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