimetic ES tumors, encompassing both the surrounding cellular milieu and extracellular matrix (ECM), and suggest potential applications to advance our understanding of ES biology, preclinical drug testing, and personalized medicine. PMID:25109853
Rohringer, Sabrina; Hofbauer, Pablo; Schneider, Karl H; Husa, Anna-Maria; Feichtinger, Georg; Peterbauer-Scherb, Anja; Redl, Heinz; Holnthoner, Wolfgang
2014-10-01
Vascularization of tissue-engineered constructs is essential to provide sufficient nutrient supply and hemostasis after implantation into target sites. Co-cultures of adipose-derived stem cells (ASC) with outgrowth endothelial cells (OEC) in fibrin gels were shown to provide an effective possibility to induce vasculogenesis in vitro. However, the mechanisms of the interaction between these two cell types remain unclear so far. The aim of this study was to evaluate differences of direct and indirect stimulation of ASC-induced vasculogenesis, the influence of ASC on network stabilization and molecular mechanisms involved in vascular structure formation. Endothelial cells (EC) were embedded in fibrin gels either containing non-coated or ASC-coated microcarrier beads as well as ASC alone. Moreover, EC-seeded constructs incubated with ASC-conditioned medium were used in addition to constructs with ASC seeded on top. Vascular network formation was visualized by green fluorescent protein expressing cells or immunostaining for CD31 and quantified. RT-qPCR of cells derived from co-cultures in fibrin was performed to evaluate changes in the expression of EC marker genes during the first week of culture. Moreover, angiogenesis-related protein levels were measured by performing angiogenesis proteome profiler arrays. The results demonstrate that proximity of endothelial cells and ASC is required for network formation and ASC stabilize EC networks by developing pericyte characteristics. We further showed that ASC induce controlled vessel growth by secreting pro-angiogenic and regulatory proteins. This study reveals angiogenic protein profiles involved in EC/ASC interactions in fibrin matrices and confirms the usability of OEC/ASC co-cultures for autologous vascular tissue engineering. PMID:25086616
Lee, Sehan; Barron, Mace G
2016-04-01
Organophosphate (OP) and carbamate esters can inhibit acetylcholinesterase (AChE) by binding covalently to a serine residue in the enzyme active site, and their inhibitory potency depends largely on affinity for the enzyme and the reactivity of the ester. Despite this understanding, there has been no mechanism-based in silico approach for classification and prediction of the inhibitory potency of ether OPs or carbamates. This prompted us to develop a three dimensional prediction framework for OPs, carbamates, and their analogs. Inhibitory structures of a compound that can form the covalent bond were identified through analysis of docked conformations of the compound and its metabolites. Inhibitory potencies of the selected structures were then predicted using a previously developed three dimensional quantitative structure-active relationship. This approach was validated with a large number of structurally diverse OP and carbamate compounds encompassing widely used insecticides and structural analogs including OP flame retardants and thio- and dithiocarbamate pesticides. The modeling revealed that: (1) in addition to classical OP metabolic activation, the toxicity of carbamate compounds can be dependent on biotransformation, (2) OP and carbamate analogs such as OP flame retardants and thiocarbamate herbicides can act as AChEI, (3) hydrogen bonds at the oxyanion hole is critical for AChE inhibition through the covalent bond, and (4) π-π interaction with Trp86 is necessary for strong inhibition of AChE. Our combined computation approach provided detailed understanding of the mechanism of action of OP and carbamate compounds and may be useful for screening a diversity of chemical structures for AChE inhibitory potency. PMID:27055524
NASA Astrophysics Data System (ADS)
Martinez, J.; Belahcen, A.; Detoni, J. G.
2016-01-01
This paper presents a coupled Finite Element Model in order to study the vibrations in induction motors under steady-state. The model utilizes a weak coupling strategy between both magnetic and elastodynamic fields on the structure. Firstly, the problem solves the magnetic vector potential in an axial cut and secondly the former solution is coupled to a three dimensional model of the stator. The coupling is performed using projection based algorithms between the computed magnetic solution and the three-dimensional mesh. The three-dimensional model of the stator includes both end-windings and end-shields in order to give a realistic picture of the motor. The present model is validated using two steps. Firstly, a modal analysis hammer test is used to validate the material characteristic of this complex structure and secondly an array of accelerometer sensors is used in order to study the rotating waves using multi-dimensional spectral techniques. The analysis of the radial vibrations presented in this paper firstly concludes that slot harmonic components are visible when the motor is loaded. Secondly, the multidimensional spectrum presents the most relevant mechanical waves on the stator such as the ones produced by the space harmonics or the saturation of the iron core. The direct retrieval of the wave-number in a multi-dimensional spectrum is able to show the internal current distribution in a non-intrusive way. Experimental results for healthy induction motors are showing mechanical imbalances in a multi-dimensional spectrum in a more straightforward form.
Piezo-actuated parallel mechanism for biological cell release at high speed.
Avci, Ebubekir; Hattori, Takayuki; Kamiyama, Kazuto; Kojima, Masaru; Horade, Mitsuhiro; Mae, Yasushi; Arai, Tatsuo
2015-10-01
In this paper, a dynamic releasing approach is proposed for high-speed biological cell manipulation. A compact parallel mechanism for grasping and releasing microobjects is used to generate controllable vibration to overcome the strong adhesion forces between the end effector and the manipulated object. To reach the required acceleration of the end effector, which is necessary for the detachment of the target object by overcoming adhesion forces, vibration in the end effector is generated by applying sinusoidal voltage to the PZT actuator of the parallel mechanism. For the necessary acceleration, we focus on the possible range of the frequency of the PZT-actuator-induced vibration, while minimizing the amplitude of the vibration (14 nm) to achieve precise positioning. The effect of the air and liquid environments on the required vibration frequency for successful release is investigated. For the first time, release results of microbeads and biological cells are compared. Release of the biological cells with 100 % success rate suggests that the proposed active release method is an appropriate solution for adhered biological cells during the release task. PMID:26343357
NASA Astrophysics Data System (ADS)
Zhao, M.; Wang, J.; Qiu, X.; Sibuet, J. C.; He, E.; Zhang, J.
2015-12-01
The post-spreading volcanic ridge (PSVR) is oriented approximately E-W in its western part called the Zhenbei-Huangyan seamount chain. Where is the extinct spreading ridge (ESR) of the East Sub-basin located? beneath the PSVR (Li et al., 2014)? Or intersecting with the PSVR by N055° orientation (Sibuet et al., submitted)? A three-dimensional Ocean Bottom Seismometer (OBS) survey covered both the central extinct spreading ridge and the Zhenbei-Huangyan seamount chain, the IODP Site U1431 (Li et al., 2014) being located just north of the chain. The results of this experiment will provide the essential information to understand the emplacement of the PSVR within the previously formed oceanic crust. The comprehensive seismic record sections of 39 OBSs are of high quality and show clear and reliable P-wave seismic phases, such as Pg, Pn and PmP. These seismic arrivals provide strong constrains for modeling the detailed three-dimensional velocity structure. We will show that the crust is oceanic on each side of the Zhenbei-Huangyan seamount chain, where is the location of the ESR and what is the genetic relationship between the magma chambers and the overlying Zhenbei-Huangyan seamount chain. We suggest that the large thickness of the upper crust is possibly due to volcanic extrusions and the thickened lower crust to magmatic underplating. Combining previous geochemical study of PSVR outcropping samples, the formation mechanism of the seamount chain might be explained by a buoyancy decompression melting mechanism (Castillo et al., 2010). This research was granted by the Natural Science Foundation of China (91028002, 91428204, 41176053). ReferencesSibuet J.-C., Yeh Y.-C. and Lee C.-S., 2015 submitted. Geodynamics of the South China Sea: A review with emphasis on solved and unsolved questions. Tectonophysics. Li, C. F., et al. 2014. Ages and magnetic structures of the South China Sea constrained by deep tow magnetic surveys and IODP Expedition 349. Geochemistry
A microfluidic device for 2D to 3D and 3D to 3D cell navigation
NASA Astrophysics Data System (ADS)
Shamloo, Amir; Amirifar, Leyla
2016-01-01
Microfluidic devices have received wide attention and shown great potential in the field of tissue engineering and regenerative medicine. Investigating cell response to various stimulations is much more accurate and comprehensive with the aid of microfluidic devices. In this study, we introduced a microfluidic device by which the matrix density as a mechanical property and the concentration profile of a biochemical factor as a chemical property could be altered. Our microfluidic device has a cell tank and a cell culture chamber to mimic both 2D to 3D and 3D to 3D migration of three types of cells. Fluid shear stress is negligible on the cells and a stable concentration gradient can be obtained by diffusion. The device was designed by a numerical simulation so that the uniformity of the concentration gradients throughout the cell culture chamber was obtained. Adult neural cells were cultured within this device and they showed different branching and axonal navigation phenotypes within varying nerve growth factor (NGF) concentration profiles. Neural stem cells were also cultured within varying collagen matrix densities while exposed to NGF concentrations and they experienced 3D to 3D collective migration. By generating vascular endothelial growth factor concentration gradients, adult human dermal microvascular endothelial cells also migrated in a 2D to 3D manner and formed a stable lumen within a specific collagen matrix density. It was observed that a minimum absolute concentration and concentration gradient were required to stimulate migration of all types of the cells. This device has the advantage of changing multiple parameters simultaneously and is expected to have wide applicability in cell studies.
Zheng, Zhong-liang; Zuo, Zhen-yu; Liu, Zhi-gang; Tsai, Keng-chang; Liu, Ai-fu; Zou, Guo-lin
2005-01-01
A three-dimensional structural model of nattokinase (NK) from Bacillus natto was constructed by homology modeling. High-resolution X-ray structures of Subtilisin BPN' (SB), Subtilisin Carlsberg (SC), Subtilisin E (SE) and Subtilisin Savinase (SS), four proteins with sequential, structural and functional homology were used as templates. Initial models of NK were built by MODELLER and analyzed by the PROCHECK programs. The best quality model was chosen for further refinement by constrained molecular dynamics simulations. The overall quality of the refined model was evaluated. The refined model NKC1 was analyzed by different protein analysis programs including PROCHECK for the evaluation of Ramachandran plot quality, PROSA for testing interaction energies and WHATIF for the calculation of packing quality. This structure was found to be satisfactory and also stable at room temperature as demonstrated by a 300ps long unconstrained molecular dynamics (MD) simulation. Further docking analysis promoted the coming of a new nucleophilic catalytic mechanism for NK, which is induced by attacking of hydroxyl rich in catalytic environment and locating of S221. PMID:15670958
NASA Astrophysics Data System (ADS)
Seidenberger, K.; Wilhelm, F.; Schmitt, T.; Lehnert, W.; Scholta, J.
Understanding of both water management in PEM fuel cells and degradation mechanisms of the gas diffusion layer (GDL) and their mutual impact is still at least incomplete. Different modelling approaches contribute to gain deeper insight into the processes occurring during fuel cell operation. Considering the GDL, the models can help to obtain information about the distribution of liquid water within the material. Especially, flooded regions can be identified, and the water distribution can be linked to the system geometry. Employed for material development, this information can help to increase the life time of the GDL as a fuel cell component and the fuel cell as the entire system. The Monte Carlo (MC) model presented here helps to simulate and analyse the water household in PEM fuel cell GDLs. This model comprises a three-dimensional, voxel-based representation of the GDL substrate, a section of the flowfield channel and the corresponding rib. Information on the water distribution within the substrate part of the GDL can be estimated.
Emerging Applications of Bedside 3D Printing in Plastic Surgery.
Chae, Michael P; Rozen, Warren M; McMenamin, Paul G; Findlay, Michael W; Spychal, Robert T; Hunter-Smith, David J
2015-01-01
Modern imaging techniques are an essential component of preoperative planning in plastic and reconstructive surgery. However, conventional modalities, including three-dimensional (3D) reconstructions, are limited by their representation on 2D workstations. 3D printing, also known as rapid prototyping or additive manufacturing, was once the province of industry to fabricate models from a computer-aided design (CAD) in a layer-by-layer manner. The early adopters in clinical practice have embraced the medical imaging-guided 3D-printed biomodels for their ability to provide tactile feedback and a superior appreciation of visuospatial relationship between anatomical structures. With increasing accessibility, investigators are able to convert standard imaging data into a CAD file using various 3D reconstruction softwares and ultimately fabricate 3D models using 3D printing techniques, such as stereolithography, multijet modeling, selective laser sintering, binder jet technique, and fused deposition modeling. However, many clinicians have questioned whether the cost-to-benefit ratio justifies its ongoing use. The cost and size of 3D printers have rapidly decreased over the past decade in parallel with the expiration of key 3D printing patents. Significant improvements in clinical imaging and user-friendly 3D software have permitted computer-aided