structured multi-block computational: Topics by Science.gov

Sample records for structured multi-block computational

Gaussian curvature analysis allows for automatic block placement in multi-block hexahedral meshing.

PubMed

Ramme, Austin J; Shivanna, Kiran H; Magnotta, Vincent A; Grosland, Nicole M

2011-10-01

Musculoskeletal finite element analysis (FEA) has been essential to research in orthopaedic biomechanics. The generation of a volumetric mesh is often the most challenging step in a FEA. Hexahedral meshing tools that are based on a multi-block approach rely on the manual placement of building blocks for their mesh generation scheme. We hypothesise that Gaussian curvature analysis could be used to automatically develop a building block structure for multi-block hexahedral mesh generation. The Automated Building Block Algorithm incorporates principles from differential geometry, combinatorics, statistical analysis and computer science to automatically generate a building block structure to represent a given surface without prior information. We have applied this algorithm to 29 bones of varying geometries and successfully generated a usable mesh in all cases. This work represents a significant advancement in automating the definition of building blocks.
An electrostatic Particle-In-Cell code on multi-block structured meshes

NASA Astrophysics Data System (ADS)

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca; Vernon, Louis J.; Moulton, J. David

2017-12-01

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. Despite the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where an arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma-material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. Compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.
An electrostatic Particle-In-Cell code on multi-block structured meshes

DOE PAGES

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca; ...

2017-09-14

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. In spite of the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where anmore » arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma–material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. And compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.« less
An electrostatic Particle-In-Cell code on multi-block structured meshes

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

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. In spite of the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where anmore » arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma–material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. And compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.« less
Investigation of upwind, multigrid, multiblock numerical schemes for three dimensional flows. Volume 1: Runge-Kutta methods for a thin layer Navier-Stokes solver

NASA Technical Reports Server (NTRS)

Cannizzaro, Frank E.; Ash, Robert L.

1992-01-01

A state-of-the-art computer code has been developed that incorporates a modified Runge-Kutta time integration scheme, upwind numerical techniques, multigrid acceleration, and multi-block capabilities (RUMM). A three-dimensional thin-layer formulation of the Navier-Stokes equations is employed. For turbulent flow cases, the Baldwin-Lomax algebraic turbulence model is used. Two different upwind techniques are available: van Leer's flux-vector splitting and Roe's flux-difference splitting. Full approximation multi-grid plus implicit residual and corrector smoothing were implemented to enhance the rate of convergence. Multi-block capabilities were developed to provide geometric flexibility. This feature allows the developed computer code to accommodate any grid topology or grid configuration with multiple topologies. The results shown in this dissertation were chosen to validate the computer code and display its geometric flexibility, which is provided by the multi-block structure.
Adaptation of a Multi-Block Structured Solver for Effective Use in a Hybrid CPU/GPU Massively Parallel Environment

NASA Astrophysics Data System (ADS)

Gutzwiller, David; Gontier, Mathieu; Demeulenaere, Alain

2014-11-01

Multi-Block structured solvers hold many advantages over their unstructured counterparts, such as a smaller memory footprint and efficient serial performance. Historically, multi-block structured solvers have not been easily adapted for use in a High Performance Computing (HPC) environment, and the recent trend towards hybrid GPU/CPU architectures has further complicated the situation. This paper will elaborate on developments and innovations applied to the NUMECA FINE/Turbo solver that have allowed near-linear scalability with real-world problems on over 250 hybrid GPU/GPU cluster nodes. Discussion will focus on the implementation of virtual partitioning and load balancing algorithms using a novel meta-block concept. This implementation is transparent to the user, allowing all pre- and post-processing steps to be performed using a simple, unpartitioned grid topology. Additional discussion will elaborate on developments that have improved parallel performance, including fully parallel I/O with the ADIOS API and the GPU porting of the computationally heavy CPUBooster convergence acceleration module. Head of HPC and Release Management, Numeca International.
GPU-accelerated computing for Lagrangian coherent structures of multi-body gravitational regimes

NASA Astrophysics Data System (ADS)

Lin, Mingpei; Xu, Ming; Fu, Xiaoyu

2017-04-01

Based on a well-established theoretical foundation, Lagrangian Coherent Structures (LCSs) have elicited widespread research on the intrinsic structures of dynamical systems in many fields, including the field of astrodynamics. Although the application of LCSs in dynamical problems seems straightforward theoretically, its associated computational cost is prohibitive. We propose a block decomposition algorithm developed on Compute Unified Device Architecture (CUDA) platform for the computation of the LCSs of multi-body gravitational regimes. In order to take advantage of GPU's outstanding computing properties, such as Shared Memory, Constant Memory, and Zero-Copy, the algorithm utilizes a block decomposition strategy to facilitate computation of finite-time Lyapunov exponent (FTLE) fields of arbitrary size and timespan. Simulation results demonstrate that this GPU-based algorithm can satisfy double-precision accuracy requirements and greatly decrease the time needed to calculate final results, increasing speed by approximately 13 times. Additionally, this algorithm can be generalized to various large-scale computing problems, such as particle filters, constellation design, and Monte-Carlo simulation.
CFD Methods and Tools for Multi-Element Airfoil Analysis

NASA Technical Reports Server (NTRS)

Rogers, Stuart E.; George, Michael W. (Technical Monitor)

1995-01-01

This lecture will discuss the computational tools currently available for high-lift multi-element airfoil analysis. It will present an overview of a number of different numerical approaches, their current capabilities, short-comings, and computational costs. The lecture will be limited to viscous methods, including inviscid/boundary layer coupling methods, and incompressible and compressible Reynolds-averaged Navier-Stokes methods. Both structured and unstructured grid generation approaches will be presented. Two different structured grid procedures are outlined, one which uses multi-block patched grids, the other uses overset chimera grids. Turbulence and transition modeling will be discussed.
Implicit gas-kinetic unified algorithm based on multi-block docking grid for multi-body reentry flows covering all flow regimes

NASA Astrophysics Data System (ADS)

Peng, Ao-Ping; Li, Zhi-Hui; Wu, Jun-Lin; Jiang, Xin-Yu

2016-12-01

Based on the previous researches of the Gas-Kinetic Unified Algorithm (GKUA) for flows from highly rarefied free-molecule transition to continuum, a new implicit scheme of cell-centered finite volume method is presented for directly solving the unified Boltzmann model equation covering various flow regimes. In view of the difficulty in generating the single-block grid system with high quality for complex irregular bodies, a multi-block docking grid generation method is designed on the basis of data transmission between blocks, and the data structure is constructed for processing arbitrary connection relations between blocks with high efficiency and reliability. As a result, the gas-kinetic unified algorithm with the implicit scheme and multi-block docking grid has been firstly established and used to solve the reentry flow problems around the multi-bodies covering all flow regimes with the whole range of Knudsen numbers from 10 to 3.7E-6. The implicit and explicit schemes are applied to computing and analyzing the supersonic flows in near-continuum and continuum regimes around a circular cylinder with careful comparison each other. It is shown that the present algorithm and modelling possess much higher computational efficiency and faster converging properties. The flow problems including two and three side-by-side cylinders are simulated from highly rarefied to near-continuum flow regimes, and the present computed results are found in good agreement with the related DSMC simulation and theoretical analysis solutions, which verify the good accuracy and reliability of the present method. It is observed that the spacing of the multi-body is smaller, the cylindrical throat obstruction is greater with the flow field of single-body asymmetrical more obviously and the normal force coefficient bigger. While in the near-continuum transitional flow regime of near-space flying surroundings, the spacing of the multi-body increases to six times of the diameter of the single-body, the interference effects of the multi-bodies tend to be negligible. The computing practice has confirmed that it is feasible for the present method to compute the aerodynamics and reveal flow mechanism around complex multi-body vehicles covering all flow regimes from the gas-kinetic point of view of solving the unified Boltzmann model velocity distribution function equation.
Progress Towards a Rad-Hydro Code for Modern Computing Architectures LA-UR-10-02825

NASA Astrophysics Data System (ADS)

Wohlbier, J. G.; Lowrie, R. B.; Bergen, B.; Calef, M.

2010-11-01

We are entering an era of high performance computing where data movement is the overwhelming bottleneck to scalable performance, as opposed to the speed of floating-point operations per processor. All multi-core hardware paradigms, whether heterogeneous or homogeneous, be it the Cell processor, GPGPU, or multi-core x86, share this common trait. In multi-physics applications such as inertial confinement fusion or astrophysics, one may be solving multi-material hydrodynamics with tabular equation of state data lookups, radiation transport, nuclear reactions, and charged particle transport in a single time cycle. The algorithms are intensely data dependent, e.g., EOS, opacity, nuclear data, and multi-core hardware memory restrictions are forcing code developers to rethink code and algorithm design. For the past two years LANL has been funding a small effort referred to as Multi-Physics on Multi-Core to explore ideas for code design as pertaining to inertial confinement fusion and astrophysics applications. The near term goals of this project are to have a multi-material radiation hydrodynamics capability, with tabular equation of state lookups, on cartesian and curvilinear block structured meshes. In the longer term we plan to add fully implicit multi-group radiation diffusion and material heat conduction, and block structured AMR. We will report on our progress to date.
Domain modeling and grid generation for multi-block structured grids with application to aerodynamic and hydrodynamic configurations

NASA Technical Reports Server (NTRS)

Spekreijse, S. P.; Boerstoel, J. W.; Vitagliano, P. L.; Kuyvenhoven, J. L.

1992-01-01

About five years ago, a joint development was started of a flow simulation system for engine-airframe integration studies on propeller as well as jet aircraft. The initial system was based on the Euler equations and made operational for industrial aerodynamic design work. The system consists of three major components: a domain modeller, for the graphical interactive subdivision of flow domains into an unstructured collection of blocks; a grid generator, for the graphical interactive computation of structured grids in blocks; and a flow solver, for the computation of flows on multi-block grids. The industrial partners of the collaboration and NLR have demonstrated that the domain modeller, grid generator and flow solver can be applied to simulate Euler flows around complete aircraft, including propulsion system simulation. Extension to Navier-Stokes flows is in progress. Delft Hydraulics has shown that both the domain modeller and grid generator can also be applied successfully for hydrodynamic configurations. An overview is given about the main aspects of both domain modelling and grid generation.
Design of convolutional tornado code

NASA Astrophysics Data System (ADS)

Zhou, Hui; Yang, Yao; Gao, Hongmin; Tan, Lu

2017-09-01

As a linear block code, the traditional tornado (tTN) code is inefficient in burst-erasure environment and its multi-level structure may lead to high encoding/decoding complexity. This paper presents a convolutional tornado (cTN) code which is able to improve the burst-erasure protection capability by applying the convolution property to the tTN code, and reduce computational complexity by abrogating the multi-level structure. The simulation results show that cTN code can provide a better packet loss protection performance with lower computation complexity than tTN code.
Hybrid Grid Techniques for Propulsion Applications

NASA Technical Reports Server (NTRS)

Koomullil, Roy P.; Soni, Bharat K.; Thornburg, Hugh J.

1996-01-01

During the past decade, computational simulation of fluid flow for propulsion activities has progressed significantly, and many notable successes have been reported in the literature. However, the generation of a high quality mesh for such problems has often been reported as a pacing item. Hence, much effort has been expended to speed this portion of the simulation process. Several approaches have evolved for grid generation. Two of the most common are structured multi-block, and unstructured based procedures. Structured grids tend to be computationally efficient, and have high aspect ratio cells necessary for efficently resolving viscous layers. Structured multi-block grids may or may not exhibit grid line continuity across the block interface. This relaxation of the continuity constraint at the interface is intended to ease the grid generation process, which is still time consuming. Flow solvers supporting non-contiguous interfaces require specialized interpolation procedures which may not ensure conservation at the interface. Unstructured or generalized indexing data structures offer greater flexibility, but require explicit connectivity information and are not easy to generate for three dimensional configurations. In addition, unstructured mesh based schemes tend to be less efficient and it is difficult to resolve viscous layers. Recently hybrid or generalized element solution and grid generation techniques have been developed with the objective of combining the attractive features of both structured and unstructured techniques. In the present work, recently developed procedures for hybrid grid generation and flow simulation are critically evaluated, and compared to existing structured and unstructured procedures in terms of accuracy and computational requirements.
Load Balancing Strategies for Multi-Block Overset Grid Applications

NASA Technical Reports Server (NTRS)

Djomehri, M. Jahed; Biswas, Rupak; Lopez-Benitez, Noe; Biegel, Bryan (Technical Monitor)

2002-01-01

The multi-block overset grid method is a powerful technique for high-fidelity computational fluid dynamics (CFD) simulations about complex aerospace configurations. The solution process uses a grid system that discretizes the problem domain by using separately generated but overlapping structured grids that periodically update and exchange boundary information through interpolation. For efficient high performance computations of large-scale realistic applications using this methodology, the individual grids must be properly partitioned among the parallel processors. Overall performance, therefore, largely depends on the quality of load balancing. In this paper, we present three different load balancing strategies far overset grids and analyze their effects on the parallel efficiency of a Navier-Stokes CFD application running on an SGI Origin2000 machine.
Methods for Computationally Efficient Structured CFD Simulations of Complex Turbomachinery Flows

NASA Technical Reports Server (NTRS)

Herrick, Gregory P.; Chen, Jen-Ping

2012-01-01

This research presents more efficient computational methods by which to perform multi-block structured Computational Fluid Dynamics (CFD) simulations of turbomachinery, thus facilitating higher-fidelity solutions of complicated geometries and their associated flows. This computational framework offers flexibility in allocating resources to balance process count and wall-clock computation time, while facilitating research interests of simulating axial compressor stall inception with more complete gridding of the flow passages and rotor tip clearance regions than is typically practiced with structured codes. The paradigm presented herein facilitates CFD simulation of previously impractical geometries and flows. These methods are validated and demonstrate improved computational efficiency when applied to complicated geometries and flows.
Adaptive mesh refinement and load balancing based on multi-level block-structured Cartesian mesh

NASA Astrophysics Data System (ADS)

Misaka, Takashi; Sasaki, Daisuke; Obayashi, Shigeru

2017-11-01

We developed a framework for a distributed-memory parallel computer that enables dynamic data management for adaptive mesh refinement and load balancing. We employed simple data structure of the building cube method (BCM) where a computational domain is divided into multi-level cubic domains and each cube has the same number of grid points inside, realising a multi-level block-structured Cartesian mesh. Solution adaptive mesh refinement, which works efficiently with the help of the dynamic load balancing, was implemented by dividing cubes based on mesh refinement criteria. The framework was investigated with the Laplace equation in terms of adaptive mesh refinement, load balancing and the parallel efficiency. It was then applied to the incompressible Navier-Stokes equations to simulate a turbulent flow around a sphere. We considered wall-adaptive cube refinement where a non-dimensional wall distance y+ near the sphere is used for a criterion of mesh refinement. The result showed the load imbalance due to y+ adaptive mesh refinement was corrected by the present approach. To utilise the BCM framework more effectively, we also tested a cube-wise algorithm switching where an explicit and implicit time integration schemes are switched depending on the local Courant-Friedrichs-Lewy (CFL) condition in each cube.
Accelerating nuclear configuration interaction calculations through a preconditioned block iterative eigensolver

NASA Astrophysics Data System (ADS)

Shao, Meiyue; Aktulga, H. Metin; Yang, Chao; Ng, Esmond G.; Maris, Pieter; Vary, James P.

2018-01-01

We describe a number of recently developed techniques for improving the performance of large-scale nuclear configuration interaction calculations on high performance parallel computers. We show the benefit of using a preconditioned block iterative method to replace the Lanczos algorithm that has traditionally been used to perform this type of computation. The rapid convergence of the block iterative method is achieved by a proper choice of starting guesses of the eigenvectors and the construction of an effective preconditioner. These acceleration techniques take advantage of special structure of the nuclear configuration interaction problem which we discuss in detail. The use of a block method also allows us to improve the concurrency of the computation, and take advantage of the memory hierarchy of modern microprocessors to increase the arithmetic intensity of the computation relative to data movement. We also discuss the implementation details that are critical to achieving high performance on massively parallel multi-core supercomputers, and demonstrate that the new block iterative solver is two to three times faster than the Lanczos based algorithm for problems of moderate sizes on a Cray XC30 system.
Facilitating higher-fidelity simulations of axial compressor instability and other turbomachinery flow conditions

NASA Astrophysics Data System (ADS)

Herrick, Gregory Paul

The quest to accurately capture flow phenomena with length-scales both short and long and to accurately represent complex flow phenomena within disparately sized geometry inspires a need for an efficient, high-fidelity, multi-block structured computational fluid dynamics (CFD) parallel computational scheme. This research presents and demonstrates a more efficient computational method by which to perform multi-block structured CFD parallel computational simulations, thus facilitating higher-fidelity solutions of complicated geometries (due to the inclusion of grids for "small'' flow areas which are often merely modeled) and their associated flows. This computational framework offers greater flexibility and user-control in allocating the resource balance between process count and wall-clock computation time. The principal modifications implemented in this revision consist of a "multiple grid block per processing core'' software infrastructure and an analytic computation of viscous flux Jacobians. The development of this scheme is largely motivated by the desire to simulate axial compressor stall inception with more complete gridding of the flow passages (including rotor tip clearance regions) than has been previously done while maintaining high computational efficiency (i.e., minimal consumption of computational resources), and thus this paradigm shall be demonstrated with an examination of instability in a transonic axial compressor. However, the paradigm presented herein facilitates CFD simulation of myriad previously impractical geometries and flows and is not limited to detailed analyses of axial compressor flows. While the simulations presented herein were technically possible under the previous structure of the subject software, they were much less computationally efficient and thus not pragmatically feasible; the previous research using this software to perform three-dimensional, full-annulus, time-accurate, unsteady, full-stage (with sliding-interface) simulations of rotating stall inception in axial compressors utilized tip clearance periodic models, while the scheme here is demonstrated by a simulation of axial compressor stall inception utilizing gridded rotor tip clearance regions. As will be discussed, much previous research---experimental, theoretical, and computational---has suggested that understanding clearance flow behavior is critical to understanding stall inception, and previous computational research efforts which have used tip clearance models have begged the question, "What about the clearance flows?''. This research begins to address that question.
Accelerating nuclear configuration interaction calculations through a preconditioned block iterative eigensolver

DOE PAGES

Shao, Meiyue; Aktulga, H. Metin; Yang, Chao; ...

2017-09-14

In this paper, we describe a number of recently developed techniques for improving the performance of large-scale nuclear configuration interaction calculations on high performance parallel computers. We show the benefit of using a preconditioned block iterative method to replace the Lanczos algorithm that has traditionally been used to perform this type of computation. The rapid convergence of the block iterative method is achieved by a proper choice of starting guesses of the eigenvectors and the construction of an effective preconditioner. These acceleration techniques take advantage of special structure of the nuclear configuration interaction problem which we discuss in detail. Themore » use of a block method also allows us to improve the concurrency of the computation, and take advantage of the memory hierarchy of modern microprocessors to increase the arithmetic intensity of the computation relative to data movement. Finally, we also discuss the implementation details that are critical to achieving high performance on massively parallel multi-core supercomputers, and demonstrate that the new block iterative solver is two to three times faster than the Lanczos based algorithm for problems of moderate sizes on a Cray XC30 system.« less
Accelerating nuclear configuration interaction calculations through a preconditioned block iterative eigensolver

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

Shao, Meiyue; Aktulga, H. Metin; Yang, Chao

In this paper, we describe a number of recently developed techniques for improving the performance of large-scale nuclear configuration interaction calculations on high performance parallel computers. We show the benefit of using a preconditioned block iterative method to replace the Lanczos algorithm that has traditionally been used to perform this type of computation. The rapid convergence of the block iterative method is achieved by a proper choice of starting guesses of the eigenvectors and the construction of an effective preconditioner. These acceleration techniques take advantage of special structure of the nuclear configuration interaction problem which we discuss in detail. Themore » use of a block method also allows us to improve the concurrency of the computation, and take advantage of the memory hierarchy of modern microprocessors to increase the arithmetic intensity of the computation relative to data movement. Finally, we also discuss the implementation details that are critical to achieving high performance on massively parallel multi-core supercomputers, and demonstrate that the new block iterative solver is two to three times faster than the Lanczos based algorithm for problems of moderate sizes on a Cray XC30 system.« less

Software Defined Radio with Parallelized Software Architecture

NASA Technical Reports Server (NTRS)

Heckler, Greg

2013-01-01

This software implements software-defined radio procession over multi-core, multi-CPU systems in a way that maximizes the use of CPU resources in the system. The software treats each processing step in either a communications or navigation modulator or demodulator system as an independent, threaded block. Each threaded block is defined with a programmable number of input or output buffers; these buffers are implemented using POSIX pipes. In addition, each threaded block is assigned a unique thread upon block installation. A modulator or demodulator system is built by assembly of the threaded blocks into a flow graph, which assembles the processing blocks to accomplish the desired signal processing. This software architecture allows the software to scale effortlessly between single CPU/single-core computers or multi-CPU/multi-core computers without recompilation. NASA spaceflight and ground communications systems currently rely exclusively on ASICs or FPGAs. This software allows low- and medium-bandwidth (100 bps to .50 Mbps) software defined radios to be designed and implemented solely in C/C++ software, while lowering development costs and facilitating reuse and extensibility.
A Multi-Level Parallelization Concept for High-Fidelity Multi-Block Solvers

NASA Technical Reports Server (NTRS)

Hatay, Ferhat F.; Jespersen, Dennis C.; Guruswamy, Guru P.; Rizk, Yehia M.; Byun, Chansup; Gee, Ken; VanDalsem, William R. (Technical Monitor)

1997-01-01

The integration of high-fidelity Computational Fluid Dynamics (CFD) analysis tools with the industrial design process benefits greatly from the robust implementations that are transportable across a wide range of computer architectures. In the present work, a hybrid domain-decomposition and parallelization concept was developed and implemented into the widely-used NASA multi-block Computational Fluid Dynamics (CFD) packages implemented in ENSAERO and OVERFLOW. The new parallel solver concept, PENS (Parallel Euler Navier-Stokes Solver), employs both fine and coarse granularity in data partitioning as well as data coalescing to obtain the desired load-balance characteristics on the available computer platforms. This multi-level parallelism implementation itself introduces no changes to the numerical results, hence the original fidelity of the packages are identically preserved. The present implementation uses the Message Passing Interface (MPI) library for interprocessor message passing and memory accessing. By choosing an appropriate combination of the available partitioning and coalescing capabilities only during the execution stage, the PENS solver becomes adaptable to different computer architectures from shared-memory to distributed-memory platforms with varying degrees of parallelism. The PENS implementation on the IBM SP2 distributed memory environment at the NASA Ames Research Center obtains 85 percent scalable parallel performance using fine-grain partitioning of single-block CFD domains using up to 128 wide computational nodes. Multi-block CFD simulations of complete aircraft simulations achieve 75 percent perfect load-balanced executions using data coalescing and the two levels of parallelism. SGI PowerChallenge, SGI Origin 2000, and a cluster of workstations are the other platforms where the robustness of the implementation is tested. The performance behavior on the other computer platforms with a variety of realistic problems will be included as this on-going study progresses.
Description of the F-16XL Geometry and Computational Grids Used in CAWAPI

NASA Technical Reports Server (NTRS)

Boelens, O. J.; Badcock, K. J.; Gortz, S.; Morton, S.; Fritz, W.; Karman, S. L., Jr.; Michal, T.; Lamar, J. E.

2009-01-01

The objective of the Cranked-Arrow Wing Aerodynamics Project International (CAWAPI) was to allow a comprehensive validation of Computational Fluid Dynamics methods against the CAWAP flight database. A major part of this work involved the generation of high-quality computational grids. Prior to the grid generation an IGES file containing the air-tight geometry of the F-16XL aircraft was generated by a cooperation of the CAWAPI partners. Based on this geometry description both structured and unstructured grids have been generated. The baseline structured (multi-block) grid (and a family of derived grids) has been generated by the National Aerospace Laboratory NLR. Although the algorithms used by NLR had become available just before CAWAPI and thus only a limited experience with their application to such a complex configuration had been gained, a grid of good quality was generated well within four weeks. This time compared favourably with that required to produce the unstructured grids in CAWAPI. The baseline all-tetrahedral and hybrid unstructured grids has been generated at NASA Langley Research Center and the USAFA, respectively. To provide more geometrical resolution, trimmed unstructured grids have been generated at EADS-MAS, the UTSimCenter, Boeing Phantom Works and KTH/FOI. All grids generated within the framework of CAWAPI will be discussed in the article. Both results obtained on the structured grids and the unstructured grids showed a significant improvement in agreement with flight test data in comparison with those obtained on the structured multi-block grid used during CAWAP.
Advanced information processing system: Local system services

NASA Technical Reports Server (NTRS)

Burkhardt, Laura; Alger, Linda; Whittredge, Roy; Stasiowski, Peter

1989-01-01

The Advanced Information Processing System (AIPS) is a multi-computer architecture composed of hardware and software building blocks that can be configured to meet a broad range of application requirements. The hardware building blocks are fault-tolerant, general-purpose computers, fault-and damage-tolerant networks (both computer and input/output), and interfaces between the networks and the computers. The software building blocks are the major software functions: local system services, input/output, system services, inter-computer system services, and the system manager. The foundation of the local system services is an operating system with the functions required for a traditional real-time multi-tasking computer, such as task scheduling, inter-task communication, memory management, interrupt handling, and time maintenance. Resting on this foundation are the redundancy management functions necessary in a redundant computer and the status reporting functions required for an operator interface. The functional requirements, functional design and detailed specifications for all the local system services are documented.
Nano-structured polymer composites and process for preparing same

DOEpatents

Hillmyer, Marc; Chen, Liang

2013-04-16

A process for preparing a polymer composite that includes reacting (a) a multi-functional monomer and (b) a block copolymer comprising (i) a first block and (ii) a second block that includes a functional group capable of reacting with the multi-functional monomer, to form a crosslinked, nano-structured, bi-continuous composite. The composite includes a continuous matrix phase and a second continuous phase comprising the first block of the block copolymer.
Software Defined Radio with Parallelized Software Architecture

NASA Technical Reports Server (NTRS)

Heckler, Greg

2013-01-01

This software implements software-defined radio procession over multicore, multi-CPU systems in a way that maximizes the use of CPU resources in the system. The software treats each processing step in either a communications or navigation modulator or demodulator system as an independent, threaded block. Each threaded block is defined with a programmable number of input or output buffers; these buffers are implemented using POSIX pipes. In addition, each threaded block is assigned a unique thread upon block installation. A modulator or demodulator system is built by assembly of the threaded blocks into a flow graph, which assembles the processing blocks to accomplish the desired signal processing. This software architecture allows the software to scale effortlessly between single CPU/single-core computers or multi-CPU/multi-core computers without recompilation. NASA spaceflight and ground communications systems currently rely exclusively on ASICs or FPGAs. This software allows low- and medium-bandwidth (100 bps to approx.50 Mbps) software defined radios to be designed and implemented solely in C/C++ software, while lowering development costs and facilitating reuse and extensibility.
Electro-Optic Computing Architectures. Volume I

DTIC Science & Technology

1998-02-01

The objective of the Electro - Optic Computing Architecture (EOCA) program was to develop multi-function electro - optic interfaces and optical...interconnect units to enhance the performance of parallel processor systems and form the building blocks for future electro - optic computing architectures...Specifically, three multi-function interface modules were targeted for development - an Electro - Optic Interface (EOI), an Optical Interconnection Unit (OW
GPU accelerated dynamic functional connectivity analysis for functional MRI data.

PubMed

Akgün, Devrim; Sakoğlu, Ünal; Esquivel, Johnny; Adinoff, Bryon; Mete, Mutlu

2015-07-01

Recent advances in multi-core processors and graphics card based computational technologies have paved the way for an improved and dynamic utilization of parallel computing techniques. Numerous applications have been implemented for the acceleration of computationally-intensive problems in various computational science fields including bioinformatics, in which big data problems are prevalent. In neuroimaging, dynamic functional connectivity (DFC) analysis is a computationally demanding method used to investigate dynamic functional interactions among different brain regions or networks identified with functional magnetic resonance imaging (fMRI) data. In this study, we implemented and analyzed a parallel DFC algorithm based on thread-based and block-based approaches. The thread-based approach was designed to parallelize DFC computations and was implemented in both Open Multi-Processing (OpenMP) and Compute Unified Device Architecture (CUDA) programming platforms. Another approach developed in this study to better utilize CUDA architecture is the block-based approach, where parallelization involves smaller parts of fMRI time-courses obtained by sliding-windows. Experimental results showed that the proposed parallel design solutions enabled by the GPUs significantly reduce the computation time for DFC analysis. Multicore implementation using OpenMP on 8-core processor provides up to 7.7× speed-up. GPU implementation using CUDA yielded substantial accelerations ranging from 18.5× to 157× speed-up once thread-based and block-based approaches were combined in the analysis. Proposed parallel programming solutions showed that multi-core processor and CUDA-supported GPU implementations accelerated the DFC analyses significantly. Developed algorithms make the DFC analyses more practical for multi-subject studies with more dynamic analyses. Copyright © 2015 Elsevier Ltd. All rights reserved.
Polar order in nanostructured organic materials

NASA Astrophysics Data System (ADS)

Sayar, M.; Olvera de la Cruz, M.; Stupp, S. I.

2003-02-01

Achiral multi-block liquid crystals are not expected to form polar domains. Recently, however, films of nanoaggregates formed by multi-block rodcoil molecules were identified as the first example of achiral single-component materials with macroscopic polar properties. By solving an Ising-like model with dipolar and asymmetric short-range interactions, we show here that polar domains are stable in films composed of aggregates as opposed to isolated molecules. Unlike classical molecular systems, these nanoaggregates have large intralayer spacings (a approx 8 nm), leading to a reduction in the repulsive dipolar interactions which oppose polar order within layers. In finite-thickness films of nanostructures, this effect enables the formation of polar domains. We compute exactly the energies of the possible structures consistent with the experiments as a function of film thickness at zero temperature (T). We also provide Monte Carlo simulations at non-zero T for a disordered hexagonal lattice that resembles the smectic-like packing in these nanofilms.
Electro-Optic Computing Architectures: Volume II. Components and System Design and Analysis

DTIC Science & Technology

1998-02-01

The objective of the Electro - Optic Computing Architecture (EOCA) program was to develop multi-function electro - optic interfaces and optical...interconnect units to enhance the performance of parallel processor systems and form the building blocks for future electro - optic computing architectures...Specifically, three multi-function interface modules were targeted for development - an Electro - Optic Interface (EOI), an Optical Interconnection Unit
Super-pixel extraction based on multi-channel pulse coupled neural network

NASA Astrophysics Data System (ADS)

Xu, GuangZhu; Hu, Song; Zhang, Liu; Zhao, JingJing; Fu, YunXia; Lei, BangJun

2018-04-01

Super-pixel extraction techniques group pixels to form over-segmented image blocks according to the similarity among pixels. Compared with the traditional pixel-based methods, the image descripting method based on super-pixel has advantages of less calculation, being easy to perceive, and has been widely used in image processing and computer vision applications. Pulse coupled neural network (PCNN) is a biologically inspired model, which stems from the phenomenon of synchronous pulse release in the visual cortex of cats. Each PCNN neuron can correspond to a pixel of an input image, and the dynamic firing pattern of each neuron contains both the pixel feature information and its context spatial structural information. In this paper, a new color super-pixel extraction algorithm based on multi-channel pulse coupled neural network (MPCNN) was proposed. The algorithm adopted the block dividing idea of SLIC algorithm, and the image was divided into blocks with same size first. Then, for each image block, the adjacent pixels of each seed with similar color were classified as a group, named a super-pixel. At last, post-processing was adopted for those pixels or pixel blocks which had not been grouped. Experiments show that the proposed method can adjust the number of superpixel and segmentation precision by setting parameters, and has good potential for super-pixel extraction.
Multi-blocking strategies for the INS3D incompressible Navier-Stokes code

NASA Technical Reports Server (NTRS)

Gatlin, Boyd

1990-01-01

With the continuing development of bigger and faster supercomputers, computational fluid dynamics (CFD) has become a useful tool for real-world engineering design and analysis. However, the number of grid points necessary to resolve realistic flow fields numerically can easily exceed the memory capacity of available computers. In addition, geometric shapes of flow fields, such as those in the Space Shuttle Main Engine (SSME) power head, may be impossible to fill with continuous grids upon which to obtain numerical solutions to the equations of fluid motion. The solution to this dilemma is simply to decompose the computational domain into subblocks of manageable size. Computer codes that are single-block by construction can be modified to handle multiple blocks, but ad-hoc changes in the FORTRAN have to be made for each geometry treated. For engineering design and analysis, what is needed is generalization so that the blocking arrangement can be specified by the user. INS3D is a computer program for the solution of steady, incompressible flow problems. It is used frequently to solve engineering problems in the CFD Branch at Marshall Space Flight Center. INS3D uses an implicit solution algorithm and the concept of artificial compressibility to provide the necessary coupling between the pressure field and the velocity field. The development of generalized multi-block capability in INS3D is described.
Multiple sequence alignment using multi-objective based bacterial foraging optimization algorithm.

PubMed

Rani, R Ranjani; Ramyachitra, D

2016-12-01

Multiple sequence alignment (MSA) is a widespread approach in computational biology and bioinformatics. MSA deals with how the sequences of nucleotides and amino acids are sequenced with possible alignment and minimum number of gaps between them, which directs to the functional, evolutionary and structural relationships among the sequences. Still the computation of MSA is a challenging task to provide an efficient accuracy and statistically significant results of alignments. In this work, the Bacterial Foraging Optimization Algorithm was employed to align the biological sequences which resulted in a non-dominated optimal solution. It employs Multi-objective, such as: Maximization of Similarity, Non-gap percentage, Conserved blocks and Minimization of gap penalty. BAliBASE 3.0 benchmark database was utilized to examine the proposed algorithm against other methods In this paper, two algorithms have been proposed: Hybrid Genetic Algorithm with Artificial Bee Colony (GA-ABC) and Bacterial Foraging Optimization Algorithm. It was found that Hybrid Genetic Algorithm with Artificial Bee Colony performed better than the existing optimization algorithms. But still the conserved blocks were not obtained using GA-ABC. Then BFO was used for the alignment and the conserved blocks were obtained. The proposed Multi-Objective Bacterial Foraging Optimization Algorithm (MO-BFO) was compared with widely used MSA methods Clustal Omega, Kalign, MUSCLE, MAFFT, Genetic Algorithm (GA), Ant Colony Optimization (ACO), Artificial Bee Colony (ABC), Particle Swarm Optimization (PSO) and Hybrid Genetic Algorithm with Artificial Bee Colony (GA-ABC). The final results show that the proposed MO-BFO algorithm yields better alignment than most widely used methods. Copyright Â© 2016 Elsevier Ireland Ltd. All rights reserved.
LAURA Users Manual: 5.3-48528

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Chirstopher O.; Kleb, Bil

2010-01-01

This users manual provides in-depth information concerning installation and execution of LAURA, version 5. LAURA is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 LAURA code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintainability by eliminating the requirement for problem-dependent re-compilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multi-physics coupling. As a result, LAURA now shares gas-physics modules, MPI modules, and other low-level modules with the FUN3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU-standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.
LAURA Users Manual: 5.5-64987

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Christopher O.; Kleb, William L.

2013-01-01

This users manual provides in-depth information concerning installation and execution of LAURA, version 5. LAURA is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 LAURA code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintain ability by eliminating the requirement for problem dependent recompilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multi-physics coupling. As a result, LAURA now shares gas-physics modules, MPI modules, and other low-level modules with the Fun3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.
LAURA Users Manual: 5.4-54166

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Christopher O.; Kleb, Bil

2011-01-01

This users manual provides in-depth information concerning installation and execution of Laura, version 5. Laura is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 Laura code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintainability by eliminating the requirement for problem dependent re-compilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multi-physics coupling. As a result, Laura now shares gas-physics modules, MPI modules, and other low-level modules with the Fun3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU-standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.
Method and structure for skewed block-cyclic distribution of lower-dimensional data arrays in higher-dimensional processor grids

DOEpatents

Chatterjee, Siddhartha [Yorktown Heights, NY; Gunnels, John A [Brewster, NY

2011-11-08

A method and structure of distributing elements of an array of data in a computer memory to a specific processor of a multi-dimensional mesh of parallel processors includes designating a distribution of elements of at least a portion of the array to be executed by specific processors in the multi-dimensional mesh of parallel processors. The pattern of the designating includes a cyclical repetitive pattern of the parallel processor mesh, as modified to have a skew in at least one dimension so that both a row of data in the array and a column of data in the array map to respective contiguous groupings of the processors such that a dimension of the contiguous groupings is greater than one.
Multi-linear sparse reconstruction for SAR imaging based on higher-order SVD

NASA Astrophysics Data System (ADS)

Gao, Yu-Fei; Gui, Guan; Cong, Xun-Chao; Yang, Yue; Zou, Yan-Bin; Wan, Qun

2017-12-01

This paper focuses on the spotlight synthetic aperture radar (SAR) imaging for point scattering targets based on tensor modeling. In a real-world scenario, scatterers usually distribute in the block sparse pattern. Such a distribution feature has been scarcely utilized by the previous studies of SAR imaging. Our work takes advantage of this structure property of the target scene, constructing a multi-linear sparse reconstruction algorithm for SAR imaging. The multi-linear block sparsity is introduced into higher-order singular value decomposition (SVD) with a dictionary constructing procedure by this research. The simulation experiments for ideal point targets show the robustness of the proposed algorithm to the noise and sidelobe disturbance which always influence the imaging quality of the conventional methods. The computational resources requirement is further investigated in this paper. As a consequence of the algorithm complexity analysis, the present method possesses the superiority on resource consumption compared with the classic matching pursuit method. The imaging implementations for practical measured data also demonstrate the effectiveness of the algorithm developed in this paper.
Vectorization, threading, and cache-blocking considerations for hydrocodes on emerging architectures

DOE PAGES

Fung, J.; Aulwes, R. T.; Bement, M. T.; ...

2015-07-14

This work reports on considerations for improving computational performance in preparation for current and expected changes to computer architecture. The algorithms studied will include increasingly complex prototypes for radiation hydrodynamics codes, such as gradient routines and diffusion matrix assembly (e.g., in [1-6]). The meshes considered for the algorithms are structured or unstructured meshes. The considerations applied for performance improvements are meant to be general in terms of architecture (not specifically graphical processing unit (GPUs) or multi-core machines, for example) and include techniques for vectorization, threading, tiling, and cache blocking. Out of a survey of optimization techniques on applications such asmore » diffusion and hydrodynamics, we make general recommendations with a view toward making these techniques conceptually accessible to the applications code developer. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.« less
Modeling and Grid Generation of Iced Airfoils

NASA Technical Reports Server (NTRS)

Vickerman, Mary B.; Baez, Marivell; Braun, Donald C.; Hackenberg, Anthony W.; Pennline, James A.; Schilling, Herbert W.

2007-01-01

SmaggIce Version 2.0 is a software toolkit for geometric modeling and grid generation for two-dimensional, singleand multi-element, clean and iced airfoils. A previous version of SmaggIce was described in Preparing and Analyzing Iced Airfoils, NASA Tech Briefs, Vol. 28, No. 8 (August 2004), page 32. To recapitulate: Ice shapes make it difficult to generate quality grids around airfoils, yet these grids are essential for predicting ice-induced complex flow. This software efficiently creates high-quality structured grids with tools that are uniquely tailored for various ice shapes. SmaggIce Version 2.0 significantly enhances the previous version primarily by adding the capability to generate grids for multi-element airfoils. This version of the software is an important step in streamlining the aeronautical analysis of ice airfoils using computational fluid dynamics (CFD) tools. The user may prepare the ice shape, define the flow domain, decompose it into blocks, generate grids, modify/divide/merge blocks, and control grid density and smoothness. All these steps may be performed efficiently even for the difficult glaze and rime ice shapes. Providing the means to generate highly controlled grids near rough ice, the software includes the creation of a wrap-around block (called the "viscous sublayer block"), which is a thin, C-type block around the wake line and iced airfoil. For multi-element airfoils, the software makes use of grids that wrap around and fill in the areas between the viscous sub-layer blocks for all elements that make up the airfoil. A scripting feature records the history of interactive steps, which can be edited and replayed later to produce other grids. Using this version of SmaggIce, ice shape handling and grid generation can become a practical engineering process, rather than a laborious research effort.

A Performance Comparison of the Parallel Preconditioners for Iterative Methods for Large Sparse Linear Systems Arising from Partial Differential Equations on Structured Grids

NASA Astrophysics Data System (ADS)

Ma, Sangback

In this paper we compare various parallel preconditioners such as Point-SSOR (Symmetric Successive OverRelaxation), ILU(0) (Incomplete LU) in the Wavefront ordering, ILU(0) in the Multi-color ordering, Multi-Color Block SOR (Successive OverRelaxation), SPAI (SParse Approximate Inverse) and pARMS (Parallel Algebraic Recursive Multilevel Solver) for solving large sparse linear systems arising from two-dimensional PDE (Partial Differential Equation)s on structured grids. Point-SSOR is well-known, and ILU(0) is one of the most popular preconditioner, but it is inherently serial. ILU(0) in the Wavefront ordering maximizes the parallelism in the natural order, but the lengths of the wave-fronts are often nonuniform. ILU(0) in the Multi-color ordering is a simple way of achieving a parallelism of the order N, where N is the order of the matrix, but its convergence rate often deteriorates as compared to that of natural ordering. We have chosen the Multi-Color Block SOR preconditioner combined with direct sparse matrix solver, since for the Laplacian matrix the SOR method is known to have a nondeteriorating rate of convergence when used with the Multi-Color ordering. By using block version we expect to minimize the interprocessor communications. SPAI computes the sparse approximate inverse directly by least squares method. Finally, ARMS is a preconditioner recursively exploiting the concept of independent sets and pARMS is the parallel version of ARMS. Experiments were conducted for the Finite Difference and Finite Element discretizations of five two-dimensional PDEs with large meshsizes up to a million on an IBM p595 machine with distributed memory. Our matrices are real positive, i. e., their real parts of the eigenvalues are positive. We have used GMRES(m) as our outer iterative method, so that the convergence of GMRES(m) for our test matrices are mathematically guaranteed. Interprocessor communications were done using MPI (Message Passing Interface) primitives. The results show that in general ILU(0) in the Multi-Color ordering ahd ILU(0) in the Wavefront ordering outperform the other methods but for symmetric and nearly symmetric 5-point matrices Multi-Color Block SOR gives the best performance, except for a few cases with a small number of processors.
Shear bond strength of computer-aided design and computer-aided manufacturing feldspathic and nano resin ceramics blocks cemented with three different generations of resin cement.

PubMed

Ab-Ghani, Zuryati; Jaafar, Wahyuni; Foo, Siew Fon; Ariffin, Zaihan; Mohamad, Dasmawati

2015-01-01

To evaluate the shear bond strength between the dentin substrate and computer-aided design and computer-aided manufacturing feldspathic ceramic and nano resin ceramics blocks cemented with resin cement. Sixty cuboidal blocks (5 mm × 5 mm × 5 mm) were fabricated in equal numbers from feldspathic ceramic CEREC(®) Blocs PC and nano resin ceramic Lava™ Ultimate, and randomly divided into six groups (n = 10). Each block was cemented to the dentin of 60 extracted human premolar using Variolink(®) II/Syntac Classic (multi-steps etch-and-rinse adhesive bonding), NX3 Nexus(®) (two-steps etch-and-rinse adhesive bonding) and RelyX™ U200 self-adhesive cement. All specimens were thermocycled, and shear bond strength testing was done using the universal testing machine at a crosshead speed of 1.0 mm/min. Data were analyzed using one-way ANOVA. Combination of CEREC(®) Blocs PC and Variolink(®) II showed the highest mean shear bond strength (8.71 Mpa), while the lowest of 2.06 Mpa were observed in Lava™ Ultimate and RelyX™ U200. There was no significant difference in the mean shear bond strength between different blocks. Variolink(®) II cement using multi-steps etch-and-rinse adhesive bonding provided a higher shear bond strength than the self-adhesive cement RelyX U200. The shear bond strength was not affected by the type of blocks used.
An adaptive block-based fusion method with LUE-SSIM for multi-focus images

NASA Astrophysics Data System (ADS)

Zheng, Jianing; Guo, Yongcai; Huang, Yukun

2016-09-01

Because of the lenses' limited depth of field, digital cameras are incapable of acquiring an all-in-focus image of objects at varying distances in a scene. Multi-focus image fusion technique can effectively solve this problem. Aiming at the block-based multi-focus image fusion methods, the problem that blocking-artifacts often occurs. An Adaptive block-based fusion method based on lifting undistorted-edge structural similarity (LUE-SSIM) is put forward. In this method, image quality metrics LUE-SSIM is firstly proposed, which utilizes the characteristics of human visual system (HVS) and structural similarity (SSIM) to make the metrics consistent with the human visual perception. Particle swarm optimization(PSO) algorithm which selects LUE-SSIM as the object function is used for optimizing the block size to construct the fused image. Experimental results on LIVE image database shows that LUE-SSIM outperform SSIM on Gaussian defocus blur images quality assessment. Besides, multi-focus image fusion experiment is carried out to verify our proposed image fusion method in terms of visual and quantitative evaluation. The results show that the proposed method performs better than some other block-based methods, especially in reducing the blocking-artifact of the fused image. And our method can effectively preserve the undistorted-edge details in focus region of the source images.
Design and Verification of Remote Sensing Image Data Center Storage Architecture Based on Hadoop

NASA Astrophysics Data System (ADS)

Tang, D.; Zhou, X.; Jing, Y.; Cong, W.; Li, C.

2018-04-01

The data center is a new concept of data processing and application proposed in recent years. It is a new method of processing technologies based on data, parallel computing, and compatibility with different hardware clusters. While optimizing the data storage management structure, it fully utilizes cluster resource computing nodes and improves the efficiency of data parallel application. This paper used mature Hadoop technology to build a large-scale distributed image management architecture for remote sensing imagery. Using MapReduce parallel processing technology, it called many computing nodes to process image storage blocks and pyramids in the background to improve the efficiency of image reading and application and sovled the need for concurrent multi-user high-speed access to remotely sensed data. It verified the rationality, reliability and superiority of the system design by testing the storage efficiency of different image data and multi-users and analyzing the distributed storage architecture to improve the application efficiency of remote sensing images through building an actual Hadoop service system.
Fluid-dynamics modelling of the human left ventricle with dynamic mesh for normal and myocardial infarction: preliminary study.

PubMed

Khalafvand, S S; Ng, E Y K; Zhong, L; Hung, T K

2012-08-01

Pulsating blood flow patterns in the left ventricular (LV) were computed for three normal subjects and three patients after myocardial infarction (MI). Cardiac magnetic resonance (MR) images were obtained, segmented and transformed into 25 frames of LV for a computational fluid dynamics (CFD) study. Multi-block structure meshes were generated for 25 frames and 75 intermediate grids. The complete LV cycle was modelled by using ANSYS-CFX 12. The flow patterns and pressure drops in the LV chamber of this study provided some useful information on intra-LV flow patterns with heart diseases. Copyright © 2012 Elsevier Ltd. All rights reserved.
A hybrid framework for coupling arbitrary summation-by-parts schemes on general meshes

NASA Astrophysics Data System (ADS)

Lundquist, Tomas; Malan, Arnaud; Nordström, Jan

2018-06-01

We develop a general interface procedure to couple both structured and unstructured parts of a hybrid mesh in a non-collocated, multi-block fashion. The target is to gain optimal computational efficiency in fluid dynamics simulations involving complex geometries. While guaranteeing stability, the proposed procedure is optimized for accuracy and requires minimal algorithmic modifications to already existing schemes. Initial numerical investigations confirm considerable efficiency gains compared to non-hybrid calculations of up to an order of magnitude.
CFD Analysis and Design Optimization Using Parallel Computers

NASA Technical Reports Server (NTRS)

Martinelli, Luigi; Alonso, Juan Jose; Jameson, Antony; Reuther, James

1997-01-01

A versatile and efficient multi-block method is presented for the simulation of both steady and unsteady flow, as well as aerodynamic design optimization of complete aircraft configurations. The compressible Euler and Reynolds Averaged Navier-Stokes (RANS) equations are discretized using a high resolution scheme on body-fitted structured meshes. An efficient multigrid implicit scheme is implemented for time-accurate flow calculations. Optimum aerodynamic shape design is achieved at very low cost using an adjoint formulation. The method is implemented on parallel computing systems using the MPI message passing interface standard to ensure portability. The results demonstrate that, by combining highly efficient algorithms with parallel computing, it is possible to perform detailed steady and unsteady analysis as well as automatic design for complex configurations using the present generation of parallel computers.
An efficient predictor-corrector-based dynamic mesh method for multi-block structured grid with extremely large deformation and its applications

NASA Astrophysics Data System (ADS)

Guo, Tongqing; Chen, Hao; Lu, Zhiliang

2018-05-01

Aiming at extremely large deformation, a novel predictor-corrector-based dynamic mesh method for multi-block structured grid is proposed. In this work, the dynamic mesh generation is completed in three steps. At first, some typical dynamic positions are selected and high-quality multi-block grids with the same topology are generated at those positions. Then, Lagrange interpolation method is adopted to predict the dynamic mesh at any dynamic position. Finally, a rapid elastic deforming technique is used to correct the small deviation between the interpolated geometric configuration and the actual instantaneous one. Compared with the traditional methods, the results demonstrate that the present method shows stronger deformation ability and higher dynamic mesh quality.
Computing Aerodynamic Performance of a 2D Iced Airfoil: Blocking Topology and Grid Generation

NASA Technical Reports Server (NTRS)

Chi, X.; Zhu, B.; Shih, T. I.-P.; Slater, J. W.; Addy, H. E.; Choo, Yung K.; Lee, Chi-Ming (Technical Monitor)

2002-01-01

The ice accrued on airfoils can have enormously complicated shapes with multiple protruded horns and feathers. In this paper, several blocking topologies are proposed and evaluated on their ability to produce high-quality structured multi-block grid systems. A transition layer grid is introduced to ensure that jaggedness on the ice-surface geometry do not to propagate into the domain. This is important for grid-generation methods based on hyperbolic PDEs (Partial Differential Equations) and algebraic transfinite interpolation. A 'thick' wrap-around grid is introduced to ensure that grid lines clustered next to solid walls do not propagate as streaks of tightly packed grid lines into the interior of the domain along block boundaries. For ice shapes that are not too complicated, a method is presented for generating high-quality single-block grids. To demonstrate the usefulness of the methods developed, grids and CFD solutions were generated for two iced airfoils: the NLF0414 airfoil with and without the 623-ice shape and the B575/767 airfoil with and without the 145m-ice shape. To validate the computations, the computed lift coefficients as a function of angle of attack were compared with available experimental data. The ice shapes and the blocking topologies were prepared by NASA Glenn's SmaggIce software. The grid systems were generated by using a four-boundary method based on Hermite interpolation with controls on clustering, orthogonality next to walls, and C continuity across block boundaries. The flow was modeled by the ensemble-averaged compressible Navier-Stokes equations, closed by the shear-stress transport turbulence model in which the integration is to the wall. All solutions were generated by using the NPARC WIND code.
Program structure-based blocking

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

Bertolli, Carlo; Eichenberger, Alexandre E.; O'Brien, John K.

2017-09-26

Embodiments relate to program structure-based blocking. An aspect includes receiving source code corresponding to a computer program by a compiler of a computer system. Another aspect includes determining a prefetching section in the source code by a marking module of the compiler. Yet another aspect includes performing, by a blocking module of the compiler, blocking of instructions located in the prefetching section into instruction blocks, such that the instruction blocks of the prefetching section only contain instructions that are located in the prefetching section.
Multi-stage decoding for multi-level block modulation codes

NASA Technical Reports Server (NTRS)

Lin, Shu

1991-01-01

In this paper, we investigate various types of multi-stage decoding for multi-level block modulation codes, in which the decoding of a component code at each stage can be either soft-decision or hard-decision, maximum likelihood or bounded-distance. Error performance of codes is analyzed for a memoryless additive channel based on various types of multi-stage decoding, and upper bounds on the probability of an incorrect decoding are derived. Based on our study and computation results, we find that, if component codes of a multi-level modulation code and types of decoding at various stages are chosen properly, high spectral efficiency and large coding gain can be achieved with reduced decoding complexity. In particular, we find that the difference in performance between the suboptimum multi-stage soft-decision maximum likelihood decoding of a modulation code and the single-stage optimum decoding of the overall code is very small: only a fraction of dB loss in SNR at the probability of an incorrect decoding for a block of 10(exp -6). Multi-stage decoding of multi-level modulation codes really offers a way to achieve the best of three worlds, bandwidth efficiency, coding gain, and decoding complexity.
Numerical Upscaling of Solute Transport in Fractured Porous Media Based on Flow Aligned Blocks

NASA Astrophysics Data System (ADS)

Leube, P.; Nowak, W.; Sanchez-Vila, X.

2013-12-01

High-contrast or fractured-porous media (FPM) pose one of the largest unresolved challenges for simulating large hydrogeological systems. The high contrast in advective transport between fast conduits and low-permeability rock matrix, including complex mass transfer processes, leads to the typical complex characteristics of early bulk arrivals and long tailings. Adequate direct representation of FPM requires enormous numerical resolutions. For large scales, e.g. the catchment scale, and when allowing for uncertainty in the fracture network architecture or in matrix properties, computational costs quickly reach an intractable level. In such cases, multi-scale simulation techniques have become useful tools. They allow decreasing the complexity of models by aggregating and transferring their parameters to coarser scales and so drastically reduce the computational costs. However, these advantages come at a loss of detail and accuracy. In this work, we develop and test a new multi-scale or upscaled modeling approach based on block upscaling. The novelty is that individual blocks are defined by and aligned with the local flow coordinates. We choose a multi-rate mass transfer (MRMT) model to represent the remaining sub-block non-Fickian behavior within these blocks on the coarse scale. To make the scale transition simple and to save computational costs, we capture sub-block features by temporal moments (TM) of block-wise particle arrival times to be matched with the MRMT model. By predicting spatial mass distributions of injected tracers in a synthetic test scenario, our coarse-scale solution matches reasonably well with the corresponding fine-scale reference solution. For predicting higher TM-orders (such as arrival time and effective dispersion), the prediction accuracy steadily decreases. This is compensated to some extent by the MRMT model. If the MRMT model becomes too complex, it loses its effect. We also found that prediction accuracy is sensitive to the choice of the effective dispersion coefficients and on the block resolution. A key advantage of the flow-aligned blocks is that the small-scale velocity field is reproduced quite accurately on the block-scale through their flow alignment. Thus, the block-scale transverse dispersivities remain in the similar magnitude as local ones, and they do not have to represent macroscopic uncertainty. Also, the flow-aligned blocks minimize numerical dispersion when solving the large-scale transport problem.
The ability of multi-site, multi-depth sacral lateral branch blocks to anesthetize the sacroiliac joint complex.

PubMed

Dreyfuss, Paul; Henning, Troy; Malladi, Niriksha; Goldstein, Barry; Bogduk, Nikolai

2009-01-01

To determine the physiologic effectiveness of multi-site, multi-depth sacral lateral branch injections. Double-blind, randomized, placebo-controlled study. Outpatient pain management center. Twenty asymptomatic volunteers. The dorsal innervation to the sacroiliac joint (SIJ) is from the L5 dorsal ramus and the S1-3 lateral branches. Multi-site, multi-depth lateral branch blocks were developed to compensate for the complex regional anatomy that limited the effectiveness of single-site, single-depth lateral branch injections. Bilateral multi-site, multi-depth lateral branch green dye injections and subsequent dissection on two cadavers revealed a 91% accuracy with this technique. Session 1: 20 asymptomatic subjects had a 25-g spinal needle probe their interosseous (IO) and dorsal sacroiliac (DSI) ligaments. The inferior dorsal SIJ was entered and capsular distension with contrast medium was performed. Discomfort had to occur with each provocation maneuver and a contained arthrogram was necessary to continue in the study. Session 2: 1 week later; computer randomized, double-blind multi-site, multi-depth lateral branch blocks injections were performed. Ten subjects received active (bupivicaine 0.75%) and 10 subjects received sham (normal saline) multi-site, multi-depth lateral branch injections. Thirty minutes later, provocation testing was repeated with identical methodology used in session 1. Presence or absence of pain for ligamentous probing and SIJ capsular distension. Seventy percent of the active group had an insensate IO and DSI ligaments, and inferior dorsal SIJ vs 0-10% of the sham group. Twenty percent of the active vs 10% of the sham group did not feel repeat capsular distension. Six of seven subjects (86%) retained the ability to feel repeat capsular distension despite an insensate dorsal SIJ complex. Multi-site, multi-depth lateral branch blocks are physiologically effective at a rate of 70%. Multi-site, multi-depth lateral branch blocks do not effectively block the intra-articular portion of the SIJ. There is physiological evidence that the intra-articular portion of the SIJ is innervated from both ventral and dorsal sources. Comparative multi-site, multi-depth lateral branch blocks should be considered a potentially valuable tool to diagnose extra-articular SIJ pain and determine if lateral branch radiofrequency neurotomy may assist one with SIJ pain.
Algorithms for the automatic generation of 2-D structured multi-block grids

NASA Technical Reports Server (NTRS)

Schoenfeld, Thilo; Weinerfelt, Per; Jenssen, Carl B.

1995-01-01

Two different approaches to the fully automatic generation of structured multi-block grids in two dimensions are presented. The work aims to simplify the user interactivity necessary for the definition of a multiple block grid topology. The first approach is based on an advancing front method commonly used for the generation of unstructured grids. The original algorithm has been modified toward the generation of large quadrilateral elements. The second method is based on the divide-and-conquer paradigm with the global domain recursively partitioned into sub-domains. For either method each of the resulting blocks is then meshed using transfinite interpolation and elliptic smoothing. The applicability of these methods to practical problems is demonstrated for typical geometries of fluid dynamics.
Genomicus 2018: karyotype evolutionary trees and on-the-fly synteny computing

PubMed Central

Nguyen, Nga Thi Thuy; Vincens, Pierre

2018-01-01

Abstract Since 2010, the Genomicus web server is available online at http://genomicus.biologie.ens.fr/genomicus. This graphical browser provides access to comparative genomic analyses in four different phyla (Vertebrate, Plants, Fungi, and non vertebrate Metazoans). Users can analyse genomic information from extant species, as well as ancestral gene content and gene order for vertebrates and flowering plants, in an integrated evolutionary context. New analyses and visualization tools have recently been implemented in Genomicus Vertebrate. Karyotype structures from several genomes can now be compared along an evolutionary pathway (Multi-KaryotypeView), and synteny blocks can be computed and visualized between any two genomes (PhylDiagView). PMID:29087490
An improved approximate network blocking probability model for all-optical WDM Networks with heterogeneous link capacities

NASA Astrophysics Data System (ADS)

Khan, Akhtar Nawaz

2017-11-01

Currently, analytical models are used to compute approximate blocking probabilities in opaque and all-optical WDM networks with the homogeneous link capacities. Existing analytical models can also be extended to opaque WDM networking with heterogeneous link capacities due to the wavelength conversion at each switch node. However, existing analytical models cannot be utilized for all-optical WDM networking with heterogeneous structure of link capacities due to the wavelength continuity constraint and unequal numbers of wavelength channels on different links. In this work, a mathematical model is extended for computing approximate network blocking probabilities in heterogeneous all-optical WDM networks in which the path blocking is dominated by the link along the path with fewer number of wavelength channels. A wavelength assignment scheme is also proposed for dynamic traffic, termed as last-fit-first wavelength assignment, in which a wavelength channel with maximum index is assigned first to a lightpath request. Due to heterogeneous structure of link capacities and the wavelength continuity constraint, the wavelength channels with maximum indexes are utilized for minimum hop routes. Similarly, the wavelength channels with minimum indexes are utilized for multi-hop routes between source and destination pairs. The proposed scheme has lower blocking probability values compared to the existing heuristic for wavelength assignments. Finally, numerical results are computed in different network scenarios which are approximately equal to values obtained from simulations. Since January 2016, he is serving as Head of Department and an Assistant Professor in the Department of Electrical Engineering at UET, Peshawar-Jalozai Campus, Pakistan. From May 2013 to June 2015, he served Department of Telecommunication Engineering as an Assistant Professor at UET, Peshawar-Mardan Campus, Pakistan. He also worked as an International Internship scholar in the Fukuda Laboratory, National Institute of Informatics, Tokyo, Japan on the topic large-scale simulation for internet topology analysis. His research interests include design and analysis of optical WDM networks, network algorithms, network routing, and network resource optimization problems.
Multi-color incomplete Cholesky conjugate gradient methods for vector computers

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

Poole, E.L.

1986-01-01

This research is concerned with the solution on vector computers of linear systems of equations. Ax = b, where A is a large, sparse symmetric positive definite matrix with non-zero elements lying only along a few diagonals of the matrix. The system is solved using the incomplete Cholesky conjugate gradient method (ICCG). Multi-color orderings are used of the unknowns in the linear system to obtain p-color matrices for which a no-fill block ICCG method is implemented on the CYBER 205 with O(N/p) length vector operations in both the decomposition of A and, more importantly, in the forward and back solvesmore » necessary at each iteration of the method. (N is the number of unknowns and p is a small constant). A p-colored matrix is a matrix that can be partitioned into a p x p block matrix where the diagonal blocks are diagonal matrices. The matrix is stored by diagonals and matrix multiplication by diagonals is used to carry out the decomposition of A and the forward and back solves. Additionally, if the vectors across adjacent blocks line up, then some of the overhead associated with vector startups can be eliminated in the matrix vector multiplication necessary at each conjugate gradient iteration. Necessary and sufficient conditions are given to determine which multi-color orderings of the unknowns correspond to p-color matrices, and a process is indicated for choosing multi-color orderings.« less
A Structured Grid Based Solution-Adaptive Technique for Complex Separated Flows

NASA Technical Reports Server (NTRS)

Thornburg, Hugh; Soni, Bharat K.; Kishore, Boyalakuntla; Yu, Robert

1996-01-01

The objective of this work was to enhance the predictive capability of widely used computational fluid dynamic (CFD) codes through the use of solution adaptive gridding. Most problems of engineering interest involve multi-block grids and widely disparate length scales. Hence, it is desirable that the adaptive grid feature detection algorithm be developed to recognize flow structures of different type as well as differing intensity, and adequately address scaling and normalization across blocks. In order to study the accuracy and efficiency improvements due to the grid adaptation, it is necessary to quantify grid size and distribution requirements as well as computational times of non-adapted solutions. Flow fields about launch vehicles of practical interest often involve supersonic freestream conditions at angle of attack exhibiting large scale separate vortical flow, vortex-vortex and vortex-surface interactions, separated shear layers and multiple shocks of different intensity. In this work, a weight function and an associated mesh redistribution procedure is presented which detects and resolves these features without user intervention. Particular emphasis has been placed upon accurate resolution of expansion regions and boundary layers. Flow past a wedge at Mach=2.0 is used to illustrate the enhanced detection capabilities of this newly developed weight function.
Efficient Blockwise Permutation Tests Preserving Exchangeability

PubMed Central

Zhou, Chunxiao; Zwilling, Chris E.; Calhoun, Vince D.; Wang, Michelle Y.

2014-01-01

In this paper, we present a new blockwise permutation test approach based on the moments of the test statistic. The method is of importance to neuroimaging studies. In order to preserve the exchangeability condition required in permutation tests, we divide the entire set of data into certain exchangeability blocks. In addition, computationally efficient moments-based permutation tests are performed by approximating the permutation distribution of the test statistic with the Pearson distribution series. This involves the calculation of the first four moments of the permutation distribution within each block and then over the entire set of data. The accuracy and efficiency of the proposed method are demonstrated through simulated experiment on the magnetic resonance imaging (MRI) brain data, specifically the multi-site voxel-based morphometry analysis from structural MRI (sMRI). PMID:25289113
Adaptive multi-GPU Exchange Monte Carlo for the 3D Random Field Ising Model

NASA Astrophysics Data System (ADS)

Navarro, Cristóbal A.; Huang, Wei; Deng, Youjin

2016-08-01

This work presents an adaptive multi-GPU Exchange Monte Carlo approach for the simulation of the 3D Random Field Ising Model (RFIM). The design is based on a two-level parallelization. The first level, spin-level parallelism, maps the parallel computation as optimal 3D thread-blocks that simulate blocks of spins in shared memory with minimal halo surface, assuming a constant block volume. The second level, replica-level parallelism, uses multi-GPU computation to handle the simulation of an ensemble of replicas. CUDA's concurrent kernel execution feature is used in order to fill the occupancy of each GPU with many replicas, providing a performance boost that is more notorious at the smallest values of L. In addition to the two-level parallel design, the work proposes an adaptive multi-GPU approach that dynamically builds a proper temperature set free of exchange bottlenecks. The strategy is based on mid-point insertions at the temperature gaps where the exchange rate is most compromised. The extra work generated by the insertions is balanced across the GPUs independently of where the mid-point insertions were performed. Performance results show that spin-level performance is approximately two orders of magnitude faster than a single-core CPU version and one order of magnitude faster than a parallel multi-core CPU version running on 16-cores. Multi-GPU performance is highly convenient under a weak scaling setting, reaching up to 99 % efficiency as long as the number of GPUs and L increase together. The combination of the adaptive approach with the parallel multi-GPU design has extended our possibilities of simulation to sizes of L = 32 , 64 for a workstation with two GPUs. Sizes beyond L = 64 can eventually be studied using larger multi-GPU systems.

SIAM Conference on Parallel Processing for Scientific Computing, 4th, Chicago, IL, Dec. 11-13, 1989, Proceedings

NASA Technical Reports Server (NTRS)

Dongarra, Jack (Editor); Messina, Paul (Editor); Sorensen, Danny C. (Editor); Voigt, Robert G. (Editor)

1990-01-01

Attention is given to such topics as an evaluation of block algorithm variants in LAPACK and presents a large-grain parallel sparse system solver, a multiprocessor method for the solution of the generalized Eigenvalue problem on an interval, and a parallel QR algorithm for iterative subspace methods on the CM2. A discussion of numerical methods includes the topics of asynchronous numerical solutions of PDEs on parallel computers, parallel homotopy curve tracking on a hypercube, and solving Navier-Stokes equations on the Cedar Multi-Cluster system. A section on differential equations includes a discussion of a six-color procedure for the parallel solution of elliptic systems using the finite quadtree structure, data parallel algorithms for the finite element method, and domain decomposition methods in aerodynamics. Topics dealing with massively parallel computing include hypercube vs. 2-dimensional meshes and massively parallel computation of conservation laws. Performance and tools are also discussed.
Integrated geometry and grid generation system for complex configurations

NASA Technical Reports Server (NTRS)

Akdag, Vedat; Wulf, Armin

1992-01-01

A grid generation system was developed that enables grid generation for complex configurations. The system called ICEM/CFD is described and its role in computational fluid dynamics (CFD) applications is presented. The capabilities of the system include full computer aided design (CAD), grid generation on the actual CAD geometry definition using robust surface projection algorithms, interfacing easily with known CAD packages through common file formats for geometry transfer, grid quality evaluation of the volume grid, coupling boundary condition set-up for block faces with grid topology generation, multi-block grid generation with or without point continuity and block to block interface requirement, and generating grid files directly compatible with known flow solvers. The interactive and integrated approach to the problem of computational grid generation not only substantially reduces manpower time but also increases the flexibility of later grid modifications and enhancements which is required in an environment where CFD is integrated into a product design cycle.
Dependency graph for code analysis on emerging architectures

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

Shashkov, Mikhail Jurievich; Lipnikov, Konstantin

Direct acyclic dependency (DAG) graph is becoming the standard for modern multi-physics codes.The ideal DAG is the true block-scheme of a multi-physics code. Therefore, it is the convenient object for insitu analysis of the cost of computations and algorithmic bottlenecks related to statistical frequent data motion and dymanical machine state.
The potential of multi-port optical memories in digital computing

NASA Technical Reports Server (NTRS)

Alford, C. O.; Gaylord, T. K.

1975-01-01

A high-capacity memory with a relatively high data transfer rate and multi-port simultaneous access capability may serve as the basis for new computer architectures. The implementation of a multi-port optical memory is discussed. Several computer structures are presented that might profitably use such a memory. These structures include (1) a simultaneous record access system, (2) a simultaneously shared memory computer system, and (3) a parallel digital processing structure.
Parallel Geospatial Data Management for Multi-Scale Environmental Data Analysis on GPUs

NASA Astrophysics Data System (ADS)

Wang, D.; Zhang, J.; Wei, Y.

2013-12-01

As the spatial and temporal resolutions of Earth observatory data and Earth system simulation outputs are getting higher, in-situ and/or post- processing such large amount of geospatial data increasingly becomes a bottleneck in scientific inquires of Earth systems and their human impacts. Existing geospatial techniques that are based on outdated computing models (e.g., serial algorithms and disk-resident systems), as have been implemented in many commercial and open source packages, are incapable of processing large-scale geospatial data and achieve desired level of performance. In this study, we have developed a set of parallel data structures and algorithms that are capable of utilizing massively data parallel computing power available on commodity Graphics Processing Units (GPUs) for a popular geospatial technique called Zonal Statistics. Given two input datasets with one representing measurements (e.g., temperature or precipitation) and the other one represent polygonal zones (e.g., ecological or administrative zones), Zonal Statistics computes major statistics (or complete distribution histograms) of the measurements in all regions. Our technique has four steps and each step can be mapped to GPU hardware by identifying its inherent data parallelisms. First, a raster is divided into blocks and per-block histograms are derived. Second, the Minimum Bounding Boxes (MBRs) of polygons are computed and are spatially matched with raster blocks; matched polygon-block pairs are tested and blocks that are either inside or intersect with polygons are identified. Third, per-block histograms are aggregated to polygons for blocks that are completely within polygons. Finally, for blocks that intersect with polygon boundaries, all the raster cells within the blocks are examined using point-in-polygon-test and cells that are within polygons are used to update corresponding histograms. As the task becomes I/O bound after applying spatial indexing and GPU hardware acceleration, we have developed a GPU-based data compression technique by reusing our previous work on Bitplane Quadtree (or BPQ-Tree) based indexing of binary bitmaps. Results have shown that our GPU-based parallel Zonal Statistic technique on 3000+ US counties over 20+ billion NASA SRTM 30 meter resolution Digital Elevation (DEM) raster cells has achieved impressive end-to-end runtimes: 101 seconds and 46 seconds a low-end workstation equipped with a Nvidia GTX Titan GPU using cold and hot cache, respectively; and, 60-70 seconds using a single OLCF TITAN computing node and 10-15 seconds using 8 nodes. Our experiment results clearly show the potentials of using high-end computing facilities for large-scale geospatial processing.
Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine.

PubMed

Zanin, Massimiliano; Chorbev, Ivan; Stres, Blaz; Stalidzans, Egils; Vera, Julio; Tieri, Paolo; Castiglione, Filippo; Groen, Derek; Zheng, Huiru; Baumbach, Jan; Schmid, Johannes A; Basilio, José; Klimek, Peter; Debeljak, Nataša; Rozman, Damjana; Schmidt, Harald H H W

2017-12-05

Systems medicine holds many promises, but has so far provided only a limited number of proofs of principle. To address this road block, possible barriers and challenges of translating systems medicine into clinical practice need to be identified and addressed. The members of the European Cooperation in Science and Technology (COST) Action CA15120 Open Multiscale Systems Medicine (OpenMultiMed) wish to engage the scientific community of systems medicine and multiscale modelling, data science and computing, to provide their feedback in a structured manner. This will result in follow-up white papers and open access resources to accelerate the clinical translation of systems medicine. © The Author 2017. Published by Oxford University Press.
Genomicus 2018: karyotype evolutionary trees and on-the-fly synteny computing.

PubMed

Nguyen, Nga Thi Thuy; Vincens, Pierre; Roest Crollius, Hugues; Louis, Alexandra

2018-01-04

Since 2010, the Genomicus web server is available online at http://genomicus.biologie.ens.fr/genomicus. This graphical browser provides access to comparative genomic analyses in four different phyla (Vertebrate, Plants, Fungi, and non vertebrate Metazoans). Users can analyse genomic information from extant species, as well as ancestral gene content and gene order for vertebrates and flowering plants, in an integrated evolutionary context. New analyses and visualization tools have recently been implemented in Genomicus Vertebrate. Karyotype structures from several genomes can now be compared along an evolutionary pathway (Multi-KaryotypeView), and synteny blocks can be computed and visualized between any two genomes (PhylDiagView). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Block-structured grids for complex aerodynamic configurations: Current status

NASA Technical Reports Server (NTRS)

Vatsa, Veer N.; Sanetrik, Mark D.; Parlette, Edward B.

1995-01-01

The status of CFD methods based on the use of block-structured grids for analyzing viscous flows over complex configurations is examined. The objective of the present study is to make a realistic assessment of the usability of such grids for routine computations typically encountered in the aerospace industry. It is recognized at the very outset that the total turnaround time, from the moment the configuration is identified until the computational results have been obtained and postprocessed, is more important than just the computational time. Pertinent examples will be cited to demonstrate the feasibility of solving flow over practical configurations of current interest on block-structured grids.
Cooperative storage of shared files in a parallel computing system with dynamic block size

DOEpatents

Bent, John M.; Faibish, Sorin; Grider, Gary

2015-11-10

Improved techniques are provided for parallel writing of data to a shared object in a parallel computing system. A method is provided for storing data generated by a plurality of parallel processes to a shared object in a parallel computing system. The method is performed by at least one of the processes and comprises: dynamically determining a block size for storing the data; exchanging a determined amount of the data with at least one additional process to achieve a block of the data having the dynamically determined block size; and writing the block of the data having the dynamically determined block size to a file system. The determined block size comprises, e.g., a total amount of the data to be stored divided by the number of parallel processes. The file system comprises, for example, a log structured virtual parallel file system, such as a Parallel Log-Structured File System (PLFS).
Multi-color incomplete Cholesky conjugate gradient methods for vector computers. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Poole, E. L.

1986-01-01

In this research, we are concerned with the solution on vector computers of linear systems of equations, Ax = b, where A is a larger, sparse symmetric positive definite matrix. We solve the system using an iterative method, the incomplete Cholesky conjugate gradient method (ICCG). We apply a multi-color strategy to obtain p-color matrices for which a block-oriented ICCG method is implemented on the CYBER 205. (A p-colored matrix is a matrix which can be partitioned into a pXp block matrix where the diagonal blocks are diagonal matrices). This algorithm, which is based on a no-fill strategy, achieves O(N/p) length vector operations in both the decomposition of A and in the forward and back solves necessary at each iteration of the method. We discuss the natural ordering of the unknowns as an ordering that minimizes the number of diagonals in the matrix and define multi-color orderings in terms of disjoint sets of the unknowns. We give necessary and sufficient conditions to determine which multi-color orderings of the unknowns correpond to p-color matrices. A performance model is given which is used both to predict execution time for ICCG methods and also to compare an ICCG method to conjugate gradient without preconditioning or another ICCG method. Results are given from runs on the CYBER 205 at NASA's Langley Research Center for four model problems.
FANS-3D Users Guide (ESTEP Project ER 201031)

DTIC Science & Technology

2016-08-01

governing laminar and turbulent flows in body-fitted curvilinear grids. The code employs multi-block overset ( chimera ) grids, including fully matched...governing incompressible flow in body-fitted grids. The code allows for multi-block overset ( chimera ) grids, which can be fully matched, arbitrarily...interested reader may consult the Chimera Overset Structured Mesh-Interpolation Code (COSMIC) Users’ Manual (Chen, 2009). The input file used for
Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks.

PubMed

Yeh, Chun-Ting; Brunette, T J; Baker, David; McIntosh-Smith, Simon; Parmeggiani, Fabio

2018-02-01

Computational protein design methods have enabled the design of novel protein structures, but they are often still limited to small proteins and symmetric systems. To expand the size of designable proteins while controlling the overall structure, we developed Elfin, a genetic algorithm for the design of novel proteins with custom shapes using structural building blocks derived from experimentally verified repeat proteins. By combining building blocks with compatible interfaces, it is possible to rapidly build non-symmetric large structures (>1000 amino acids) that match three-dimensional geometric descriptions provided by the user. A run time of about 20min on a laptop computer for a 3000 amino acid structure makes Elfin accessible to users with limited computational resources. Protein structures with controlled geometry will allow the systematic study of the effect of spatial arrangement of enzymes and signaling molecules, and provide new scaffolds for functional nanomaterials. Copyright © 2017 Elsevier Inc. All rights reserved.
Fast Physically Correct Refocusing for Sparse Light Fields Using Block-Based Multi-Rate View Interpolation.

PubMed

Huang, Chao-Tsung; Wang, Yu-Wen; Huang, Li-Ren; Chin, Jui; Chen, Liang-Gee

2017-02-01

Digital refocusing has a tradeoff between complexity and quality when using sparsely sampled light fields for low-storage applications. In this paper, we propose a fast physically correct refocusing algorithm to address this issue in a twofold way. First, view interpolation is adopted to provide photorealistic quality at infocus-defocus hybrid boundaries. Regarding its conventional high complexity, we devised a fast line-scan method specifically for refocusing, and its 1D kernel can be 30× faster than the benchmark View Synthesis Reference Software (VSRS)-1D-Fast. Second, we propose a block-based multi-rate processing flow for accelerating purely infocused or defocused regions, and a further 3- 34× speedup can be achieved for high-resolution images. All candidate blocks of variable sizes can interpolate different numbers of rendered views and perform refocusing in different subsampled layers. To avoid visible aliasing and block artifacts, we determine these parameters and the simulated aperture filter through a localized filter response analysis using defocus blur statistics. The final quadtree block partitions are then optimized in terms of computation time. Extensive experimental results are provided to show superior refocusing quality and fast computation speed. In particular, the run time is comparable with the conventional single-image blurring, which causes serious boundary artifacts.
Algorithms for parallel flow solvers on message passing architectures

NASA Technical Reports Server (NTRS)

Vanderwijngaart, Rob F.

1995-01-01

The purpose of this project has been to identify and test suitable technologies for implementation of fluid flow solvers -- possibly coupled with structures and heat equation solvers -- on MIMD parallel computers. In the course of this investigation much attention has been paid to efficient domain decomposition strategies for ADI-type algorithms. Multi-partitioning derives its efficiency from the assignment of several blocks of grid points to each processor in the parallel computer. A coarse-grain parallelism is obtained, and a near-perfect load balance results. In uni-partitioning every processor receives responsibility for exactly one block of grid points instead of several. This necessitates fine-grain pipelined program execution in order to obtain a reasonable load balance. Although fine-grain parallelism is less desirable on many systems, especially high-latency networks of workstations, uni-partition methods are still in wide use in production codes for flow problems. Consequently, it remains important to achieve good efficiency with this technique that has essentially been superseded by multi-partitioning for parallel ADI-type algorithms. Another reason for the concentration on improving the performance of pipeline methods is their applicability in other types of flow solver kernels with stronger implied data dependence. Analytical expressions can be derived for the size of the dynamic load imbalance incurred in traditional pipelines. From these it can be determined what is the optimal first-processor retardation that leads to the shortest total completion time for the pipeline process. Theoretical predictions of pipeline performance with and without optimization match experimental observations on the iPSC/860 very well. Analysis of pipeline performance also highlights the effect of uncareful grid partitioning in flow solvers that employ pipeline algorithms. If grid blocks at boundaries are not at least as large in the wall-normal direction as those immediately adjacent to them, then the first processor in the pipeline will receive a computational load that is less than that of subsequent processors, magnifying the pipeline slowdown effect. Extra compensation is needed for grid boundary effects, even if all grid blocks are equally sized.
Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler.

PubMed

Bindewald, Eckart; Grunewald, Calvin; Boyle, Brett; O'Connor, Mary; Shapiro, Bruce A

2008-10-01

One approach to designing RNA nanoscale structures is to use known RNA structural motifs such as junctions, kissing loops or bulges and to construct a molecular model by connecting these building blocks with helical struts. We previously developed an algorithm for detecting internal loops, junctions and kissing loops in RNA structures. Here we present algorithms for automating or assisting many of the steps that are involved in creating RNA structures from building blocks: (1) assembling building blocks into nanostructures using either a combinatorial search or constraint satisfaction; (2) optimizing RNA 3D ring structures to improve ring closure; (3) sequence optimisation; (4) creating a unique non-degenerate RNA topology descriptor. This effectively creates a computational pipeline for generating molecular models of RNA nanostructures and more specifically RNA ring structures with optimized sequences from RNA building blocks. We show several examples of how the algorithms can be utilized to generate RNA tecto-shapes.
Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler☆

PubMed Central

Bindewald, Eckart; Grunewald, Calvin; Boyle, Brett; O’Connor, Mary; Shapiro, Bruce A.

2013-01-01

One approach to designing RNA nanoscale structures is to use known RNA structural motifs such as junctions, kissing loops or bulges and to construct a molecular model by connecting these building blocks with helical struts. We previously developed an algorithm for detecting internal loops, junctions and kissing loops in RNA structures. Here we present algorithms for automating or assisting many of the steps that are involved in creating RNA structures from building blocks: (1) assembling building blocks into nanostructures using either a combinatorial search or constraint satisfaction; (2) optimizing RNA 3D ring structures to improve ring closure; (3) sequence optimisation; (4) creating a unique non-degenerate RNA topology descriptor. This effectively creates a computational pipeline for generating molecular models of RNA nanostructures and more specifically RNA ring structures with optimized sequences from RNA building blocks. We show several examples of how the algorithms can be utilized to generate RNA tecto-shapes. PMID:18838281
Simulation requirements for the Large Deployable Reflector (LDR)

NASA Technical Reports Server (NTRS)

Soosaar, K.

1984-01-01

Simulation tools for the large deployable reflector (LDR) are discussed. These tools are often the transfer function variety equations. However, transfer functions are inadequate to represent time-varying systems for multiple control systems with overlapping bandwidths characterized by multi-input, multi-output features. Frequency domain approaches are the useful design tools, but a full-up simulation is needed. Because of the need for a dedicated computer for high frequency multi degree of freedom components encountered, non-real time smulation is preferred. Large numerical analysis software programs are useful only to receive inputs and provide output to the next block, and should be kept out of the direct loop of simulation. The following blocks make up the simulation. The thermal model block is a classical heat transfer program. It is a non-steady state program. The quasistatic block deals with problems associated with rigid body control of reflector segments. The steady state block assembles data into equations of motion and dynamics. A differential raytrace is obtained to establish a change in wave aberrations. The observation scene is described. The focal plane module converts the photon intensity impinging on it into electron streams or into permanent film records.
Atmospheric Blocking and Atlantic Multi-Decadal Ocean Variability

NASA Technical Reports Server (NTRS)

Hakkinen, Sirpa; Rhines, Peter B.; Worthen, Denise L.

2011-01-01

Atmospheric blocking over the northern North Atlantic involves isolation of large regions of air from the westerly circulation for 5-14 days or more. From a recent 20th century atmospheric reanalysis (1,2) winters with more frequent blocking persist over several decades and correspond to a warm North Atlantic Ocean, in-phase with Atlantic multi-decadal ocean variability (AMV). Ocean circulation is forced by wind-stress curl and related air/sea heat exchange, and we find that their space-time structure is associated with dominant blocking patterns: weaker ocean gyres and weaker heat exchange contribute to the warm phase of AMV. Increased blocking activity extending from Greenland to British Isles is evident when winter blocking days of the cold years (1900-1929) are subtracted from those of the warm years (1939-1968).
Performance Analysis of a Hybrid Overset Multi-Block Application on Multiple Architectures

NASA Technical Reports Server (NTRS)

Djomehri, M. Jahed; Biswas, Rupak

2003-01-01

This paper presents a detailed performance analysis of a multi-block overset grid compu- tational fluid dynamics app!ication on multiple state-of-the-art computer architectures. The application is implemented using a hybrid MPI+OpenMP programming paradigm that exploits both coarse and fine-grain parallelism; the former via MPI message passing and the latter via OpenMP directives. The hybrid model also extends the applicability of multi-block programs to large clusters of SNIP nodes by overcoming the restriction that the number of processors be less than the number of grid blocks. A key kernel of the application, namely the LU-SGS linear solver, had to be modified to enhance the performance of the hybrid approach on the target machines. Investigations were conducted on cacheless Cray SX6 vector processors, cache-based IBM Power3 and Power4 architectures, and single system image SGI Origin3000 platforms. Overall results for complex vortex dynamics simulations demonstrate that the SX6 achieves the highest performance and outperforms the RISC-based architectures; however, the best scaling performance was achieved on the Power3.
Numerical simulation of rough-surface aerodynamics

NASA Astrophysics Data System (ADS)

Chi, Xingkai

Computational fluid dynamics (CFD) simulations of flow over surfaces with roughness in which the details of the surface geometry must be resolved pose major challenges. The objective of this study is to address these challenges through two important engineering problems, where roughness play a critical role---flow over airfoils with accrued ice and flow and heat transfer over turbine blade surfaces roughened by erosion and/or deposition. CFD simulations of iced airfoils face two major challenges. The first is how to generate high-quality single- and multi-block structured grids for highly convoluted convex and concave surface geometries with multiple scales. In this study, two methods were developed for the generation of high-quality grids for such geometries. The method developed for single-block grids involves generating a grid about the clean airfoil, carving out a portion of that grid about the airfoil, replacing that portion with a grid that accounts for the accrued ice geometry, and performing elliptic smoothing. The method developed for multi-block grids involves a transition-layer grid to ensure jaggedness in the ice geometry does not propagate into the domain. It also involves a "thick" wrap-around grid about the ice to ensure grid lines clustered next to solid surfaces do not propagate as streaks of tightly packed grid lines into the domain along block boundaries. For multi-block grids, this study also developed blocking topologies that ensure solutions to multi-block grids converge to steady state as quickly as single-block grids. The second major challenge in CFD simulations of iced airfoils is not knowing when it will predict reliably because of uncertainties in the turbulence modeling. In this study, the effects of turbulence models in predicting lift, drag, and moment coefficients were examined for airfoils with rime ice (i.e., ice with jaggedness only) and with glaze ice (i.e., ice with multiple protruding horns and surface jaggedness) as a function of angle of attack. In this examination, three different CFD codes---WIND, FLUENT, and PowerFLOW were used to examine a variety of turbulence models, including Spalart-Allmaras, RNG k-epsilon, shear-stress transport, v2-f, and differential Reynolds stress with and without non-equilibrium wall functions. The accuracy of the CFD predictions was evaluated by comparing grid-independent solutions with measured experimental data. Results obtained show CFD with WIND and FLUENT to predict the aerodynamics of airfoils with rime ice reliably up to near stall for all turbulence models investigated. (Abstract shortened by UMI.)

Navier-Stokes simulation of external/internal transonic flow on the forebody/inlet of the AV-8B Harrier II

NASA Technical Reports Server (NTRS)

Mysko, Stephen J.; Chyu, Wei J.; Stortz, Michael W.; Chow, Chuen-Yen

1993-01-01

In this work, the computation of combined external/internal transonic flow on the complex forebody/inlet configuration of the AV-8B Harrier II is performed. The actual aircraft has been measured and its surface and surrounding domain, in which the fuselage and inlet have a common wall, have been described using structured grids. The 'thin-layer' Navier-Stokes equations were used to model the flow along with the Chimera embedded multi-block technique. A fully conservative, alternating direction implicit (ADI), approximately factored, partially fluxsplit algorithm was employed to perform the computation. Comparisons to some experimental wind tunnel data yielded good agreement for flow at zero incidence and angle of attack. The aim of this paper is to provide a methodology or computational tool for the numerical solution of complex external/internal flows.
A study of the parallel algorithm for large-scale DC simulation of nonlinear systems

NASA Astrophysics Data System (ADS)

Cortés Udave, Diego Ernesto; Ogrodzki, Jan; Gutiérrez de Anda, Miguel Angel

Newton-Raphson DC analysis of large-scale nonlinear circuits may be an extremely time consuming process even if sparse matrix techniques and bypassing of nonlinear models calculation are used. A slight decrease in the time required for this task may be enabled on multi-core, multithread computers if the calculation of the mathematical models for the nonlinear elements as well as the stamp management of the sparse matrix entries are managed through concurrent processes. This numerical complexity can be further reduced via the circuit decomposition and parallel solution of blocks taking as a departure point the BBD matrix structure. This block-parallel approach may give a considerable profit though it is strongly dependent on the system topology and, of course, on the processor type. This contribution presents the easy-parallelizable decomposition-based algorithm for DC simulation and provides a detailed study of its effectiveness.
A software tool for modeling and simulation of numerical P systems.

PubMed

Buiu, Catalin; Arsene, Octavian; Cipu, Corina; Patrascu, Monica

2011-03-01

A P system represents a distributed and parallel bio-inspired computing model in which basic data structures are multi-sets or strings. Numerical P systems have been recently introduced and they use numerical variables and local programs (or evolution rules), usually in a deterministic way. They may find interesting applications in areas such as computational biology, process control or robotics. The first simulator of numerical P systems (SNUPS) has been designed, implemented and made available to the scientific community by the authors of this paper. SNUPS allows a wide range of applications, from modeling and simulation of ordinary differential equations, to the use of membrane systems as computational blocks of cognitive architectures, and as controllers for autonomous mobile robots. This paper describes the functioning of a numerical P system and presents an overview of SNUPS capabilities together with an illustrative example. SNUPS is freely available to researchers as a standalone application and may be downloaded from a dedicated website, http://snups.ics.pub.ro/, which includes an user manual and sample membrane structures. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.
Multi-purpose greenhouse of changeable geometry (MGCG)

NASA Astrophysics Data System (ADS)

Kordium, V.; Kornejchuk, A.

In the frames of scientific program of National Cosmic Agency of Ukraine the multipurpose greenhouse is being developed. It is destined for the performance of biological and biotechnological experiments as well as for planting of fast growing vegetable cultures for crew ration enrichment and positive psychological influence under the conditions of long-term flight in the international space station or in other cosmic flying objects. Main principle of greenhouse arrangement is the existence of unified modules. Their sets and combinations permit to form executively different space greenhouse configurations. The minimal structural greenhouse unit suitable either for construction of total configuration or for autonomous functioning, is a carrying composite platform (CCP). The experimental vegetative module (EVM) and the module, supporting microclimate needed inside EVM, are launched to CCP. The amount of these modules and their configuration depend on quantity and complexity of tasks to be solved as well as on duration of their performance. These modules form the experimental block. Four modules of much larger sizes, which form experimentally technological block, are used for further studies of objectives approved in the experimental block. The technologies developed for growing plants are used in the third, technological block, which is a one large vegetative module. All three greenhouse blocks can be changed in their sizes in three dimensions, and function either in a complete greenhouse structure, or autonomously. The control is performed from a board computer, or, if necessary, it is governed with automation devices placed on a front panel of blocks. All three blocks are pulled out along the directing base into the station passage, and this makes free access to the base modules, convenient work with them, and à good survey.
Large calculation of the flow over a hypersonic vehicle using a GPU

NASA Astrophysics Data System (ADS)

Elsen, Erich; LeGresley, Patrick; Darve, Eric

2008-12-01

Graphics processing units are capable of impressive computing performance up to 518 Gflops peak performance. Various groups have been using these processors for general purpose computing; most efforts have focussed on demonstrating relatively basic calculations, e.g. numerical linear algebra, or physical simulations for visualization purposes with limited accuracy. This paper describes the simulation of a hypersonic vehicle configuration with detailed geometry and accurate boundary conditions using the compressible Euler equations. To the authors' knowledge, this is the most sophisticated calculation of this kind in terms of complexity of the geometry, the physical model, the numerical methods employed, and the accuracy of the solution. The Navier-Stokes Stanford University Solver (NSSUS) was used for this purpose. NSSUS is a multi-block structured code with a provably stable and accurate numerical discretization which uses a vertex-based finite-difference method. A multi-grid scheme is used to accelerate the solution of the system. Based on a comparison of the Intel Core 2 Duo and NVIDIA 8800GTX, speed-ups of over 40× were demonstrated for simple test geometries and 20× for complex geometries.
Multistage Computerized Adaptive Testing with Uniform Item Exposure

ERIC Educational Resources Information Center

Edwards, Michael C.; Flora, David B.; Thissen, David

2012-01-01

This article describes a computerized adaptive test (CAT) based on the uniform item exposure multi-form structure (uMFS). The uMFS is a specialization of the multi-form structure (MFS) idea described by Armstrong, Jones, Berliner, and Pashley (1998). In an MFS CAT, the examinee first responds to a small fixed block of items. The items comprising…
Modeling self-organization of novel organic materials

NASA Astrophysics Data System (ADS)

Sayar, Mehmet

In this thesis, the structural organization of oligomeric multi-block molecules is analyzed by computational analysis of coarse-grained models. These molecules form nanostructures with different dimensionalities, and the nanostructured nature of these materials leads to novel structural properties at different length scales. Previously, a number of oligomeric triblock rodcoil molecules have been shown to self-organize into mushroom shaped noncentrosymmetric nanostructures. Interestingly, thin films of these molecules contain polar domains and a finite macroscopic polarization. However, the fully polarized state is not the equilibrium state. In the first chapter, by solving a model with dipolar and Ising-like short range interactions, we show that polar domains are stable in films composed of aggregates as opposed to isolated molecules. Unlike classical molecular systems, these nanoaggregates have large intralayer spacings (a ≈ 6 nm), leading to a reduction in the repulsive dipolar interactions that oppose polar order within layers. This enables the formation of a striped pattern with polar domains of alternating directions. The energies of the possible structures at zero temperature are computed exactly and results of Monte Carlo simulations are provided at non-zero temperatures. In the second chapter, the macroscopic polarization of such nanostructured films is analyzed in the presence of a short range surface interaction. The surface interaction leads to a periodic domain structure where the balance between the up and down domains is broken, and therefore films of finite thickness have a net macroscopic polarization. The polarization per unit volume is a function of film thickness and strength of the surface interaction. Finally, in chapter three, self-organization of organic molecules into a network of one dimensional objects is analyzed. Multi-block organic dendron rodcoil molecules were found to self-organize into supramolecular nanoribbons (threads) and form gels at very low concentrations. Here, the formation and structural properties of these networks are studied with Monte Carlo simulations. The model gelators can form intra and inter-thread bonds, and the threads have a finite stiffness. The results suggest that the high persistence length is a result of the interplay of thread stiffness and inter-thread interactions. Furthermore, this high persistence length enables the formation of networks at low concentrations.
Multi-GPU hybrid programming accelerated three-dimensional phase-field model in binary alloy

NASA Astrophysics Data System (ADS)

Zhu, Changsheng; Liu, Jieqiong; Zhu, Mingfang; Feng, Li

2018-03-01

In the process of dendritic growth simulation, the computational efficiency and the problem scales have extremely important influence on simulation efficiency of three-dimensional phase-field model. Thus, seeking for high performance calculation method to improve the computational efficiency and to expand the problem scales has a great significance to the research of microstructure of the material. A high performance calculation method based on MPI+CUDA hybrid programming model is introduced. Multi-GPU is used to implement quantitative numerical simulations of three-dimensional phase-field model in binary alloy under the condition of multi-physical processes coupling. The acceleration effect of different GPU nodes on different calculation scales is explored. On the foundation of multi-GPU calculation model that has been introduced, two optimization schemes, Non-blocking communication optimization and overlap of MPI and GPU computing optimization, are proposed. The results of two optimization schemes and basic multi-GPU model are compared. The calculation results show that the use of multi-GPU calculation model can improve the computational efficiency of three-dimensional phase-field obviously, which is 13 times to single GPU, and the problem scales have been expanded to 8193. The feasibility of two optimization schemes is shown, and the overlap of MPI and GPU computing optimization has better performance, which is 1.7 times to basic multi-GPU model, when 21 GPUs are used.
Multi-scale analysis of the effect of nano-filler particle diameter on the physical properties of CAD/CAM composite resin blocks.

PubMed

Yamaguchi, Satoshi; Inoue, Sayuri; Sakai, Takahiko; Abe, Tomohiro; Kitagawa, Haruaki; Imazato, Satoshi

2017-05-01

The objective of this study was to assess the effect of silica nano-filler particle diameters in a computer-aided design/manufacturing (CAD/CAM) composite resin (CR) block on physical properties at the multi-scale in silico. CAD/CAM CR blocks were modeled, consisting of silica nano-filler particles (20, 40, 60, 80, and 100 nm) and matrix (Bis-GMA/TEGDMA), with filler volume contents of 55.161%. Calculation of Young's moduli and Poisson's ratios for the block at macro-scale were analyzed by homogenization. Macro-scale CAD/CAM CR blocks (3 × 3 × 3 mm) were modeled and compressive strengths were defined when the fracture loads exceeded 6075 N. MPS values of the nano-scale models were compared by localization analysis. As the filler size decreased, Young's moduli and compressive strength increased, while Poisson's ratios and MPS decreased. All parameters were significantly correlated with the diameters of the filler particles (Pearson's correlation test, r = -0.949, 0.943, -0.951, 0.976, p < 0.05). The in silico multi-scale model established in this study demonstrates that the Young's moduli, Poisson's ratios, and compressive strengths of CAD/CAM CR blocks can be enhanced by loading silica nanofiller particles of smaller diameter. CAD/CAM CR blocks by using smaller silica nano-filler particles have a potential to increase fracture resistance.
Automatic Blocking Of QR and LU Factorizations for Locality

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

Yi, Q; Kennedy, K; You, H

2004-03-26

QR and LU factorizations for dense matrices are important linear algebra computations that are widely used in scientific applications. To efficiently perform these computations on modern computers, the factorization algorithms need to be blocked when operating on large matrices to effectively exploit the deep cache hierarchy prevalent in today's computer memory systems. Because both QR (based on Householder transformations) and LU factorization algorithms contain complex loop structures, few compilers can fully automate the blocking of these algorithms. Though linear algebra libraries such as LAPACK provides manually blocked implementations of these algorithms, by automatically generating blocked versions of the computations, moremore » benefit can be gained such as automatic adaptation of different blocking strategies. This paper demonstrates how to apply an aggressive loop transformation technique, dependence hoisting, to produce efficient blockings for both QR and LU with partial pivoting. We present different blocking strategies that can be generated by our optimizer and compare the performance of auto-blocked versions with manually tuned versions in LAPACK, both using reference BLAS, ATLAS BLAS and native BLAS specially tuned for the underlying machine architectures.« less
ASIC-based architecture for the real-time computation of 2D convolution with large kernel size

NASA Astrophysics Data System (ADS)

Shao, Rui; Zhong, Sheng; Yan, Luxin

2015-12-01

Bidimensional convolution is a low-level processing algorithm of interest in many areas, but its high computational cost constrains the size of the kernels, especially in real-time embedded systems. This paper presents a hardware architecture for the ASIC-based implementation of 2-D convolution with medium-large kernels. Aiming to improve the efficiency of storage resources on-chip, reducing off-chip bandwidth of these two issues, proposed construction of a data cache reuse. Multi-block SPRAM to cross cached images and the on-chip ping-pong operation takes full advantage of the data convolution calculation reuse, design a new ASIC data scheduling scheme and overall architecture. Experimental results show that the structure can achieve 40× 32 size of template real-time convolution operations, and improve the utilization of on-chip memory bandwidth and on-chip memory resources, the experimental results show that the structure satisfies the conditions to maximize data throughput output , reducing the need for off-chip memory bandwidth.
Emerging CFD technologies and aerospace vehicle design

NASA Technical Reports Server (NTRS)

Aftosmis, Michael J.

1995-01-01

With the recent focus on the needs of design and applications CFD, research groups have begun to address the traditional bottlenecks of grid generation and surface modeling. Now, a host of emerging technologies promise to shortcut or dramatically simplify the simulation process. This paper discusses the current status of these emerging technologies. It will argue that some tools are already available which can have positive impact on portions of the design cycle. However, in most cases, these tools need to be integrated into specific engineering systems and process cycles to be used effectively. The rapidly maturing status of unstructured and Cartesian approaches for inviscid simulations makes suggests the possibility of highly automated Euler-boundary layer simulations with application to loads estimation and even preliminary design. Similarly, technology is available to link block structured mesh generation algorithms with topology libraries to avoid tedious re-meshing of topologically similar configurations. Work in algorithmic based auto-blocking suggests that domain decomposition and point placement operations in multi-block mesh generation may be properly posed as problems in Computational Geometry, and following this approach may lead to robust algorithmic processes for automatic mesh generation.
Parallel block schemes for large scale least squares computations

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

Golub, G.H.; Plemmons, R.J.; Sameh, A.

1986-04-01

Large scale least squares computations arise in a variety of scientific and engineering problems, including geodetic adjustments and surveys, medical image analysis, molecular structures, partial differential equations and substructuring methods in structural engineering. In each of these problems, matrices often arise which possess a block structure which reflects the local connection nature of the underlying physical problem. For example, such super-large nonlinear least squares computations arise in geodesy. Here the coordinates of positions are calculated by iteratively solving overdetermined systems of nonlinear equations by the Gauss-Newton method. The US National Geodetic Survey will complete this year (1986) the readjustment ofmore » the North American Datum, a problem which involves over 540 thousand unknowns and over 6.5 million observations (equations). The observation matrix for these least squares computations has a block angular form with 161 diagnonal blocks, each containing 3 to 4 thousand unknowns. In this paper parallel schemes are suggested for the orthogonal factorization of matrices in block angular form and for the associated backsubstitution phase of the least squares computations. In addition, a parallel scheme for the calculation of certain elements of the covariance matrix for such problems is described. It is shown that these algorithms are ideally suited for multiprocessors with three levels of parallelism such as the Cedar system at the University of Illinois. 20 refs., 7 figs.« less
CFD-ACE+: a CAD system for simulation and modeling of MEMS

NASA Astrophysics Data System (ADS)

Stout, Phillip J.; Yang, H. Q.; Dionne, Paul; Leonard, Andy; Tan, Zhiqiang; Przekwas, Andrzej J.; Krishnan, Anantha

1999-03-01

Computer aided design (CAD) systems are a key to designing and manufacturing MEMS with higher performance/reliability, reduced costs, shorter prototyping cycles and improved time- to-market. One such system is CFD-ACE+MEMS, a modeling and simulation environment for MEMS which includes grid generation, data visualization, graphical problem setup, and coupled fluidic, thermal, mechanical, electrostatic, and magnetic physical models. The fluid model is a 3D multi- block, structured/unstructured/hybrid, pressure-based, implicit Navier-Stokes code with capabilities for multi- component diffusion, multi-species transport, multi-step gas phase chemical reactions, surface reactions, and multi-media conjugate heat transfer. The thermal model solves the total enthalpy from of the energy equation. The energy equation includes unsteady, convective, conductive, species energy, viscous dissipation, work, and radiation terms. The electrostatic model solves Poisson's equation. Both the finite volume method and the boundary element method (BEM) are available for solving Poisson's equation. The BEM method is useful for unbounded problems. The magnetic model solves for the vector magnetic potential from Maxwell's equations including eddy currents but neglecting displacement currents. The mechanical model is a finite element stress/deformation solver which has been coupled to the flow, heat, electrostatic, and magnetic calculations to study flow, thermal electrostatically, and magnetically included deformations of structures. The mechanical or structural model can accommodate elastic and plastic materials, can handle large non-linear displacements, and can model isotropic and anisotropic materials. The thermal- mechanical coupling involves the solution of the steady state Navier equation with thermoelastic deformation. The electrostatic-mechanical coupling is a calculation of the pressure force due to surface charge on the mechanical structure. Results of CFD-ACE+MEMS modeling of MEMS such as cantilever beams, accelerometers, and comb drives are discussed.
LAURA Users Manual: 5.2-43231

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Christopher O.; Kleb, Bil

2009-01-01

This users manual provides in-depth information concerning installation and execution of LAURA, version 5. LAURA is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 LAURA code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintainability by eliminating the requirement for problem-dependent re-compilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multiphysics coupling. As a result, LAURA now shares gas-physics modules, MPI modules, and other low-level modules with the FUN3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU-standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.
Laura Users Manual: 5.1-41601

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Christopher O.; Kleb, Bil

2009-01-01

This users manual provides in-depth information concerning installation and execution of LAURA, version 5. LAURA is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 LAURA code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintainability by eliminating the requirement for problem-dependent re-compilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multiphysics coupling. As a result, LAURA now shares gas-physics modules, MPI modules, and other low-level modules with the FUN3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU-standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.
A Scalable, Parallel Approach for Multi-Point, High-Fidelity Aerostructural Optimization of Aircraft Configurations

NASA Astrophysics Data System (ADS)

Kenway, Gaetan K. W.

This thesis presents new tools and techniques developed to address the challenging problem of high-fidelity aerostructural optimization with respect to large numbers of design variables. A new mesh-movement scheme is developed that is both computationally efficient and sufficiently robust to accommodate large geometric design changes and aerostructural deformations. A fully coupled Newton-Krylov method is presented that accelerates the convergence of aerostructural systems and provides a 20% performance improvement over the traditional nonlinear block Gauss-Seidel approach and can handle more exible structures. A coupled adjoint method is used that efficiently computes derivatives for a gradient-based optimization algorithm. The implementation uses only machine accurate derivative techniques and is verified to yield fully consistent derivatives by comparing against the complex step method. The fully-coupled large-scale coupled adjoint solution method is shown to have 30% better performance than the segregated approach. The parallel scalability of the coupled adjoint technique is demonstrated on an Euler Computational Fluid Dynamics (CFD) model with more than 80 million state variables coupled to a detailed structural finite-element model of the wing with more than 1 million degrees of freedom. Multi-point high-fidelity aerostructural optimizations of a long-range wide-body, transonic transport aircraft configuration are performed using the developed techniques. The aerostructural analysis employs Euler CFD with a 2 million cell mesh and a structural finite element model with 300 000 DOF. Two design optimization problems are solved: one where takeoff gross weight is minimized, and another where fuel burn is minimized. Each optimization uses a multi-point formulation with 5 cruise conditions and 2 maneuver conditions. The optimization problems have 476 design variables are optimal results are obtained within 36 hours of wall time using 435 processors. The TOGW minimization results in a 4.2% reduction in TOGW with a 6.6% fuel burn reduction, while the fuel burn optimization resulted in a 11.2% fuel burn reduction with no change to the takeoff gross weight.
Chemical and morphological characterization of III-V strained layered heterostructures

NASA Astrophysics Data System (ADS)

Gray, Allen Lindsay

This dissertation describes investigations into the chemical and morphological characterization of III-V strained layered heterostructures by high-resolution x-ray diffraction. The purpose of this work is two-fold. The first was to use high-resolution x-ray diffraction coupled with transmission electron microscopy to characterize structurally a quaternary AlGaAsSb/InGaAsSb multiple quantum well heterostructure laser device. A method for uniquely determining the chemical composition of the strain quaternary quantum well, information previously thought to be unattainable using high resolution x-ray diffraction is thoroughly described. The misconception that high-resolution x-ray diffraction can separately find the well and barrier thickness of a multi-quantum well from the pendellosung fringe spacing is corrected, and thus the need for transmission electron microscopy is motivated. Computer simulations show that the key in finding the well composition is the intensity of the -3rd order satellite peaks in the diffraction pattern. The second part of this work addresses the evolution of strain relief in metastable multi-period InGaAs/GaAs multi-layered structures by high-resolution x-ray reciprocal space maps. Results are accompanied by transmission electron and differential contrast microscopy. The evolution of strain relief is tracked from a coherent "pseudomorphic" growth to a dislocated state as a function of period number by examining the x-ray diffuse scatter emanating from the average composition (zeroth-order) of the multi-layer. Relaxation is determined from the relative positions of the substrate with respect to the zeroth-order peak. For the low period number, the diffuse scatter from the multi-layer structure region arises from periodic, coherent crystallites. For the intermediate period number, the displacement fields around the multi-layer structure region transition to random coherent crystallites. At the higher period number, displacement fields of overlapping dislocations from relaxation of the random crystallites cause the initial stages of relaxation of the multi-layer structure. At the highest period number studied, relaxation of the multi-layer structure becomes bi-modal characterized by overlapping dislocations caused by mosaic block relaxation and periodically spaced misfit dislocations formed by 60°-type dislocations. The relaxation of the multi-layer structure has an exponential dependence on the diffuse scatter length-scale, which is shown to be a sensitive measure of the onset of relaxation.
Adaptive Numerical Algorithms in Space Weather Modeling

NASA Technical Reports Server (NTRS)

Toth, Gabor; vanderHolst, Bart; Sokolov, Igor V.; DeZeeuw, Darren; Gombosi, Tamas I.; Fang, Fang; Manchester, Ward B.; Meng, Xing; Nakib, Dalal; Powell, Kenneth G.;

2010-01-01

Space weather describes the various processes in the Sun-Earth system that present danger to human health and technology. The goal of space weather forecasting is to provide an opportunity to mitigate these negative effects. Physics-based space weather modeling is characterized by disparate temporal and spatial scales as well as by different physics in different domains. A multi-physics system can be modeled by a software framework comprising of several components. Each component corresponds to a physics domain, and each component is represented by one or more numerical models. The publicly available Space Weather Modeling Framework (SWMF) can execute and couple together several components distributed over a parallel machine in a flexible and efficient manner. The framework also allows resolving disparate spatial and temporal scales with independent spatial and temporal discretizations in the various models. Several of the computationally most expensive domains of the framework are modeled by the Block-Adaptive Tree Solar wind Roe Upwind Scheme (BATS-R-US) code that can solve various forms of the magnetohydrodynamics (MHD) equations, including Hall, semi-relativistic, multi-species and multi-fluid MHD, anisotropic pressure, radiative transport and heat conduction. Modeling disparate scales within BATS-R-US is achieved by a block-adaptive mesh both in Cartesian and generalized coordinates. Most recently we have created a new core for BATS-R-US: the Block-Adaptive Tree Library (BATL) that provides a general toolkit for creating, load balancing and message passing in a 1, 2 or 3 dimensional block-adaptive grid. We describe the algorithms of BATL and demonstrate its efficiency and scaling properties for various problems. BATS-R-US uses several time-integration schemes to address multiple time-scales: explicit time stepping with fixed or local time steps, partially steady-state evolution, point-implicit, semi-implicit, explicit/implicit, and fully implicit numerical schemes. Depending on the application, we find that different time stepping methods are optimal. Several of the time integration schemes exploit the block-based granularity of the grid structure. The framework and the adaptive algorithms enable physics based space weather modeling and even forecasting.

Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

PubMed Central

Putz, Mihai V.; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

2016-01-01

Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. PMID:27399692

A computer-guided bone block harvesting procedure: a proof-of-principle case report and technical notes.

PubMed

De Stavola, Luca; Fincato, Andrea; Albiero, Alberto Maria

2015-01-01

During autogenous mandibular bone harvesting, there is a risk of damage to anatomical structures, as the surgeon has no three-dimensional control of the osteotomy planes. The aim of this proof-of-principle case report is to describe a procedure for harvesting a mandibular bone block that applies a computer-guided surgery concept. A partially dentate patient who presented with two vertical defects (one in the maxilla and one in the mandible) was selected for an autogenous mandibular bone block graft. The bone block was planned using a computer-aided design process, with ideal bone osteotomy planes defined beforehand to prevent damage to anatomical structures (nerves, dental roots, etc) and to generate a surgical guide, which defined the working directions in three dimensions for the bone-cutting instrument. Bone block dimensions were planned so that both defects could be repaired. The projected bone block was 37.5 mm in length, 10 mm in height, and 5.7 mm in thickness, and it was grafted in two vertical bone augmentations: an 8 × 21-mm mandibular defect and a 6.5 × 18-mm defect in the maxilla. Supraimposition of the preoperative and postoperative computed tomographic images revealed a procedure accuracy of 0.25 mm. This computer-guided bone harvesting technique enables clinicians to obtain sufficient autogenous bone to manage multiple defects safely.
Numerical grid generation in computational field simulations. Volume 1

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

Soni, B.K.; Thompson, J.F.; Haeuser, J.

1996-12-31

To enhance the CFS technology to its next level of applicability (i.e., to create acceptance of CFS in an integrated product and process development involving multidisciplinary optimization) the basic requirements are: rapid turn-around time, reliable and accurate simulation, affordability and appropriate linkage to other engineering disciplines. In response to this demand, there has been a considerable growth in the grid generation related research activities involving automization, parallel processing, linkage with the CAD-CAM systems, CFS with dynamic motion and moving boundaries, strategies and algorithms associated with multi-block structured, unstructured, hybrid, hexahedral, and Cartesian grids, along with its applicability to various disciplinesmore » including biomedical, semiconductor, geophysical, ocean modeling, and multidisciplinary optimization.« less
Demonstration Of Ultra HI-FI (UHF) Methods

NASA Technical Reports Server (NTRS)

Dyson, Rodger W.

2004-01-01

Computational aero-acoustics (CAA) requires efficient, high-resolution simulation tools. Most current techniques utilize finite-difference approaches because high order accuracy is considered too difficult or expensive to achieve with finite volume or finite element methods. However, a novel finite volume approach (Ultra HI-FI or UHF) which utilizes Hermite fluxes is presented which can achieve both arbitrary accuracy and fidelity in space and time. The technique can be applied to unstructured grids with some loss of fidelity or with multi-block structured grids for maximum efficiency and resolution. In either paradigm, it is possible to resolve ultra-short waves (less than 2 PPW). This is demonstrated here by solving the 4th CAA workshop Category 1 Problem 1.
A Comparative Study of Multi-material Data Structures for Computational Physics Applications

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

Garimella, Rao Veerabhadra; Robey, Robert W.

The data structures used to represent the multi-material state of a computational physics application can have a drastic impact on the performance of the application. We look at efficient data structures for sparse applications where there may be many materials, but only one or few in most computational cells. We develop simple performance models for use in selecting possible data structures and programming patterns. We verify the analytic models of performance through a small test program of the representative cases.
User's guide to the Fault Inferring Nonlinear Detection System (FINDS) computer program

NASA Technical Reports Server (NTRS)

Caglayan, A. K.; Godiwala, P. M.; Satz, H. S.

1988-01-01

Described are the operation and internal structure of the computer program FINDS (Fault Inferring Nonlinear Detection System). The FINDS algorithm is designed to provide reliable estimates for aircraft position, velocity, attitude, and horizontal winds to be used for guidance and control laws in the presence of possible failures in the avionics sensors. The FINDS algorithm was developed with the use of a digital simulation of a commercial transport aircraft and tested with flight recorded data. The algorithm was then modified to meet the size constraints and real-time execution requirements on a flight computer. For the real-time operation, a multi-rate implementation of the FINDS algorithm has been partitioned to execute on a dual parallel processor configuration: one based on the translational dynamics and the other on the rotational kinematics. The report presents an overview of the FINDS algorithm, the implemented equations, the flow charts for the key subprograms, the input and output files, program variable indexing convention, subprogram descriptions, and the common block descriptions used in the program.
Synergistic Anti-arrhythmic Effects in Human Atria with Combined Use of Sodium Blockers and Acacetin

PubMed Central

Ni, Haibo; Whittaker, Dominic G.; Wang, Wei; Giles, Wayne R.; Narayan, Sanjiv M.; Zhang, Henggui

2017-01-01

Atrial fibrillation (AF) is the most common cardiac arrhythmia. Developing effective and safe anti-AF drugs remains an unmet challenge. Simultaneous block of both atrial-specific ultra-rapid delayed rectifier potassium (K+) current (IKur) and the Na+ current (INa) has been hypothesized to be anti-AF, without inducing significant QT prolongation and ventricular side effects. However, the antiarrhythmic advantage of simultaneously blocking these two channels vs. individual block in the setting of AF-induced electrical remodeling remains to be documented. Furthermore, many IKur blockers such as acacetin and AVE0118, partially inhibit other K+ currents in the atria. Whether this multi-K+-block produces greater anti-AF effects compared with selective IKur-block has not been fully understood. The aim of this study was to use computer models to (i) assess the impact of multi-K+-block as exhibited by many IKur blokers, and (ii) evaluate the antiarrhythmic effect of blocking IKur and INa, either alone or in combination, on atrial and ventricular electrical excitation and recovery in the setting of AF-induced electrical-remodeling. Contemporary mathematical models of human atrial and ventricular cells were modified to incorporate dose-dependent actions of acacetin (a multichannel blocker primarily inhibiting IKur while less potently blocking Ito, IKr, and IKs). Rate- and atrial-selective inhibition of INa was also incorporated into the models. These single myocyte models were then incorporated into multicellular two-dimensional (2D) and three-dimensional (3D) anatomical models of the human atria. As expected, application of IKur blocker produced pronounced action potential duration (APD) prolongation in atrial myocytes. Furthermore, combined multiple K+-channel block that mimicked the effects of acacetin exhibited synergistic APD prolongations. Synergistically anti-AF effects following inhibition of INa and combined IKur/K+-channels were also observed. The attainable maximal AF-selectivity of INa inhibition was greatly augmented by blocking IKur or multiple K+-currents in the atrial myocytes. This enhanced anti-arrhythmic effects of combined block of Na+- and K+-channels were also seen in 2D and 3D simulations; specially, there was an enhanced efficacy in terminating re-entrant excitation waves, exerting improved antiarrhythmic effects in the human atria as compared to a single-channel block. However, in the human ventricular myocytes and tissue, cellular repolarization and computed QT intervals were modestly affected in the presence of actions of acacetin and INa blockers (either alone or in combination). In conclusion, this study demonstrates synergistic antiarrhythmic benefits of combined block of IKur and INa, as well as those of INa and combined multi K+-current block of acacetin, without significant alterations of ventricular repolarization and QT intervals. This approach may be a valuable strategy for the treatment of AF. PMID:29218016
A taxonomy and comparison of parallel block multi-level preconditioners for the incompressible Navier-Stokes equations.

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

Shadid, John Nicolas; Elman, Howard; Shuttleworth, Robert R.

2007-04-01

In recent years, considerable effort has been placed on developing efficient and robust solution algorithms for the incompressible Navier-Stokes equations based on preconditioned Krylov methods. These include physics-based methods, such as SIMPLE, and purely algebraic preconditioners based on the approximation of the Schur complement. All these techniques can be represented as approximate block factorization (ABF) type preconditioners. The goal is to decompose the application of the preconditioner into simplified sub-systems in which scalable multi-level type solvers can be applied. In this paper we develop a taxonomy of these ideas based on an adaptation of a generalized approximate factorization of themore » Navier-Stokes system first presented in [25]. This taxonomy illuminates the similarities and differences among these preconditioners and the central role played by efficient approximation of certain Schur complement operators. We then present a parallel computational study that examines the performance of these methods and compares them to an additive Schwarz domain decomposition (DD) algorithm. Results are presented for two and three-dimensional steady state problems for enclosed domains and inflow/outflow systems on both structured and unstructured meshes. The numerical experiments are performed using MPSalsa, a stabilized finite element code.« less
Vision-Based UAV Flight Control and Obstacle Avoidance

DTIC Science & Technology

2006-01-01

denoted it by Vb = (Vb1, Vb2 , Vb3). Fig. 2 shows the block diagram of the proposed vision-based motion analysis and obstacle avoidance system. We denote...structure analysis often involve computation- intensive computer vision tasks, such as feature extraction and geometric modeling. Computation-intensive...First, we extract a set of features from each block. 2) Second, we compute the distance between these two sets of features. In conventional motion
A design philosophy for multi-layer neural networks with applications to robot control

NASA Technical Reports Server (NTRS)

Vadiee, Nader; Jamshidi, MO

1989-01-01

A system is proposed which receives input information from many sensors that may have diverse scaling, dimension, and data representations. The proposed system tolerates sensory information with faults. The proposed self-adaptive processing technique has great promise in integrating the techniques of artificial intelligence and neural networks in an attempt to build a more intelligent computing environment. The proposed architecture can provide a detailed decision tree based on the input information, information stored in a long-term memory, and the adapted rule-based knowledge. A mathematical model for analysis will be obtained to validate the cited hypotheses. An extensive software program will be developed to simulate a typical example of pattern recognition problem. It is shown that the proposed model displays attention, expectation, spatio-temporal, and predictory behavior which are specific to the human brain. The anticipated results of this research project are: (1) creation of a new dynamic neural network structure, and (2) applications to and comparison with conventional multi-layer neural network structures. The anticipated benefits from this research are vast. The model can be used in a neuro-computer architecture as a building block which can perform complicated, nonlinear, time-varying mapping from a multitude of input excitory classes to an output or decision environment. It can be used for coordinating different sensory inputs and past experience of a dynamic system and actuating signals. The commercial applications of this project can be the creation of a special-purpose neuro-computer hardware which can be used in spatio-temporal pattern recognitions in such areas as air defense systems, e.g., target tracking, and recognition. Potential robotics-related applications are trajectory planning, inverse dynamics computations, hierarchical control, task-oriented control, and collision avoidance.
A joint precoding scheme for indoor downlink multi-user MIMO VLC systems

NASA Astrophysics Data System (ADS)

Zhao, Qiong; Fan, Yangyu; Kang, Bochao

2017-11-01

In this study, we aim to improve the system performance and reduce the implementation complexity of precoding scheme for visible light communication (VLC) systems. By incorporating the power-method algorithm and the block diagonalization (BD) algorithm, we propose a joint precoding scheme for indoor downlink multi-user multi-input-multi-output (MU-MIMO) VLC systems. In this scheme, we apply the BD algorithm to eliminate the co-channel interference (CCI) among users firstly. Secondly, the power-method algorithm is used to search the precoding weight for each user based on the optimal criterion of signal to interference plus noise ratio (SINR) maximization. Finally, the optical power restrictions of VLC systems are taken into account to constrain the precoding weight matrix. Comprehensive computer simulations in two scenarios indicate that the proposed scheme always has better bit error rate (BER) performance and lower computation complexity than that of the traditional scheme.
Performance Enhancement Strategies for Multi-Block Overset Grid CFD Applications

NASA Technical Reports Server (NTRS)

Djomehri, M. Jahed; Biswas, Rupak

2003-01-01

The overset grid methodology has significantly reduced time-to-solution of highfidelity computational fluid dynamics (CFD) simulations about complex aerospace configurations. The solution process resolves the geometrical complexity of the problem domain by using separately generated but overlapping structured discretization grids that periodically exchange information through interpolation. However, high performance computations of such large-scale realistic applications must be handled efficiently on state-of-the-art parallel supercomputers. This paper analyzes the effects of various performance enhancement strategies on the parallel efficiency of an overset grid Navier-Stokes CFD application running on an SGI Origin2000 machinc. Specifically, the role of asynchronous communication, grid splitting, and grid grouping strategies are presented and discussed. Details of a sophisticated graph partitioning technique for grid grouping are also provided. Results indicate that performance depends critically on the level of latency hiding and the quality of load balancing across the processors.
Numerical study of supersonic combustors by multi-block grids with mismatched interfaces

NASA Technical Reports Server (NTRS)

Moon, Young J.

1990-01-01

A three dimensional, finite rate chemistry, Navier-Stokes code was extended to a multi-block code with mismatched interface for practical calculations of supersonic combustors. To ensure global conservation, a conservative algorithm was used for the treatment of mismatched interfaces. The extended code was checked against one test case, i.e., a generic supersonic combustor with transverse fuel injection, examining solution accuracy, convergence, and local mass flux error. After testing, the code was used to simulate the chemically reacting flow fields in a scramjet combustor with parallel fuel injectors (unswept and swept ramps). Computational results were compared with experimental shadowgraph and pressure measurements. Fuel-air mixing characteristics of the unswept and swept ramps were compared and investigated.
Persistence of Amygdala-Hippocampal Connectivity and Multi-Voxel Correlation Structures During Awake Rest After Fear Learning Predicts Long-Term Expression of Fear.

PubMed

Hermans, Erno J; Kanen, Jonathan W; Tambini, Arielle; Fernández, Guillén; Davachi, Lila; Phelps, Elizabeth A

2017-05-01

After encoding, memories undergo a process of consolidation that determines long-term retention. For conditioned fear, animal models postulate that consolidation involves reactivations of neuronal assemblies supporting fear learning during postlearning "offline" periods. However, no human studies to date have investigated such processes, particularly in relation to long-term expression of fear. We tested 24 participants using functional MRI on 2 consecutive days in a fear conditioning paradigm involving 1 habituation block, 2 acquisition blocks, and 2 extinction blocks on day 1, and 2 re-extinction blocks on day 2. Conditioning blocks were preceded and followed by 4.5-min rest blocks. Strength of spontaneous recovery of fear on day 2 served as a measure of long-term expression of fear. Amygdala connectivity primarily with hippocampus increased progressively during postacquisition and postextinction rest on day 1. Intraregional multi-voxel correlation structures within amygdala and hippocampus sampled during a block of differential fear conditioning furthermore persisted after fear learning. Critically, both these main findings were stronger in participants who exhibited spontaneous recovery 24 h later. Our findings indicate that neural circuits activated during fear conditioning exhibit persistent postlearning activity that may be functionally relevant in promoting consolidation of the fear memory. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Innovative architectures for dense multi-microprocessor computers

NASA Technical Reports Server (NTRS)

Larson, Robert E.

1989-01-01

The purpose is to summarize a Phase 1 SBIR project performed for the NASA/Langley Computational Structural Mechanics Group. The project was performed from February to August 1987. The main objectives of the project were to: (1) expand upon previous research into the application of chordal ring architectures to the general problem of designing multi-microcomputer architectures, (2) attempt to identify a family of chordal rings such that each chordal ring can be simply expanded to produce the next member of the family, (3) perform a preliminary, high-level design of an expandable multi-microprocessor computer based upon chordal rings, (4) analyze the potential use of chordal ring based multi-microprocessors for sparse matrix problems and other applications arising in computational structural mechanics.
The Comparison of the Effect of Block Flute Accompanied Song Teaching with Multi-Sound Notation and Vocalization Program Accompanied Song Teaching on the Success of Students' Song Learning Behavior

ERIC Educational Resources Information Center

Saktanli, S. Cem

2011-01-01

This experimental study was done to see if using computer supported notation and vocalization program for teaching songs instead of using block flute accompanied song teaching has any significant effect on students' singing behavior. The study group is composed of the 5th, 6th and 7th graders of 2008-2009 educational term in T.O.K.I. Yahya Kemal…
Full Multigrid Flow Solver

NASA Technical Reports Server (NTRS)

Mineck, Raymond E.; Thomas, James L.; Biedron, Robert T.; Diskin, Boris

2005-01-01

FMG3D (full multigrid 3 dimensions) is a pilot computer program that solves equations of fluid flow using a finite difference representation on a structured grid. Infrastructure exists for three dimensions but the current implementation treats only two dimensions. Written in Fortran 90, FMG3D takes advantage of the recursive subroutine feature, dynamic memory allocation, and structured-programming constructs of that language. FMG3D supports multi-block grids with three types of block-to-block interfaces: periodic, C-zero, and C-infinity. For all three types, grid points must match at interfaces. For periodic and C-infinity types, derivatives of grid metrics must be continuous at interfaces. The available equation sets are as follows: scalar elliptic equations, scalar convection equations, and the pressure-Poisson formulation of the Navier-Stokes equations for an incompressible fluid. All the equation sets are implemented with nonzero forcing functions to enable the use of user-specified solutions to assist in verification and validation. The equations are solved with a full multigrid scheme using a full approximation scheme to converge the solution on each succeeding grid level. Restriction to the next coarser mesh uses direct injection for variables and full weighting for residual quantities; prolongation of the coarse grid correction from the coarse mesh to the fine mesh uses bilinear interpolation; and prolongation of the coarse grid solution uses bicubic interpolation.
Improved 3-D turbomachinery CFD algorithm

NASA Technical Reports Server (NTRS)

Janus, J. Mark; Whitfield, David L.

1988-01-01

The building blocks of a computer algorithm developed for the time-accurate flow analysis of rotating machines are described. The flow model is a finite volume method utilizing a high resolution approximate Riemann solver for interface flux definitions. This block LU implicit numerical scheme possesses apparent unconditional stability. Multi-block composite gridding is used to orderly partition the field into a specified arrangement. Block interfaces, including dynamic interfaces, are treated such as to mimic interior block communication. Special attention is given to the reduction of in-core memory requirements by placing the burden on secondary storage media. Broad applicability is implied, although the results presented are restricted to that of an even blade count configuration. Several other configurations are presently under investigation, the results of which will appear in subsequent publications.
Atmospheric Blocking and Atlantic Multi-Decadal Ocean Variability

NASA Technical Reports Server (NTRS)

Haekkinen, Sirpa; Rhines, Peter B.; Worthlen, Denise L.

2011-01-01

Based on the 20th century atmospheric reanalysis, winters with more frequent blocking, in a band of blocked latitudes from Greenland to Western Europe, are found to persist over several decades and correspond to a warm North Atlantic Ocean, in-phase with Atlantic multi-decadal ocean variability. Atmospheric blocking over the northern North Atlantic, which involves isolation of large regions of air from the westerly circulation for 5 days or more, influences fundamentally the ocean circulation and upper ocean properties by impacting wind patterns. Winters with clusters of more frequent blocking between Greenland and western Europe correspond to a warmer, more saline subpolar ocean. The correspondence between blocked westerly winds and warm ocean holds in recent decadal episodes (especially, 1996-2010). It also describes much longer-timescale Atlantic multidecadal ocean variability (AMV), including the extreme, pre-greenhouse-gas, northern warming of the 1930s-1960s. The space-time structure of the wind forcing associated with a blocked regime leads to weaker ocean gyres and weaker heat-exchange, both of which contribute to the warm phase of AMV.
Combinatorics of γ-structures.

PubMed

Han, Hillary S W; Li, Thomas J X; Reidys, Christian M

2014-08-01

In this article we study canonical γ-structures, a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A γ-structure is composed of specific building blocks that have topological genus less than or equal to γ, where composition means concatenation and nesting of such blocks. Our main result is the derivation of the generating function of γ-structures via symbolic enumeration using so called irreducible shadows. We furthermore recursively compute the generating polynomials of irreducible shadows of genus ≤ γ. The γ-structures are constructed via γ-matchings. For 1 ≤ γ ≤ 10, we compute Puiseux expansions at the unique, dominant singularities, allowing us to derive simple asymptotic formulas for the number of γ-structures.
Novel Self-Assembling Amino Acid-Derived Block Copolymer with Changeable Polymer Backbone Structure.

PubMed

Koga, Tomoyuki; Aso, Eri; Higashi, Nobuyuki

2016-11-29

Block copolymers have attracted much attention as potentially interesting building blocks for the development of novel nanostructured materials in recent years. Herein, we report a new type of self-assembling block copolymer with changeable polymer backbone structure, poly(Fmoc-Ser) ester -b-PSt, which was synthesized by combining the polycondensation of 9-fluorenylmethoxycarbonyl-serine (Fmoc-Ser) with the reversible addition-fragmentation chain transfer (RAFT) polymerization of styrene (St). This block copolymer showed the direct conversion of the backbone structure from polyester to polypeptide through a multi O,N-acyl migration triggered by base-induced deprotection of Fmoc groups in organic solvent. Such polymer-to-polymer conversion was found to occur quantitatively without decrease in degree of polymerization and to cause a drastic change in self-assembling property of the block copolymer. On the basis of several morphological analyses using FTIR spectroscopy, atomic force, and transmission and scanning electron microscopies, the resulting peptide block copolymer was found to self-assemble into a vesicle-like hollow nanosphere with relatively uniform diameter of ca. 300 nm in toluene. In this case, the peptide block generated from polyester formed β-sheet structure, indicating the self-assembly via peptide-guided route. We believe the findings presented in this study offer a new concept for the development of self-assembling block copolymer system.

Carpet: Adaptive Mesh Refinement for the Cactus Framework

NASA Astrophysics Data System (ADS)

Schnetter, Erik; Hawley, Scott; Hawke, Ian

2016-11-01

Carpet is an adaptive mesh refinement and multi-patch driver for the Cactus Framework (ascl:1102.013). Cactus is a software framework for solving time-dependent partial differential equations on block-structured grids, and Carpet acts as driver layer providing adaptive mesh refinement, multi-patch capability, as well as parallelization and efficient I/O.
Morphing the feature-based multi-blocks of normative/healthy vertebral geometries to scoliosis vertebral geometries: development of personalized finite element models.

PubMed

Hadagali, Prasannaah; Peters, James R; Balasubramanian, Sriram

2018-03-01

Personalized Finite Element (FE) models and hexahedral elements are preferred for biomechanical investigations. Feature-based multi-block methods are used to develop anatomically accurate personalized FE models with hexahedral mesh. It is tedious to manually construct multi-blocks for large number of geometries on an individual basis to develop personalized FE models. Mesh-morphing method mitigates the aforementioned tediousness in meshing personalized geometries every time, but leads to element warping and loss of geometrical data. Such issues increase in magnitude when normative spine FE model is morphed to scoliosis-affected spinal geometry. The only way to bypass the issue of hex-mesh distortion or loss of geometry as a result of morphing is to rely on manually constructing the multi-blocks for scoliosis-affected spine geometry of each individual, which is time intensive. A method to semi-automate the construction of multi-blocks on the geometry of scoliosis vertebrae from the existing multi-blocks of normative vertebrae is demonstrated in this paper. High-quality hexahedral elements were generated on the scoliosis vertebrae from the morphed multi-blocks of normative vertebrae. Time taken was 3 months to construct the multi-blocks for normative spine and less than a day for scoliosis. Efforts taken to construct multi-blocks on personalized scoliosis spinal geometries are significantly reduced by morphing existing multi-blocks.
Distributed collaborative probabilistic design of multi-failure structure with fluid-structure interaction using fuzzy neural network of regression

NASA Astrophysics Data System (ADS)

Song, Lu-Kai; Wen, Jie; Fei, Cheng-Wei; Bai, Guang-Chen

2018-05-01

To improve the computing efficiency and precision of probabilistic design for multi-failure structure, a distributed collaborative probabilistic design method-based fuzzy neural network of regression (FR) (called as DCFRM) is proposed with the integration of distributed collaborative response surface method and fuzzy neural network regression model. The mathematical model of DCFRM is established and the probabilistic design idea with DCFRM is introduced. The probabilistic analysis of turbine blisk involving multi-failure modes (deformation failure, stress failure and strain failure) was investigated by considering fluid-structure interaction with the proposed method. The distribution characteristics, reliability degree, and sensitivity degree of each failure mode and overall failure mode on turbine blisk are obtained, which provides a useful reference for improving the performance and reliability of aeroengine. Through the comparison of methods shows that the DCFRM reshapes the probability of probabilistic analysis for multi-failure structure and improves the computing efficiency while keeping acceptable computational precision. Moreover, the proposed method offers a useful insight for reliability-based design optimization of multi-failure structure and thereby also enriches the theory and method of mechanical reliability design.
Heat Transfer on a Film-Cooled Rotating Blade

NASA Technical Reports Server (NTRS)

Garg, Vijay K.

1999-01-01

A multi-block, three-dimensional Navier-Stokes code has been used to compute heat transfer coefficient on the blade, hub and shroud for a rotating high-pressure turbine blade with 172 film-cooling holes in eight rows. Film cooling effectiveness is also computed on the adiabatic blade. Wilcox's k-omega model is used for modeling the turbulence. Of the eight rows of holes, three are staggered on the shower-head with compound-angled holes. With so many holes on the blade it was somewhat of a challenge to get a good quality grid on and around the blade and in the tip clearance region. The final multi-block grid consists of 4784 elementary blocks which were merged into 276 super blocks. The viscous grid has over 2.2 million cells. Each hole exit, in its true oval shape, has 80 cells within it so that coolant velocity, temperature, k and omega distributions can be specified at these hole exits. It is found that for the given parameters, heat transfer coefficient on the cooled, isothermal blade is highest in the leading edge region and in the tip region. Also, the effectiveness over the cooled, adiabatic blade is the lowest in these regions. Results for an uncooled blade are also shown, providing a direct comparison with those for the cooled blade. Also, the heat transfer coefficient is much higher on the shroud as compared to that on the hub for both the cooled and the uncooled cases.
NASA Workshop on Computational Structural Mechanics 1987, part 3

NASA Technical Reports Server (NTRS)

Sykes, Nancy P. (Editor)

1989-01-01

Computational Structural Mechanics (CSM) topics are explored. Algorithms and software for nonlinear structural dynamics, concurrent algorithms for transient finite element analysis, computational methods and software systems for dynamics and control of large space structures, and the use of multi-grid for structural analysis are discussed.
Two-Dimensional Computational Model for Wave Rotor Flow Dynamics

NASA Technical Reports Server (NTRS)

Welch, Gerard E.

1996-01-01

A two-dimensional (theta,z) Navier-Stokes solver for multi-port wave rotor flow simulation is described. The finite-volume form of the unsteady thin-layer Navier-Stokes equations are integrated in time on multi-block grids that represent the stationary inlet and outlet ports and the moving rotor passages of the wave rotor. Computed results are compared with three-port wave rotor experimental data. The model is applied to predict the performance of a planned four-port wave rotor experiment. Two-dimensional flow features that reduce machine performance and influence rotor blade and duct wall thermal loads are identified. The performance impact of rounding the inlet port wall, to inhibit separation during passage gradual opening, is assessed.
Structure and Dynamics of Ionic Block Copolymer Melts: Computational Study

DOE PAGES

Aryal, Dipak; Agrawal, Anupriya; Perahia, Dvora; ...

2017-09-06

Structure and dynamics of melts of copolymers with an ABCBA topology, where C is an ionizable block, have been studied by fully atomistic molecular dynamics (MD) simulations. Introducing an ionizable block for functionality adds a significant element to the coupled set of interactions that determine the structure and dynamics of the macromolecule. The polymer consists of a randomly sulfonated polystyrene C block tethered to a flexible poly(ethylene-r-propylene) bridge B and end-capped with poly(tert-butylstyrene) A. The chemical structure and topology of these polymers constitute a model for incorporation of ionic blocks within a framework that provides tactility and mechanical stability. Heremore » in this paper we resolve the structure and dynamics of a structured polymer on the nanoscale constrained by ionic clusters. We find that the melts form intertwined networks of the A and C blocks independent of the degree of sulfonation of the C block with no long-range order. The cluster cohesiveness and morphology affect both macroscopic translational motion and segmental dynamics of all the blocks.« less
Structure and Dynamics of Ionic Block Copolymer Melts: Computational Study

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

Aryal, Dipak; Agrawal, Anupriya; Perahia, Dvora

Structure and dynamics of melts of copolymers with an ABCBA topology, where C is an ionizable block, have been studied by fully atomistic molecular dynamics (MD) simulations. Introducing an ionizable block for functionality adds a significant element to the coupled set of interactions that determine the structure and dynamics of the macromolecule. The polymer consists of a randomly sulfonated polystyrene C block tethered to a flexible poly(ethylene-r-propylene) bridge B and end-capped with poly(tert-butylstyrene) A. The chemical structure and topology of these polymers constitute a model for incorporation of ionic blocks within a framework that provides tactility and mechanical stability. Heremore » in this paper we resolve the structure and dynamics of a structured polymer on the nanoscale constrained by ionic clusters. We find that the melts form intertwined networks of the A and C blocks independent of the degree of sulfonation of the C block with no long-range order. The cluster cohesiveness and morphology affect both macroscopic translational motion and segmental dynamics of all the blocks.« less
Conformally encapsulated multi-electrode arrays with seamless insulation

DOEpatents

Tabada, Phillipe J.; Shah, Kedar G.; Tolosa, Vanessa; Pannu, Satinderall S.; Tooker, Angela; Delima, Terri; Sheth, Heeral; Felix, Sarah

2016-11-22

Thin-film multi-electrode arrays (MEA) having one or more electrically conductive beams conformally encapsulated in a seamless block of electrically insulating material, and methods of fabricating such MEAs using reproducible, microfabrication processes. One or more electrically conductive traces are formed on scaffold material that is subsequently removed to suspend the traces over a substrate by support portions of the trace beam in contact with the substrate. By encapsulating the suspended traces, either individually or together, with a single continuous layer of an electrically insulating material, a seamless block of electrically insulating material is formed that conforms to the shape of the trace beam structure, including any trace backings which provide suspension support. Electrical contacts, electrodes, or leads of the traces are exposed from the encapsulated trace beam structure by removing the substrate.
Dynamic clustering scheme based on the coordination of management and control in multi-layer and multi-region intelligent optical network

NASA Astrophysics Data System (ADS)

Niu, Xiaoliang; Yuan, Fen; Huang, Shanguo; Guo, Bingli; Gu, Wanyi

2011-12-01

A Dynamic clustering scheme based on coordination of management and control is proposed to reduce network congestion rate and improve the blocking performance of hierarchical routing in Multi-layer and Multi-region intelligent optical network. Its implement relies on mobile agent (MA) technology, which has the advantages of efficiency, flexibility, functional and scalability. The paper's major contribution is to adjust dynamically domain when the performance of working network isn't in ideal status. And the incorporation of centralized NMS and distributed MA control technology migrate computing process to control plane node which releases the burden of NMS and improves process efficiently. Experiments are conducted on Multi-layer and multi-region Simulation Platform for Optical Network (MSPON) to assess the performance of the scheme.
A novel method for a multi-level hierarchical composite with brick-and-mortar structure

PubMed Central

Brandt, Kristina; Wolff, Michael F. H.; Salikov, Vitalij; Heinrich, Stefan; Schneider, Gerold A.

2013-01-01

The fascination for hierarchically structured hard tissues such as enamel or nacre arises from their unique structure-properties-relationship. During the last decades this numerously motivated the synthesis of composites, mimicking the brick-and-mortar structure of nacre. However, there is still a lack in synthetic engineering materials displaying a true hierarchical structure. Here, we present a novel multi-step processing route for anisotropic 2-level hierarchical composites by combining different coating techniques on different length scales. It comprises polymer-encapsulated ceramic particles as building blocks for the first level, followed by spouted bed spray granulation for a second level, and finally directional hot pressing to anisotropically consolidate the composite. The microstructure achieved reveals a brick-and-mortar hierarchical structure with distinct, however not yet optimized mechanical properties on each level. It opens up a completely new processing route for the synthesis of multi-level hierarchically structured composites, giving prospects to multi-functional structure-properties relationships. PMID:23900554
A novel method for a multi-level hierarchical composite with brick-and-mortar structure.

PubMed

Brandt, Kristina; Wolff, Michael F H; Salikov, Vitalij; Heinrich, Stefan; Schneider, Gerold A

2013-01-01

The fascination for hierarchically structured hard tissues such as enamel or nacre arises from their unique structure-properties-relationship. During the last decades this numerously motivated the synthesis of composites, mimicking the brick-and-mortar structure of nacre. However, there is still a lack in synthetic engineering materials displaying a true hierarchical structure. Here, we present a novel multi-step processing route for anisotropic 2-level hierarchical composites by combining different coating techniques on different length scales. It comprises polymer-encapsulated ceramic particles as building blocks for the first level, followed by spouted bed spray granulation for a second level, and finally directional hot pressing to anisotropically consolidate the composite. The microstructure achieved reveals a brick-and-mortar hierarchical structure with distinct, however not yet optimized mechanical properties on each level. It opens up a completely new processing route for the synthesis of multi-level hierarchically structured composites, giving prospects to multi-functional structure-properties relationships.
A novel method for a multi-level hierarchical composite with brick-and-mortar structure

NASA Astrophysics Data System (ADS)

Brandt, Kristina; Wolff, Michael F. H.; Salikov, Vitalij; Heinrich, Stefan; Schneider, Gerold A.

2013-07-01

The fascination for hierarchically structured hard tissues such as enamel or nacre arises from their unique structure-properties-relationship. During the last decades this numerously motivated the synthesis of composites, mimicking the brick-and-mortar structure of nacre. However, there is still a lack in synthetic engineering materials displaying a true hierarchical structure. Here, we present a novel multi-step processing route for anisotropic 2-level hierarchical composites by combining different coating techniques on different length scales. It comprises polymer-encapsulated ceramic particles as building blocks for the first level, followed by spouted bed spray granulation for a second level, and finally directional hot pressing to anisotropically consolidate the composite. The microstructure achieved reveals a brick-and-mortar hierarchical structure with distinct, however not yet optimized mechanical properties on each level. It opens up a completely new processing route for the synthesis of multi-level hierarchically structured composites, giving prospects to multi-functional structure-properties relationships.
Level-Set Simulation of Viscous Free Surface Flow Around a Commercial Hull Form

DTIC Science & Technology

2005-04-15

Abstract The viscous free surface flow around a 3600 TEU KRISO Container Ship is computed using the finite volume based multi-block RANS code, WAVIS...developed at KRISO . The free surface is captured with the Level-set method and the realizable k-ε model is employed for turbulence closure. The...computations are done for a 3600 TEU container ship of Korea Research Institute of Ships & Ocean Engineering, KORDI (hereafter, KRISO ) selected as
Computation of Flow Over a Drag Prediction Workshop Wing/Body Transport Configuration Using CFL3D

NASA Technical Reports Server (NTRS)

Rumsey, Christopher L.; Biedron, Robert T.

2001-01-01

A Drag Prediction Workshop was held in conjunction with the 19th AIAA Applied Aerodynamics Conference in June 2001. The purpose of the workshop was to assess the prediction of drag by computational methods for a wing/body configuration (DLR-F4) representative of subsonic transport aircraft. This report details computed results submitted to this workshop using the Reynolds-averaged Navier-Stokes code CFL3D. Two supplied grids were used: a point-matched 1-to-1 multi-block grid, and an overset multi-block grid. The 1-to-1 grid, generally of much poorer quality and with less streamwise resolution than the overset grid, is found to be too coarse to adequately resolve the surface pressures. However, the global forces and moments are nonetheless similar to those computed using the overset grid. The effect of three different turbulence models is assessed using the 1-to-1 grid. Surface pressures are very similar overall, and the drag variation due to turbulence model is 18 drag counts. Most of this drag variation is in the friction component, and is attributed in part to insufficient grid resolution of the 1-to-1 grid. The misnomer of 'fully turbulent' computations is discussed; comparisons are made using different transition locations and their effects on the global forces and moments are quantified. Finally, the effect of two different versions of a widely used one-equation turbulence model is explored.
A Distributed-Memory Package for Dense Hierarchically Semi-Separable Matrix Computations Using Randomization

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

Rouet, François-Henry; Li, Xiaoye S.; Ghysels, Pieter

In this paper, we present a distributed-memory library for computations with dense structured matrices. A matrix is considered structured if its off-diagonal blocks can be approximated by a rank-deficient matrix with low numerical rank. Here, we use Hierarchically Semi-Separable (HSS) representations. Such matrices appear in many applications, for example, finite-element methods, boundary element methods, and so on. Exploiting this structure allows for fast solution of linear systems and/or fast computation of matrix-vector products, which are the two main building blocks of matrix computations. The compression algorithm that we use, that computes the HSS form of an input dense matrix, reliesmore » on randomized sampling with a novel adaptive sampling mechanism. We discuss the parallelization of this algorithm and also present the parallelization of structured matrix-vector product, structured factorization, and solution routines. The efficiency of the approach is demonstrated on large problems from different academic and industrial applications, on up to 8,000 cores. Finally, this work is part of a more global effort, the STRUctured Matrices PACKage (STRUMPACK) software package for computations with sparse and dense structured matrices. Hence, although useful on their own right, the routines also represent a step in the direction of a distributed-memory sparse solver.« less
A Distributed-Memory Package for Dense Hierarchically Semi-Separable Matrix Computations Using Randomization

DOE PAGES

Rouet, François-Henry; Li, Xiaoye S.; Ghysels, Pieter; ...

2016-06-30

In this paper, we present a distributed-memory library for computations with dense structured matrices. A matrix is considered structured if its off-diagonal blocks can be approximated by a rank-deficient matrix with low numerical rank. Here, we use Hierarchically Semi-Separable (HSS) representations. Such matrices appear in many applications, for example, finite-element methods, boundary element methods, and so on. Exploiting this structure allows for fast solution of linear systems and/or fast computation of matrix-vector products, which are the two main building blocks of matrix computations. The compression algorithm that we use, that computes the HSS form of an input dense matrix, reliesmore » on randomized sampling with a novel adaptive sampling mechanism. We discuss the parallelization of this algorithm and also present the parallelization of structured matrix-vector product, structured factorization, and solution routines. The efficiency of the approach is demonstrated on large problems from different academic and industrial applications, on up to 8,000 cores. Finally, this work is part of a more global effort, the STRUctured Matrices PACKage (STRUMPACK) software package for computations with sparse and dense structured matrices. Hence, although useful on their own right, the routines also represent a step in the direction of a distributed-memory sparse solver.« less
Adaptive 3D single-block grids for the computation of viscous flows around wings

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

Hagmeijer, R.; Kok, J.C.

1996-12-31

A robust algorithm for the adaption of a 3D single-block structured grid suitable for the computation of viscous flows around a wing is presented and demonstrated by application to the ONERA M6 wing. The effects of grid adaption on the flow solution and accuracy improvements is analyzed. Reynolds number variations are studied.
Molecular dynamics study of the encapsulation capability of a PCL-PEO based block copolymer for hydrophobic drugs with different spatial distributions of hydrogen bond donors and acceptors.

PubMed

Patel, Sarthak K; Lavasanifar, Afsaneh; Choi, Phillip

2010-03-01

Molecular dynamics simulation was used to study the potential of using a block copolymer containing three poly(epsilon-caprolactone) (PCL) blocks of equal length connected to one end of a poly(ethylene oxide) (PEO) block, designated as PEO-b-3PCL, to encapsulate two classes of hydrophobic drugs with distinctively different molecular structures. In particular, the first class of drugs consisted of two cucurbitacin drugs (CuB and CuI) that contain multiple hydrogen bond donors and acceptors evenly distributed on their molecules while the other class of drugs (fenofibrate and nimodipine) contain essentially only clustered hydrogen bond acceptors. In the case of cucurbitacin drugs, the results showed that PEO-b-3PCL lowered the Flory-Huggins interaction parameters (chi) considerably (i.e., increased the drug solubility) compared to the linear di-block copolymer PEO-b-PCL with the same PCL/PEO (w/w) ratio of 1.0. However, the opposite effect was observed for fenofibrate and nimodipine. Analysis of the intermolecular interactions indicates that the number of hydrogen bonds formed between the three PCL blocks and cucurbitacin drugs is significantly higher than that of the linear di-block copolymer. On the other hand, owing to the absence of hydrogen bond donors and the clustering of the hydrogen bond acceptors on the fenofibrate and nimodipine molecules, this significantly reduces the number of hydrogen bonds formed in the multi-PCL block environment, leading to unfavourable chi values. The findings of the present work suggest that multi-hydrophobic block architecture could potentially increase the drug loading for hydrophobic drugs with structures containing evenly distributed multiple hydrogen bond donors and acceptors. (c) 2009 Elsevier Ltd. All rights reserved.
Mesozoic Deformation and Its Geological Significance in the Southern Margin of the South China Sea

NASA Astrophysics Data System (ADS)

Zhu, Rongwei; Liu, Hailing; Yao, Yongjian; Wang, Yin

2018-05-01

The pre-Eocene history of the region around the present South China Sea is not well known. New multi-channel seismic profiles provide valuable insights into the probable Mesozoic history of this region. Detailed structural and stratigraphic interpretations of the multi-channel seismic profiles, calibrated with relevant drilling and dredging data, show major Mesozoic structural features. A structural restoration was done to remove the Cenozoic tectonic influence and calculate the Mesozoic tectonic compression ratios. The results indicate that two groups of compressive stress with diametrically opposite orientations, S(S)E-N(N)W and N(N)W-S(S)E, were active during the Mesozoic. The compression ratio values gradually decrease from north to south and from west to east in each stress orientation. The phenomena may be related to the opening of the proto-South China Sea (then located in south of the Nansha block) and the rate at which the Nansha block drifted northward in the late Jurassic to late Cretaceous. The Nansha block drifted northward until it collided and sutured with the southern China margin. The opening of the present South China Sea may be related to this suture zone, which was a tectonic zone of weakness.

ParallelStructure: A R Package to Distribute Parallel Runs of the Population Genetics Program STRUCTURE on Multi-Core Computers

PubMed Central

Besnier, Francois; Glover, Kevin A.

2013-01-01

This software package provides an R-based framework to make use of multi-core computers when running analyses in the population genetics program STRUCTURE. It is especially addressed to those users of STRUCTURE dealing with numerous and repeated data analyses, and who could take advantage of an efficient script to automatically distribute STRUCTURE jobs among multiple processors. It also consists of additional functions to divide analyses among combinations of populations within a single data set without the need to manually produce multiple projects, as it is currently the case in STRUCTURE. The package consists of two main functions: MPI_structure() and parallel_structure() as well as an example data file. We compared the performance in computing time for this example data on two computer architectures and showed that the use of the present functions can result in several-fold improvements in terms of computation time. ParallelStructure is freely available at https://r-forge.r-project.org/projects/parallstructure/. PMID:23923012
Study on turbulent flow and heat transfer performance of tubes with internal fins in EGR cooler

NASA Astrophysics Data System (ADS)

Liu, Lin; Ling, Xiang; Peng, Hao

2015-07-01

In this paper, flow and heat transfer performances of the tubes with internal longitudinal fins in Exhaust Gas Recirculation (EGR ) cooler were investigated by three-dimension computation and experiment . Each test tube was a single-pipe structure, without inner tube. Three-dimension computation was performed to determine the thermal characteristics difference between the two kinds of tubes, that is, the tube with an inner solid staff as a blocked structure and the tube without the blocked structure. The effects of fin width and fin height on heat transfer and flow are examined. For proving the validity of numerical method, the calculated results were compared with corresponding experimental data. The tube-side friction factor and heat transfer coefficient were examined. As a result, the maximum deviations between the numerical results and the experimental data are approximately 5.4 % for friction factor and 8.6 % for heat transfer coefficient, respectively. It is found that two types of internally finned tubes enhance significantly heat transfer. The heat transfer of the tube with blocked structure is better, while the pressure drop of the tube without blocked structure is lower. The comprehensive performance of the unblocked tube is better to applied in EGR cooler.
Concurrent Probabilistic Simulation of High Temperature Composite Structural Response

NASA Technical Reports Server (NTRS)

Abdi, Frank

1996-01-01

A computational structural/material analysis and design tool which would meet industry's future demand for expedience and reduced cost is presented. This unique software 'GENOA' is dedicated to parallel and high speed analysis to perform probabilistic evaluation of high temperature composite response of aerospace systems. The development is based on detailed integration and modification of diverse fields of specialized analysis techniques and mathematical models to combine their latest innovative capabilities into a commercially viable software package. The technique is specifically designed to exploit the availability of processors to perform computationally intense probabilistic analysis assessing uncertainties in structural reliability analysis and composite micromechanics. The primary objectives which were achieved in performing the development were: (1) Utilization of the power of parallel processing and static/dynamic load balancing optimization to make the complex simulation of structure, material and processing of high temperature composite affordable; (2) Computational integration and synchronization of probabilistic mathematics, structural/material mechanics and parallel computing; (3) Implementation of an innovative multi-level domain decomposition technique to identify the inherent parallelism, and increasing convergence rates through high- and low-level processor assignment; (4) Creating the framework for Portable Paralleled architecture for the machine independent Multi Instruction Multi Data, (MIMD), Single Instruction Multi Data (SIMD), hybrid and distributed workstation type of computers; and (5) Market evaluation. The results of Phase-2 effort provides a good basis for continuation and warrants Phase-3 government, and industry partnership.
CUDA Optimization Strategies for Compute- and Memory-Bound Neuroimaging Algorithms

PubMed Central

Lee, Daren; Dinov, Ivo; Dong, Bin; Gutman, Boris; Yanovsky, Igor; Toga, Arthur W.

2011-01-01

As neuroimaging algorithms and technology continue to grow faster than CPU performance in complexity and image resolution, data-parallel computing methods will be increasingly important. The high performance, data-parallel architecture of modern graphical processing units (GPUs) can reduce computational times by orders of magnitude. However, its massively threaded architecture introduces challenges when GPU resources are exceeded. This paper presents optimization strategies for compute- and memory-bound algorithms for the CUDA architecture. For compute-bound algorithms, the registers are reduced through variable reuse via shared memory and the data throughput is increased through heavier thread workloads and maximizing the thread configuration for a single thread block per multiprocessor. For memory-bound algorithms, fitting the data into the fast but limited GPU resources is achieved through reorganizing the data into self-contained structures and employing a multi-pass approach. Memory latencies are reduced by selecting memory resources whose cache performance are optimized for the algorithm's access patterns. We demonstrate the strategies on two computationally expensive algorithms and achieve optimized GPU implementations that perform up to 6× faster than unoptimized ones. Compared to CPU implementations, we achieve peak GPU speedups of 129× for the 3D unbiased nonlinear image registration technique and 93× for the non-local means surface denoising algorithm. PMID:21159404
CUDA optimization strategies for compute- and memory-bound neuroimaging algorithms.

PubMed

Lee, Daren; Dinov, Ivo; Dong, Bin; Gutman, Boris; Yanovsky, Igor; Toga, Arthur W

2012-06-01

As neuroimaging algorithms and technology continue to grow faster than CPU performance in complexity and image resolution, data-parallel computing methods will be increasingly important. The high performance, data-parallel architecture of modern graphical processing units (GPUs) can reduce computational times by orders of magnitude. However, its massively threaded architecture introduces challenges when GPU resources are exceeded. This paper presents optimization strategies for compute- and memory-bound algorithms for the CUDA architecture. For compute-bound algorithms, the registers are reduced through variable reuse via shared memory and the data throughput is increased through heavier thread workloads and maximizing the thread configuration for a single thread block per multiprocessor. For memory-bound algorithms, fitting the data into the fast but limited GPU resources is achieved through reorganizing the data into self-contained structures and employing a multi-pass approach. Memory latencies are reduced by selecting memory resources whose cache performance are optimized for the algorithm's access patterns. We demonstrate the strategies on two computationally expensive algorithms and achieve optimized GPU implementations that perform up to 6× faster than unoptimized ones. Compared to CPU implementations, we achieve peak GPU speedups of 129× for the 3D unbiased nonlinear image registration technique and 93× for the non-local means surface denoising algorithm. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.
Dynamics of propagation of premature impulses in structurally remodeled infarcted myocardium: a computational analysis

PubMed Central

Cabo, Candido

2014-01-01

Initiation of cardiac arrhythmias typically follows one or more premature impulses either occurring spontaneously or applied externally. In this study, we characterize the dynamics of propagation of single (S2) and double premature impulses (S3), and the mechanisms of block of premature impulses at structural heterogeneities caused by remodeling of gap junctional conductance (Gj) in infarcted myocardium. Using a sub-cellular computer model of infarcted tissue, we found that |INa,max|, prematurity (coupling interval with the previous impulse), and conduction velocity (CV) of premature impulses change dynamically as they propagate away from the site of initiation. There are fundamental differences between the dynamics of propagation of S2 and S3 premature impulses: for S2 impulses |INa,max| recovers fast, prematurity decreases and CV increases as propagation proceeds; for S3 impulses low values of |INa,max| persist, prematurity could increase, and CV could decrease as impulses propagate away from the site of initiation. As a consequence it is more likely that S3 impulses block at sites of structural heterogeneities causing source/sink mismatch than S2 impulses block. Whether premature impulses block at Gj heterogeneities or not is also determined by the values of Gj (and the space constant λ) in the regions proximal and distal to the heterogeneity: when λ in the direction of propagation increases >40%, premature impulses could block. The maximum slope of CV restitution curves for S2 impulses is larger than for S3 impulses. In conclusion: (1) The dynamics of propagation of premature impulses make more likely that S3 impulses block at sites of structural heterogeneities than S2 impulses block; (2) Structural heterogeneities causing an increase in λ (or CV) of >40% could result in block of premature impulses; (3) A decrease in the maximum slope of CV restitution curves of propagating premature impulses is indicative of an increased potential for block at structural heterogeneities. PMID:25566085
Dynamics of propagation of premature impulses in structurally remodeled infarcted myocardium: a computational analysis.

PubMed

Cabo, Candido

2014-01-01

Initiation of cardiac arrhythmias typically follows one or more premature impulses either occurring spontaneously or applied externally. In this study, we characterize the dynamics of propagation of single (S2) and double premature impulses (S3), and the mechanisms of block of premature impulses at structural heterogeneities caused by remodeling of gap junctional conductance (Gj) in infarcted myocardium. Using a sub-cellular computer model of infarcted tissue, we found that |INa,max|, prematurity (coupling interval with the previous impulse), and conduction velocity (CV) of premature impulses change dynamically as they propagate away from the site of initiation. There are fundamental differences between the dynamics of propagation of S2 and S3 premature impulses: for S2 impulses |INa,max| recovers fast, prematurity decreases and CV increases as propagation proceeds; for S3 impulses low values of |INa,max| persist, prematurity could increase, and CV could decrease as impulses propagate away from the site of initiation. As a consequence it is more likely that S3 impulses block at sites of structural heterogeneities causing source/sink mismatch than S2 impulses block. Whether premature impulses block at Gj heterogeneities or not is also determined by the values of Gj (and the space constant λ) in the regions proximal and distal to the heterogeneity: when λ in the direction of propagation increases >40%, premature impulses could block. The maximum slope of CV restitution curves for S2 impulses is larger than for S3 impulses. (1) The dynamics of propagation of premature impulses make more likely that S3 impulses block at sites of structural heterogeneities than S2 impulses block; (2) Structural heterogeneities causing an increase in λ (or CV) of >40% could result in block of premature impulses; (3) A decrease in the maximum slope of CV restitution curves of propagating premature impulses is indicative of an increased potential for block at structural heterogeneities.
A multi-block adaptive solving technique based on lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Zhang, Yang; Xie, Jiahua; Li, Xiaoyue; Ma, Zhenghai; Zou, Jianfeng; Zheng, Yao

2018-05-01

In this paper, a CFD parallel adaptive algorithm is self-developed by combining the multi-block Lattice Boltzmann Method (LBM) with Adaptive Mesh Refinement (AMR). The mesh refinement criterion of this algorithm is based on the density, velocity and vortices of the flow field. The refined grid boundary is obtained by extending outward half a ghost cell from the coarse grid boundary, which makes the adaptive mesh more compact and the boundary treatment more convenient. Two numerical examples of the backward step flow separation and the unsteady flow around circular cylinder demonstrate the vortex structure of the cold flow field accurately and specifically.
Topology Optimization of Lightweight Lattice Structural Composites Inspired by Cuttlefish Bone

NASA Astrophysics Data System (ADS)

Hu, Zhong; Gadipudi, Varun Kumar; Salem, David R.

2018-03-01

Lattice structural composites are of great interest to various industries where lightweight multifunctionality is important, especially aerospace. However, strong coupling among the composition, microstructure, porous topology, and fabrication of such materials impedes conventional trial-and-error experimental development. In this work, a discontinuous carbon fiber reinforced polymer matrix composite was adopted for structural design. A reliable and robust design approach for developing lightweight multifunctional lattice structural composites was proposed, inspired by biomimetics and based on topology optimization. Three-dimensional periodic lattice blocks were initially designed, inspired by the cuttlefish bone microstructure. The topologies of the three-dimensional periodic blocks were further optimized by computer modeling, and the mechanical properties of the topology optimized lightweight lattice structures were characterized by computer modeling. The lattice structures with optimal performance were identified.
Composite sandwich structure and method for making same

NASA Technical Reports Server (NTRS)

Magurany, Charles J. (Inventor)

1995-01-01

A core for a sandwich structure which has multi-ply laminate ribs separated by voids is made as an integral unit in one single curing step. Tooling blocks corresponding to the voids are first wrapped by strips of prepreg layup equal to one half of each rib laminate so a continuous wall of prepreg material is formed around the tooling blocks. The wrapped tooling blocks are next pressed together laterally, like tiles, so adjoining walls from two tooling blocks are joined. The assembly is then cured by conventional methods, and afterwards the tooling blocks are removed so voids are formed. The ribs can be provided with integral tabs forming bonding areas for face sheets, and face sheets may be co-cured with the core ribs. The new core design is suitable for discrete ribcores used in space telescopes and reflector panels, where quasiisotropic properties and zero coefficient of thermal expansion are required.
Coupled multi-disciplinary simulation of composite engine structures in propulsion environment

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Singhal, Surendra N.

1992-01-01

A computational simulation procedure is described for the coupled response of multi-layered multi-material composite engine structural components which are subjected to simultaneous multi-disciplinary thermal, structural, vibration, and acoustic loadings including the effect of hostile environments. The simulation is based on a three dimensional finite element analysis technique in conjunction with structural mechanics codes and with acoustic analysis methods. The composite material behavior is assessed at the various composite scales, i.e., the laminate/ply/constituents (fiber/matrix), via a nonlinear material characterization model. Sample cases exhibiting nonlinear geometrical, material, loading, and environmental behavior of aircraft engine fan blades, are presented. Results for deformed shape, vibration frequency, mode shapes, and acoustic noise emitted from the fan blade, are discussed for their coupled effect in hot and humid environments. Results such as acoustic noise for coupled composite-mechanics/heat transfer/structural/vibration/acoustic analyses demonstrate the effectiveness of coupled multi-disciplinary computational simulation and the various advantages of composite materials compared to metals.
Investigation of obstacle effect to improve conjugate heat transfer in backward facing step channel using fast simulation of incompressible flow

NASA Astrophysics Data System (ADS)

Nouri-Borujerdi, Ali; Moazezi, Arash

2018-01-01

The current study investigates the conjugate heat transfer characteristics for laminar flow in backward facing step channel. All of the channel walls are insulated except the lower thick wall under a constant temperature. The upper wall includes a insulated obstacle perpendicular to flow direction. The effect of obstacle height and location on the fluid flow and heat transfer are numerically explored for the Reynolds number in the range of 10 ≤ Re ≤ 300. Incompressible Navier-Stokes and thermal energy equations are solved simultaneously in fluid region by the upwind compact finite difference scheme based on flux-difference splitting in conjunction with artificial compressibility method. In the thick wall, the energy equation is obtained by Laplace equation. A multi-block approach is used to perform parallel computing to reduce the CPU time. Each block is modeled separately by sharing boundary conditions with neighbors. The developed program for modeling was written in FORTRAN language with OpenMP API. The obtained results showed that using of the multi-block parallel computing method is a simple robust scheme with high performance and high-order accurate. Moreover, the obtained results demonstrated that the increment of Reynolds number and obstacle height as well as decrement of horizontal distance between the obstacle and the step improve the heat transfer.
Multishaker modal testing

NASA Technical Reports Server (NTRS)

Craig, Roy R., Jr.

1987-01-01

The major accomplishments of this research are: (1) the refinement and documentation of a multi-input, multi-output modal parameter estimation algorithm which is applicable to general linear, time-invariant dynamic systems; (2) the development and testing of an unsymmetric block-Lanzcos algorithm for reduced-order modeling of linear systems with arbitrary damping; and (3) the development of a control-structure-interaction (CSI) test facility.
Application of RNAMlet to surface defect identification of steels

NASA Astrophysics Data System (ADS)

Xu, Ke; Xu, Yang; Zhou, Peng; Wang, Lei

2018-06-01

As three main production lines of steels, continuous casting slabs, hot rolled steel plates and cold rolled steel strips have different surface appearances and are produced at different speeds of their production lines. Therefore, the algorithms for the surface defect identifications of the three steel products have different requirements for real-time and anti-interference. The existing algorithms cannot be adaptively applied to surface defect identification of the three steel products. A new method of adaptive multi-scale geometric analysis named RNAMlet was proposed. The idea of RNAMlet came from the non-symmetry anti-packing pattern representation model (NAM). The image is decomposed into a set of rectangular blocks asymmetrically according to gray value changes of image pixels. Then two-dimensional Haar wavelet transform is applied to all blocks. If the image background is complex, the number of blocks is large, and more details of the image are utilized. If the image background is simple, the number of blocks is small, and less computation time is needed. RNAMlet was tested with image samples of the three steel products, and compared with three classical methods of multi-scale geometric analysis, including Contourlet, Shearlet and Tetrolet. For the image samples with complicated backgrounds, such as continuous casting slabs and hot rolled steel plates, the defect identification rate obtained by RNAMlet was 1% higher than other three methods. For the image samples with simple backgrounds, such as cold rolled steel strips, the computation time of RNAMlet was one-tenth of the other three MGA methods, while the defect identification rates obtained by RNAMlet were higher than the other three methods.
Advanced flight computer. Special study

NASA Technical Reports Server (NTRS)

Coo, Dennis

1995-01-01

This report documents a special study to define a 32-bit radiation hardened, SEU tolerant flight computer architecture, and to investigate current or near-term technologies and development efforts that contribute to the Advanced Flight Computer (AFC) design and development. An AFC processing node architecture is defined. Each node may consist of a multi-chip processor as needed. The modular, building block approach uses VLSI technology and packaging methods that demonstrate a feasible AFC module in 1998 that meets that AFC goals. The defined architecture and approach demonstrate a clear low-risk, low-cost path to the 1998 production goal, with intermediate prototypes in 1996.
An Investigation into the Postbuckling Response of a Single Blade-Stiffened Composite Panel

NASA Astrophysics Data System (ADS)

Spediacci, Alexander Daniel

The large strength reserves of stiffened composite structures in the postbuckling range appeal to the aerospace industry because of the high strength-to weight-ratio. Design and analysis of these large-scale, complex structures is technical, and requires major computational effort. Using the building-block approach, a smaller, single-stringer panel can be a useful and efficient tool for initial design, and can reveal critical behavior of a larger, multi-stringer panel. A characterization, through finite element modeling, of buckling and postbuckling response of a single blade-stiffened composite panel is proposed. Several factors affecting buckling and postbuckling behavior are investigated, including specimen length, initial imperfections, mode switching, and skin stringer separation. Two specimens are repeatedly tested under quasi- static compression loading well into the postbuckling range, showing no sign of damage. The test data from the specimens are used to compare and validate the nonlinear finite element models, show good correlation with the models. Ultimately, this work will serve to demonstrate the safety of stiffened structures operating in the postbuckling range and allow for thinner, lighter structures, which can increase the overall efficiency of aircraft.
An immersed-boundary method for flow–structure interaction in biological systems with application to phonation

PubMed Central

Luo, Haoxiang; Mittal, Rajat; Zheng, Xudong; Bielamowicz, Steven A.; Walsh, Raymond J.; Hahn, James K.

2008-01-01

A new numerical approach for modeling a class of flow–structure interaction problems typically encountered in biological systems is presented. In this approach, a previously developed, sharp-interface, immersed-boundary method for incompressible flows is used to model the fluid flow and a new, sharp-interface Cartesian grid, immersed boundary method is devised to solve the equations of linear viscoelasticity that governs the solid. The two solvers are coupled to model flow–structure interaction. This coupled solver has the advantage of simple grid generation and efficient computation on simple, single-block structured grids. The accuracy of the solid-mechanics solver is examined by applying it to a canonical problem. The solution methodology is then applied to the problem of laryngeal aerodynamics and vocal fold vibration during human phonation. This includes a three-dimensional eigen analysis for a multi-layered vocal fold prototype as well as two-dimensional, flow-induced vocal fold vibration in a modeled larynx. Several salient features of the aerodynamics as well as vocal-fold dynamics are presented. PMID:19936017
Expansion and improvements of the FORMA system for response and load analysis. Volume 1: Programming manual

NASA Technical Reports Server (NTRS)

Wohlen, R. L.

1976-01-01

Techniques are presented for the solution of structural dynamic systems on an electronic digital computer using FORMA (FORTRAN Matrix Analysis). FORMA is a library of subroutines coded in FORTRAN 4 for the efficient solution of structural dynamics problems. These subroutines are in the form of building blocks that can be put together to solve a large variety of structural dynamics problems. The obvious advantage of the building block approach is that programming and checkout time are limited to that required for putting the blocks together in the proper order.
Computationally efficient algorithm for high sampling-frequency operation of active noise control

NASA Astrophysics Data System (ADS)

Rout, Nirmal Kumar; Das, Debi Prasad; Panda, Ganapati

2015-05-01

In high sampling-frequency operation of active noise control (ANC) system the length of the secondary path estimate and the ANC filter are very long. This increases the computational complexity of the conventional filtered-x least mean square (FXLMS) algorithm. To reduce the computational complexity of long order ANC system using FXLMS algorithm, frequency domain block ANC algorithms have been proposed in past. These full block frequency domain ANC algorithms are associated with some disadvantages such as large block delay, quantization error due to computation of large size transforms and implementation difficulties in existing low-end DSP hardware. To overcome these shortcomings, the partitioned block ANC algorithm is newly proposed where the long length filters in ANC are divided into a number of equal partitions and suitably assembled to perform the FXLMS algorithm in the frequency domain. The complexity of this proposed frequency domain partitioned block FXLMS (FPBFXLMS) algorithm is quite reduced compared to the conventional FXLMS algorithm. It is further reduced by merging one fast Fourier transform (FFT)-inverse fast Fourier transform (IFFT) combination to derive the reduced structure FPBFXLMS (RFPBFXLMS) algorithm. Computational complexity analysis for different orders of filter and partition size are presented. Systematic computer simulations are carried out for both the proposed partitioned block ANC algorithms to show its accuracy compared to the time domain FXLMS algorithm.
NASA National Combustion Code Simulations

NASA Technical Reports Server (NTRS)

Iannetti, Anthony; Davoudzadeh, Farhad

2001-01-01

A systematic effort is in progress to further validate the National Combustion Code (NCC) that has been developed at NASA Glenn Research Center (GRC) for comprehensive modeling and simulation of aerospace combustion systems. The validation efforts include numerical simulation of the gas-phase combustor experiments conducted at the Center for Turbulence Research (CTR), Stanford University, followed by comparison and evaluation of the computed results with the experimental data. Presently, at GRC, a numerical model of the experimental gaseous combustor is built to simulate the experimental model. The constructed numerical geometry includes the flow development sections for air annulus and fuel pipe, 24 channel air and fuel swirlers, hub, combustor, and tail pipe. Furthermore, a three-dimensional multi-block, multi-grid grid (1.6 million grid points, 3-levels of multi-grid) is generated. Computational simulation of the gaseous combustor flow field operating on methane fuel has started. The computational domain includes the whole flow regime starting from the fuel pipe and the air annulus, through the 12 air and 12 fuel channels, in the combustion region and through the tail pipe.

Hybrid architecture for encoded measurement-based quantum computation

PubMed Central

Zwerger, M.; Briegel, H. J.; Dür, W.

2014-01-01

We present a hybrid scheme for quantum computation that combines the modular structure of elementary building blocks used in the circuit model with the advantages of a measurement-based approach to quantum computation. We show how to construct optimal resource states of minimal size to implement elementary building blocks for encoded quantum computation in a measurement-based way, including states for error correction and encoded gates. The performance of the scheme is determined by the quality of the resource states, where within the considered error model a threshold of the order of 10% local noise per particle for fault-tolerant quantum computation and quantum communication. PMID:24946906
Block-Parallel Data Analysis with DIY2

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

Morozov, Dmitriy; Peterka, Tom

DIY2 is a programming model and runtime for block-parallel analytics on distributed-memory machines. Its main abstraction is block-structured data parallelism: data are decomposed into blocks; blocks are assigned to processing elements (processes or threads); computation is described as iterations over these blocks, and communication between blocks is defined by reusable patterns. By expressing computation in this general form, the DIY2 runtime is free to optimize the movement of blocks between slow and fast memories (disk and flash vs. DRAM) and to concurrently execute blocks residing in memory with multiple threads. This enables the same program to execute in-core, out-of-core, serial,more » parallel, single-threaded, multithreaded, or combinations thereof. This paper describes the implementation of the main features of the DIY2 programming model and optimizations to improve performance. DIY2 is evaluated on benchmark test cases to establish baseline performance for several common patterns and on larger complete analysis codes running on large-scale HPC machines.« less
Collaborating CPU and GPU for large-scale high-order CFD simulations with complex grids on the TianHe-1A supercomputer

NASA Astrophysics Data System (ADS)

Xu, Chuanfu; Deng, Xiaogang; Zhang, Lilun; Fang, Jianbin; Wang, Guangxue; Jiang, Yi; Cao, Wei; Che, Yonggang; Wang, Yongxian; Wang, Zhenghua; Liu, Wei; Cheng, Xinghua

2014-12-01

Programming and optimizing complex, real-world CFD codes on current many-core accelerated HPC systems is very challenging, especially when collaborating CPUs and accelerators to fully tap the potential of heterogeneous systems. In this paper, with a tri-level hybrid and heterogeneous programming model using MPI + OpenMP + CUDA, we port and optimize our high-order multi-block structured CFD software HOSTA on the GPU-accelerated TianHe-1A supercomputer. HOSTA adopts two self-developed high-order compact definite difference schemes WCNS and HDCS that can simulate flows with complex geometries. We present a dual-level parallelization scheme for efficient multi-block computation on GPUs and perform particular kernel optimizations for high-order CFD schemes. The GPU-only approach achieves a speedup of about 1.3 when comparing one Tesla M2050 GPU with two Xeon X5670 CPUs. To achieve a greater speedup, we collaborate CPU and GPU for HOSTA instead of using a naive GPU-only approach. We present a novel scheme to balance the loads between the store-poor GPU and the store-rich CPU. Taking CPU and GPU load balance into account, we improve the maximum simulation problem size per TianHe-1A node for HOSTA by 2.3×, meanwhile the collaborative approach can improve the performance by around 45% compared to the GPU-only approach. Further, to scale HOSTA on TianHe-1A, we propose a gather/scatter optimization to minimize PCI-e data transfer times for ghost and singularity data of 3D grid blocks, and overlap the collaborative computation and communication as far as possible using some advanced CUDA and MPI features. Scalability tests show that HOSTA can achieve a parallel efficiency of above 60% on 1024 TianHe-1A nodes. With our method, we have successfully simulated an EET high-lift airfoil configuration containing 800M cells and China's large civil airplane configuration containing 150M cells. To our best knowledge, those are the largest-scale CPU-GPU collaborative simulations that solve realistic CFD problems with both complex configurations and high-order schemes.
Collaborating CPU and GPU for large-scale high-order CFD simulations with complex grids on the TianHe-1A supercomputer

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

Xu, Chuanfu, E-mail: xuchuanfu@nudt.edu.cn; Deng, Xiaogang; Zhang, Lilun

Programming and optimizing complex, real-world CFD codes on current many-core accelerated HPC systems is very challenging, especially when collaborating CPUs and accelerators to fully tap the potential of heterogeneous systems. In this paper, with a tri-level hybrid and heterogeneous programming model using MPI + OpenMP + CUDA, we port and optimize our high-order multi-block structured CFD software HOSTA on the GPU-accelerated TianHe-1A supercomputer. HOSTA adopts two self-developed high-order compact definite difference schemes WCNS and HDCS that can simulate flows with complex geometries. We present a dual-level parallelization scheme for efficient multi-block computation on GPUs and perform particular kernel optimizations formore » high-order CFD schemes. The GPU-only approach achieves a speedup of about 1.3 when comparing one Tesla M2050 GPU with two Xeon X5670 CPUs. To achieve a greater speedup, we collaborate CPU and GPU for HOSTA instead of using a naive GPU-only approach. We present a novel scheme to balance the loads between the store-poor GPU and the store-rich CPU. Taking CPU and GPU load balance into account, we improve the maximum simulation problem size per TianHe-1A node for HOSTA by 2.3×, meanwhile the collaborative approach can improve the performance by around 45% compared to the GPU-only approach. Further, to scale HOSTA on TianHe-1A, we propose a gather/scatter optimization to minimize PCI-e data transfer times for ghost and singularity data of 3D grid blocks, and overlap the collaborative computation and communication as far as possible using some advanced CUDA and MPI features. Scalability tests show that HOSTA can achieve a parallel efficiency of above 60% on 1024 TianHe-1A nodes. With our method, we have successfully simulated an EET high-lift airfoil configuration containing 800M cells and China's large civil airplane configuration containing 150M cells. To our best knowledge, those are the largest-scale CPU–GPU collaborative simulations that solve realistic CFD problems with both complex configurations and high-order schemes.« less
Parallel Program Systems for the Analysis of Wave Processes in Elastic-Plastic, Granular, Porous and Multi-Blocky Media

NASA Astrophysics Data System (ADS)

Sadovskaya, Oxana; Sadovskii, Vladimir

2017-04-01

Under modeling the wave propagation processes in geomaterials (granular and porous media, soils and rocks) it is necessary to take into account the structural inhomogeneity of these materials. Parallel program systems for numerical solution of 2D and 3D problems of the dynamics of deformable media with constitutive relationships of rather general form on the basis of universal mathematical model describing small strains of elastic, elastic-plastic, granular and porous materials are worked out. In the case of an elastic material, the model is reduced to the system of equations, hyperbolic by Friedrichs, written in terms of velocities and stresses in a symmetric form. In the case of an elastic-plastic material, the model is a special formulation of the Prandtl-Reuss theory in the form of variational inequality with one-sided constraints on the stress tensor. Generalization of the model to describe granularity and the collapse of pores is obtained by means of the rheological approach, taking into account different resistance of materials to tension and compression. Rotational motion of particles in the material microstructure is considered within the framework of a mathematical model of the Cosserat continuum. Computational domain may have a blocky structure, composed of an arbitrary number of layers, strips in a layer and blocks in a strip from different materials with self-consistent curvilinear interfaces. At the external boundaries of computational domain the main types of dissipative boundary conditions in terms of velocities, stresses or mixed boundary conditions can be given. Shock-capturing algorithm is proposed for implementation of the model on supercomputers with cluster architecture. It is based on the two-cyclic splitting method with respect to spatial variables and the special procedures of the stresses correction to take into account plasticity, granularity or porosity of a material. An explicit monotone ENO-scheme is applied for solving one-dimensional systems of equations at the stages of splitting method. The parallelizing of computations is carried out using the MPI library and the SPMD technology. The data exchange between processors occurs at step "predictor" of the finite-difference scheme. Program systems allow simulate the propagation of waves produced by external mechanical effects in a medium, aggregated of arbitrary number of heterogeneous blocks. Some computations of dynamic problems with and without taking into account the moment properties of a material were performed on clusters of ICM SB RAS (Krasnoyarsk) and JSCC RAS (Moscow). Parallel program systems 2Dyn_Granular, 3Dyn_Granular, 2Dyn_Cosserat, 3Dyn_Cosserat and 2Dyn_Blocks_MPI for numerical solution of 2D and 3D elastic-plastic problems of the dynamics of granular media and problems of the Cosserat elasticity theory, as well as for modeling of the dynamic processes in multi-blocky media with pliant viscoelastic, porous and fluid-saturated interlayers on cluster systems were registered by Rospatent.
Dynamic Load-Balancing for Distributed Heterogeneous Computing of Parallel CFD Problems

NASA Technical Reports Server (NTRS)

Ecer, A.; Chien, Y. P.; Boenisch, T.; Akay, H. U.

2000-01-01

The developed methodology is aimed at improving the efficiency of executing block-structured algorithms on parallel, distributed, heterogeneous computers. The basic approach of these algorithms is to divide the flow domain into many sub- domains called blocks, and solve the governing equations over these blocks. Dynamic load balancing problem is defined as the efficient distribution of the blocks among the available processors over a period of several hours of computations. In environments with computers of different architecture, operating systems, CPU speed, memory size, load, and network speed, balancing the loads and managing the communication between processors becomes crucial. Load balancing software tools for mutually dependent parallel processes have been created to efficiently utilize an advanced computation environment and algorithms. These tools are dynamic in nature because of the chances in the computer environment during execution time. More recently, these tools were extended to a second operating system: NT. In this paper, the problems associated with this application will be discussed. Also, the developed algorithms were combined with the load sharing capability of LSF to efficiently utilize workstation clusters for parallel computing. Finally, results will be presented on running a NASA based code ADPAC to demonstrate the developed tools for dynamic load balancing.
Hydrophobic duck feathers and their simulation on textile substrates for water repellent treatment.

PubMed

Liu, Yuyang; Chen, Xianqiong; Xin, J H

2008-12-01

Inspired by the non-wetting phenomena of duck feathers, the water repellent property of duck feathers was studied at the nanoscale. The microstructures of the duck feather were investigated by a scanning electron microscope (SEM) imaging method through a step-by-step magnifying procedure. The SEM results show that duck feathers have a multi-scale structure and that this multi-scale structure as well as the preening oil are responsible for their super hydrophobic behavior. The microstructures of the duck feather were simulated on textile substrates using the biopolymer chitosan as building blocks through a novel surface solution precipitation (SSP) method, and then the textile substrates were further modified with a silicone compound to achieve low surface energy. The resultant textiles exhibit super water repellent properties, thus providing a simple bionic way to create super hydrophobic surfaces on soft substrates using flexible material as building blocks.
Multi-DSP and FPGA based Multi-channel Direct IF/RF Digital receiver for atmospheric radar

NASA Astrophysics Data System (ADS)

Yasodha, Polisetti; Jayaraman, Achuthan; Kamaraj, Pandian; Durga rao, Meka; Thriveni, A.

2016-07-01

Modern phased array radars depend highly on digital signal processing (DSP) to extract the echo signal information and to accomplish reliability along with programmability and flexibility. The advent of ASIC technology has made various digital signal processing steps to be realized in one DSP chip, which can be programmed as per the application and can handle high data rates, to be used in the radar receiver to process the received signal. Further, recent days field programmable gate array (FPGA) chips, which can be re-programmed, also present an opportunity to utilize them to process the radar signal. A multi-channel direct IF/RF digital receiver (MCDRx) is developed at NARL, taking the advantage of high speed ADCs and high performance DSP chips/FPGAs, to be used for atmospheric radars working in HF/VHF bands. Multiple channels facilitate the radar t be operated in multi-receiver modes and also to obtain the wind vector with improved time resolution, without switching the antenna beam. MCDRx has six channels, implemented on a custom built digital board, which is realized using six numbers of ADCs for simultaneous processing of the six input signals, Xilinx vertex5 FPGA and Spartan6 FPGA, and two ADSPTS201 DSP chips, each of which performs one phase of processing. MCDRx unit interfaces with the data storage/display computer via two gigabit ethernet (GbE) links. One of the six channels is used for Doppler beam swinging (DBS) mode and the other five channels are used for multi-receiver mode operations, dedicatedly. Each channel has (i) ADC block, to digitize RF/IF signal, (ii) DDC block for digital down conversion of the digitized signal, (iii) decoding block to decode the phase coded signal, and (iv) coherent integration block for integrating the data preserving phase intact. ADC block consists of Analog devices make AD9467 16-bit ADCs, to digitize the input signal at 80 MSPS. The output of ADC is centered around (80 MHz - input frequency). The digitized data is fed to DDC block, which down converts the data to base-band. The DDC block has NCO, mixer and two chains of Bessel filters (fifth order cascaded integration comb filter, two FIR filters, two half band filters and programmable FIR filters) for in-phase (I) and Quadrature phase (Q) channels. The NCO has 32 bits and is set to match the output frequency of ADC. Further, DDC down samples (decimation) the data and reduces the data rate to 16 MSPS. This data is further decimated and the data rate is reduced down to 4/2/1/0.5/0.25/0.125/0.0625 MSPS for baud lengths 0.25/0.5/1/2/4/8/16 μs respectively. The down sampled data is then fed to decoding block, which performs cross correlation to achieve pulse compression of the binary-phase coded data to obtain better range resolution with maximum possible height coverage. This step improves the signal power by a factor equal to the length of the code. Coherent integration block integrates the decoded data coherently for successive pulses, which improves the signal to noise ratio and reduces the data volume. DDC, decoding and coherent integration blocks are implemented in Xilinx vertex5 FPGA. Till this point, function of all six channels is same for DBS mode and multi-receiver modes. Data from vertex5 FPGA is transferred to PC via GbE-1 interface for multi-modes or to two Analog devices make ADSP-TS201 DSP chips (A and B), via link port for DBS mode. ADSP-TS201 chips perform the normalization, DC removal, windowing, FFT computation and spectral averaging on the data, which is transferred to storage/display PC via GbE-2 interface for real-time data display and data storing. Physical layer of GbE interface is implemented in an external chip (Marvel 88E1111) and MAC layer is implemented internal to vertex5 FPGA. The MCDRx has total 4 GB of DDR2 memory for data storage. Spartan6 FPGA is used for generating timing signals, required for basic operation of the radar and testing of the MCDRx.
Layer-oriented multigrid wavefront reconstruction algorithms for multi-conjugate adaptive optics

NASA Astrophysics Data System (ADS)

Gilles, Luc; Ellerbroek, Brent L.; Vogel, Curtis R.

2003-02-01

Multi-conjugate adaptive optics (MCAO) systems with 104-105 degrees of freedom have been proposed for future giant telescopes. Using standard matrix methods to compute, optimize, and implement wavefront control algorithms for these systems is impractical, since the number of calculations required to compute and apply the reconstruction matrix scales respectively with the cube and the square of the number of AO degrees of freedom. In this paper, we develop an iterative sparse matrix implementation of minimum variance wavefront reconstruction for telescope diameters up to 32m with more than 104 actuators. The basic approach is the preconditioned conjugate gradient method, using a multigrid preconditioner incorporating a layer-oriented (block) symmetric Gauss-Seidel iterative smoothing operator. We present open-loop numerical simulation results to illustrate algorithm convergence.
Block-suffix shifting: fast, simultaneous medical concept set identification in large medical record corpora.

PubMed

Liu, Ying; Lita, Lucian Vlad; Niculescu, Radu Stefan; Mitra, Prasenjit; Giles, C Lee

2008-11-06

Owing to new advances in computer hardware, large text databases have become more prevalent than ever.Automatically mining information from these databases proves to be a challenge due to slow pattern/string matching techniques. In this paper we present a new, fast multi-string pattern matching method based on the well known Aho-Chorasick algorithm. Advantages of our algorithm include:the ability to exploit the natural structure of text, the ability to perform significant character shifting, avoiding backtracking jumps that are not useful, efficiency in terms of matching time and avoiding the typical "sub-string" false positive errors.Our algorithm is applicable to many fields with free text, such as the health care domain and the scientific document field. In this paper, we apply the BSS algorithm to health care data and mine hundreds of thousands of medical concepts from a large Electronic Medical Record (EMR) corpora simultaneously and efficiently. Experimental results show the superiority of our algorithm when compared with the top of the line multi-string matching algorithms.
Chondrocyte Deformations as a Function of Tibiofemoral Joint Loading Predicted by a Generalized High-Throughput Pipeline of Multi-Scale Simulations

PubMed Central

Sibole, Scott C.; Erdemir, Ahmet

2012-01-01

Cells of the musculoskeletal system are known to respond to mechanical loading and chondrocytes within the cartilage are not an exception. However, understanding how joint level loads relate to cell level deformations, e.g. in the cartilage, is not a straightforward task. In this study, a multi-scale analysis pipeline was implemented to post-process the results of a macro-scale finite element (FE) tibiofemoral joint model to provide joint mechanics based displacement boundary conditions to micro-scale cellular FE models of the cartilage, for the purpose of characterizing chondrocyte deformations in relation to tibiofemoral joint loading. It was possible to identify the load distribution within the knee among its tissue structures and ultimately within the cartilage among its extracellular matrix, pericellular environment and resident chondrocytes. Various cellular deformation metrics (aspect ratio change, volumetric strain, cellular effective strain and maximum shear strain) were calculated. To illustrate further utility of this multi-scale modeling pipeline, two micro-scale cartilage constructs were considered: an idealized single cell at the centroid of a 100×100×100 μm block commonly used in past research studies, and an anatomically based (11 cell model of the same volume) representation of the middle zone of tibiofemoral cartilage. In both cases, chondrocytes experienced amplified deformations compared to those at the macro-scale, predicted by simulating one body weight compressive loading on the tibiofemoral joint. In the 11 cell case, all cells experienced less deformation than the single cell case, and also exhibited a larger variance in deformation compared to other cells residing in the same block. The coupling method proved to be highly scalable due to micro-scale model independence that allowed for exploitation of distributed memory computing architecture. The method’s generalized nature also allows for substitution of any macro-scale and/or micro-scale model providing application for other multi-scale continuum mechanics problems. PMID:22649535
Review on modeling of the anode solid electrolyte interphase (SEI) for lithium-ion batteries

NASA Astrophysics Data System (ADS)

Wang, Aiping; Kadam, Sanket; Li, Hong; Shi, Siqi; Qi, Yue

2018-03-01

A passivation layer called the solid electrolyte interphase (SEI) is formed on electrode surfaces from decomposition products of electrolytes. The SEI allows Li+ transport and blocks electrons in order to prevent further electrolyte decomposition and ensure continued electrochemical reactions. The formation and growth mechanism of the nanometer thick SEI films are yet to be completely understood owing to their complex structure and lack of reliable in situ experimental techniques. Significant advances in computational methods have made it possible to predictively model the fundamentals of SEI. This review aims to give an overview of state-of-the-art modeling progress in the investigation of SEI films on the anodes, ranging from electronic structure calculations to mesoscale modeling, covering the thermodynamics and kinetics of electrolyte reduction reactions, SEI formation, modification through electrolyte design, correlation of SEI properties with battery performance, and the artificial SEI design. Multi-scale simulations have been summarized and compared with each other as well as with experiments. Computational details of the fundamental properties of SEI, such as electron tunneling, Li-ion transport, chemical/mechanical stability of the bulk SEI and electrode/(SEI/) electrolyte interfaces have been discussed. This review shows the potential of computational approaches in the deconvolution of SEI properties and design of artificial SEI. We believe that computational modeling can be integrated with experiments to complement each other and lead to a better understanding of the complex SEI for the development of a highly efficient battery in the future.
Compute-unified device architecture implementation of a block-matching algorithm for multiple graphical processing unit cards

PubMed Central

Massanes, Francesc; Cadennes, Marie; Brankov, Jovan G.

2012-01-01

In this paper we describe and evaluate a fast implementation of a classical block matching motion estimation algorithm for multiple Graphical Processing Units (GPUs) using the Compute Unified Device Architecture (CUDA) computing engine. The implemented block matching algorithm (BMA) uses summed absolute difference (SAD) error criterion and full grid search (FS) for finding optimal block displacement. In this evaluation we compared the execution time of a GPU and CPU implementation for images of various sizes, using integer and non-integer search grids. The results show that use of a GPU card can shorten computation time by a factor of 200 times for integer and 1000 times for a non-integer search grid. The additional speedup for non-integer search grid comes from the fact that GPU has built-in hardware for image interpolation. Further, when using multiple GPU cards, the presented evaluation shows the importance of the data splitting method across multiple cards, but an almost linear speedup with a number of cards is achievable. In addition we compared execution time of the proposed FS GPU implementation with two existing, highly optimized non-full grid search CPU based motion estimations methods, namely implementation of the Pyramidal Lucas Kanade Optical flow algorithm in OpenCV and Simplified Unsymmetrical multi-Hexagon search in H.264/AVC standard. In these comparisons, FS GPU implementation still showed modest improvement even though the computational complexity of FS GPU implementation is substantially higher than non-FS CPU implementation. We also demonstrated that for an image sequence of 720×480 pixels in resolution, commonly used in video surveillance, the proposed GPU implementation is sufficiently fast for real-time motion estimation at 30 frames-per-second using two NVIDIA C1060 Tesla GPU cards. PMID:22347787
Compute-unified device architecture implementation of a block-matching algorithm for multiple graphical processing unit cards.

PubMed

Massanes, Francesc; Cadennes, Marie; Brankov, Jovan G

2011-07-01

In this paper we describe and evaluate a fast implementation of a classical block matching motion estimation algorithm for multiple Graphical Processing Units (GPUs) using the Compute Unified Device Architecture (CUDA) computing engine. The implemented block matching algorithm (BMA) uses summed absolute difference (SAD) error criterion and full grid search (FS) for finding optimal block displacement. In this evaluation we compared the execution time of a GPU and CPU implementation for images of various sizes, using integer and non-integer search grids.The results show that use of a GPU card can shorten computation time by a factor of 200 times for integer and 1000 times for a non-integer search grid. The additional speedup for non-integer search grid comes from the fact that GPU has built-in hardware for image interpolation. Further, when using multiple GPU cards, the presented evaluation shows the importance of the data splitting method across multiple cards, but an almost linear speedup with a number of cards is achievable.In addition we compared execution time of the proposed FS GPU implementation with two existing, highly optimized non-full grid search CPU based motion estimations methods, namely implementation of the Pyramidal Lucas Kanade Optical flow algorithm in OpenCV and Simplified Unsymmetrical multi-Hexagon search in H.264/AVC standard. In these comparisons, FS GPU implementation still showed modest improvement even though the computational complexity of FS GPU implementation is substantially higher than non-FS CPU implementation.We also demonstrated that for an image sequence of 720×480 pixels in resolution, commonly used in video surveillance, the proposed GPU implementation is sufficiently fast for real-time motion estimation at 30 frames-per-second using two NVIDIA C1060 Tesla GPU cards.
Fabrication of SiO2@ZrO2@Y2O3:Eu3+ core-multi-shell structured phosphor.

PubMed

Gao, Xuan; He, Diping; Jiao, Huan; Chen, Juan; Meng, Xin

2011-08-01

ZrO2 interface was designed to block the reaction between SiO2 and Y2O3 in SiO2@Y2O3:Eu coreshell structure phosphor. SiO2@ZrO2@Y2O3:Eu core-multi-shell phosphors were successfully synthesized by combing an LBL method with a Sol-gel process. Based on electron microscopy, X-ray diffraction, and spectroscopy experiments, compelling evidence for the formation of the Y2O3:Eu outer shell on ZrO2 were presented. The presence of ZrO2 layer on SiO2 core can block the reaction of SiO2 core and Y2O3 shell effectively. By this kind of structure, the reaction temperature of the SiO2 core and Y2O3 shell in the SiO2@Y2O3:Eu core-shell structure phosphor can be increased about 200-300 degrees C and the luminescent intensity of this structure phosphor can be improved obviously. Under the excitation of ultraviolet (254 nm), the Eu3+ ion mainly shows its characteristic red (611 nm, 5D0-7F2) emissions in the core-multi-shell particles from Y2O3:Eu3+ shells. The emission intensity of Eu3+ ions can be tuned by the annealing temperatures, the number of coating times, and the thickness of ZrO2 interface, respectively.
Shaping Crystal-Crystal Phase Transitions

NASA Astrophysics Data System (ADS)

Du, Xiyu; van Anders, Greg; Dshemuchadse, Julia; Glotzer, Sharon

Previous computational and experimental studies have shown self-assembled structure depends strongly on building block shape. New synthesis techniques have led to building blocks with reconfigurable shape and it has been demonstrated that building block reconfiguration can induce bulk structural reconfiguration. However, we do not understand systematically how this transition happens as a function of building block shape. Using a recently developed ``digital alchemy'' framework, we study the thermodynamics of shape-driven crystal-crystal transitions. We find examples of shape-driven bulk reconfiguration that are accompanied by first-order phase transitions, and bulk reconfiguration that occurs without any thermodynamic phase transition. Our results suggest that for well-chosen shapes and structures, there exist facile means of bulk reconfiguration, and that shape-driven bulk reconfiguration provides a viable mechanism for developing functional materials.
How do bendy straws bend? A study of re-configurability of multi-stable corrugated shells

NASA Astrophysics Data System (ADS)

Bende, Nakul; Selden, Sarah; Evans, Arthur; Santangelo, Christian; Hayward, Ryan

Shape programmable systems have evolved to allow for reconfiguration of structures through a variety of mechanisms including swelling, stress-relaxation, and thermal expansion. Particularly, there has been a recent interest in systems that exhibit bi-stability or multi-stability to achieve transformation between two or more pre-programmed states. Here, we study the ubiquitous architecture of corrugated shells, such as drinking straws or bellows, which has been well known for centuries. Some of these structures exhibit almost continuous stability amongst a wide range of reconfigurable shapes, but the underlying mechanisms are not well understood. To understand multi-stability in `bendy-straw' structures, we study the unit bi-conical segment using experiments and finite element modeling to elucidate the key geometrical and mechanical factors responsible for its multi-stability. The simple transformations of a unit segment - a change in length or angle can impart complex re-configurability of a structure containing many of these units. The fundamental understanding provided of this simple multi-stable building block could yield improvements in shape re-configurability for a wide array of applications such as corrugated medical tubing, robotics, and deployable structures. NSF EFRI ODISSEI-1240441.
Simulations of Turbine Cooling Flows Using a Multiblock-Multigrid Scheme

NASA Technical Reports Server (NTRS)

Steinthorsson, Erlendur; Ameri, Ali A.; Rigby, David L.

1996-01-01

Results from numerical simulations of air flow and heat transfer in a 'branched duct' geometry are presented. The geometry contains features, including pins and a partition, as are found in coolant passages of turbine blades. The simulations were performed using a multi-block structured grid system and a finite volume discretization of the governing equations (the compressible Navier-Stokes equations). The effects of turbulence on the mean flow and heat transfer were modeled using the Baldwin-Lomax turbulence model. The computed results are compared to experimental data. It was found that the extent of some regions of high heat transfer was somewhat under predicted. It is conjectured that the underlying reason is the local nature of the turbulence model which cannot account for upstream influence on the turbulence field. In general, however, the comparison with the experimental data is favorable.
Geometry modeling and multi-block grid generation for turbomachinery configurations

NASA Technical Reports Server (NTRS)

Shih, Ming H.; Soni, Bharat K.

1992-01-01

An interactive 3D grid generation code, Turbomachinery Interactive Grid genERation (TIGER), was developed for general turbomachinery configurations. TIGER features the automatic generation of multi-block structured grids around multiple blade rows for either internal, external, or internal-external turbomachinery flow fields. Utilization of the Bezier's curves achieves a smooth grid and better orthogonality. TIGER generates the algebraic grid automatically based on geometric information provided by its built-in pseudo-AI algorithm. However, due to the large variation of turbomachinery configurations, this initial grid may not always be as good as desired. TIGER therefore provides graphical user interactions during the process which allow the user to design, modify, as well as manipulate the grid, including the capability of elliptic surface grid generation.
Multi-Functional Macromers for Hydrogel Design in Biomedical Engineering and Regenerative Medicine

PubMed Central

Hacker, Michael C.; Nawaz, Hafiz Awais

2015-01-01

Contemporary biomaterials are expected to provide tailored mechanical, biological and structural cues to encapsulated or invading cells in regenerative applications. In addition, the degradative properties of the material also have to be adjustable to the desired application. Oligo- or polymeric building blocks that can be further cross-linked into hydrogel networks, here addressed as macromers, appear as the prime option to assemble gels with the necessary degrees of freedom in the adjustment of the mentioned key parameters. Recent developments in the design of multi-functional macromers with two or more chemically different types of functionalities are summarized and discussed in this review illustrating recent trends in the development of advanced hydrogel building blocks for regenerative applications. PMID:26610468

Multi-Functional Macromers for Hydrogel Design in Biomedical Engineering and Regenerative Medicine.

PubMed

Hacker, Michael C; Nawaz, Hafiz Awais

2015-11-19

Contemporary biomaterials are expected to provide tailored mechanical, biological and structural cues to encapsulated or invading cells in regenerative applications. In addition, the degradative properties of the material also have to be adjustable to the desired application. Oligo- or polymeric building blocks that can be further cross-linked into hydrogel networks, here addressed as macromers, appear as the prime option to assemble gels with the necessary degrees of freedom in the adjustment of the mentioned key parameters. Recent developments in the design of multi-functional macromers with two or more chemically different types of functionalities are summarized and discussed in this review illustrating recent trends in the development of advanced hydrogel building blocks for regenerative applications.
Scalable, High-performance 3D Imaging Software Platform: System Architecture and Application to Virtual Colonoscopy

PubMed Central

Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli; Brett, Bevin

2013-01-01

One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. In this work, we have developed a software platform that is designed to support high-performance 3D medical image processing for a wide range of applications using increasingly available and affordable commodity computing systems: multi-core, clusters, and cloud computing systems. To achieve scalable, high-performance computing, our platform (1) employs size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D image processing algorithms; (2) supports task scheduling for efficient load distribution and balancing; and (3) consists of a layered parallel software libraries that allow a wide range of medical applications to share the same functionalities. We evaluated the performance of our platform by applying it to an electronic cleansing system in virtual colonoscopy, with initial experimental results showing a 10 times performance improvement on an 8-core workstation over the original sequential implementation of the system. PMID:23366803
High-Order Implicit-Explicit Multi-Block Time-stepping Method for Hyperbolic PDEs

NASA Technical Reports Server (NTRS)

Nielsen, Tanner B.; Carpenter, Mark H.; Fisher, Travis C.; Frankel, Steven H.

2014-01-01

This work seeks to explore and improve the current time-stepping schemes used in computational fluid dynamics (CFD) in order to reduce overall computational time. A high-order scheme has been developed using a combination of implicit and explicit (IMEX) time-stepping Runge-Kutta (RK) schemes which increases numerical stability with respect to the time step size, resulting in decreased computational time. The IMEX scheme alone does not yield the desired increase in numerical stability, but when used in conjunction with an overlapping partitioned (multi-block) domain significant increase in stability is observed. To show this, the Overlapping-Partition IMEX (OP IMEX) scheme is applied to both one-dimensional (1D) and two-dimensional (2D) problems, the nonlinear viscous Burger's equation and 2D advection equation, respectively. The method uses two different summation by parts (SBP) derivative approximations, second-order and fourth-order accurate. The Dirichlet boundary conditions are imposed using the Simultaneous Approximation Term (SAT) penalty method. The 6-stage additive Runge-Kutta IMEX time integration schemes are fourth-order accurate in time. An increase in numerical stability 65 times greater than the fully explicit scheme is demonstrated to be achievable with the OP IMEX method applied to 1D Burger's equation. Results from the 2D, purely convective, advection equation show stability increases on the order of 10 times the explicit scheme using the OP IMEX method. Also, the domain partitioning method in this work shows potential for breaking the computational domain into manageable sizes such that implicit solutions for full three-dimensional CFD simulations can be computed using direct solving methods rather than the standard iterative methods currently used.
A Mixtures-of-Trees Framework for Multi-Label Classification

PubMed Central

Hong, Charmgil; Batal, Iyad; Hauskrecht, Milos

2015-01-01

We propose a new probabilistic approach for multi-label classification that aims to represent the class posterior distribution P(Y|X). Our approach uses a mixture of tree-structured Bayesian networks, which can leverage the computational advantages of conditional tree-structured models and the abilities of mixtures to compensate for tree-structured restrictions. We develop algorithms for learning the model from data and for performing multi-label predictions using the learned model. Experiments on multiple datasets demonstrate that our approach outperforms several state-of-the-art multi-label classification methods. PMID:25927011
A system for aerodynamic design and analysis of supersonic aircraft. Part 3: Computer program description

NASA Technical Reports Server (NTRS)

Middleton, W. D.; Lundry, J. L.; Coleman, R. G.

1980-01-01

The computer program documentation for the design and analysis of supersonic configurations is presented. Schematics and block diagrams of the major program structure, together with subroutine descriptions for each module are included.
ComDim for explorative multi-block data analysis of Cantal-type cheeses: Effects of salts, gentle heating and ripening.

PubMed

Loudiyi, M; Rutledge, D N; Aït-Kaddour, A

2018-10-30

Common Dimension (ComDim) chemometrics method for multi-block data analysis was employed to evaluate the impact of different added salts and ripening times on physicochemical, color, dynamic low amplitude oscillatory rheology, texture profile, and molecular structure (fluorescence and MIR spectroscopies) of five Cantal-type cheeses. Firstly, Independent Components Analysis (ICA) was applied separately on fluorescence and MIR spectra in order to extract the relevant signal source and the associated proportions related to molecular structure characteristics. ComDim was then applied on the 31 data tables corresponding to the proportion of ICA signals obtained for spectral methods and the global analysis of cheeses by the other techniques. The ComDim results indicated that generally cheeses made with 50% NaCl or with 75:25% NaCl/KCl exhibit the equivalent characteristics in structural, textural, meltability and color properties. The proposed methodology demonstrates the applicability of ComDim for the characterization of samples when different techniques describe the same samples. Copyright © 2018 Elsevier Ltd. All rights reserved.
Transient Signal Distortion and Coupling in Multilayer Multiconductor MIC Microstrips

DTIC Science & Technology

1990-05-22

cess.ar1 and identify by block number) I FIELD GROUP I $..)3-{; ’\\0-:: Transient signals, distortion, dispersion, microstrip J 1 i nes , multi...printed circuit design; complex microstrip structures {multiple lines and/or dielectric layers), coupling between lines, distortion of non -periodic...signals on complex structures, and a new method to control coupling on multilayer structures, as well as presenting numerical results for each of these
Encoders for block-circulant LDPC codes

NASA Technical Reports Server (NTRS)

Andrews, Kenneth; Dolinar, Sam; Thorpe, Jeremy

2005-01-01

In this paper, we present two encoding methods for block-circulant LDPC codes. The first is an iterative encoding method based on the erasure decoding algorithm, and the computations required are well organized due to the block-circulant structure of the parity check matrix. The second method uses block-circulant generator matrices, and the encoders are very similar to those for recursive convolutional codes. Some encoders of the second type have been implemented in a small Field Programmable Gate Array (FPGA) and operate at 100 Msymbols/second.
Aeroelastic Analyses of the SemiSpan SuperSonic Transport (S4T) Wind Tunnel Model at Mach 0.95

NASA Technical Reports Server (NTRS)

Hur, Jiyoung

2014-01-01

Detailed aeroelastic analyses of the SemiSpan SuperSonic Transport (S4T) wind tunnel model at Mach 0.95 with a 1.75deg fixed angle of attack are presented. First, a numerical procedure using the Computational Fluids Laboratory 3-Dimensional (CFL3D) Version 6.4 flow solver is investigated. The mesh update method for structured multi-block grids was successfully applied to the Navier-Stokes simulations. Second, the steady aerodynamic analyses with a rigid structure of the S4T wind tunnel model are reviewed in transonic flow. Third, the static analyses were performed for both the Euler and Navier-Stokes equations. Both the Euler and Navier-Stokes equations predicted a significant increase of lift forces, compared to the results from the rigid structure of the S4T wind-tunnel model, over various dynamic pressures. Finally, dynamic aeroelastic analyses were performed to investigate the flutter condition of the S4T wind tunnel model at the transonic Mach number. The condition of flutter was observed at a dynamic pressure of approximately 75.0-psf for the Navier-Stokes simulations. However, it was observed that the flutter condition occurred a dynamic pressure of approximately 47.27-psf for the Euler simulations. Also, the computational efficiency of the aeroelastic analyses for the S4T wind tunnel model has been assessed.
Multidimensional Predictors of Fatigue among Octogenarians and Centenarians

PubMed Central

Cho, Jinmyoung; Martin, Peter; Margrett, Jennifer; MacDonald, Maurice; Johnson, Mary Ann; Poon, Leonard W.

2012-01-01

Background Fatigue is a common and frequently observed complaint among older adults. However, knowledge about the nature and correlates of fatigue in old age is very limited. Objective: This study examined the relationship of functional indicators, psychological and situational factors and fatigue for 210 octogenarians and centenarians from the Georgia Centenarian Study. Methods Three indicators of functional capacity (self-rated health, instrumental activities of daily living, physical activities of daily living), two indicators of psychological well-being (positive and negative affect), two indicators of situational factors (social network and social support), and a multidimensional fatigue scale were used. Blocked multiple regression analyses were computed to examine significant factors related to fatigue. In addition, multi-group analysis in structural equation modeling was used to investigate residential differences (i.e., long-term care facilities vs. private homes) in the relationship between significant factors and fatigue. Results Blocked multiple regression analyses indicated that two indicators of functional capacity, self-rated health and instrumental activities of daily living, both positive and negative affect, and social support were significant predictors of fatigue among oldest-old adults. The multiple group analysis in structural equation modeling revealed a significant difference among oldest-old adults based on residential status. Conclusion The results suggest that we should not consider fatigue as merely an unpleasant physical symptom, but rather adopt a perspective that different factors such as psychosocial aspects can influence fatigue in advanced later life. PMID:22094445
Multidimensional predictors of fatigue among octogenarians and centenarians.

PubMed

Cho, Jinmyoung; Martin, Peter; Margrett, Jennifer; MacDonald, Maurice; Johnson, Mary Ann; Poon, Leonard W; Jazwinski, S M; Green, R C; Gearing, M; Woodard, J L; Tenover, J S; Siegler, I C; Rott, C; Rodgers, W L; Hausman, D; Arnold, J; Davey, A

2012-01-01

Fatigue is a common and frequently observed complaint among older adults. However, knowledge about the nature and correlates of fatigue in old age is very limited. This study examined the relationship of functional indicators, psychological and situational factors and fatigue for 210 octogenarians and centenarians from the Georgia Centenarian Study. Three indicators of functional capacity (self-rated health, instrumental activities of daily living, physical activities of daily living), two indicators of psychological well-being (positive and negative affect), two indicators of situational factors (social network and social support), and a multidimensional fatigue scale were used. Blocked multiple regression analyses were computed to examine significant factors related to fatigue. In addition, multi-group analysis in structural equation modeling was used to investigate residential differences (i.e., long-term care facilities vs. private homes) in the relationship between significant factors and fatigue. Blocked multiple regression analyses indicated that two indicators of functional capacity, self-rated health and instrumental activities of daily living, both positive and negative affect, and social support were significant predictors of fatigue among oldest-old adults. The multiple group analysis in structural equation modeling revealed a significant difference among oldest-old adults based on residential status. The results suggest that we should not consider fatigue as merely an unpleasant physical symptom, but rather adopt a perspective that different factors such as psychosocial aspects can influence fatigue in advanced later life. Copyright © 2011 S. Karger AG, Basel.
Computational and experimental study of atmospheric moisture in ceramic blocks filled with waste fibres in winter season

NASA Astrophysics Data System (ADS)

Stastnik, S.

2016-06-01

Development of materials for vertical outer building structures tends to application of hollow clay blocks filled with some appropriate insulation material. Ceramic fittings provide high thermal resistance, but the walls built from them suffer from condensation of air humidity in winter season frequently. The paper presents the computational simulation and experimental laboratory validation of moisture behaviour of such masonry with insulation prepared from waste fibres under the Central European climatic conditions.
Implementation of a block Lanczos algorithm for Eigenproblem solution of gyroscopic systems

NASA Technical Reports Server (NTRS)

Gupta, Kajal K.; Lawson, Charles L.

1987-01-01

The details of implementation of a general numerical procedure developed for the accurate and economical computation of natural frequencies and associated modes of any elastic structure rotating along an arbitrary axis are described. A block version of the Lanczos algorithm is derived for the solution that fully exploits associated matrix sparsity and employs only real numbers in all relevant computations. It is also capable of determining multiple roots and proves to be most efficient when compared to other, similar, exisiting techniques.
Argumentation in a Multi Party Asynchronous Computer Mediated Conference: A Generic Analysis

ERIC Educational Resources Information Center

Coffin, Caroline; Painter, Clare; Hewings, Ann

2005-01-01

This paper draws on systemic functional linguistic genre analysis to illuminate the way in which post graduate applied linguistics students structure their argumentation within a multi party asynchronous computer mediated conference. Two conference discussions within the same postgraduate course are compared in order to reveal the way in which…
Time-efficient simulations of tight-binding electronic structures with Intel Xeon PhiTM many-core processors

NASA Astrophysics Data System (ADS)

Ryu, Hoon; Jeong, Yosang; Kang, Ji-Hoon; Cho, Kyu Nam

2016-12-01

Modelling of multi-million atomic semiconductor structures is important as it not only predicts properties of physically realizable novel materials, but can accelerate advanced device designs. This work elaborates a new Technology-Computer-Aided-Design (TCAD) tool for nanoelectronics modelling, which uses a sp3d5s∗ tight-binding approach to describe multi-million atomic structures, and simulate electronic structures with high performance computing (HPC), including atomic effects such as alloy and dopant disorders. Being named as Quantum simulation tool for Advanced Nanoscale Devices (Q-AND), the tool shows nice scalability on traditional multi-core HPC clusters implying the strong capability of large-scale electronic structure simulations, particularly with remarkable performance enhancement on latest clusters of Intel Xeon PhiTM coprocessors. A review of the recent modelling study conducted to understand an experimental work of highly phosphorus-doped silicon nanowires, is presented to demonstrate the utility of Q-AND. Having been developed via Intel Parallel Computing Center project, Q-AND will be open to public to establish a sound framework of nanoelectronics modelling with advanced HPC clusters of a many-core base. With details of the development methodology and exemplary study of dopant electronics, this work will present a practical guideline for TCAD development to researchers in the field of computational nanoelectronics.
Automatic Orientation of Large Blocks of Oblique Images

NASA Astrophysics Data System (ADS)

Rupnik, E.; Nex, F.; Remondino, F.

2013-05-01

Nowadays, multi-camera platforms combining nadir and oblique cameras are experiencing a revival. Due to their advantages such as ease of interpretation, completeness through mitigation of occluding areas, as well as system accessibility, they have found their place in numerous civil applications. However, automatic post-processing of such imagery still remains a topic of research. Configuration of cameras poses a challenge on the traditional photogrammetric pipeline used in commercial software and manual measurements are inevitable. For large image blocks it is certainly an impediment. Within theoretical part of the work we review three common least square adjustment methods and recap on possible ways for a multi-camera system orientation. In the practical part we present an approach that successfully oriented a block of 550 images acquired with an imaging system composed of 5 cameras (Canon Eos 1D Mark III) with different focal lengths. Oblique cameras are rotated in the four looking directions (forward, backward, left and right) by 45° with respect to the nadir camera. The workflow relies only upon open-source software: a developed tool to analyse image connectivity and Apero to orient the image block. The benefits of the connectivity tool are twofold: in terms of computational time and success of Bundle Block Adjustment. It exploits the georeferenced information provided by the Applanix system in constraining feature point extraction to relevant images only, and guides the concatenation of images during the relative orientation. Ultimately an absolute transformation is performed resulting in mean re-projection residuals equal to 0.6 pix.
Applications of Multi-Agent Technology to Power Systems

NASA Astrophysics Data System (ADS)

Nagata, Takeshi

Currently, agents are focus of intense on many sub-fields of computer science and artificial intelligence. Agents are being used in an increasingly wide variety of applications. Many important computing applications such as planning, process control, communication networks and concurrent systems will benefit from using multi-agent system approach. A multi-agent system is a structure given by an environment together with a set of artificial agents capable to act on this environment. Multi-agent models are oriented towards interactions, collaborative phenomena, and autonomy. This article presents the applications of multi-agent technology to the power systems.
Self-assembly assisted polymerization (SAAP): approaching long multi-block copolymers with an ordered chain sequence and controllable block length.

PubMed

Wu, Chi; Xie, Zuowei; Zhang, Guangzhao; Zi, Guofu; Tu, Yingfeng; Yang, Yali; Cai, Ping; Nie, Ting

2002-12-07

A combination of polymer physics and synthetic chemistry has enabled us to develop self-assembly assisted polymerization (SAAP), leading to the preparation of long multi-block copolymers with an ordered chain sequence and controllable block lengths.
Thermal Analysis of Magnetically-Coupled Pump for Cryogenic Applications

NASA Technical Reports Server (NTRS)

Senocak, Inanc; Udaykumar, H. S.; Ndri, Narcisse; Francois, Marianne; Shyy, Wei

1999-01-01

Magnetically-coupled pump is under evaluation at Kennedy Space Center for possible cryogenic applications. A major concern is the impact of low temperature fluid flows on the pump performance. As a first step toward addressing this and related issues, a computational fluid dynamics and heat transfer tool has been adopted in a pump geometry. The computational tool includes (i) a commercial grid generator to handle multiple grid blocks and complicated geometric definitions, and (ii) an in-house computational fluid dynamics and heat transfer software developed in the Principal Investigator's group at the University of Florida. Both pure-conduction and combined convection-conduction computations have been conducted. A pure-conduction analysis gives insufficient information about the overall thermal distribution. Combined convection-conduction analysis indicates the significant influence of the coolant over the entire flow path. Since 2-D simulation is of limited help, future work on full 3-D modeling of the pump using multi-materials is needed. A comprehensive and accurate model can be developed to take into account the effect of multi-phase flow in the cooling flow loop, and the magnetic interactions.
Plane Smoothers for Multiblock Grids: Computational Aspects

NASA Technical Reports Server (NTRS)

Llorente, Ignacio M.; Diskin, Boris; Melson, N. Duane

1999-01-01

Standard multigrid methods are not well suited for problems with anisotropic discrete operators, which can occur, for example, on grids that are stretched in order to resolve a boundary layer. One of the most efficient approaches to yield robust methods is the combination of standard coarsening with alternating-direction plane relaxation in the three dimensions. However, this approach may be difficult to implement in codes with multiblock structured grids because there may be no natural definition of global lines or planes. This inherent obstacle limits the range of an implicit smoother to only the portion of the computational domain in the current block. This report studies in detail, both numerically and analytically, the behavior of blockwise plane smoothers in order to provide guidance to engineers who use block-structured grids. The results obtained so far show alternating-direction plane smoothers to be very robust, even on multiblock grids. In common computational fluid dynamics multiblock simulations, where the number of subdomains crossed by the line of a strong anisotropy is low (up to four), textbook multigrid convergence rates can be obtained with a small overlap of cells between neighboring blocks.

Rotorcraft application of advanced computational aerodynamics

NASA Technical Reports Server (NTRS)

Stanaway, Sharon

1991-01-01

The objective was to develop the capability to compute the unsteady viscous flow around rotor-body combinations. In the interest of tractability, the problem was divided into subprograms for: (1) computing the flow around a rotor blade in isolation; (2) computing the flow around a fuselage in isolation, and (3) integrating the pieces. Considerable progress has already been made by others toward computing the rotor in isolation (Srinivasen) and this work focused on the remaining tasks. These tasks required formulating a multi-block strategy for combining rotating blades and nonrotating components (i.e., a fuselage). Then an appropriate configuration was chosen for which suitable rotor body interference test data exists. Next, surface and volume grids were generated and state-of-the-art CFD codes were modified and applied to the problem.
Computer aided design environment for the analysis and design of multi-body flexible structures

NASA Technical Reports Server (NTRS)

Ramakrishnan, Jayant V.; Singh, Ramen P.

1989-01-01

A computer aided design environment consisting of the programs NASTRAN, TREETOPS and MATLAB is presented in this paper. With links for data transfer between these programs, the integrated design of multi-body flexible structures is significantly enhanced. The CAD environment is used to model the Space Shuttle/Pinhole Occulater Facility. Then a controller is designed and evaluated in the nonlinear time history sense. Recent enhancements and ongoing research to add more capabilities are also described.
Evaluating forensic DNA mixtures with contributors of different structured ethnic origins: a computer software.

PubMed

Hu, Yue-Qing; Fung, Wing K

2003-08-01

The effect of a structured population on the likelihood ratio of a DNA mixture has been studied by the current authors and others. In practice, contributors of a DNA mixture may belong to different ethnic/racial origins, a situation especially common in multi-racial countries such as the USA and Singapore. We have developed a computer software which is available on the web for evaluating DNA mixtures in multi-structured populations. The software can deal with various DNA mixture problems that cannot be handled by the methods given in a recent article of Fung and Hu.
GENIE(++): A Multi-Block Structured Grid System

NASA Technical Reports Server (NTRS)

Williams, Tonya; Nadenthiran, Naren; Thornburg, Hugh; Soni, Bharat K.

1996-01-01

The computer code GENIE++ is a continuously evolving grid system containing a multitude of proven geometry/grid techniques. The generation process in GENIE++ is based on an earlier version. The process uses several techniques either separately or in combination to quickly and economically generate sculptured geometry descriptions and grids for arbitrary geometries. The computational mesh is formed by using an appropriate algebraic method. Grid clustering is accomplished with either exponential or hyperbolic tangent routines which allow the user to specify a desired point distribution. Grid smoothing can be accomplished by using an elliptic solver with proper forcing functions. B-spline and Non-Uniform Rational B-splines (NURBS) algorithms are used for surface definition and redistribution. The built in sculptured geometry definition with desired distribution of points, automatic Bezier curve/surface generation for interior boundaries/surfaces, and surface redistribution is based on NURBS. Weighted Lagrance/Hermite transfinite interpolation methods, interactive geometry/grid manipulation modules, and on-line graphical visualization of the generation process are salient features of this system which result in a significant time savings for a given geometry/grid application.
Mechanical Behaviour of Light Metal Alloys at High Strain Rates. Computer Simulation on Mesoscale Levels

NASA Astrophysics Data System (ADS)

Skripnyak, Vladimir; Skripnyak, Evgeniya; Meyer, Lothar W.; Herzig, Norman; Skripnyak, Nataliya

2012-02-01

Researches of the last years have allowed to establish that the laws of deformation and fracture of bulk ultrafine-grained and coarse-grained materials are various both in static and in dynamic loading conditions. Development of adequate constitutive equations for the description of mechanical behavior of bulk ultrafine-grained materials at intensive dynamic influences is complicated in consequence of insufficient knowledge about general rules of inelastic deformation and nucleation and growth of cracks. Multi-scale computational model was used for the investigation of deformation and fracture of bulk structured aluminum and magnesium alloys under stress pulse loadings on mesoscale level. The increment of plastic deformation is defined by the sum of the increments caused by a nucleation and gliding of dislocations, the twinning, meso-blocks movement, and grain boundary sliding. The model takes into account the influence on mechanical properties of alloys an average grains size, grain sizes distribution of and concentration of precipitates. It was obtained the nucleation and gliding of dislocations caused the high attenuation rate of the elastic precursor of ultrafine-grained alloys than in coarse grained counterparts.
Finite Macro-Element Mesh Deformation in a Structured Multi-Block Navier-Stokes Code

NASA Technical Reports Server (NTRS)

Bartels, Robert E.

2005-01-01

A mesh deformation scheme is developed for a structured multi-block Navier-Stokes code consisting of two steps. The first step is a finite element solution of either user defined or automatically generated macro-elements. Macro-elements are hexagonal finite elements created from a subset of points from the full mesh. When assembled, the finite element system spans the complete flow domain. Macro-element moduli vary according to the distance to the nearest surface, resulting in extremely stiff elements near a moving surface and very pliable elements away from boundaries. Solution of the finite element system for the imposed boundary deflections generally produces smoothly varying nodal deflections. The manner in which distance to the nearest surface has been found to critically influence the quality of the element deformation. The second step is a transfinite interpolation which distributes the macro-element nodal deflections to the remaining fluid mesh points. The scheme is demonstrated for several two-dimensional applications.
Charge splitters and charge transport junctions based on guanine quadruplexes

NASA Astrophysics Data System (ADS)

Sha, Ruojie; Xiang, Limin; Liu, Chaoren; Balaeff, Alexander; Zhang, Yuqi; Zhang, Peng; Li, Yueqi; Beratan, David N.; Tao, Nongjian; Seeman, Nadrian C.

2018-04-01

Self-assembling circuit elements, such as current splitters or combiners at the molecular scale, require the design of building blocks with three or more terminals. A promising material for such building blocks is DNA, wherein multiple strands can self-assemble into multi-ended junctions, and nucleobase stacks can transport charge over long distances. However, nucleobase stacking is often disrupted at junction points, hindering electric charge transport between the two terminals of the junction. Here, we show that a guanine-quadruplex (G4) motif can be used as a connector element for a multi-ended DNA junction. By attaching specific terminal groups to the motif, we demonstrate that charges can enter the structure from one terminal at one end of a three-way G4 motif, and can exit from one of two terminals at the other end with minimal carrier transport attenuation. Moreover, we study four-way G4 junction structures by performing theoretical calculations to assist in the design and optimization of these connectors.
Time delay estimation using new spectral and adaptive filtering methods with applications to underwater target detection

NASA Astrophysics Data System (ADS)

Hasan, Mohammed A.

1997-11-01

In this dissertation, we present several novel approaches for detection and identification of targets of arbitrary shapes from the acoustic backscattered data and using the incident waveform. This problem is formulated as time- delay estimation and sinusoidal frequency estimation problems which both have applications in many other important areas in signal processing. Solving time-delay estimation problem allows the identification of the specular components in the backscattered signal from elastic and non-elastic targets. Thus, accurate estimation of these time delays would help in determining the existence of certain clues for detecting targets. Several new methods for solving these two problems in the time, frequency and wavelet domains are developed. In the time domain, a new block fast transversal filter (BFTF) is proposed for a fast implementation of the least squares (LS) method. This BFTF algorithm is derived by using data-related constrained block-LS cost function to guarantee global optimality. The new soft-constrained algorithm provides an efficient way of transferring weight information between blocks of data and thus it is computationally very efficient compared with other LS- based schemes. Additionally, the tracking ability of the algorithm can be controlled by varying the block length and/or a soft constrained parameter. The effectiveness of this algorithm is tested on several underwater acoustic backscattered data for elastic targets and non-elastic (cement chunk) objects. In the frequency domain, the time-delay estimation problem is converted to a sinusoidal frequency estimation problem by using the discrete Fourier transform. Then, the lagged sample covariance matrices of the resulting signal are computed and studied in terms of their eigen- structure. These matrices are shown to be robust and effective in extracting bases for the signal and noise subspaces. New MUSIC and matrix pencil-based methods are derived these subspaces. The effectiveness of the method is demonstrated on the problem of detection of multiple specular components in the acoustic backscattered data. Finally, a method for the estimation of time delays using wavelet decomposition is derived. The sub-band adaptive filtering uses discrete wavelet transform for multi- resolution or sub-band decomposition. Joint time delay estimation for identifying multi-specular components and subsequent adaptive filtering processes are performed on the signal in each sub-band. This would provide multiple 'look' of the signal at different resolution scale which results in more accurate estimates for delays associated with the specular components. Simulation results on the simulated and real shallow water data are provided which show the promise of this new scheme for target detection in a heavy cluttered environment.
Multi-hop path tracing of mobile robot with multi-range image

NASA Astrophysics Data System (ADS)

Choudhury, Ramakanta; Samal, Chandrakanta; Choudhury, Umakanta

2010-02-01

It is well known that image processing depends heavily upon image representation technique . This paper intends to find out the optimal path of mobile robots for a specified area where obstacles are predefined as well as modified. Here the optimal path is represented by using the Quad tree method. Since there has been rising interest in the use of quad tree, we have tried to use the successive subdivision of images into quadrants from which the quad tree is developed. In the quad tree, obstacles-free area and the partial filled area are represented with different notations. After development of quad tree the algorithm is used to find the optimal path by employing neighbor finding technique, with a view to move the robot from the source to destination. The algorithm, here , permeates through the entire tree, and tries to locate the common ancestor for computation. The computation and the algorithm, aim at easing the ability of the robot to trace the optimal path with the help of adjacencies between the neighboring nodes as well as determining such adjacencies in the horizontal, vertical and diagonal directions. In this paper efforts have been made to determine the movement of the adjacent block in the quad tree and to detect the transition between the blocks equal size and finally generate the result.
Rosetta:MSF: a modular framework for multi-state computational protein design.

PubMed

Löffler, Patrick; Schmitz, Samuel; Hupfeld, Enrico; Sterner, Reinhard; Merkl, Rainer

2017-06-01

Computational protein design (CPD) is a powerful technique to engineer existing proteins or to design novel ones that display desired properties. Rosetta is a software suite including algorithms for computational modeling and analysis of protein structures and offers many elaborate protocols created to solve highly specific tasks of protein engineering. Most of Rosetta's protocols optimize sequences based on a single conformation (i. e. design state). However, challenging CPD objectives like multi-specificity design or the concurrent consideration of positive and negative design goals demand the simultaneous assessment of multiple states. This is why we have developed the multi-state framework MSF that facilitates the implementation of Rosetta's single-state protocols in a multi-state environment and made available two frequently used protocols. Utilizing MSF, we demonstrated for one of these protocols that multi-state design yields a 15% higher performance than single-state design on a ligand-binding benchmark consisting of structural conformations. With this protocol, we designed de novo nine retro-aldolases on a conformational ensemble deduced from a (βα)8-barrel protein. All variants displayed measurable catalytic activity, testifying to a high success rate for this concept of multi-state enzyme design.
Rosetta:MSF: a modular framework for multi-state computational protein design

PubMed Central

Hupfeld, Enrico; Sterner, Reinhard

2017-01-01

Computational protein design (CPD) is a powerful technique to engineer existing proteins or to design novel ones that display desired properties. Rosetta is a software suite including algorithms for computational modeling and analysis of protein structures and offers many elaborate protocols created to solve highly specific tasks of protein engineering. Most of Rosetta’s protocols optimize sequences based on a single conformation (i. e. design state). However, challenging CPD objectives like multi-specificity design or the concurrent consideration of positive and negative design goals demand the simultaneous assessment of multiple states. This is why we have developed the multi-state framework MSF that facilitates the implementation of Rosetta’s single-state protocols in a multi-state environment and made available two frequently used protocols. Utilizing MSF, we demonstrated for one of these protocols that multi-state design yields a 15% higher performance than single-state design on a ligand-binding benchmark consisting of structural conformations. With this protocol, we designed de novo nine retro-aldolases on a conformational ensemble deduced from a (βα)8-barrel protein. All variants displayed measurable catalytic activity, testifying to a high success rate for this concept of multi-state enzyme design. PMID:28604768
Computational Assessment of Blood Flow Heterogeneity in Peritoneal Dialysis Patients' Cardiac Ventricles

PubMed Central

Kharche, Sanjay R.; So, Aaron; Salerno, Fabio; Lee, Ting-Yim; Ellis, Chris; Goldman, Daniel; McIntyre, Christopher W.

2018-01-01

Dialysis prolongs life but augments cardiovascular mortality. Imaging data suggests that dialysis increases myocardial blood flow (BF) heterogeneity, but its causes remain poorly understood. A biophysical model of human coronary vasculature was used to explain the imaging observations, and highlight causes of coronary BF heterogeneity. Post-dialysis CT images from patients under control, pharmacological stress (adenosine), therapy (cooled dialysate), and adenosine and cooled dialysate conditions were obtained. The data presented disparate phenotypes. To dissect vascular mechanisms, a 3D human vasculature model based on known experimental coronary morphometry and a space filling algorithm was implemented. Steady state simulations were performed to investigate the effects of altered aortic pressure and blood vessel diameters on myocardial BF heterogeneity. Imaging showed that stress and therapy potentially increased mean and total BF, while reducing heterogeneity. BF histograms of one patient showed multi-modality. Using the model, it was found that total coronary BF increased as coronary perfusion pressure was increased. BF heterogeneity was differentially affected by large or small vessel blocking. BF heterogeneity was found to be inversely related to small blood vessel diameters. Simulation of large artery stenosis indicates that BF became heterogeneous (increase relative dispersion) and gave multi-modal histograms. The total transmural BF as well as transmural BF heterogeneity reduced due to large artery stenosis, generating large patches of very low BF regions downstream. Blocking of arteries at various orders showed that blocking larger arteries results in multi-modal BF histograms and large patches of low BF, whereas smaller artery blocking results in augmented relative dispersion and fractal dimension. Transmural heterogeneity was also affected. Finally, the effects of augmented aortic pressure in the presence of blood vessel blocking shows differential effects on BF heterogeneity as well as transmural BF. Improved aortic blood pressure may improve total BF. Stress and therapy may be effective if they dilate small vessels. A potential cause for the observed complex BF distributions (multi-modal BF histograms) may indicate existing large vessel stenosis. The intuitive BF heterogeneity methods used can be readily used in clinical studies. Further development of the model and methods will permit personalized assessment of patient BF status. PMID:29867555
Multigrid Methods for Aerodynamic Problems in Complex Geometries

NASA Technical Reports Server (NTRS)

Caughey, David A.

1995-01-01

Work has been directed at the development of efficient multigrid methods for the solution of aerodynamic problems involving complex geometries, including the development of computational methods for the solution of both inviscid and viscous transonic flow problems. The emphasis is on problems of complex, three-dimensional geometry. The methods developed are based upon finite-volume approximations to both the Euler and the Reynolds-Averaged Navier-Stokes equations. The methods are developed for use on multi-block grids using diagonalized implicit multigrid methods to achieve computational efficiency. The work is focused upon aerodynamic problems involving complex geometries, including advanced engine inlets.
Multi-block sulfonated poly(phenylene) copolymer proton exchange membranes

DOEpatents

Fujimoto, Cy H [Albuquerque, NM; Hibbs, Michael [Albuquerque, NM; Ambrosini, Andrea [Albuquerque, NM

2012-02-07

Improved multi-block sulfonated poly(phenylene) copolymer compositions, methods of making the same, and their use as proton exchange membranes (PEM) in hydrogen fuel cells, direct methanol fuel cells, in electrode casting solutions and electrodes. The multi-block architecture has defined, controllable hydrophobic and hydrophilic segments. These improved membranes have better ion transport (proton conductivity) and water swelling properties.
A general multiblock Euler code for propulsion integration. Volume 1: Theory document

NASA Technical Reports Server (NTRS)

Chen, H. C.; Su, T. Y.; Kao, T. J.

1991-01-01

A general multiblock Euler solver was developed for the analysis of flow fields over geometrically complex configurations either in free air or in a wind tunnel. In this approach, the external space around a complex configuration was divided into a number of topologically simple blocks, so that surface-fitted grids and an efficient flow solution algorithm could be easily applied in each block. The computational grid in each block is generated using a combination of algebraic and elliptic methods. A grid generation/flow solver interface program was developed to facilitate the establishment of block-to-block relations and the boundary conditions for each block. The flow solver utilizes a finite volume formulation and an explicit time stepping scheme to solve the Euler equations. A multiblock version of the multigrid method was developed to accelerate the convergence of the calculations. The generality of the method was demonstrated through the analysis of two complex configurations at various flow conditions. Results were compared to available test data. Two accompanying volumes, user manuals for the preparation of multi-block grids (vol. 2) and for the Euler flow solver (vol. 3), provide information on input data format and program execution.
MultiLIS: A Description of the System Design and Operational Features.

ERIC Educational Resources Information Center

Kelly, Glen J.; And Others

1988-01-01

Describes development, hardware requirements, and features of the MultiLIS integrated library software package. A system profile provides pricing information, operational characteristics, and technical specifications. Sidebars discuss MultiLIS integration structure, incremental architecture, and NCR Tower Computers. (4 references) (MES)
Lithosphere structure of the west Qinling orogenic belt revealed by deep seismic reflection profile

NASA Astrophysics Data System (ADS)

Wang, H.

2009-12-01

The west Qinling orogen located in the northeastern margin of the Qinghai-Tibet plateau, is transformation zone between the N-S-trending and E-W-trending tectonics in the Chinese continent. Further study of the fine crust structure of the west Qinling orogen and its relationships with surrounding basins have very important significance for understanding tectonic response of the northeastern margin of the plateau about collision convergence of the Indian block and Asian block and learning formation and evolution of the plateau. In 2009, we reprocessed the data of the Tangke-Hezuo deep seismic reflection profiles collected in 2004 across the west Qinling orogen and the northern Songpan block. The new results show the lithosphere fine structure of the west Qinling orogen. Reflection features indicate that an interface at 6.0-7.0s (TWT) divided the crust into the upper and lower crust, whose structural style and deformation are totally different. Integrating geological data, we deduce that the interface at 6.0-7.0s (depth with 18-21 km) was the basement detachment, which made deformation decoupled of the upper and lower crust. The multi-layered reflections in the upper crust reveal the sedimentary covers of the west Qinling orogen, disclose the thickness of the various structure layer and deformation degree, and provide a basis for the prospective evaluation of a multi-metallic mineral and energy exploration. The north dipping strong reflection characteristics of the lower crust in the west Qinling orogen constituted imbricate structure, such imbricate structural features provide seismology evidence for researching the west Qinling thrusting toward the northern Songpan block, and have great significance for studying formation and evolution of the Songpan-Garze structure. Moho reflections are observed around 17.0-17.2s, characterized by nearly horizontal reflections, which implies the west Qinling orogen underwent an intense extension post orogeny caused the lithosphere extensional thinning formed a nearly level Moho reflections. The study was financed by National Natural Science Foundation of china (No. 40830316 and 40604010),the Basic outlay of scientific research work from Ministry of Science and Technology of the People’s Republic of China and SINOPPROBE-02.
The three-dimensional Multi-Block Advanced Grid Generation System (3DMAGGS)

NASA Technical Reports Server (NTRS)

Alter, Stephen J.; Weilmuenster, Kenneth J.

1993-01-01

As the size and complexity of three dimensional volume grids increases, there is a growing need for fast and efficient 3D volumetric elliptic grid solvers. Present day solvers are limited by computational speed and do not have all the capabilities such as interior volume grid clustering control, viscous grid clustering at the wall of a configuration, truncation error limiters, and convergence optimization residing in one code. A new volume grid generator, 3DMAGGS (Three-Dimensional Multi-Block Advanced Grid Generation System), which is based on the 3DGRAPE code, has evolved to meet these needs. This is a manual for the usage of 3DMAGGS and contains five sections, including the motivations and usage, a GRIDGEN interface, a grid quality analysis tool, a sample case for verifying correct operation of the code, and a comparison to both 3DGRAPE and GRIDGEN3D. Since it was derived from 3DGRAPE, this technical memorandum should be used in conjunction with the 3DGRAPE manual (NASA TM-102224).
An Adaptive Mesh Algorithm: Mesh Structure and Generation

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

Scannapieco, Anthony J.

2016-06-21

The purpose of Adaptive Mesh Refinement is to minimize spatial errors over the computational space not to minimize the number of computational elements. The additional result of the technique is that it may reduce the number of computational elements needed to retain a given level of spatial accuracy. Adaptive mesh refinement is a computational technique used to dynamically select, over a region of space, a set of computational elements designed to minimize spatial error in the computational model of a physical process. The fundamental idea is to increase the mesh resolution in regions where the physical variables are represented bymore » a broad spectrum of modes in k-space, hence increasing the effective global spectral coverage of those physical variables. In addition, the selection of the spatially distributed elements is done dynamically by cyclically adjusting the mesh to follow the spectral evolution of the system. Over the years three types of AMR schemes have evolved; block, patch and locally refined AMR. In block and patch AMR logical blocks of various grid sizes are overlaid to span the physical space of interest, whereas in locally refined AMR no logical blocks are employed but locally nested mesh levels are used to span the physical space. The distinction between block and patch AMR is that in block AMR the original blocks refine and coarsen entirely in time, whereas in patch AMR the patches change location and zone size with time. The type of AMR described herein is a locally refi ned AMR. In the algorithm described, at any point in physical space only one zone exists at whatever level of mesh that is appropriate for that physical location. The dynamic creation of a locally refi ned computational mesh is made practical by a judicious selection of mesh rules. With these rules the mesh is evolved via a mesh potential designed to concentrate the nest mesh in regions where the physics is modally dense, and coarsen zones in regions where the physics is modally sparse.« less
Multi-disciplinary coupling effects for integrated design of propulsion systems

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Singhal, S. N.

1993-01-01

Effective computational simulation procedures are described for modeling the inherent multi-disciplinary interactions which govern the accurate response of propulsion systems. Results are presented for propulsion system responses including multi-disciplinary coupling effects using coupled multi-discipline thermal, structural, and acoustic tailoring; an integrated system of multi-disciplinary simulators; coupled material behavior/fabrication process tailoring; sensitivities using a probabilistic simulator; and coupled materials, structures, fracture, and probabilistic behavior simulator. The results demonstrate that superior designs can be achieved if the analysis/tailoring methods account for the multi-disciplinary coupling effects. The coupling across disciplines can be used to develop an integrated coupled multi-discipline numerical propulsion system simulator.

Multi-resonant scatterers in sonic crystals: Locally multi-resonant acoustic metamaterial

NASA Astrophysics Data System (ADS)

Romero-García, V.; Krynkin, A.; Garcia-Raffi, L. M.; Umnova, O.; Sánchez-Pérez, J. V.

2013-01-01

An acoustic metamaterial made of a two-dimensional (2D) periodic array of multi-resonant acoustic scatterers is analyzed both experimentally and theoretically. The building blocks consist of a combination of elastic beams of low-density polyethylene foam (LDPF) with cavities of known area. Elastic resonances of the beams and acoustic resonances of the cavities can be excited by sound producing several attenuation peaks in the low frequency range. Due to this behavior the periodic array with long wavelength multi-resonant structural units can be classified as a locally multi-resonant acoustic metamaterial (LMRAM) with strong dispersion of its effective properties.The results presented in this paper could be used to design effective tunable acoustic filters for the low frequency range.
[The research on bidirectional reflectance computer simulation of forest canopy at pixel scale].

PubMed

Song, Jin-Ling; Wang, Jin-Di; Shuai, Yan-Min; Xiao, Zhi-Qiang

2009-08-01

Computer simulation is based on computer graphics to generate the realistic 3D structure scene of vegetation, and to simulate the canopy regime using radiosity method. In the present paper, the authors expand the computer simulation model to simulate forest canopy bidirectional reflectance at pixel scale. But usually, the trees are complex structures, which are tall and have many branches. So there is almost a need for hundreds of thousands or even millions of facets to built up the realistic structure scene for the forest It is difficult for the radiosity method to compute so many facets. In order to make the radiosity method to simulate the forest scene at pixel scale, in the authors' research, the authors proposed one idea to simplify the structure of forest crowns, and abstract the crowns to ellipsoids. And based on the optical characteristics of the tree component and the characteristics of the internal energy transmission of photon in real crown, the authors valued the optical characteristics of ellipsoid surface facets. In the computer simulation of the forest, with the idea of geometrical optics model, the gap model is considered to get the forest canopy bidirectional reflectance at pixel scale. Comparing the computer simulation results with the GOMS model, and Multi-angle Imaging SpectroRadiometer (MISR) multi-angle remote sensing data, the simulation results are in agreement with the GOMS simulation result and MISR BRF. But there are also some problems to be solved. So the authors can conclude that the study has important value for the application of multi-angle remote sensing and the inversion of vegetation canopy structure parameters.
A procedure for automating CFD simulations of an inlet-bleed problem

NASA Technical Reports Server (NTRS)

Chyu, Wei J.; Rimlinger, Mark J.; Shih, Tom I.-P.

1995-01-01

A procedure was developed to improve the turn-around time for computational fluid dynamics (CFD) simulations of an inlet-bleed problem involving oblique shock-wave/boundary-layer interactions on a flat plate with bleed into a plenum through one or more circular holes. This procedure is embodied in a preprocessor called AUTOMAT. With AUTOMAT, once data for the geometry and flow conditions have been specified (either interactively or via a namelist), it will automatically generate all input files needed to perform a three-dimensional Navier-Stokes simulation of the prescribed inlet-bleed problem by using the PEGASUS and OVERFLOW codes. The input files automatically generated by AUTOMAT include those for the grid system and those for the initial and boundary conditions. The grid systems automatically generated by AUTOMAT are multi-block structured grids of the overlapping type. Results obtained by using AUTOMAT are presented to illustrate its capability.
Application of the Geophysical Scale Multi-Block Transport Modeling System to Hydrodynamic Forcing of Dredged Material Placement Sediment Transport within the James River Estuary

NASA Astrophysics Data System (ADS)

Kim, S. C.; Hayter, E. J.; Pruhs, R.; Luong, P.; Lackey, T. C.

2016-12-01

The geophysical scale circulation of the Mid Atlantic Bight and hydrologic inputs from adjacent Chesapeake Bay watersheds and tributaries influences the hydrodynamics and transport of the James River estuary. Both barotropic and baroclinic transport govern the hydrodynamics of this partially stratified estuary. Modeling the placement of dredged sediment requires accommodating this wide spectrum of atmospheric and hydrodynamic scales. The Geophysical Scale Multi-Block (GSMB) Transport Modeling System is a collection of multiple well established and USACE approved process models. Taking advantage of the parallel computing capability of multi-block modeling, we performed one year three-dimensional modeling of hydrodynamics in supporting simulation of dredged sediment placements transport and morphology changes. Model forcing includes spatially and temporally varying meteorological conditions and hydrological inputs from the watershed. Surface heat flux estimates were derived from the National Solar Radiation Database (NSRDB). The open water boundary condition for water level was obtained from an ADCIRC model application of the U. S. East Coast. Temperature-salinity boundary conditions were obtained from the Environmental Protection Agency (EPA) Chesapeake Bay Program (CBP) long-term monitoring stations database. Simulated water levels were calibrated and verified by comparison with National Oceanic and Atmospheric Administration (NOAA) tide gage locations. A harmonic analysis of the modeled tides was performed and compared with NOAA tide prediction data. In addition, project specific circulation was verified using US Army Corps of Engineers (USACE) drogue data. Salinity and temperature transport was verified at seven CBP long term monitoring stations along the navigation channel. Simulation and analysis of model results suggest that GSMB is capable of resolving the long duration, multi-scale processes inherent to practical engineering problems such as dredged material placement stability.
Structure and Dynamics Ionic Block co-Polymer Melts: Computational Study

NASA Astrophysics Data System (ADS)

Aryal, Dipak; Perahia, Dvora; Grest, Gary S.

Tethering ionomer blocks into co-polymers enables engineering of polymeric systems designed to encompass transport while controlling structure. Here the structure and dynamics of symmetric pentablock copolymers melts are probed by fully atomistic molecular dynamics simulations. The center block consists of randomly sulfonated polystyrene with sulfonation fractions f = 0 to 0.55 tethered to a hydrogenated polyisoprene (PI), end caped with poly(t-butyl styrene). We find that melts with f = 0.15 and 0.30 consist of isolated ionic clusters whereas melts with f = 0.55 exhibit a long-range percolating ionic network. Similar to polystyrene sulfonate, a small number of ionic clusters slow the mobility of the center of mass of the co-polymer, however, formation of the ionic clusters is slower and they are often intertwined with PI segments. Surprisingly, the segmental dynamics of the other blocks are also affected. NSF DMR-1611136; NERSC; Palmetto Cluster Clemson University; Kraton Polymers US, LLC.
Adapting hierarchical bidirectional inter prediction on a GPU-based platform for 2D and 3D H.264 video coding

NASA Astrophysics Data System (ADS)

Rodríguez-Sánchez, Rafael; Martínez, José Luis; Cock, Jan De; Fernández-Escribano, Gerardo; Pieters, Bart; Sánchez, José L.; Claver, José M.; de Walle, Rik Van

2013-12-01

The H.264/AVC video coding standard introduces some improved tools in order to increase compression efficiency. Moreover, the multi-view extension of H.264/AVC, called H.264/MVC, adopts many of them. Among the new features, variable block-size motion estimation is one which contributes to high coding efficiency. Furthermore, it defines a different prediction structure that includes hierarchical bidirectional pictures, outperforming traditional Group of Pictures patterns in both scenarios: single-view and multi-view. However, these video coding techniques have high computational complexity. Several techniques have been proposed in the literature over the last few years which are aimed at accelerating the inter prediction process, but there are no works focusing on bidirectional prediction or hierarchical prediction. In this article, with the emergence of many-core processors or accelerators, a step forward is taken towards an implementation of an H.264/AVC and H.264/MVC inter prediction algorithm on a graphics processing unit. The results show a negligible rate distortion drop with a time reduction of up to 98% for the complete H.264/AVC encoder.
Productive High Performance Parallel Programming with Auto-tuned Domain-Specific Embedded Languages

DTIC Science & Technology

2013-01-02

Compilation JVM Java Virtual Machine KB Kilobyte KDT Knowledge Discovery Toolbox LAPACK Linear Algebra Package LLVM Low-Level Virtual Machine LOC Lines...different starting points. Leo Meyerovich also helped solidify some of the ideas here in discussions during Par Lab retreats. I would also like to thank...multi-timestep computations by blocking in both time and space. 88 Implementation Output Approx DSL Type Language Language Parallelism LoC Graphite
Boosting Contextual Information for Deep Neural Network Based Voice Activity Detection

DTIC Science & Technology

2015-02-01

multi-resolution stacking (MRS), which is a stack of ensemble classifiers. Each classifier in a building block inputs the concatenation of the predictions ...a base classifier in MRS, named boosted deep neural network (bDNN). bDNN first generates multiple base predictions from different contexts of a single...frame by only one DNN and then aggregates the base predictions for a better prediction of the frame, and it is different from computationally
Artificial Neuron Based on Integrated Semiconductor Quantum Dot Mode-Locked Lasers

NASA Astrophysics Data System (ADS)

Mesaritakis, Charis; Kapsalis, Alexandros; Bogris, Adonis; Syvridis, Dimitris

2016-12-01

Neuro-inspired implementations have attracted strong interest as a power efficient and robust alternative to the digital model of computation with a broad range of applications. Especially, neuro-mimetic systems able to produce and process spike-encoding schemes can offer merits like high noise-resiliency and increased computational efficiency. Towards this direction, integrated photonics can be an auspicious platform due to its multi-GHz bandwidth, its high wall-plug efficiency and the strong similarity of its dynamics under excitation with biological spiking neurons. Here, we propose an integrated all-optical neuron based on an InAs/InGaAs semiconductor quantum-dot passively mode-locked laser. The multi-band emission capabilities of these lasers allows, through waveband switching, the emulation of the excitation and inhibition modes of operation. Frequency-response effects, similar to biological neural circuits, are observed just as in a typical two-section excitable laser. The demonstrated optical building block can pave the way for high-speed photonic integrated systems able to address tasks ranging from pattern recognition to cognitive spectrum management and multi-sensory data processing.
Flexible feature-space-construction architecture and its VLSI implementation for multi-scale object detection

NASA Astrophysics Data System (ADS)

Luo, Aiwen; An, Fengwei; Zhang, Xiangyu; Chen, Lei; Huang, Zunkai; Jürgen Mattausch, Hans

2018-04-01

Feature extraction techniques are a cornerstone of object detection in computer-vision-based applications. The detection performance of vison-based detection systems is often degraded by, e.g., changes in the illumination intensity of the light source, foreground-background contrast variations or automatic gain control from the camera. In order to avoid such degradation effects, we present a block-based L1-norm-circuit architecture which is configurable for different image-cell sizes, cell-based feature descriptors and image resolutions according to customization parameters from the circuit input. The incorporated flexibility in both the image resolution and the cell size for multi-scale image pyramids leads to lower computational complexity and power consumption. Additionally, an object-detection prototype for performance evaluation in 65 nm CMOS implements the proposed L1-norm circuit together with a histogram of oriented gradients (HOG) descriptor and a support vector machine (SVM) classifier. The proposed parallel architecture with high hardware efficiency enables real-time processing, high detection robustness, small chip-core area as well as low power consumption for multi-scale object detection.
Artificial Neuron Based on Integrated Semiconductor Quantum Dot Mode-Locked Lasers

PubMed Central

Mesaritakis, Charis; Kapsalis, Alexandros; Bogris, Adonis; Syvridis, Dimitris

2016-01-01

Neuro-inspired implementations have attracted strong interest as a power efficient and robust alternative to the digital model of computation with a broad range of applications. Especially, neuro-mimetic systems able to produce and process spike-encoding schemes can offer merits like high noise-resiliency and increased computational efficiency. Towards this direction, integrated photonics can be an auspicious platform due to its multi-GHz bandwidth, its high wall-plug efficiency and the strong similarity of its dynamics under excitation with biological spiking neurons. Here, we propose an integrated all-optical neuron based on an InAs/InGaAs semiconductor quantum-dot passively mode-locked laser. The multi-band emission capabilities of these lasers allows, through waveband switching, the emulation of the excitation and inhibition modes of operation. Frequency-response effects, similar to biological neural circuits, are observed just as in a typical two-section excitable laser. The demonstrated optical building block can pave the way for high-speed photonic integrated systems able to address tasks ranging from pattern recognition to cognitive spectrum management and multi-sensory data processing. PMID:27991574
Market-based control strategy for long-span structures considering the multi-time delay issue

NASA Astrophysics Data System (ADS)

Li, Hongnan; Song, Jianzhu; Li, Gang

2017-01-01

To solve the different time delays that exist in the control device installed on spatial structures, in this study, discrete analysis using a 2 N precise algorithm was selected to solve the multi-time-delay issue for long-span structures based on the market-based control (MBC) method. The concept of interval mixed energy was introduced from computational structural mechanics and optimal control research areas, and it translates the design of the MBC multi-time-delay controller into a solution for the segment matrix. This approach transforms the serial algorithm in time to parallel computing in space, greatly improving the solving efficiency and numerical stability. The designed controller is able to consider the issue of time delay with a linear controlling force combination and is especially effective for large time-delay conditions. A numerical example of a long-span structure was selected to demonstrate the effectiveness of the presented controller, and the time delay was found to have a significant impact on the results.
Innovative architectures for dense multi-microprocessor computers

NASA Technical Reports Server (NTRS)

Donaldson, Thomas; Doty, Karl; Engle, Steven W.; Larson, Robert E.; O'Reilly, John G.

1988-01-01

The results of a Phase I Small Business Innovative Research (SBIR) project performed for the NASA Langley Computational Structural Mechanics Group are described. The project resulted in the identification of a family of chordal-ring interconnection architectures with excellent potential to serve as the basis for new multimicroprocessor (MMP) computers. The paper presents examples of how computational algorithms from structural mechanics can be efficiently implemented on the chordal-ring architecture.
Cathepsin S-cleavable, multi-block HPMA copolymers for improved SPECT/CT imaging of pancreatic cancer.

PubMed

Fan, Wei; Shi, Wen; Zhang, Wenting; Jia, Yinnong; Zhou, Zhengyuan; Brusnahan, Susan K; Garrison, Jered C

2016-10-01

This work continues our efforts to improve the diagnostic and radiotherapeutic effectiveness of nanomedicine platforms by developing approaches to reduce the non-target accumulation of these agents. Herein, we developed multi-block HPMA copolymers with backbones that are susceptible to cleavage by cathepsin S, a protease that is abundantly expressed in tissues of the mononuclear phagocyte system (MPS). Specifically, a bis-thiol terminated HPMA telechelic copolymer containing 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) was synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization. Three maleimide modified linkers with different sequences, including cathepsin S degradable oligopeptide, scramble oligopeptide and oligo ethylene glycol, were subsequently synthesized and used for the extension of the HPMA copolymers by thiol-maleimide click chemistry. All multi-block HPMA copolymers could be labeled by (177)Lu with high labeling efficiency and exhibited high serum stability. In vitro cleavage studies demonstrated highly selective and efficient cathepsin S mediated cleavage of the cathepsin S-susceptible multi-block HPMA copolymer. A modified multi-block HPMA copolymer series capable of Förster Resonance Energy Transfer (FRET) was utilized to investigate the rate of cleavage of the multi-block HPMA copolymers in monocyte-derived macrophages. Confocal imaging and flow cytometry studies revealed substantially higher rates of cleavage for the multi-block HPMA copolymers containing the cathepsin S-susceptible linker. The efficacy of the cathepsin S-cleavable multi-block HPMA copolymer was further examined using an in vivo model of pancreatic ductal adenocarcinoma. Based on the biodistribution and SPECT/CT studies, the copolymer extended with the cathepsin S susceptible linker exhibited significantly faster clearance and lower non-target retention without compromising tumor targeting. Overall, these results indicate that exploitation of the cathepsin S activity in MPS tissues can be utilized to substantially lower non-target accumulation, suggesting this is a promising approach for the development of diagnostic and radiotherapeutic nanomedicine platforms. Copyright © 2016 Elsevier Ltd. All rights reserved.
East Cameron Block 270, offshore Louisiana: a Pleistocene field

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

Holland, D.S.; Sutley, C.E.; Berlitz, R.E.

1976-01-01

Exploration of the Plio-Pleistocene in the Gulf of Mexico since 1970 has led to the discovery of significant hydrocarbon reserves. One of the better gas fields found to date has been the East Cameron Block 270 field, offshore Louisiana. Utilization of a coordinated exploitation plan with Schlumberger Offshore Services has allowed Pennzoil Co., as operator, to develop and put the Block 270 field on production in minimum time. The structure at Block 270 field is a north-south-trending, faulted nose at 6000 ft (1825 m). At the depth of the ''G'' sandstone (8700 ft or 2650 m), the structure is closed;more » it is elongated north-south and dips in all directions from the Block 270 area. Closure is the result of contemporaneous growth of the east-bounding regional fault. Structural and stratigraphic interpretations from dipmeters were used to determine the most favorable offset locations. The producing zones consist of various combinations of bar-like, channel-like, and distributary-front sandstones. The sediment source for most of the producing zones was southwest of the area, except for two zones which derived their sediments from the north through a system of channels paralleling the east-bounding fault. Computed logs were used to convert conventional logging measurements into a more readily usable form for evaluation. The computed results were used for reserve calculations, reservoir-quality determinations, and confirmation of depositional environments as determined from other sources.« less
Development of an Aeroelastic Modeling Capability for Transient Nozzle Side Load Analysis

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Zhao, Xiang; Zhang, Sijun; Chen, Yen-Sen

2013-01-01

Lateral nozzle forces are known to cause severe structural damage to any new rocket engine in development during test. While three-dimensional, transient, turbulent, chemically reacting computational fluid dynamics methodology has been demonstrated to capture major side load physics with rigid nozzles, hot-fire tests often show nozzle structure deformation during major side load events, leading to structural damages if structural strengthening measures were not taken. The modeling picture is incomplete without the capability to address the two-way responses between the structure and fluid. The objective of this study is to develop a coupled aeroelastic modeling capability by implementing the necessary structural dynamics component into an anchored computational fluid dynamics methodology. The computational fluid dynamics component is based on an unstructured-grid, pressure-based computational fluid dynamics formulation, while the computational structural dynamics component is developed in the framework of modal analysis. Transient aeroelastic nozzle startup analyses of the Block I Space Shuttle Main Engine at sea level were performed. The computed results from the aeroelastic nozzle modeling are presented.
Predicting multi-wall structural response to hypervelocity impact using the hull code

NASA Technical Reports Server (NTRS)

Schonberg, William P.

1993-01-01

Previously, multi-wall structures have been analyzed extensively, primarily through experiment, as a means of increasing the meteoroid/space debris impact protection of spacecraft. As structural configurations become more varied, the number of tests required to characterize their response increases dramatically. As an alternative to experimental testing, numerical modeling of high-speed impact phenomena is often being used to predict the response of a variety of structural systems under different impact loading conditions. The results of comparing experimental tests to Hull Hydrodynamic Computer Code predictions are reported. Also, the results of a numerical parametric study of multi-wall structural response to hypervelocity cylindrical projectile impact are presented.
Code Optimization Techniques

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

MAGEE,GLEN I.

Computers transfer data in a number of different ways. Whether through a serial port, a parallel port, over a modem, over an ethernet cable, or internally from a hard disk to memory, some data will be lost. To compensate for that loss, numerous error detection and correction algorithms have been developed. One of the most common error correction codes is the Reed-Solomon code, which is a special subset of BCH (Bose-Chaudhuri-Hocquenghem) linear cyclic block codes. In the AURA project, an unmanned aircraft sends the data it collects back to earth so it can be analyzed during flight and possible flightmore » modifications made. To counter possible data corruption during transmission, the data is encoded using a multi-block Reed-Solomon implementation with a possibly shortened final block. In order to maximize the amount of data transmitted, it was necessary to reduce the computation time of a Reed-Solomon encoding to three percent of the processor's time. To achieve such a reduction, many code optimization techniques were employed. This paper outlines the steps taken to reduce the processing time of a Reed-Solomon encoding and the insight into modern optimization techniques gained from the experience.« less
Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures.

PubMed

Stamatakis, Alexandros; Ott, Michael

2008-12-27

The continuous accumulation of sequence data, for example, due to novel wet-laboratory techniques such as pyrosequencing, coupled with the increasing popularity of multi-gene phylogenies and emerging multi-core processor architectures that face problems of cache congestion, poses new challenges with respect to the efficient computation of the phylogenetic maximum-likelihood (ML) function. Here, we propose two approaches that can significantly speed up likelihood computations that typically represent over 95 per cent of the computational effort conducted by current ML or Bayesian inference programs. Initially, we present a method and an appropriate data structure to efficiently compute the likelihood score on 'gappy' multi-gene alignments. By 'gappy' we denote sampling-induced gaps owing to missing sequences in individual genes (partitions), i.e. not real alignment gaps. A first proof-of-concept implementation in RAXML indicates that this approach can accelerate inferences on large and gappy alignments by approximately one order of magnitude. Moreover, we present insights and initial performance results on multi-core architectures obtained during the transition from an OpenMP-based to a Pthreads-based fine-grained parallelization of the ML function.
Effect of Configuration Pitching Motion on Twin Tail Buffet Response

NASA Technical Reports Server (NTRS)

Sheta, Essam F.; Kandil, Osama A.

1998-01-01

The effect of dynamic pitch-up motion of delta wing on twin-tail buffet response is investigated. The computational model consists of a delta wing-twin tail configuration. The computations are carried out on a dynamic multi-block grid structure. This multidisciplinary problem is solved using three sets of equations which consists of the unsteady Navier-Stokes equations, the aeroelastic equations, and the grid displacement equations. The configuration is pitched-up from zero up to 60 deg. angle of attack, and the freestream Mach number and Reynolds number are 0.3 and 1.25 million, respectively. With the twin tail fixed as rigid surfaces and with no-forced pitch-up motion, the problem is solved for the initial flow conditions. Next, the problem is solved for the twin-tail response for uncoupled bending and torsional vibrations due to the unsteady loads on the twin tail and due to the forced pitch-up motion. The dynamic pitch-up problem is also solved for the flow response with the twin tail kept rigid. The configuration is investigated for inboard position of the twin tail which corresponds to a separation distance between the twin tail of 33% wing chord. The computed results are compared with the available experimental data.

Multi-layered nanocomposite dielectrics for high density organic memory devices

NASA Astrophysics Data System (ADS)

Kang, Moonyeong; Chung, Kyungwha; Baeg, Kang-Jun; Kim, Dong Ha; Kim, Choongik

2015-01-01

We fabricated organic memory devices with metal-pentacene-insulator-silicon structure which contain double dielectric layers comprising 3D pattern of Au nanoparticles (Au NPs) and block copolymer (PS-b-P2VP). The role of Au NPs is to charge/discharge carriers upon applied voltage, while block copolymer helps to form highly ordered Au NP patterns in the dielectric layer. Double-layered nanocomposite dielectrics enhanced the charge trap density (i.e., trapped charge per unit area) by Au NPs, resulting in increase of the memory window (ΔVth).
Experiences in teaching of modeling and simulation with emphasize on equation-based and acausal modeling techniques.

PubMed

Kulhánek, Tomáš; Ježek, Filip; Mateják, Marek; Šilar, Jan; Kofránek, Jří

2015-08-01

This work introduces experiences of teaching modeling and simulation for graduate students in the field of biomedical engineering. We emphasize the acausal and object-oriented modeling technique and we have moved from teaching block-oriented tool MATLAB Simulink to acausal and object oriented Modelica language, which can express the structure of the system rather than a process of computation. However, block-oriented approach is allowed in Modelica language too and students have tendency to express the process of computation. Usage of the exemplar acausal domains and approach allows students to understand the modeled problems much deeper. The causality of the computation is derived automatically by the simulation tool.
Development of an Innovative Algorithm for Aerodynamics-Structure Interaction Using Lattice Boltzmann Method

NASA Technical Reports Server (NTRS)

Mei, Ren-Wei; Shyy, Wei; Yu, Da-Zhi; Luo, Li-Shi; Rudy, David (Technical Monitor)

2001-01-01

The lattice Boltzmann equation (LBE) is a kinetic formulation which offers an alternative computational method capable of solving fluid dynamics for various systems. Major advantages of the method are owing to the fact that the solution for the particle distribution functions is explicit, easy to implement, and the algorithm is natural to parallelize. In this final report, we summarize the works accomplished in the past three years. Since most works have been published, the technical details can be found in the literature. Brief summary will be provided in this report. In this project, a second-order accurate treatment of boundary condition in the LBE method is developed for a curved boundary and tested successfully in various 2-D and 3-D configurations. To evaluate the aerodynamic force on a body in the context of LBE method, several force evaluation schemes have been investigated. A simple momentum exchange method is shown to give reliable and accurate values for the force on a body in both 2-D and 3-D cases. Various 3-D LBE models have been assessed in terms of efficiency, accuracy, and robustness. In general, accurate 3-D results can be obtained using LBE methods. The 3-D 19-bit model is found to be the best one among the 15-bit, 19-bit, and 27-bit LBE models. To achieve desired grid resolution and to accommodate the far field boundary conditions in aerodynamics computations, a multi-block LBE method is developed by dividing the flow field into various blocks each having constant lattice spacing. Substantial contribution to the LBE method is also made through the development of a new, generalized lattice Boltzmann equation constructed in the moment space in order to improve the computational stability, detailed theoretical analysis on the stability, dispersion, and dissipation characteristics of the LBE method, and computational studies of high Reynolds number flows with singular gradients. Finally, a finite difference-based lattice Boltzmann method is developed for inviscid compressible flows.
CELES: CUDA-accelerated simulation of electromagnetic scattering by large ensembles of spheres

NASA Astrophysics Data System (ADS)

Egel, Amos; Pattelli, Lorenzo; Mazzamuto, Giacomo; Wiersma, Diederik S.; Lemmer, Uli

2017-09-01

CELES is a freely available MATLAB toolbox to simulate light scattering by many spherical particles. Aiming at high computational performance, CELES leverages block-diagonal preconditioning, a lookup-table approach to evaluate costly functions and massively parallel execution on NVIDIA graphics processing units using the CUDA computing platform. The combination of these techniques allows to efficiently address large electrodynamic problems (>104 scatterers) on inexpensive consumer hardware. In this paper, we validate near- and far-field distributions against the well-established multi-sphere T-matrix (MSTM) code and discuss the convergence behavior for ensembles of different sizes, including an exemplary system comprising 105 particles.
A rate-constrained fast full-search algorithm based on block sum pyramid.

PubMed

Song, Byung Cheol; Chun, Kang-Wook; Ra, Jong Beom

2005-03-01

This paper presents a fast full-search algorithm (FSA) for rate-constrained motion estimation. The proposed algorithm, which is based on the block sum pyramid frame structure, successively eliminates unnecessary search positions according to rate-constrained criterion. This algorithm provides the identical estimation performance to a conventional FSA having rate constraint, while achieving considerable reduction in computation.
A Tabu-Search Heuristic for Deterministic Two-Mode Blockmodeling of Binary Network Matrices.

PubMed

Brusco, Michael; Steinley, Douglas

2011-10-01

Two-mode binary data matrices arise in a variety of social network contexts, such as the attendance or non-attendance of individuals at events, the participation or lack of participation of groups in projects, and the votes of judges on cases. A popular method for analyzing such data is two-mode blockmodeling based on structural equivalence, where the goal is to identify partitions for the row and column objects such that the clusters of the row and column objects form blocks that are either complete (all 1s) or null (all 0s) to the greatest extent possible. Multiple restarts of an object relocation heuristic that seeks to minimize the number of inconsistencies (i.e., 1s in null blocks and 0s in complete blocks) with ideal block structure is the predominant approach for tackling this problem. As an alternative, we propose a fast and effective implementation of tabu search. Computational comparisons across a set of 48 large network matrices revealed that the new tabu-search heuristic always provided objective function values that were better than those of the relocation heuristic when the two methods were constrained to the same amount of computation time.
Simultaneous Multi-Scale Diffusion Estimation and Tractography Guided by Entropy Spectrum Pathways

PubMed Central

Galinsky, Vitaly L.; Frank, Lawrence R.

2015-01-01

We have developed a method for the simultaneous estimation of local diffusion and the global fiber tracts based upon the information entropy flow that computes the maximum entropy trajectories between locations and depends upon the global structure of the multi-dimensional and multi-modal diffusion field. Computation of the entropy spectrum pathways requires only solving a simple eigenvector problem for the probability distribution for which efficient numerical routines exist, and a straight forward integration of the probability conservation through ray tracing of the convective modes guided by a global structure of the entropy spectrum coupled with a small scale local diffusion. The intervoxel diffusion is sampled by multi b-shell multi q-angle DWI data expanded in spherical waves. This novel approach to fiber tracking incorporates global information about multiple fiber crossings in every individual voxel and ranks it in the most scientifically rigorous way. This method has potential significance for a wide range of applications, including studies of brain connectivity. PMID:25532167
Description and texts for the auxiliary programs for processing video information on the YeS computer. Part 3: Test program 2

NASA Technical Reports Server (NTRS)

Borisenko, V. I., G.g.; Stetsenko, Z. A.

1980-01-01

The functions were discribed and the operating instructions, the block diagram and the proposed versions are given for modifying the program in order to obtain the statistical characteristics of multi-channel video information. The program implements certain man-machine methods for investigating video information. It permits representation of the material and its statistical characteristics in a form which is convenient for the user.
Rapid construction of mechanically- confined multi- cellular structures using dendrimeric intercellular linker.

PubMed

Mo, Xuejun; Li, Qiushi; Yi Lui, Lena Wai; Zheng, Baixue; Kang, Chiang Huen; Nugraha, Bramasta; Yue, Zhilian; Jia, Rui Rui; Fu, Hong Xia; Choudhury, Deepak; Arooz, Talha; Yan, Jie; Lim, Chwee Teck; Shen, Shali; Hong Tan, Choon; Yu, Hanry

2010-10-01

Tissue constructs that mimic the in vivo cell-cell and cell-matrix interactions are especially useful for applications involving the cell- dense and matrix- poor internal organs. Rapid and precise arrangement of cells into functional tissue constructs remains a challenge in tissue engineering. We demonstrate rapid assembly of C3A cells into multi- cell structures using a dendrimeric intercellular linker. The linker is composed of oleyl- polyethylene glycol (PEG) derivatives conjugated to a 16 arms- polypropylenimine hexadecaamine (DAB) dendrimer. The positively charged multivalent dendrimer concentrates the linker onto the negatively charged cell surface to facilitate efficient insertion of the hydrophobic oleyl groups into the cellular membrane. Bringing linker- treated cells into close proximity to each other via mechanical means such as centrifugation and micromanipulation enables their rapid assembly into multi- cellular structures within minutes. The cells exhibit high levels of viability, proliferation, three- dimensional (3D) cell morphology and other functions in the constructs. We constructed defined multi- cellular structures such as rings, sheets or branching rods that can serve as potential tissue building blocks to be further assembled into complex 3D tissue constructs for biomedical applications. 2010 Elsevier Ltd. All rights reserved.
Soft hydrogel materials from elastomeric gluten-mimetic proteins

NASA Astrophysics Data System (ADS)

Bagheri, Mehran; Scott, Shane; Wan, Fan; Dick, Scott; Harden, James; Biomolecular Assemblies Team

2014-03-01

Elastomeric proteins are ubiquitous in both animal and plant tissues, where they are responsible for the elastic response and mechanical resilience of tissues. In addition to fundamental interest in the molecular origins of their elastic behaviour, this class of proteins has great potential for use in biomaterial applications. The structural and elastomeric properties of these proteins are thought to be controlled by a subtle balance between hydrophobic interactions and entropic effects, and in many cases their characteristic properties can be recapitulated by multi-block protein polymers formed from repeats of short, characteristic polypeptide motifs. We have developed biomimetic multi-block protein polymers based on variants of several elastomeric gluten consensus sequences. These proteins include constituents designed to maximize their solubility in aqueous solution and minimize the formation of extended secondary structure. Thus, they are examples of elastic intrinsically disordered proteins. In addition, the proteins have distributed tyrosine residues which allow for inter-molecular crosslinking to form hydrogel networks. In this talk, we present experimental and simulation studies of the molecular and materials properties of these proteins and their assemblies.
A novel partitioning method for block-structured adaptive meshes

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

Fu, Lin, E-mail: lin.fu@tum.de; Litvinov, Sergej, E-mail: sergej.litvinov@aer.mw.tum.de; Hu, Xiangyu Y., E-mail: xiangyu.hu@tum.de

We propose a novel partitioning method for block-structured adaptive meshes utilizing the meshless Lagrangian particle concept. With the observation that an optimum partitioning has high analogy to the relaxation of a multi-phase fluid to steady state, physically motivated model equations are developed to characterize the background mesh topology and are solved by multi-phase smoothed-particle hydrodynamics. In contrast to well established partitioning approaches, all optimization objectives are implicitly incorporated and achieved during the particle relaxation to stationary state. Distinct partitioning sub-domains are represented by colored particles and separated by a sharp interface with a surface tension model. In order to obtainmore » the particle relaxation, special viscous and skin friction models, coupled with a tailored time integration algorithm are proposed. Numerical experiments show that the present method has several important properties: generation of approximately equal-sized partitions without dependence on the mesh-element type, optimized interface communication between distinct partitioning sub-domains, continuous domain decomposition which is physically localized and implicitly incremental. Therefore it is particularly suitable for load-balancing of high-performance CFD simulations.« less
A novel partitioning method for block-structured adaptive meshes

NASA Astrophysics Data System (ADS)

Fu, Lin; Litvinov, Sergej; Hu, Xiangyu Y.; Adams, Nikolaus A.

2017-07-01

We propose a novel partitioning method for block-structured adaptive meshes utilizing the meshless Lagrangian particle concept. With the observation that an optimum partitioning has high analogy to the relaxation of a multi-phase fluid to steady state, physically motivated model equations are developed to characterize the background mesh topology and are solved by multi-phase smoothed-particle hydrodynamics. In contrast to well established partitioning approaches, all optimization objectives are implicitly incorporated and achieved during the particle relaxation to stationary state. Distinct partitioning sub-domains are represented by colored particles and separated by a sharp interface with a surface tension model. In order to obtain the particle relaxation, special viscous and skin friction models, coupled with a tailored time integration algorithm are proposed. Numerical experiments show that the present method has several important properties: generation of approximately equal-sized partitions without dependence on the mesh-element type, optimized interface communication between distinct partitioning sub-domains, continuous domain decomposition which is physically localized and implicitly incremental. Therefore it is particularly suitable for load-balancing of high-performance CFD simulations.
Utilization of a CRT display light pen in the design of feedback control systems

NASA Technical Reports Server (NTRS)

Thompson, J. G.; Young, K. R.

1972-01-01

A hierarchical structure of the interlinked programs was developed to provide a flexible computer-aided design tool. A graphical input technique and a data structure are considered which provide the capability of entering the control system model description into the computer in block diagram form. An information storage and retrieval system was developed to keep track of the system description, and analysis and simulation results, and to provide them to the correct routines for further manipulation or display. Error analysis and diagnostic capabilities are discussed, and a technique was developed to reduce a transfer function to a set of nested integrals suitable for digital simulation. A general, automated block diagram reduction procedure was set up to prepare the system description for the analysis routines.
Adaptive/learning control of large space structures - System identification techniques. [for multi-configuration flexible spacecraft

NASA Technical Reports Server (NTRS)

Thau, F. E.; Montgomery, R. C.

1980-01-01

Techniques developed for the control of aircraft under changing operating conditions are used to develop a learning control system structure for a multi-configuration, flexible space vehicle. A configuration identification subsystem that is to be used with a learning algorithm and a memory and control process subsystem is developed. Adaptive gain adjustments can be achieved by this learning approach without prestoring of large blocks of parameter data and without dither signal inputs which will be suppressed during operations for which they are not compatible. The Space Shuttle Solar Electric Propulsion (SEP) experiment is used as a sample problem for the testing of adaptive/learning control system algorithms.
Interactive communication channel

NASA Astrophysics Data System (ADS)

Chan, R. H.; Mann, M. R.; Ciarrocchi, J. A.

1985-10-01

Discussed is an interactive communications channel (ICC) for providing a digital computer with high-performance multi-channel interfaces. Sixteen full duplex channels can be serviced in the ICC with the sequence or scan pattern being programmable and dependent upon the number or channels and their speed. A channel buffer system is used for line interface, and character exchange. The channel buffer system is on a byte basis. The ICC performs frame start and frame end functions, bit stripping and bit stuffing. Data is stored in a memory in block format (256 bytes maximum) by a program control and the ICC maintains byte address information and a block byte count. Data exchange with a memory is made by cycle steals. Error detection is also provided for using a cyclic redundancy check technique.
Nesting in an Object Oriented Language is NOT for the Birds

NASA Astrophysics Data System (ADS)

Buhr, P. A.; Zarnke, C. R.

The notion of nested blocks has come into disfavour or has been ignored in recent program language design. Many of the current object oriented programming languages use subclassing as the sole mechanism to establish relationships between classes and have no general notion of nesting. We argue that nesting (and, more generally, hierarchical organization) is a powerful mechanism that provides facilities that are not otherwise possible in a class based programming language. We agree that traditional block structure and its associated nesting have severe problems, and we suggest several extensions to the notion of blocks and block structure that indirectly make nesting a useful and powerful mechanism, particularly in an object oriented programming system. The main extension is to allow references to definitions from outside of the containing block, thereby making the contained definitions available in a larger scope. References are made using either the name of the containing entity or an instance of the containing entity. The extensions suggest a way to organize the programming environment for a large, multi-user system. These facilities are not available with subclassing, and subclassing provides facilities not available by nesting; hence, an object oriented language can benefit by providing nesting as well.
Flow effects of blood constitutive equations in 3D models of vascular anomalies

NASA Astrophysics Data System (ADS)

Neofytou, Panagiotis; Tsangaris, Sokrates

2006-06-01

The effects of different blood rheological models are investigated numerically utilizing two three- dimensional (3D) models of vascular anomalies, namely a stenosis and an abdominal aortic aneurysm model. The employed CFD code incorporates the SIMPLE scheme in conjunction with the finite-volume method with collocated arrangement of variables. The approximation of the convection terms is carried out using the QUICK differencing scheme, whereas the code enables also multi-block computations, which are useful in order to cope with the two-block grid structure of the current computational domain. Three non-Newtonian models are employed, namely the Casson, Power-Law and Quemada models, which have been introduced in the past for modelling the rheological behaviour of blood and cover both the viscous as well as the two-phase character of blood. In view of the haemodynamical mechanisms related to abnormalities in the vascular network and the role of the wall shear stress in initiating and further developing of arterial diseases, the present study focuses on the 3D flow field and in particular on the distribution as well as on both low and high values of the wall shear stress in the vicinity of the anomaly. Finally, a comparison is made between the effects of each rheological model on the aforementioned parameters. Results show marked differences between simulating blood as Newtonian and non-Newtonian fluid and furthermore the Power-Law model exhibits different behaviour in all cases compared to the other models whereas Quemada and Casson models exhibit similar behaviour in the case of the stenosis but different behaviour in the case of the aneurysm.
An interactive multi-block grid generation system

NASA Technical Reports Server (NTRS)

Kao, T. J.; Su, T. Y.; Appleby, Ruth

1992-01-01

A grid generation procedure combining interactive and batch grid generation programs was put together to generate multi-block grids for complex aircraft configurations. The interactive section provides the tools for 3D geometry manipulation, surface grid extraction, boundary domain construction for 3D volume grid generation, and block-block relationships and boundary conditions for flow solvers. The procedure improves the flexibility and quality of grid generation to meet the design/analysis requirements.
A scalable parallel black oil simulator on distributed memory parallel computers

NASA Astrophysics Data System (ADS)

Wang, Kun; Liu, Hui; Chen, Zhangxin

2015-11-01

This paper presents our work on developing a parallel black oil simulator for distributed memory computers based on our in-house parallel platform. The parallel simulator is designed to overcome the performance issues of common simulators that are implemented for personal computers and workstations. The finite difference method is applied to discretize the black oil model. In addition, some advanced techniques are employed to strengthen the robustness and parallel scalability of the simulator, including an inexact Newton method, matrix decoupling methods, and algebraic multigrid methods. A new multi-stage preconditioner is proposed to accelerate the solution of linear systems from the Newton methods. Numerical experiments show that our simulator is scalable and efficient, and is capable of simulating extremely large-scale black oil problems with tens of millions of grid blocks using thousands of MPI processes on parallel computers.
Multi-equilibrium property of metabolic networks: SSI module.

PubMed

Lei, Hong-Bo; Zhang, Ji-Feng; Chen, Luonan

2011-06-20

Revealing the multi-equilibrium property of a metabolic network is a fundamental and important topic in systems biology. Due to the complexity of the metabolic network, it is generally a difficult task to study the problem as a whole from both analytical and numerical viewpoint. On the other hand, the structure-oriented modularization idea is a good choice to overcome such a difficulty, i.e. decomposing the network into several basic building blocks and then studying the whole network through investigating the dynamical characteristics of the basic building blocks and their interactions. Single substrate and single product with inhibition (SSI) metabolic module is one type of the basic building blocks of metabolic networks, and its multi-equilibrium property has important influence on that of the whole metabolic networks. In this paper, we describe what the SSI metabolic module is, characterize the rates of the metabolic reactions by Hill kinetics and give a unified model for SSI modules by using a set of nonlinear ordinary differential equations with multi-variables. Specifically, a sufficient and necessary condition is first given to describe the injectivity of a class of nonlinear systems, and then, the sufficient condition is used to study the multi-equilibrium property of SSI modules. As a main theoretical result, for the SSI modules in which each reaction has no more than one inhibitor, a sufficient condition is derived to rule out multiple equilibria, i.e. the Jacobian matrix of its rate function is nonsingular everywhere. In summary, we describe SSI modules and give a general modeling framework based on Hill kinetics, and provide a sufficient condition for ruling out multiple equilibria of a key type of SSI module.

Multi-equilibrium property of metabolic networks: SSI module

PubMed Central

2011-01-01

Background Revealing the multi-equilibrium property of a metabolic network is a fundamental and important topic in systems biology. Due to the complexity of the metabolic network, it is generally a difficult task to study the problem as a whole from both analytical and numerical viewpoint. On the other hand, the structure-oriented modularization idea is a good choice to overcome such a difficulty, i.e. decomposing the network into several basic building blocks and then studying the whole network through investigating the dynamical characteristics of the basic building blocks and their interactions. Single substrate and single product with inhibition (SSI) metabolic module is one type of the basic building blocks of metabolic networks, and its multi-equilibrium property has important influence on that of the whole metabolic networks. Results In this paper, we describe what the SSI metabolic module is, characterize the rates of the metabolic reactions by Hill kinetics and give a unified model for SSI modules by using a set of nonlinear ordinary differential equations with multi-variables. Specifically, a sufficient and necessary condition is first given to describe the injectivity of a class of nonlinear systems, and then, the sufficient condition is used to study the multi-equilibrium property of SSI modules. As a main theoretical result, for the SSI modules in which each reaction has no more than one inhibitor, a sufficient condition is derived to rule out multiple equilibria, i.e. the Jacobian matrix of its rate function is nonsingular everywhere. Conclusions In summary, we describe SSI modules and give a general modeling framework based on Hill kinetics, and provide a sufficient condition for ruling out multiple equilibria of a key type of SSI module. PMID:21689474
PETSc Users Manual Revision 3.7

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

Balay, Satish; Abhyankar, S.; Adams, M.

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication.
PETSc Users Manual Revision 3.8

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

Balay, S.; Abhyankar, S.; Adams, M.

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication.
Technique for Calculating Solution Derivatives With Respect to Geometry Parameters in a CFD Code

NASA Technical Reports Server (NTRS)

Mathur, Sanjay

2011-01-01

A solution has been developed to the challenges of computation of derivatives with respect to geometry, which is not straightforward because these are not typically direct inputs to the computational fluid dynamics (CFD) solver. To overcome these issues, a procedure has been devised that can be used without having access to the mesh generator, while still being applicable to all types of meshes. The basic approach is inspired by the mesh motion algorithms used to deform the interior mesh nodes in a smooth manner when the surface nodes, for example, are in a fluid structure interaction problem. The general idea is to model the mesh edges and nodes as constituting a spring-mass system. Changes to boundary node locations are propagated to interior nodes by allowing them to assume their new equilibrium positions, for instance, one where the forces on each node are in balance. The main advantage of the technique is that it is independent of the volumetric mesh generator, and can be applied to structured, unstructured, single- and multi-block meshes. It essentially reduces the problem down to defining the surface mesh node derivatives with respect to the geometry parameters of interest. For analytical geometries, this is quite straightforward. In the more general case, one would need to be able to interrogate the underlying parametric CAD (computer aided design) model and to evaluate the derivatives either analytically, or by a finite difference technique. Because the technique is based on a partial differential equation (PDE), it is applicable not only to forward mode problems (where derivatives of all the output quantities are computed with respect to a single input), but it could also be extended to the adjoint problem, either by using an analytical adjoint of the PDE or a discrete analog.
GPU COMPUTING FOR PARTICLE TRACKING

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

Nishimura, Hiroshi; Song, Kai; Muriki, Krishna

2011-03-25

This is a feasibility study of using a modern Graphics Processing Unit (GPU) to parallelize the accelerator particle tracking code. To demonstrate the massive parallelization features provided by GPU computing, a simplified TracyGPU program is developed for dynamic aperture calculation. Performances, issues, and challenges from introducing GPU are also discussed. General purpose Computation on Graphics Processing Units (GPGPU) bring massive parallel computing capabilities to numerical calculation. However, the unique architecture of GPU requires a comprehensive understanding of the hardware and programming model to be able to well optimize existing applications. In the field of accelerator physics, the dynamic aperture calculationmore » of a storage ring, which is often the most time consuming part of the accelerator modeling and simulation, can benefit from GPU due to its embarrassingly parallel feature, which fits well with the GPU programming model. In this paper, we use the Tesla C2050 GPU which consists of 14 multi-processois (MP) with 32 cores on each MP, therefore a total of 448 cores, to host thousands ot threads dynamically. Thread is a logical execution unit of the program on GPU. In the GPU programming model, threads are grouped into a collection of blocks Within each block, multiple threads share the same code, and up to 48 KB of shared memory. Multiple thread blocks form a grid, which is executed as a GPU kernel. A simplified code that is a subset of Tracy++ [2] is developed to demonstrate the possibility of using GPU to speed up the dynamic aperture calculation by having each thread track a particle.« less
Adaptive surrogate model based multi-objective transfer trajectory optimization between different libration points

NASA Astrophysics Data System (ADS)

Peng, Haijun; Wang, Wei

2016-10-01

An adaptive surrogate model-based multi-objective optimization strategy that combines the benefits of invariant manifolds and low-thrust control toward developing a low-computational-cost transfer trajectory between libration orbits around the L1 and L2 libration points in the Sun-Earth system has been proposed in this paper. A new structure for a multi-objective transfer trajectory optimization model that divides the transfer trajectory into several segments and gives the dominations for invariant manifolds and low-thrust control in different segments has been established. To reduce the computational cost of multi-objective transfer trajectory optimization, a mixed sampling strategy-based adaptive surrogate model has been proposed. Numerical simulations show that the results obtained from the adaptive surrogate-based multi-objective optimization are in agreement with the results obtained using direct multi-objective optimization methods, and the computational workload of the adaptive surrogate-based multi-objective optimization is only approximately 10% of that of direct multi-objective optimization. Furthermore, the generating efficiency of the Pareto points of the adaptive surrogate-based multi-objective optimization is approximately 8 times that of the direct multi-objective optimization. Therefore, the proposed adaptive surrogate-based multi-objective optimization provides obvious advantages over direct multi-objective optimization methods.
Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy

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

King, Neil P.; Sheffler, William; Sawaya, Michael R.

2015-09-17

We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method canmore » be used to design a wide variety of self-assembling protein nanomaterials.« less
A projected preconditioned conjugate gradient algorithm for computing many extreme eigenpairs of a Hermitian matrix [A projected preconditioned conjugate gradient algorithm for computing a large eigenspace of a Hermitian matrix

DOE PAGES

Vecharynski, Eugene; Yang, Chao; Pask, John E.

2015-02-25

Here, we present an iterative algorithm for computing an invariant subspace associated with the algebraically smallest eigenvalues of a large sparse or structured Hermitian matrix A. We are interested in the case in which the dimension of the invariant subspace is large (e.g., over several hundreds or thousands) even though it may still be small relative to the dimension of A. These problems arise from, for example, density functional theory (DFT) based electronic structure calculations for complex materials. The key feature of our algorithm is that it performs fewer Rayleigh–Ritz calculations compared to existing algorithms such as the locally optimalmore » block preconditioned conjugate gradient or the Davidson algorithm. It is a block algorithm, and hence can take advantage of efficient BLAS3 operations and be implemented with multiple levels of concurrency. We discuss a number of practical issues that must be addressed in order to implement the algorithm efficiently on a high performance computer.« less
Performance of a Block Structured, Hierarchical Adaptive MeshRefinement Code on the 64k Node IBM BlueGene/L Computer

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

Greenough, Jeffrey A.; de Supinski, Bronis R.; Yates, Robert K.

2005-04-25

We describe the performance of the block-structured Adaptive Mesh Refinement (AMR) code Raptor on the 32k node IBM BlueGene/L computer. This machine represents a significant step forward towards petascale computing. As such, it presents Raptor with many challenges for utilizing the hardware efficiently. In terms of performance, Raptor shows excellent weak and strong scaling when running in single level mode (no adaptivity). Hardware performance monitors show Raptor achieves an aggregate performance of 3:0 Tflops in the main integration kernel on the 32k system. Results from preliminary AMR runs on a prototype astrophysical problem demonstrate the efficiency of the current softwaremore » when running at large scale. The BG/L system is enabling a physics problem to be considered that represents a factor of 64 increase in overall size compared to the largest ones of this type computed to date. Finally, we provide a description of the development work currently underway to address our inefficiencies.« less
Heat Transfer on a Film-Cooled Blade - Effect of Hole Physics

NASA Technical Reports Server (NTRS)

Garg, Vijay K.; Rigby, David L.

1998-01-01

A multi-block, three-dimensional Navier-Stokes code has been used to study the within-hole and near-hole physics in relation to heat transfer on a film-cooled blade. The flow domain consists of the coolant flow through the plenum and hole-pipes for the three staggered rows of shower-head holes on the VK1 rotor, and the main flow over the blade. A multi-block grid is generated that is nearly orthogonal to the various surfaces. It may be noted that for the VK1 rotor the shower-head holes are inclined at 30 deg. to the spanwise direction, and are normal to the streamwise direction on the blade. Wilcox's k-omega turbulence model is used. The present study provides a much better comparison for the heat transfer coefficient at the blade mid-span with the experimental data than an earlier analysis wherein coolant velocity and temperature distributions were specified at the hole exits rather than extending the computational domain into the hole-pipe and plenum. Details of the distributions of coolant velocity, temperature, k and omega at the hole exits are also presented.
Simulation of RCC Crack Growth Due to Carbon Oxidation in High-Temperature Gas Environments

NASA Technical Reports Server (NTRS)

Titov, E. V.; Levin, D. A.; Picetti, Donald J.; Anderson, Brian P.

2009-01-01

The carbon wall oxidation technique coupled with a CFD technique was employed to study the flow in the expanding crack channel caused by the oxidation of the channel carbon walls. The recessing 3D surface morphing procedure was developed and tested in comparison with the arcjet experimental results. The multi-block structured adaptive meshing was used to model the computational domain changes due to the wall recession. Wall regression rates for a reinforced carbon-carbon (RCC) samples, that were tested in a high enthalpy arcjet environment, were computationally obtained and used to assess the channel expansion. The test geometry and flow conditions render the flow regime as the transitional to continuum, therefore Navier-Stokes gas dynamic approach with the temperature jump and velocity slip correction to the boundary conditions was used. The modeled mechanism for wall material loss was atomic oxygen reaction with bare carbon. The predicted channel growth was found to agree with arcjet observations. Local gas flow field results were found to affect the oxidation rate in a manner that cannot be predicted by previous mass loss correlations. The method holds promise for future modeling of materials gas-dynamic interactions for hypersonic flight.
Computation of multi-dimensional viscous supersonic jet flow

NASA Technical Reports Server (NTRS)

Kim, Y. N.; Buggeln, R. C.; Mcdonald, H.

1986-01-01

A new method has been developed for two- and three-dimensional computations of viscous supersonic flows with embedded subsonic regions adjacent to solid boundaries. The approach employs a reduced form of the Navier-Stokes equations which allows solution as an initial-boundary value problem in space, using an efficient noniterative forward marching algorithm. Numerical instability associated with forward marching algorithms for flows with embedded subsonic regions is avoided by approximation of the reduced form of the Navier-Stokes equations in the subsonic regions of the boundary layers. Supersonic and subsonic portions of the flow field are simultaneously calculated by a consistently split linearized block implicit computational algorithm. The results of computations for a series of test cases relevant to internal supersonic flow is presented and compared with data. Comparison between data and computation are in general excellent thus indicating that the computational technique has great promise as a tool for calculating supersonic flow with embedded subsonic regions. Finally, a User's Manual is presented for the computer code used to perform the calculations.
Reynolds-averaged Navier-Stokes based ice accretion for aircraft wings

NASA Astrophysics Data System (ADS)

Lashkajani, Kazem Hasanzadeh

This thesis addresses one of the current issues in flight safety towards increasing icing simulation capabilities for prediction of complex 2D and 3D glaze ice shapes over aircraft surfaces. During the 1980's and 1990's, the field of aero-icing was established to support design and certification of aircraft flying in icing conditions. The multidisciplinary technologies used in such codes were: aerodynamics (panel method), droplet trajectory calculations (Lagrangian framework), thermodynamic module (Messinger model) and geometry module (ice accretion). These are embedded in a quasi-steady module to simulate the time-dependent ice accretion process (multi-step procedure). The objectives of the present research are to upgrade the aerodynamic module from Laplace to Reynolds-Average Navier-Stokes equations solver. The advantages are many. First, the physical model allows accounting for viscous effects in the aerodynamic module. Second, the solution of the aero-icing module directly provides the means for characterizing the aerodynamic effects of icing, such as loss of lift and increased drag. Third, the use of a finite volume approach to solving the Partial Differential Equations allows rigorous mesh and time convergence analysis. Finally, the approaches developed in 2D can be easily transposed to 3D problems. The research was performed in three major steps, each providing insights into the overall numerical approaches. The most important realization comes from the need to develop specific mesh generation algorithms to ensure feasible solutions in very complex multi-step aero-icing calculations. The contributions are presented in chronological order of their realization. First, a new framework for RANS based two-dimensional ice accretion code, CANICE2D-NS, is developed. A multi-block RANS code from U. of Liverpool (named PMB) is providing the aerodynamic field using the Spalart-Allmaras turbulence model. The ICEM-CFD commercial tool is used for the iced airfoil remeshing and field smoothing. The new coupling is fully automated and capable of multi-step ice accretion simulations via a quasi-steady approach. In addition, the framework allows for flow analysis and aerodynamic performance prediction of the iced airfoils. The convergence of the quasi-steady algorithm is verified and identifies the need for an order of magnitude increase in the number of multi-time steps in icing simulations to achieve solver independent solutions. Second, a Multi-Block Navier-Stokes code, NSMB, is coupled with the CANICE2D icing framework. Attention is paid to the roughness implementation of the ONERA roughness model within the Spalart-Allmaras turbulence model, and to the convergence of the steady and quasi-steady iterative procedure. Effects of uniform surface roughness in quasi-steady ice accretion simulation are analyzed through different validation test cases. The results of CANICE2D-NS show good agreement with experimental data both in terms of predicted ice shapes as well as aerodynamic analysis of predicted and experimental ice shapes. Third, an efficient single-block structured Navier-Stokes CFD code, NSCODE, is coupled with the CANICE2D-NS icing framework. Attention is paid to the roughness implementation of the Boeing model within the Spalart-Allmaras turbulence model, and to acceleration of the convergence of the steady and quasi-steady iterative procedures. Effects of uniform surface roughness in quasi-steady ice accretion simulation are analyzed through different validation test cases, including code to code comparisons with the same framework coupled with the NSMB Navier-Stokes solver. The efficiency of the J-multigrid approach to solve the flow equations on complex iced geometries is demonstrated. Since it was noted in all these calculations that the ICEM-CFD grid generation package produced a number of issues such as inefficient mesh quality and smoothing deficiencies (notably grid shocks), a fourth study proposes a new mesh generation algorithm. A PDE based multi-block structured grid generation code, NSGRID, is developed for this purpose. The study includes the developments of novel mesh generation algorithms over complex glaze ice shapes containing multi-curvature ice accretion geometries, such as single/double ice horns. The twofold approaches tackle surface geometry discretization as well as field mesh generation. An adaptive curvilinear curvature control algorithm is constructed solving a 1D elliptic PDE equation with periodic source terms. This method controls the arclength grid spacing so that high convex and concave curvature regions around ice horns are appropriately captured and is shown to effectively treat the grid shock problem. Then, a novel blended method is developed by defining combinations of source terms with 2D elliptic equations. The source terms include two common control functions, Sorenson and Spekreijse, and an additional third source term to improve orthogonality. This blended method is shown to be very effective for improving grid quality metrics for complex glaze ice meshes with RANS resolution. The performance in terms of residual reduction per non-linear iteration of several solution algorithms (Point-Jacobi, Gauss-Seidel, ADI, Point and Line SOR) are discussed within the context of a full Multi-grid operator. Details are given on the various formulations used in the linearization process. It is shown that the performance of the solution algorithm depends on the type of control function used. Finally, the algorithms are validated on standard complex experimental ice shapes, demonstrating the applicability of the methods. Finally, the automated framework of RANS based two-dimensional multi-step ice accretion, CANICE2D-NS is developed, coupled with a Multi-Block Navier-Stokes CFD code, NSCODE2D, a Multi-Block elliptic grid generation code, NSGRID2D, and a Multi-Block Eulerian droplet solver, NSDROP2D (developed at Polytechnique Montreal). The framework allows Lagrangian and Eulerian droplet computations within a chimera approach treating multi-elements geometries. The code was tested on public and confidential validation test cases including standard NATO cases. In addition, up to 10 times speedup is observed in the mesh generation procedure by using the implicit line SOR and ADI smoothers within a multigrid procedure. The results demonstrate the benefits and robustness of the new framework in predicting ice shapes and aerodynamic performance parameters.
Manyscale Computing for Sensor Processing in Support of Space Situational Awareness

NASA Astrophysics Data System (ADS)

Schmalz, M.; Chapman, W.; Hayden, E.; Sahni, S.; Ranka, S.

2014-09-01

Increasing image and signal data burden associated with sensor data processing in support of space situational awareness implies continuing computational throughput growth beyond the petascale regime. In addition to growing applications data burden and diversity, the breadth, diversity and scalability of high performance computing architectures and their various organizations challenge the development of a single, unifying, practicable model of parallel computation. Therefore, models for scalable parallel processing have exploited architectural and structural idiosyncrasies, yielding potential misapplications when legacy programs are ported among such architectures. In response to this challenge, we have developed a concise, efficient computational paradigm and software called Manyscale Computing to facilitate efficient mapping of annotated application codes to heterogeneous parallel architectures. Our theory, algorithms, software, and experimental results support partitioning and scheduling of application codes for envisioned parallel architectures, in terms of work atoms that are mapped (for example) to threads or thread blocks on computational hardware. Because of the rigor, completeness, conciseness, and layered design of our manyscale approach, application-to-architecture mapping is feasible and scalable for architectures at petascales, exascales, and above. Further, our methodology is simple, relying primarily on a small set of primitive mapping operations and support routines that are readily implemented on modern parallel processors such as graphics processing units (GPUs) and hybrid multi-processors (HMPs). In this paper, we overview the opportunities and challenges of manyscale computing for image and signal processing in support of space situational awareness applications. We discuss applications in terms of a layered hardware architecture (laboratory > supercomputer > rack > processor > component hierarchy). Demonstration applications include performance analysis and results in terms of execution time as well as storage, power, and energy consumption for bus-connected and/or networked architectures. The feasibility of the manyscale paradigm is demonstrated by addressing four principal challenges: (1) architectural/structural diversity, parallelism, and locality, (2) masking of I/O and memory latencies, (3) scalability of design as well as implementation, and (4) efficient representation/expression of parallel applications. Examples will demonstrate how manyscale computing helps solve these challenges efficiently on real-world computing systems.
Frequency stability of on-orbit GPS Block-I and Block-II Navstar clocks

NASA Astrophysics Data System (ADS)

McCaskill, Thomas B.; Reid, Wilson G.; Buisson, James A.

On-orbit analysis of the Global Positioning System (GPS) Block-I and Block-II Navstar clocks has been performed by the Naval Research Laboratory using a multi-year database. The Navstar clock phase-offset measurements were computed from pseudorange measurements made by the five GPS monitor sites and from the U.S. Naval Observatory precise-time site using single or dual frequency GPS receivers. Orbital data was obtained from the Navstar broadcast ephemeris and from the best-fit, postprocessed orbital ephemerides supplied by the Naval Surface Weapons Center or by the Defense Mapping Agency. Clock performance in the time domain is characterized using frequency-stability profiles with sample times that vary from 1 to 100 days. Composite plots of Navstar frequency stability and time-prediction uncertainty are included as a summary of clock analysis results. The analysis includes plots of the clock phase offset and frequency offset histories with the eclipse seasons superimposed on selected plots to demonstrate the temperature sensitivity of one of the Block-I Navstar rubidium clocks. The potential impact on navigation and on transferring precise time of the degradation in the long-term frequency stability of the rubidium clocks is discussed.
A new routing enhancement scheme based on node blocking state advertisement in wavelength-routed WDM networks

NASA Astrophysics Data System (ADS)

Hu, Peigang; Jin, Yaohui; Zhang, Chunlei; He, Hao; Hu, WeiSheng

2005-02-01

The increasing switching capacity brings the optical node with considerable complexity. Due to the limitation in cost and technology, an optical node is often designed with partial switching capability and partial resource sharing. It means that the node is of blocking to some extent, for example multi-granularity switching node, which in fact is a structure using pass wavelength to reduce the dimension of OXC, and partial sharing wavelength converter (WC) OXC. It is conceivable that these blocking nodes will have great effects on the problem of routing and wavelength assignment. Some previous works studied the blocking case, partial WC OXC, using complicated wavelength assignment algorithm. But the complexities of these schemes decide them to be not in practice in real networks. In this paper, we propose a new scheme based on the node blocking state advertisement to reduce the retry or rerouting probability and improve the efficiency of routing in the networks with blocking nodes. In the scheme, node blocking state are advertised to the other nodes in networks, which will be used for subsequent route calculation to find a path with lowest blocking probability. The performance of the scheme is evaluated using discrete event model in 14-node NSFNET, all the nodes of which employ a kind of partial sharing WC OXC structure. In the simulation, a simple First-Fit wavelength assignment algorithm is used. The simulation results demonstrate that the new scheme considerably reduces the retry or rerouting probability in routing process.
Computational Simulation of the Formation and Material Behavior of Ice

NASA Technical Reports Server (NTRS)

Tong, Michael T.; Singhal, Surendra N.; Chamis, Christos C.

1994-01-01

Computational methods are described for simulating the formation and the material behavior of ice in prevailing transient environments. The methodology developed at the NASA Lewis Research Center was adopted. A three dimensional finite-element heat transfer analyzer was used to predict the thickness of ice formed under prevailing environmental conditions. A multi-factor interaction model for simulating the material behavior of time-variant ice layers is presented. The model, used in conjunction with laminated composite mechanics, updates the material properties of an ice block as its thickness increases with time. A sample case of ice formation in a body of water was used to demonstrate the methodology. The results showed that the formation and the material behavior of ice can be computationally simulated using the available composites technology.
Benchmarking high performance computing architectures with CMS’ skeleton framework

NASA Astrophysics Data System (ADS)

Sexton-Kennedy, E.; Gartung, P.; Jones, C. D.

2017-10-01

In 2012 CMS evaluated which underlying concurrency technology would be the best to use for its multi-threaded framework. The available technologies were evaluated on the high throughput computing systems dominating the resources in use at that time. A skeleton framework benchmarking suite that emulates the tasks performed within a CMSSW application was used to select Intel’s Thread Building Block library, based on the measured overheads in both memory and CPU on the different technologies benchmarked. In 2016 CMS will get access to high performance computing resources that use new many core architectures; machines such as Cori Phase 1&2, Theta, Mira. Because of this we have revived the 2012 benchmark to test it’s performance and conclusions on these new architectures. This talk will discuss the results of this exercise.
A new implementation of full resolution SBAS-DInSAR processing chain for the effective monitoring of structures and infrastructures

NASA Astrophysics Data System (ADS)

Bonano, Manuela; Buonanno, Sabatino; Ojha, Chandrakanta; Berardino, Paolo; Lanari, Riccardo; Zeni, Giovanni; Manunta, Michele

2017-04-01

The advanced DInSAR technique referred to as Small BAseline Subset (SBAS) algorithm has already largely demonstrated its effectiveness to carry out multi-scale and multi-platform surface deformation analyses relevant to both natural and man-made hazards. Thanks to its capability to generate displacement maps and long-term deformation time series at both regional (low resolution analysis) and local (full resolution analysis) spatial scales, it allows to get more insights on the spatial and temporal patterns of localized displacements relevant to single buildings and infrastructures over extended urban areas, with a key role in supporting risk mitigation and preservation activities. The extensive application of the multi-scale SBAS-DInSAR approach in many scientific contexts has gone hand in hand with new SAR satellite mission development, characterized by different frequency bands, spatial resolution, revisit times and ground coverage. This brought to the generation of huge DInSAR data stacks to be efficiently handled, processed and archived, with a strong impact on both the data storage and the computational requirements needed for generating the full resolution SBAS-DInSAR results. Accordingly, innovative and effective solutions for the automatic processing of massive SAR data archives and for the operational management of the derived SBAS-DInSAR products need to be designed and implemented, by exploiting the high efficiency (in terms of portability, scalability and computing performances) of the new ICT methodologies. In this work, we present a novel parallel implementation of the full resolution SBAS-DInSAR processing chain, aimed at investigating localized displacements affecting single buildings and infrastructures relevant to very large urban areas, relying on different granularity level parallelization strategies. The image granularity level is applied in most steps of the SBAS-DInSAR processing chain and exploits the multiprocessor systems with distributed memory. Moreover, in some processing steps very heavy from the computational point of view, the Graphical Processing Units (GPU) are exploited for the processing of blocks working on a pixel-by-pixel basis, requiring strong modifications on some key parts of the sequential full resolution SBAS-DInSAR processing chain. GPU processing is implemented by efficiently exploiting parallel processing architectures (as CUDA) for increasing the computing performances, in terms of optimization of the available GPU memory, as well as reduction of the Input/Output operations on the GPU and of the whole processing time for specific blocks w.r.t. the corresponding sequential implementation, particularly critical in presence of huge DInSAR datasets. Moreover, to efficiently handle the massive amount of DInSAR measurements provided by the new generation SAR constellations (CSK and Sentinel-1), we perform a proper re-design strategy aimed at the robust assimilation of the full resolution SBAS-DInSAR results into the web-based Geonode platform of the Spatial Data Infrastructure, thus allowing the efficient management, analysis and integration of the interferometric results with different data sources.
Next Generation Space Telescope Integrated Science Module Data System

NASA Technical Reports Server (NTRS)

Schnurr, Richard G.; Greenhouse, Matthew A.; Jurotich, Matthew M.; Whitley, Raymond; Kalinowski, Keith J.; Love, Bruce W.; Travis, Jeffrey W.; Long, Knox S.

1999-01-01

The Data system for the Next Generation Space Telescope (NGST) Integrated Science Module (ISIM) is the primary data interface between the spacecraft, telescope, and science instrument systems. This poster includes block diagrams of the ISIM data system and its components derived during the pre-phase A Yardstick feasibility study. The poster details the hardware and software components used to acquire and process science data for the Yardstick instrument compliment, and depicts the baseline external interfaces to science instruments and other systems. This baseline data system is a fully redundant, high performance computing system. Each redundant computer contains three 150 MHz power PC processors. All processors execute a commercially available real time multi-tasking operating system supporting, preemptive multi-tasking, file management and network interfaces. These six processors in the system are networked together. The spacecraft interface baseline is an extension of the network, which links the six processors. The final selection for Processor busses, processor chips, network interfaces, and high-speed data interfaces will be made during mid 2002.

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.
Obfuscatable multi-recipient re-encryption for secure privacy-preserving personal health record services.

PubMed

Shi, Yang; Fan, Hongfei; Xiong, Guoyue

2015-01-01

With the rapid development of cloud computing techniques, it is attractive for personal health record (PHR) service providers to deploy their PHR applications and store the personal health data in the cloud. However, there could be a serious privacy leakage if the cloud-based system is intruded by attackers, which makes it necessary for the PHR service provider to encrypt all patients' health data on cloud servers. Existing techniques are insufficiently secure under circumstances where advanced threats are considered, or being inefficient when many recipients are involved. Therefore, the objectives of our solution are (1) providing a secure implementation of re-encryption in white-box attack contexts and (2) assuring the efficiency of the implementation even in multi-recipient cases. We designed the multi-recipient re-encryption functionality by randomness-reusing and protecting the implementation by obfuscation. The proposed solution is secure even in white-box attack contexts. Furthermore, a comparison with other related work shows that the computational cost of the proposed solution is lower. The proposed technique can serve as a building block for supporting secure, efficient and privacy-preserving personal health record service systems.
Advanced Structures: 2000-2004

NASA Technical Reports Server (NTRS)

2004-01-01

This custom bibliography from the NASA Scientific and Technical Information Program lists a sampling of records found in the NASA Aeronautics and Space Database. The scope of this topic includes technologies for extremely lightweight, multi-function structures with modular interfaces - the building-block technology for advanced spacecraft. This area of focus is one of the enabling technologies as defined by NASA s Report of the President s Commission on Implementation of United States Space Exploration Policy, published in June 2004.
Software Design Strategies for Multidisciplinary Computational Fluid Dynamics

DTIC Science & Technology

2012-07-01

on the left-hand-side of Figure 3. The resulting unstructured grid system does a good job of representing the flowfield locally around the solid... Laboratory [16–19]. It uses Cartesian block structured grids, which lead to a substantially more efficient computational execution compared to the...including blade sectional lift and pitching moment. These Helios-computed airloads show good agreement with the experimental data. Many of the
Spectroscopic investigation of some building blocks of organic conductors: A comparative study

NASA Astrophysics Data System (ADS)

Mukherjee, V.; Yadav, T.

2017-04-01

Theoretical molecular structures and IR and Raman spectra of di and tetra methyl substituted tetrathiafulvalene and tetraselenafulvalene molecules have been studied. These molecules belong to the organic conductor family and are immensely used as building blocks of several organic conducting devices. The Hartree-Fock and density functional theory with exchange functional B3LYP have been employed for computational purpose. We have also performed normal coordinate analysis to scale the theoretical frequencies and to calculate potential energy distributions for the conspicuous assignments. The exciting frequency and temperature dependent Raman spectra have also presented. Optimization results reveal that the sulphur derivatives possess boat shape while selenium derivatives possess planner structures. Natural bond orbitals analysis has also been performed to study second order interaction between donors and acceptors and to compute molecular orbital occupancy and energy.
Computations of Unsteady Viscous Compressible Flows Using Adaptive Mesh Refinement in Curvilinear Body-fitted Grid Systems

NASA Technical Reports Server (NTRS)

Steinthorsson, E.; Modiano, David; Colella, Phillip

1994-01-01

A methodology for accurate and efficient simulation of unsteady, compressible flows is presented. The cornerstones of the methodology are a special discretization of the Navier-Stokes equations on structured body-fitted grid systems and an efficient solution-adaptive mesh refinement technique for structured grids. The discretization employs an explicit multidimensional upwind scheme for the inviscid fluxes and an implicit treatment of the viscous terms. The mesh refinement technique is based on the AMR algorithm of Berger and Colella. In this approach, cells on each level of refinement are organized into a small number of topologically rectangular blocks, each containing several thousand cells. The small number of blocks leads to small overhead in managing data, while their size and regular topology means that a high degree of optimization can be achieved on computers with vector processors.
UNIX: A Tool for Information Management.

ERIC Educational Resources Information Center

Frey, Dean

1989-01-01

Describes UNIX, a computer operating system that supports multi-task and multi-user operations. Characteristics that make it especially suitable for library applications are discussed, including a hierarchical file structure and utilities for text processing, database activities, and bibliographic work. Sources of information on hardware…
Multi-atlas pancreas segmentation: Atlas selection based on vessel structure.

PubMed

Karasawa, Ken'ichi; Oda, Masahiro; Kitasaka, Takayuki; Misawa, Kazunari; Fujiwara, Michitaka; Chu, Chengwen; Zheng, Guoyan; Rueckert, Daniel; Mori, Kensaku

2017-07-01

Automated organ segmentation from medical images is an indispensable component for clinical applications such as computer-aided diagnosis (CAD) and computer-assisted surgery (CAS). We utilize a multi-atlas segmentation scheme, which has recently been used in different approaches in the literature to achieve more accurate and robust segmentation of anatomical structures in computed tomography (CT) volume data. Among abdominal organs, the pancreas has large inter-patient variability in its position, size and shape. Moreover, the CT intensity of the pancreas closely resembles adjacent tissues, rendering its segmentation a challenging task. Due to this, conventional intensity-based atlas selection for pancreas segmentation often fails to select atlases that are similar in pancreas position and shape to those of the unlabeled target volume. In this paper, we propose a new atlas selection strategy based on vessel structure around the pancreatic tissue and demonstrate its application to a multi-atlas pancreas segmentation. Our method utilizes vessel structure around the pancreas to select atlases with high pancreatic resemblance to the unlabeled volume. Also, we investigate two types of applications of the vessel structure information to the atlas selection. Our segmentations were evaluated on 150 abdominal contrast-enhanced CT volumes. The experimental results showed that our approach can segment the pancreas with an average Jaccard index of 66.3% and an average Dice overlap coefficient of 78.5%. Copyright © 2017 Elsevier B.V. All rights reserved.
Application of a multi-block CFD code to investigate the impact of geometry modeling on centrifugal compressor flow field predictions

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

Hathaway, M.D.; Wood, J.R.

1997-10-01

CFD codes capable of utilizing multi-block grids provide the capability to analyze the complete geometry of centrifugal compressors. Attendant with this increased capability is potentially increased grid setup time and more computational overhead with the resultant increase in wall clock time to obtain a solution. If the increase in difficulty of obtaining a solution significantly improves the solution from that obtained by modeling the features of the tip clearance flow or the typical bluntness of a centrifugal compressor`s trailing edge, then the additional burden is worthwhile. However, if the additional information obtained is of marginal use, then modeling of certainmore » features of the geometry may provide reasonable solutions for designers to make comparative choices when pursuing a new design. In this spirit a sequence of grids were generated to study the relative importance of modeling versus detailed gridding of the tip gap and blunt trailing edge regions of the NASA large low-speed centrifugal compressor for which there is considerable detailed internal laser anemometry data available for comparison. The results indicate: (1) There is no significant difference in predicted tip clearance mass flow rate whether the tip gap is gridded or modeled. (2) Gridding rather than modeling the trailing edge results in better predictions of some flow details downstream of the impeller, but otherwise appears to offer no great benefits. (3) The pitchwise variation of absolute flow angle decreases rapidly up to 8% impeller radius ratio and much more slowly thereafter. Although some improvements in prediction of flow field details are realized as a result of analyzing the actual geometry there is no clear consensus that any of the grids investigated produced superior results in every case when compared to the measurements. However, if a multi-block code is available, it should be used, as it has the propensity for enabling better predictions than a single block code.« less
Block-diagonalization as a tool for the robust diabatization of high-dimensional potential energy surfaces

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

Venghaus, Florian; Eisfeld, Wolfgang, E-mail: wolfgang.eisfeld@uni-bielefeld.de

2016-03-21

Robust diabatization techniques are key for the development of high-dimensional coupled potential energy surfaces (PESs) to be used in multi-state quantum dynamics simulations. In the present study we demonstrate that, besides the actual diabatization technique, common problems with the underlying electronic structure calculations can be the reason why a diabatization fails. After giving a short review of the theoretical background of diabatization, we propose a method based on the block-diagonalization to analyse the electronic structure data. This analysis tool can be used in three different ways: First, it allows to detect issues with the ab initio reference data and ismore » used to optimize the setup of the electronic structure calculations. Second, the data from the block-diagonalization are utilized for the development of optimal parametrized diabatic model matrices by identifying the most significant couplings. Third, the block-diagonalization data are used to fit the parameters of the diabatic model, which yields an optimal initial guess for the non-linear fitting required by standard or more advanced energy based diabatization methods. The new approach is demonstrated by the diabatization of 9 electronic states of the propargyl radical, yielding fully coupled full-dimensional (12D) PESs in closed form.« less
Multiscale Space-Time Computational Methods for Fluid-Structure Interactions

DTIC Science & Technology

2015-09-13

prescribed fully or partially, is from an actual locust, extracted from high-speed, multi-camera video recordings of the locust in a wind tunnel . We use...With creative methods for coupling the fluid and structure, we can increase the scope and efficiency of the FSI modeling . Multiscale methods, which now...play an important role in computational mathematics, can also increase the accuracy and efficiency of the computer modeling techniques. The main
Nanoscale superstructures assembled by polymerase chain reaction (PCR): programmable construction, structural diversity, and emerging applications.

PubMed

Kuang, Hua; Ma, Wei; Xu, Liguang; Wang, Libing; Xu, Chuanlai

2013-11-19

Polymerase chain reaction (PCR) is an essential tool in biotechnology laboratories and is becoming increasingly important in other areas of research. Extensive data obtained over the last 12 years has shown that the combination of PCR with nanoscale dispersions can resolve issues in the preparation DNA-based materials that include both inorganic and organic nanoscale components. Unlike conventional DNA hybridization and antibody-antigen complexes, PCR provides a new, effective assembly platform that both increases the yield of DNA-based nanomaterials and allows researchers to program and control assembly with predesigned parameters including those assisted and automated by computers. As a result, this method allows researchers to optimize to the combinatorial selection of the DNA strands for their nanoparticle conjugates. We have developed a PCR approach for producing various nanoscale assemblies including organic motifs such as small molecules, macromolecules, and inorganic building blocks, such as nanorods (NRs), metal, semiconductor, and magnetic nanoparticles (NPs). We start with a nanoscale primer and then modify that building block using the automated steps of PCR-based assembly including initialization, denaturation, annealing, extension, final elongation, and final hold. The intermediate steps of denaturation, annealing, and extension are cyclic, and we use computer control so that the assembled superstructures reach their predetermined complexity. The structures assembled using a small number of PCR cycles show a lower polydispersity than similar discrete structures obtained by direct hybridization between the nanoscale building blocks. Using different building blocks, we assembled the following structural motifs by PCR: (1) discrete nanostructures (NP dimers, NP multimers including trimers, pyramids, tetramers or hexamers, etc.), (2) branched NP superstructures and heterochains, (3) NP satellite-like superstructures, (4) Y-shaped nanostructures and DNA networks, (5) protein-DNA co-assembly structures, and (6) DNA block copolymers including trimers and pentamers. These results affirm that this method can produce a variety of chemical structures and in yields that are tunable. Using PCR-based preparation of DNA-bridged nanostructures, we can program the assembly of the nanoscale blocks through the adjustment of the primer intensity on the assembled units, the number of PCR cycles, or both. The resulting structures are highly complex and diverse and have interesting dynamics and collective properties. Potential applications of these materials include chirooptical materials, probe fabrication, and environmental and biomedical sensors.
Integrated Design and Simulation of Tunable, Multi-State Structures Fabricated Monolithically with Multi-Material 3D Printing.

PubMed

Chen, Tian; Mueller, Jochen; Shea, Kristina

2017-03-31

Multi-material 3D printing has created new opportunities for fabricating deployable structures. We design reversible, deployable structures that are fabricated flat, have defined load bearing capacity, and multiple, predictable activated geometries. These structures are designed with a hierarchical framework where the proposed bistable actuator serves as the base building block. The actuator is designed to maximise its stroke length, with the expansion ratio approaching one when serially connected. The activation force of the actuator is parameterised through its joint material and joint length. Simulation and experimental results show that the bistability triggering force can be tuned between 0.5 and 5.0 N. Incorporating this bistable actuator, the first group of hierarchical designs demonstrate the deployment of space frame structures with a tetrahedron module consisting of three active edges, each containing four serially connected actuators. The second group shows the design of flat structures that assume either positive or negative Gaussian curvature once activated. By flipping the initial configuration of the unit actuators, structures such as a dome and an enclosure are demonstrated. A modified Dynamic Relaxation method is used to simulate all possible geometries of the hierarchical structures. Measured geometries differ by less than 5% compared to simulation results.
Integrated Design and Simulation of Tunable, Multi-State Structures Fabricated Monolithically with Multi-Material 3D Printing

PubMed Central

Chen, Tian; Mueller, Jochen; Shea, Kristina

2017-01-01

Multi-material 3D printing has created new opportunities for fabricating deployable structures. We design reversible, deployable structures that are fabricated flat, have defined load bearing capacity, and multiple, predictable activated geometries. These structures are designed with a hierarchical framework where the proposed bistable actuator serves as the base building block. The actuator is designed to maximise its stroke length, with the expansion ratio approaching one when serially connected. The activation force of the actuator is parameterised through its joint material and joint length. Simulation and experimental results show that the bistability triggering force can be tuned between 0.5 and 5.0 N. Incorporating this bistable actuator, the first group of hierarchical designs demonstrate the deployment of space frame structures with a tetrahedron module consisting of three active edges, each containing four serially connected actuators. The second group shows the design of flat structures that assume either positive or negative Gaussian curvature once activated. By flipping the initial configuration of the unit actuators, structures such as a dome and an enclosure are demonstrated. A modified Dynamic Relaxation method is used to simulate all possible geometries of the hierarchical structures. Measured geometries differ by less than 5% compared to simulation results. PMID:28361891
Random and Block Sulfonated Polyaramides as Advanced Proton Exchange Membranes

DOE PAGES

Kinsinger, Corey L.; Liu, Yuan; Liu, Feilong; ...

2015-10-09

We present here the experimental and computational characterization of two novel copolyaramide proton exchange membranes (PEMs) with higher conductivity than Nafion at relatively high temperatures, good mechanical properties, high thermal stability, and the capability to operate in low humidity conditions. The random and block copolyaramide PEMs are found to possess different ion exchange capacities (IEC) in addition to subtle structural and morphological differences, which impact the stability and conductivity of the membranes. SAXS patterns indicate the ionomer peak for the dry block copolymer resides at q = 0.1 Å –1, which increases in amplitude when initially hydrated to 25% relativemore » humidity, but then decrease in amplitude with additional hydration. This pattern is hypothesized to signal the transport of water into the polymer matrix resulting in a reduced degree of phase separation. Coupled to these morphological changes, the enhanced proton transport characteristics and structural/mechanical stability for the block copolymer are hypothesized to be primarily due to the ordered structure of ionic clusters that create connected proton transport pathways while reducing swelling upon hydration. Interestingly, the random copolymer did not possess an ionomer peak at any of the hydration levels investigated, indicating a lack of any significant ionomer structure. The random copolymer also demonstrated higher proton conductivity than the block copolymer, which is opposite to the trend normally seen in polymer membranes. However, it has reduced structural/mechanical stability as compared to the block copolymer. In conclusion, this reduction in stability is due to the random morphology formed by entanglements of polymer chains and the adverse swelling characteristics upon hydration. Therefore, the block copolymer with its enhanced proton conductivity characteristics, as compared to Nafion, and favorable structural/mechanical stability, as compared to the random copolymer, represents a viable alternative to current proton exchange membranes.« less
TOPICAL REVIEW: Smart aggregates: multi-functional sensors for concrete structures—a tutorial and a review

NASA Astrophysics Data System (ADS)

Song, Gangbing; Gu, Haichang; Mo, Yi-Lung

2008-06-01

This paper summarizes the authors' recent pioneering research work in piezoceramic-based smart aggregates and their innovative applications in concrete civil structures. The basic operating principle of smart aggregates is first introduced. The proposed smart aggregate is formed by embedding a waterproof piezoelectric patch with lead wires into a small concrete block. The proposed smart aggregates are multi-functional and can perform three major tasks: early-age concrete strength monitoring, impact detection and structural health monitoring. The proposed smart aggregates are embedded into the desired location before the casting of the concrete structure. The concrete strength development is monitored by observing the high frequency harmonic wave response of the smart aggregate. Impact on the concrete structure is detected by observing the open-circuit voltage of the piezoceramic patch in the smart aggregate. For structural health monitoring purposes, a smart aggregate-based active sensing system is designed for the concrete structure. Wavelet packet analysis is used as a signal-processing tool to analyze the sensor signal. A damage index based on the wavelet packet analysis is used to determine the structural health status. To better describe the time-history and location information of damage, two types of damage index matrices are proposed: a sensor-history damage index matrix and an actuator-sensor damage index matrix. To demonstrate the multi-functionality of the proposed smart aggregates, different types of concrete structures have been used as test objects, including concrete bridge bent-caps, concrete cylinders and a concrete frame. Experimental results have verified the effectiveness and the multi-functionality of the proposed smart aggregates. The multi-functional smart aggregates have the potential to be applied to the comprehensive monitoring of concrete structures from their earliest stages and throughout their lifetime.
An adaptive multi-moment FVM approach for incompressible flows

NASA Astrophysics Data System (ADS)

Liu, Cheng; Hu, Changhong

2018-04-01

In this study, a multi-moment finite volume method (FVM) based on block-structured adaptive Cartesian mesh is proposed for simulating incompressible flows. A conservative interpolation scheme following the idea of the constrained interpolation profile (CIP) method is proposed for the prolongation operation of the newly created mesh. A sharp immersed boundary (IB) method is used to model the immersed rigid body. A moving least squares (MLS) interpolation approach is applied for reconstruction of the velocity field around the solid surface. An efficient method for discretization of Laplacian operators on adaptive meshes is proposed. Numerical simulations on several test cases are carried out for validation of the proposed method. For the case of viscous flow past an impulsively started cylinder (Re = 3000 , 9500), the computed surface vorticity coincides with the result of the body-fitted method. For the case of a fast pitching NACA 0015 airfoil at moderate Reynolds numbers (Re = 10000 , 45000), the predicted drag coefficient (CD) and lift coefficient (CL) agree well with other numerical or experimental results. For 2D and 3D simulations of viscous flow past a pitching plate with prescribed motions (Re = 5000 , 40000), the predicted CD, CL and CM (moment coefficient) are in good agreement with those obtained by other numerical methods.
Ground Software Maintenance Facility (GSMF) system manual

NASA Technical Reports Server (NTRS)

Derrig, D.; Griffith, G.

1986-01-01

The Ground Software Maintenance Facility (GSMF) is designed to support development and maintenance of spacelab ground support software. THE GSMF consists of a Perkin Elmer 3250 (Host computer) and a MITRA 125s (ATE computer), with appropriate interface devices and software to simulate the Electrical Ground Support Equipment (EGSE). This document is presented in three sections: (1) GSMF Overview; (2) Software Structure; and (3) Fault Isolation Capability. The overview contains information on hardware and software organization along with their corresponding block diagrams. The Software Structure section describes the modes of software structure including source files, link information, and database files. The Fault Isolation section describes the capabilities of the Ground Computer Interface Device, Perkin Elmer host, and MITRA ATE.
Multiple-length-scale deformation analysis in a thermoplastic polyurethane

PubMed Central

Sui, Tan; Baimpas, Nikolaos; Dolbnya, Igor P.; Prisacariu, Cristina; Korsunsky, Alexander M.

2015-01-01

Thermoplastic polyurethane elastomers enjoy an exceptionally wide range of applications due to their remarkable versatility. These block co-polymers are used here as an example of a structurally inhomogeneous composite containing nano-scale gradients, whose internal strain differs depending on the length scale of consideration. Here we present a combined experimental and modelling approach to the hierarchical characterization of block co-polymer deformation. Synchrotron-based small- and wide-angle X-ray scattering and radiography are used for strain evaluation across the scales. Transmission electron microscopy image-based finite element modelling and fast Fourier transform analysis are used to develop a multi-phase numerical model that achieves agreement with the combined experimental data using a minimal number of adjustable structural parameters. The results highlight the importance of fuzzy interfaces, that is, regions of nanometre-scale structure and property gradients, in determining the mechanical properties of hierarchical composites across the scales. PMID:25758945
Computation of multi-dimensional viscous supersonic flow

NASA Technical Reports Server (NTRS)

Buggeln, R. C.; Kim, Y. N.; Mcdonald, H.

1986-01-01

A method has been developed for two- and three-dimensional computations of viscous supersonic jet flows interacting with an external flow. The approach employs a reduced form of the Navier-Stokes equations which allows solution as an initial-boundary value problem in space, using an efficient noniterative forward marching algorithm. Numerical instability associated with forward marching algorithms for flows with embedded subsonic regions is avoided by approximation of the reduced form of the Navier-Stokes equations in the subsonic regions of the boundary layers. Supersonic and subsonic portions of the flow field are simultaneously calculated by a consistently split linearized block implicit computational algorithm. The results of computations for a series of test cases associated with supersonic jet flow is presented and compared with other calculations for axisymmetric cases. Demonstration calculations indicate that the computational technique has great promise as a tool for calculating a wide range of supersonic flow problems including jet flow. Finally, a User's Manual is presented for the computer code used to perform the calculations.

Neuromorphic Kalman filter implementation in IBM’s TrueNorth

NASA Astrophysics Data System (ADS)

Carney, R.; Bouchard, K.; Calafiura, P.; Clark, D.; Donofrio, D.; Garcia-Sciveres, M.; Livezey, J.

2017-10-01

Following the advent of a post-Moore’s law field of computation, novel architectures continue to emerge. With composite, multi-million connection neuromorphic chips like IBM’s TrueNorth, neural engineering has now become a feasible technology in this novel computing paradigm. High Energy Physics experiments are continuously exploring new methods of computation and data handling, including neuromorphic, to support the growing challenges of the field and be prepared for future commodity computing trends. This work details the first instance of a Kalman filter implementation in IBM’s neuromorphic architecture, TrueNorth, for both parallel and serial spike trains. The implementation is tested on multiple simulated systems and its performance is evaluated with respect to an equivalent non-spiking Kalman filter. The limits of the implementation are explored whilst varying the size of weight and threshold registers, the number of spikes used to encode a state, size of neuron block for spatial encoding, and neuron potential reset schemes.
Comparison of Measured and Block Structured Simulations for the F-16XL Aircraft

NASA Technical Reports Server (NTRS)

Boelens, O. J.; Badcock, K. J.; Elmilgui, A.; Abdol-Hamid, K. S.; Massey, S. J.

2008-01-01

This article presents a comparison of the predictions of three RANS codes for flight conditions of the F-16XL aircraft which feature vortical flow. The three codes, ENSOLV, PMB and PAB3D, solve on structured multi-block grids. Flight data for comparison was available in the form of surface pressures, skin friction, boundary layer data and photographs of tufts. The three codes provided predictions which were consistent with expectations based on the turbulence modelling used, which was k- , k- with vortex corrections and an Algebraic Stress Model. The agreement with flight data was good, with the exception of the outer wing primary vortex strength. The confidence in the application of the CFD codes to complex fighter configurations increased significantly through this study.
An Informal Overview of the Unitary Group Approach

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

Sonnad, V.; Escher, J.; Kruse, M.

The Unitary Groups Approach (UGA) is an elegant and conceptually unified approach to quantum structure calculations. It has been widely used in molecular structure calculations, and holds the promise of a single computational approach to structure calculations in a variety of different fields. We explore the possibility of extending the UGA to computations in atomic and nuclear structure as a simpler alternative to traditional Racah algebra-based approaches. We provide a simple introduction to the basic UGA and consider some of the issues in using the UGA with spin-dependent, multi-body Hamiltonians requiring multi-shell bases adapted to additional symmetries. While the UGAmore » is perfectly capable of dealing with such problems, it is seen that the complexity rises dramatically, and the UGA is not at this time, a simpler alternative to Racah algebra-based approaches.« less
Nanoscale integration is the next frontier for nanotechnology

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

Picraux, Samuel T

2009-01-01

Nanoscale integration of materials and structures is the next critical step to exploit the promise of nanomaterials. Many novel and fascinating properties have been revealed for nanostructured materials. But if nanotechnology is to live up to its promise we must incorporate these nanoscale building blocks into functional systems that connect to the micro- and macroscale world. To do this we will inevitably need to understand and exploit the resulting combined unique properties of these integrated nanosystems. Much science waits to be discovered in the process. Nanoscale integration extends from the synthesis and fabrication of individual nanoscale building blocks, to themore » assembly of these building blocks into composite structures, and finally to the formation of complex functional systems. As illustrated in Figure 1, the building blocks may be homogeneous or heterogeneous, the composite materials may be nanocomposite or patterned structures, and the functional systems will involve additional combinations of materials. Nanoscale integration involves assembling diverse nanoscale materials across length scales to design and achieve new properties and functionality. At each stage size-dependent properties, the influence of surfaces in close proximity, and a multitude of interfaces all come into play. Whether the final system involves coherent electrons in a quantum computing approach, the combined flow of phonons and electrons for a high efficiency thermoelectric micro-generator, or a molecular recognition structure for bio-sensing, the combined effects of size, surface, and interface will be critical. In essence, one wants to combine the novel functions available through nanoscale science to achieve unique multi-functionalities not available in bulk materials. Perhaps the best-known example of integration is that of combining electronic components together into very large scale integrated circuits (VLSI). The integrated circuit has revolutionized electronics in many ways, from exploiting field-effect transistor devices and low power complementary logic to enable the electronic watch and hand calculator in the 1970's, to today's microprocessors and memories with billions of devices and a computational power not imagined a few decades ago. The manipulation of charges on a chip, the new concepts in combining devices for logic functions, and the new approaches to computation, information processing, and imaging have all emerged from Kilby and Noyce's simple concept of integrating devices on a single chip. Moving from hard to soft materials, a second more recent example of integration is the DNA microarray. These microarrays, with up to millions of elements in a planar array that can be optically read out, can simultaneously measure the expression of 10's of thousands of genes to study the effects of disease and treatment, or screen for single nucleotide polymorphisms for uses ranging from forensics to predisposition to disease. While still at an early stage, microarrays have revolutionized biosciences by providing the means to interrogate the complex genetic control of biological functions. Just as integrated circuits and microarrays have led to completely new functionalities and performance, the integration of nanoscale materials and structures is anticipated to lead to new performance and enable the design of new functionalities not previously envisioned. The fundamental questions underlying integration go beyond just complex fabrication or the engineering of known solutions; they lead to new discoveries and new science. The scientific challenges around nanoscale integration necessitate the development of new knowledge that is central to the advance of nanotechnology. To move forward one must address key science questions that arise in nanoscience integration and go beyond a single system or materials area. New science and discoveries especially await around three questions. How does one: (1) Control energy transfer and other interactions across interfaces and over mUltiple length scales? (2) Understand and control the interactions between nanoscale building blocks to assemble specific integrated structures? (3) Design and exploit interactions within assembled structures to achieve new properties and specific functionalities? These high level questions can serve to drive research, and to advance understanding of the complex phenomena and multifunctionality that may emerge from integration. For example, in photonics there is considerable effort to understand and control the response of nanoscale conducting structures on dielectrics, to allow one to localize, manipulate, and control electromagnetic energy in integrated systems such as in the field known as metamaterials. Essential to this area is a fundamental understanding of energy transfer across multiple length scales (question 1 above).« less
Rapid and annealing-free self-assembly of DNA building blocks for 3D hydrogel chaperoned by cationic comb-type copolymers.

PubMed

Zhang, Zheng; Wu, Yuyang; Yu, Feng; Niu, Chaoqun; Du, Zhi; Chen, Yong; Du, Jie

2017-10-01

The construction and self-assembly of DNA building blocks are the foundation of bottom-up development of three-dimensional DNA nanostructures or hydrogels. However, most self-assembly from DNA components is impeded by the mishybridized intermediates or the thermodynamic instability. To enable rapid production of complicated DNA objects with high yields no need for annealing process, herein different DNA building blocks (Y-shaped, L- and L'-shaped units) were assembled in presence of a cationic comb-type copolymer, poly (L-lysine)-graft-dextran (PLL-g-Dex), under physiological conditions. The results demonstrated that PLL-g-Dex not only significantly promoted the self-assembly of DNA blocks with high efficiency, but also stabilized the assembled multi-level structures especially for promoting the complicated 3D DNA hydrogel formation. This study develops a novel strategy for rapid and high-yield production of DNA hydrogel even derived from instable building blocks at relatively low DNA concentrations, which would endow DNA nanotechnology for more practical applications.
Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities

PubMed Central

Breuer, Marian; Rosso, Kevin M.; Blumberger, Jochen; Butt, Julea N.

2015-01-01

Multi-haem cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometres. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-haem cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-haem cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward, there are opportunities to engage multi-haem cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence, it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-haem cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-haem cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies. PMID:25411412
Spectral partitioning in equitable graphs.

PubMed

Barucca, Paolo

2017-06-01

Graph partitioning problems emerge in a wide variety of complex systems, ranging from biology to finance, but can be rigorously analyzed and solved only for a few graph ensembles. Here, an ensemble of equitable graphs, i.e., random graphs with a block-regular structure, is studied, for which analytical results can be obtained. In particular, the spectral density of this ensemble is computed exactly for a modular and bipartite structure. Kesten-McKay's law for random regular graphs is found analytically to apply also for modular and bipartite structures when blocks are homogeneous. An exact solution to graph partitioning for two equal-sized communities is proposed and verified numerically, and a conjecture on the absence of an efficient recovery detectability transition in equitable graphs is suggested. A final discussion summarizes results and outlines their relevance for the solution of graph partitioning problems in other graph ensembles, in particular for the study of detectability thresholds and resolution limits in stochastic block models.
Spectral partitioning in equitable graphs

NASA Astrophysics Data System (ADS)

Barucca, Paolo

2017-06-01

Graph partitioning problems emerge in a wide variety of complex systems, ranging from biology to finance, but can be rigorously analyzed and solved only for a few graph ensembles. Here, an ensemble of equitable graphs, i.e., random graphs with a block-regular structure, is studied, for which analytical results can be obtained. In particular, the spectral density of this ensemble is computed exactly for a modular and bipartite structure. Kesten-McKay's law for random regular graphs is found analytically to apply also for modular and bipartite structures when blocks are homogeneous. An exact solution to graph partitioning for two equal-sized communities is proposed and verified numerically, and a conjecture on the absence of an efficient recovery detectability transition in equitable graphs is suggested. A final discussion summarizes results and outlines their relevance for the solution of graph partitioning problems in other graph ensembles, in particular for the study of detectability thresholds and resolution limits in stochastic block models.
Using block pulse functions for seismic vibration semi-active control of structures with MR dampers

NASA Astrophysics Data System (ADS)

Rahimi Gendeshmin, Saeed; Davarnia, Daniel

2018-03-01

This article applied the idea of block pulse functions in the semi-active control of structures. The BP functions give effective tools to approximate complex problems. The applied control algorithm has a major effect on the performance of the controlled system and the requirements of the control devices. In control problems, it is important to devise an accurate analytical technique with less computational cost. It is proved that the BP functions are fundamental tools in approximation problems which have been applied in disparate areas in last decades. This study focuses on the employment of BP functions in control algorithm concerning reduction the computational cost. Magneto-rheological (MR) dampers are one of the well-known semi-active tools that can be used to control the response of civil Structures during earthquake. For validation purposes, numerical simulations of a 5-story shear building frame with MR dampers are presented. The results of suggested method were compared with results obtained by controlling the frame by the optimal control method based on linear quadratic regulator theory. It can be seen from simulation results that the suggested method can be helpful in reducing seismic structural responses. Besides, this method has acceptable accuracy and is in agreement with optimal control method with less computational costs.
Application of welding simulation to block joints in shipbuilding and assessment of welding-induced residual stresses and distortions

NASA Astrophysics Data System (ADS)

Fricke, Wolfgang; Zacke, Sonja

2014-06-01

During ship design, welding-induced distortions are roughly estimated as a function of the size of the component as well as the welding process and residual stresses are assumed to be locally in the range of the yield stress. Existing welding simulation methods are very complex and time-consuming and therefore not applicable to large structures like ships. Simplified methods for the estimation of welding effects were and still are subject of several research projects, but mostly concerning smaller structures. The main goal of this paper is the application of a multi-layer welding simulation to the block joint of a ship structure. When welding block joints, high constraints occur due to the ship structure which are assumed to result in accordingly high residual stresses. Constraints measured during construction were realized in a test plant for small-scale welding specimens in order to investigate their and other effects on the residual stresses. Associated welding simulations were successfully performed with fine-mesh finite element models. Further analyses showed that a courser mesh was also able to reproduce the welding-induced reaction forces and hence the residual stresses after some calibration. Based on the coarse modeling it was possible to perform the welding simulation at a block joint in order to investigate the influence of the resulting residual stresses on the behavior of the real structure, showing quite interesting stress distributions. Finally it is discussed whether smaller and idealized models of definite areas of the block joint can be used to achieve the same results offering possibilities to consider residual stresses in the design process.
Structured Problem Solving and the Basic Graphic Methods within a Total Quality Leadership Setting: Case Study

DTIC Science & Technology

1992-02-01

develop,, and maintains computer programs for the Department of the Navy. It provides life cycle support for over 50 computer programs installed at over...the computer programs . Table 4 presents a list of possible product or output measures of functionality for ACDS Block 0 programs . Examples of output...were identified as important "causes" of process performance. Functionality of the computer programs was the result or "effect" of the combination of
Progress in multi-dimensional upwind differencing

NASA Technical Reports Server (NTRS)

Vanleer, Bram

1992-01-01

Multi-dimensional upwind-differencing schemes for the Euler equations are reviewed. On the basis of the first-order upwind scheme for a one-dimensional convection equation, the two approaches to upwind differencing are discussed: the fluctuation approach and the finite-volume approach. The usual extension of the finite-volume method to the multi-dimensional Euler equations is not entirely satisfactory, because the direction of wave propagation is always assumed to be normal to the cell faces. This leads to smearing of shock and shear waves when these are not grid-aligned. Multi-directional methods, in which upwind-biased fluxes are computed in a frame aligned with a dominant wave, overcome this problem, but at the expense of robustness. The same is true for the schemes incorporating a multi-dimensional wave model not based on multi-dimensional data but on an 'educated guess' of what they could be. The fluctuation approach offers the best possibilities for the development of genuinely multi-dimensional upwind schemes. Three building blocks are needed for such schemes: a wave model, a way to achieve conservation, and a compact convection scheme. Recent advances in each of these components are discussed; putting them all together is the present focus of a worldwide research effort. Some numerical results are presented, illustrating the potential of the new multi-dimensional schemes.
Large Scale Document Inversion using a Multi-threaded Computing System

PubMed Central

Jung, Sungbo; Chang, Dar-Jen; Park, Juw Won

2018-01-01

Current microprocessor architecture is moving towards multi-core/multi-threaded systems. This trend has led to a surge of interest in using multi-threaded computing devices, such as the Graphics Processing Unit (GPU), for general purpose computing. We can utilize the GPU in computation as a massive parallel coprocessor because the GPU consists of multiple cores. The GPU is also an affordable, attractive, and user-programmable commodity. Nowadays a lot of information has been flooded into the digital domain around the world. Huge volume of data, such as digital libraries, social networking services, e-commerce product data, and reviews, etc., is produced or collected every moment with dramatic growth in size. Although the inverted index is a useful data structure that can be used for full text searches or document retrieval, a large number of documents will require a tremendous amount of time to create the index. The performance of document inversion can be improved by multi-thread or multi-core GPU. Our approach is to implement a linear-time, hash-based, single program multiple data (SPMD), document inversion algorithm on the NVIDIA GPU/CUDA programming platform utilizing the huge computational power of the GPU, to develop high performance solutions for document indexing. Our proposed parallel document inversion system shows 2-3 times faster performance than a sequential system on two different test datasets from PubMed abstract and e-commerce product reviews. CCS Concepts •Information systems➝Information retrieval • Computing methodologies➝Massively parallel and high-performance simulations. PMID:29861701
Large Scale Document Inversion using a Multi-threaded Computing System.

PubMed

Jung, Sungbo; Chang, Dar-Jen; Park, Juw Won

2017-06-01

Current microprocessor architecture is moving towards multi-core/multi-threaded systems. This trend has led to a surge of interest in using multi-threaded computing devices, such as the Graphics Processing Unit (GPU), for general purpose computing. We can utilize the GPU in computation as a massive parallel coprocessor because the GPU consists of multiple cores. The GPU is also an affordable, attractive, and user-programmable commodity. Nowadays a lot of information has been flooded into the digital domain around the world. Huge volume of data, such as digital libraries, social networking services, e-commerce product data, and reviews, etc., is produced or collected every moment with dramatic growth in size. Although the inverted index is a useful data structure that can be used for full text searches or document retrieval, a large number of documents will require a tremendous amount of time to create the index. The performance of document inversion can be improved by multi-thread or multi-core GPU. Our approach is to implement a linear-time, hash-based, single program multiple data (SPMD), document inversion algorithm on the NVIDIA GPU/CUDA programming platform utilizing the huge computational power of the GPU, to develop high performance solutions for document indexing. Our proposed parallel document inversion system shows 2-3 times faster performance than a sequential system on two different test datasets from PubMed abstract and e-commerce product reviews. •Information systems➝Information retrieval • Computing methodologies➝Massively parallel and high-performance simulations.
Vortex Generators in a Two-Dimensional, External-Compression Supersonic Inlet

NASA Technical Reports Server (NTRS)

Baydar, Ezgihan; Lu, Frank K.; Slater, John W.

2016-01-01

Vortex generators within a two-dimensional, external-compression supersonic inlet for Mach 1.6 were investigated to determine their ability to increase total pressure recovery, reduce total pressure distortion, and improve the boundary layer. The vortex generators studied included vanes and ramps. The geometric factors of the vortex generators studied included height, length, spacing, and positions upstream and downstream of the inlet terminal shock. The flow through the inlet was simulated through the computational solution of the steady-state Reynolds-averaged Navier-Stokes equations on multi-block, structured grids. The vortex generators were simulated by either gridding the geometry of the vortex generators or modeling the vortices generated by the vortex generators. The inlet performance was characterized by the inlet total pressure recovery, total pressure distortion, and incompressible shape factor of the boundary-layer at the engine face. The results suggested that downstream vanes reduced the distortion and improved the boundary layer. The height of the vortex generators had the greatest effect of the geometric factors.
The Power of the Test for Treatment Effects in Three-Level Block Randomized Designs

ERIC Educational Resources Information Center

Konstantopoulos, Spyros

2008-01-01

Experiments that involve nested structures may assign treatment conditions either to subgroups (such as classrooms) or individuals within subgroups (such as students). The design of such experiments requires knowledge of the intraclass correlation structure to compute the sample sizes necessary to achieve adequate power to detect the treatment…
Cpu/gpu Computing for AN Implicit Multi-Block Compressible Navier-Stokes Solver on Heterogeneous Platform

NASA Astrophysics Data System (ADS)

Deng, Liang; Bai, Hanli; Wang, Fang; Xu, Qingxin

2016-06-01

CPU/GPU computing allows scientists to tremendously accelerate their numerical codes. In this paper, we port and optimize a double precision alternating direction implicit (ADI) solver for three-dimensional compressible Navier-Stokes equations from our in-house Computational Fluid Dynamics (CFD) software on heterogeneous platform. First, we implement a full GPU version of the ADI solver to remove a lot of redundant data transfers between CPU and GPU, and then design two fine-grain schemes, namely “one-thread-one-point” and “one-thread-one-line”, to maximize the performance. Second, we present a dual-level parallelization scheme using the CPU/GPU collaborative model to exploit the computational resources of both multi-core CPUs and many-core GPUs within the heterogeneous platform. Finally, considering the fact that memory on a single node becomes inadequate when the simulation size grows, we present a tri-level hybrid programming pattern MPI-OpenMP-CUDA that merges fine-grain parallelism using OpenMP and CUDA threads with coarse-grain parallelism using MPI for inter-node communication. We also propose a strategy to overlap the computation with communication using the advanced features of CUDA and MPI programming. We obtain speedups of 6.0 for the ADI solver on one Tesla M2050 GPU in contrast to two Xeon X5670 CPUs. Scalability tests show that our implementation can offer significant performance improvement on heterogeneous platform.
Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction.

PubMed

Kuhn, Stefan; Egert, Björn; Neumann, Steffen; Steinbeck, Christoph

2008-09-25

Current efforts in Metabolomics, such as the Human Metabolome Project, collect structures of biological metabolites as well as data for their characterisation, such as spectra for identification of substances and measurements of their concentration. Still, only a fraction of existing metabolites and their spectral fingerprints are known. Computer-Assisted Structure Elucidation (CASE) of biological metabolites will be an important tool to leverage this lack of knowledge. Indispensable for CASE are modules to predict spectra for hypothetical structures. This paper evaluates different statistical and machine learning methods to perform predictions of proton NMR spectra based on data from our open database NMRShiftDB. A mean absolute error of 0.18 ppm was achieved for the prediction of proton NMR shifts ranging from 0 to 11 ppm. Random forest, J48 decision tree and support vector machines achieved similar overall errors. HOSE codes being a notably simple method achieved a comparatively good result of 0.17 ppm mean absolute error. NMR prediction methods applied in the course of this work delivered precise predictions which can serve as a building block for Computer-Assisted Structure Elucidation for biological metabolites.
FAST: A fully asynchronous and status-tracking pattern for geoprocessing services orchestration

NASA Astrophysics Data System (ADS)

Wu, Huayi; You, Lan; Gui, Zhipeng; Gao, Shuang; Li, Zhenqiang; Yu, Jingmin

2014-09-01

Geoprocessing service orchestration (GSO) provides a unified and flexible way to implement cross-application, long-lived, and multi-step geoprocessing service workflows by coordinating geoprocessing services collaboratively. Usually, geoprocessing services and geoprocessing service workflows are data and/or computing intensive. The intensity feature may make the execution process of a workflow time-consuming. Since it initials an execution request without blocking other interactions on the client side, an asynchronous mechanism is especially appropriate for GSO workflows. Many critical problems remain to be solved in existing asynchronous patterns for GSO including difficulties in improving performance, status tracking, and clarifying the workflow structure. These problems are a challenge when orchestrating performance efficiency, making statuses instantly available, and constructing clearly structured GSO workflows. A Fully Asynchronous and Status-Tracking (FAST) pattern that adopts asynchronous interactions throughout the whole communication tier of a workflow is proposed for GSO. The proposed FAST pattern includes a mechanism that actively pushes the latest status to clients instantly and economically. An independent proxy was designed to isolate the status tracking logic from the geoprocessing business logic, which assists the formation of a clear GSO workflow structure. A workflow was implemented in the FAST pattern to simulate the flooding process in the Poyang Lake region. Experimental results show that the proposed FAST pattern can efficiently tackle data/computing intensive geoprocessing tasks. The performance of all collaborative partners was improved due to the asynchronous mechanism throughout communication tier. A status-tracking mechanism helps users retrieve the latest running status of a GSO workflow in an efficient and instant way. The clear structure of the GSO workflow lowers the barriers for geospatial domain experts and model designers to compose asynchronous GSO workflows. Most importantly, it provides better support for locating and diagnosing potential exceptions.
Interactive Volume Exploration of Petascale Microscopy Data Streams Using a Visualization-Driven Virtual Memory Approach.

PubMed

Hadwiger, M; Beyer, J; Jeong, Won-Ki; Pfister, H

2012-12-01

This paper presents the first volume visualization system that scales to petascale volumes imaged as a continuous stream of high-resolution electron microscopy images. Our architecture scales to dense, anisotropic petascale volumes because it: (1) decouples construction of the 3D multi-resolution representation required for visualization from data acquisition, and (2) decouples sample access time during ray-casting from the size of the multi-resolution hierarchy. Our system is designed around a scalable multi-resolution virtual memory architecture that handles missing data naturally, does not pre-compute any 3D multi-resolution representation such as an octree, and can accept a constant stream of 2D image tiles from the microscopes. A novelty of our system design is that it is visualization-driven: we restrict most computations to the visible volume data. Leveraging the virtual memory architecture, missing data are detected during volume ray-casting as cache misses, which are propagated backwards for on-demand out-of-core processing. 3D blocks of volume data are only constructed from 2D microscope image tiles when they have actually been accessed during ray-casting. We extensively evaluate our system design choices with respect to scalability and performance, compare to previous best-of-breed systems, and illustrate the effectiveness of our system for real microscopy data from neuroscience.

Fast Algorithms for Structured Least Squares and Total Least Squares Problems

PubMed Central

Kalsi, Anoop; O’Leary, Dianne P.

2006-01-01

We consider the problem of solving least squares problems involving a matrix M of small displacement rank with respect to two matrices Z1 and Z2. We develop formulas for the generators of the matrix M HM in terms of the generators of M and show that the Cholesky factorization of the matrix M HM can be computed quickly if Z1 is close to unitary and Z2 is triangular and nilpotent. These conditions are satisfied for several classes of matrices, including Toeplitz, block Toeplitz, Hankel, and block Hankel, and for matrices whose blocks have such structure. Fast Cholesky factorization enables fast solution of least squares problems, total least squares problems, and regularized total least squares problems involving these classes of matrices. PMID:27274922
Fast Algorithms for Structured Least Squares and Total Least Squares Problems.

PubMed

Kalsi, Anoop; O'Leary, Dianne P

2006-01-01

We consider the problem of solving least squares problems involving a matrix M of small displacement rank with respect to two matrices Z 1 and Z 2. We develop formulas for the generators of the matrix M (H) M in terms of the generators of M and show that the Cholesky factorization of the matrix M (H) M can be computed quickly if Z 1 is close to unitary and Z 2 is triangular and nilpotent. These conditions are satisfied for several classes of matrices, including Toeplitz, block Toeplitz, Hankel, and block Hankel, and for matrices whose blocks have such structure. Fast Cholesky factorization enables fast solution of least squares problems, total least squares problems, and regularized total least squares problems involving these classes of matrices.
Parallel computer vision

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

Uhr, L.

1987-01-01

This book is written by research scientists involved in the development of massively parallel, but hierarchically structured, algorithms, architectures, and programs for image processing, pattern recognition, and computer vision. The book gives an integrated picture of the programs and algorithms that are being developed, and also of the multi-computer hardware architectures for which these systems are designed.
Parallel Adaptive Mesh Refinement Library

NASA Technical Reports Server (NTRS)

Mac-Neice, Peter; Olson, Kevin

2005-01-01

Parallel Adaptive Mesh Refinement Library (PARAMESH) is a package of Fortran 90 subroutines designed to provide a computer programmer with an easy route to extension of (1) a previously written serial code that uses a logically Cartesian structured mesh into (2) a parallel code with adaptive mesh refinement (AMR). Alternatively, in its simplest use, and with minimal effort, PARAMESH can operate as a domain-decomposition tool for users who want to parallelize their serial codes but who do not wish to utilize adaptivity. The package builds a hierarchy of sub-grids to cover the computational domain of a given application program, with spatial resolution varying to satisfy the demands of the application. The sub-grid blocks form the nodes of a tree data structure (a quad-tree in two or an oct-tree in three dimensions). Each grid block has a logically Cartesian mesh. The package supports one-, two- and three-dimensional models.
Multivariable frequency domain identification via 2-norm minimization

NASA Technical Reports Server (NTRS)

Bayard, David S.

1992-01-01

The author develops a computational approach to multivariable frequency domain identification, based on 2-norm minimization. In particular, a Gauss-Newton (GN) iteration is developed to minimize the 2-norm of the error between frequency domain data and a matrix fraction transfer function estimate. To improve the global performance of the optimization algorithm, the GN iteration is initialized using the solution to a particular sequentially reweighted least squares problem, denoted as the SK iteration. The least squares problems which arise from both the SK and GN iterations are shown to involve sparse matrices with identical block structure. A sparse matrix QR factorization method is developed to exploit the special block structure, and to efficiently compute the least squares solution. A numerical example involving the identification of a multiple-input multiple-output (MIMO) plant having 286 unknown parameters is given to illustrate the effectiveness of the algorithm.
WE-E-18A-01: Large Area Avalanche Amorphous Selenium Sensors for Low Dose X-Ray Imaging

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

Scheuermann, J; Goldan, A; Zhao, W

2014-06-15

Purpose: A large area indirect flat panel imager (FPI) with avalanche gain is being developed to achieve x-ray quantum noise limited low dose imaging. It uses a thin optical sensing layer of amorphous selenium (a-Se), known as High-Gain Avalanche Rushing Photoconductor (HARP), to detect optical photons generated from a high resolution x-ray scintillator. We will report initial results in the fabrication of a solid-state HARP structure suitable for a large area FPI. Our objective is to establish the blocking layer structures and defect suppression mechanisms that provide stable and uniform avalanche gain. Methods: Samples were fabricated as follows: (1) ITOmore » signal electrode. (2) Electron blocking layer. (3) A 15 micron layer of intrinsic a-Se. (4) Transparent hole blocking layer. (5) Multiple semitransparent bias electrodes to investigate avalanche gain uniformity over a large area. The sample was exposed to 50ps optical excitation pulses through the bias electrode. Transient time of flight (TOF) and integrated charge was measured. A charge transport simulation was developed to investigate the effects of varying blocking layer charge carrier mobility on defect suppression, avalanche gain and temporal performance. Results: Avalanche gain of ∼200 was achieved experimentally with our multi-layer HARP samples. Simulations using the experimental sensor structure produced the same magnitude of gain as a function of electric field. The simulation predicted that the high dark current at a point defect can be reduced by two orders of magnitude by blocking layer optimization which can prevent irreversible damage while normal operation remained unaffected. Conclusion: We presented the first solid state HARP structure directly scalable to a large area FPI. We have shown reproducible and uniform avalanche gain of 200. By reducing mobility of the blocking layers we can suppress defects and maintain stable avalanche. Future work will optimize the blocking layers to prevent lag and ghosting.« less
Benchmarking high performance computing architectures with CMS’ skeleton framework

DOE PAGES

Sexton-Kennedy, E.; Gartung, P.; Jones, C. D.

2017-11-23

Here, in 2012 CMS evaluated which underlying concurrency technology would be the best to use for its multi-threaded framework. The available technologies were evaluated on the high throughput computing systems dominating the resources in use at that time. A skeleton framework benchmarking suite that emulates the tasks performed within a CMSSW application was used to select Intel’s Thread Building Block library, based on the measured overheads in both memory and CPU on the different technologies benchmarked. In 2016 CMS will get access to high performance computing resources that use new many core architectures; machines such as Cori Phase 1&2, Theta,more » Mira. Because of this we have revived the 2012 benchmark to test it’s performance and conclusions on these new architectures. This talk will discuss the results of this exercise.« less
Benchmarking high performance computing architectures with CMS’ skeleton framework

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

Sexton-Kennedy, E.; Gartung, P.; Jones, C. D.

Here, in 2012 CMS evaluated which underlying concurrency technology would be the best to use for its multi-threaded framework. The available technologies were evaluated on the high throughput computing systems dominating the resources in use at that time. A skeleton framework benchmarking suite that emulates the tasks performed within a CMSSW application was used to select Intel’s Thread Building Block library, based on the measured overheads in both memory and CPU on the different technologies benchmarked. In 2016 CMS will get access to high performance computing resources that use new many core architectures; machines such as Cori Phase 1&2, Theta,more » Mira. Because of this we have revived the 2012 benchmark to test it’s performance and conclusions on these new architectures. This talk will discuss the results of this exercise.« less
Low-Dissipation Advection Schemes Designed for Large Eddy Simulations of Hypersonic Propulsion Systems

NASA Technical Reports Server (NTRS)

White, Jeffrey A.; Baurle, Robert A.; Fisher, Travis C.; Quinlan, Jesse R.; Black, William S.

2012-01-01

The 2nd-order upwind inviscid flux scheme implemented in the multi-block, structured grid, cell centered, finite volume, high-speed reacting flow code VULCAN has been modified to reduce numerical dissipation. This modification was motivated by the desire to improve the codes ability to perform large eddy simulations. The reduction in dissipation was accomplished through a hybridization of non-dissipative and dissipative discontinuity-capturing advection schemes that reduces numerical dissipation while maintaining the ability to capture shocks. A methodology for constructing hybrid-advection schemes that blends nondissipative fluxes consisting of linear combinations of divergence and product rule forms discretized using 4th-order symmetric operators, with dissipative, 3rd or 4th-order reconstruction based upwind flux schemes was developed and implemented. A series of benchmark problems with increasing spatial and fluid dynamical complexity were utilized to examine the ability of the candidate schemes to resolve and propagate structures typical of turbulent flow, their discontinuity capturing capability and their robustness. A realistic geometry typical of a high-speed propulsion system flowpath was computed using the most promising of the examined schemes and was compared with available experimental data to demonstrate simulation fidelity.
Summary of the Fourth AIAA CFD Drag Prediction Workshop

NASA Technical Reports Server (NTRS)

Vassberg, John C.; Tinoco, Edward N.; Mani, Mori; Rider, Ben; Zickuhr, Tom; Levy, David W.; Brodersen, Olaf P.; Eisfeld, Bernhard; Crippa, Simone; Wahls, Richard A.;

2010-01-01

Results from the Fourth AIAA Drag Prediction Workshop (DPW-IV) are summarized. The workshop focused on the prediction of both absolute and differential drag levels for wing-body and wing-body-horizontal-tail configurations that are representative of transonic transport air- craft. Numerical calculations are performed using industry-relevant test cases that include lift- specific flight conditions, trimmed drag polars, downwash variations, dragrises and Reynolds- number effects. Drag, lift and pitching moment predictions from numerous Reynolds-Averaged Navier-Stokes computational fluid dynamics methods are presented. Solutions are performed on structured, unstructured and hybrid grid systems. The structured-grid sets include point- matched multi-block meshes and over-set grid systems. The unstructured and hybrid grid sets are comprised of tetrahedral, pyramid, prismatic, and hexahedral elements. Effort is made to provide a high-quality and parametrically consistent family of grids for each grid type about each configuration under study. The wing-body-horizontal families are comprised of a coarse, medium and fine grid; an optional extra-fine grid augments several of the grid families. These mesh sequences are utilized to determine asymptotic grid-convergence characteristics of the solution sets, and to estimate grid-converged absolute drag levels of the wing-body-horizontal configuration using Richardson extrapolation.

Computer Science Research in Europe.

DTIC Science & Technology

1984-08-29

most attention, multi- database and its structure, and (3) the dependencies between databases Distributed Systems and multi- databases . Having...completed a multi- database Newcastle University, UK system for distributed data management, At the University of Newcastle the INRIA is now working on a real...communications re- INRIA quirements of distributed database A project called SIRIUS was estab- systems, protocols for checking the lished in 1977 at the
Molecular Building Block-Based Electronic Charges for High-Throughput Screening of Metal-Organic Frameworks for Adsorption Applications.

PubMed

Argueta, Edwin; Shaji, Jeena; Gopalan, Arun; Liao, Peilin; Snurr, Randall Q; Gómez-Gualdrón, Diego A

2018-01-09

Metal-organic frameworks (MOFs) are porous crystalline materials with attractive properties for gas separation and storage. Their remarkable tunability makes it possible to create millions of MOF variations but creates the need for fast material screening to identify promising structures. Computational high-throughput screening (HTS) is a possible solution, but its usefulness is tied to accurate predictions of MOF adsorption properties. Accurate adsorption simulations often require an accurate description of electrostatic interactions, which depend on the electronic charges of the MOF atoms. HTS-compatible methods to assign charges to MOF atoms need to accurately reproduce electrostatic potentials (ESPs) and be computationally affordable, but current methods present an unsatisfactory trade-off between computational cost and accuracy. We illustrate a method to assign charges to MOF atoms based on ab initio calculations on MOF molecular building blocks. A library of building blocks with built-in charges is thus created and used by an automated MOF construction code to create hundreds of MOFs with charges "inherited" from the constituent building blocks. The molecular building block-based (MBBB) charges are similar to REPEAT charges-which are charges that reproduce ESPs obtained from ab initio calculations on crystallographic unit cells of nanoporous crystals-and thus similar predictions of adsorption loadings, heats of adsorption, and Henry's constants are obtained with either method. The presented results indicate that the MBBB method to assign charges to MOF atoms is suitable for use in computational high-throughput screening of MOFs for applications that involve adsorption of molecules such as carbon dioxide.
Decorating multi-walled carbon nanotubes with quantum dots for construction of multi-color fluorescent nanoprobes.

PubMed

Jia, Nengqin; Lian, Qiong; Tian, Zhong; Duan, Xin; Yin, Min; Jing, Lihong; Chen, Shouhui; Shen, Hebai; Gao, Mingyuan

2010-01-29

Novel multi-color fluorescent nanoprobes were prepared by electrostatically assembling differently sized CdTe quantum dots on polyethylenimine (PEI) functionalized multi-walled carbon nanotubes (MWNTs). The structural and optical properties of the nano-assemblies (MWNTs-PEI-CdTe) were characterized by transmission electron microscopy (TEM), electron diffraction spectra (EDS), Raman spectroscopy, confocal microscopy and photoluminescence spectroscopy (PL), respectively. Electrochemical impedance spectroscopy (EIS) was also applied to investigate the electrostatic assembling among oxidized MWNTs, PEI and CdTe. Furthermore, confocal fluorescence microscopy was used to monitor the nano-assemblies' delivery into tumor cells. It was found that the nano-assemblies exhibit efficient intracellular transporting and strong intracellular tracking. These properties would make this luminescent nano-assembly an excellent building block for the construction of intracellular nanoprobes, which could hold great promise for biomedical applications.
Homogeneous-oxide stack in IGZO thin-film transistors for multi-level-cell NAND memory application

NASA Astrophysics Data System (ADS)

Ji, Hao; Wei, Yehui; Zhang, Xinlei; Jiang, Ran

2017-11-01

A nonvolatile charge-trap-flash memory that is based on amorphous indium-gallium-zinc-oxide thin film transistors was fabricated with a homogeneous-oxide structure for a multi-level-cell application. All oxide layers, i.e., tunneling layer, charge trapping layer, and blocking layer, were fabricated with Al2O3 films. The fabrication condition (including temperature and deposition method) of the charge trapping layer was different from those of the other oxide layers. This device demonstrated a considerable large memory window of 4 V between the states fully erased and programmed with the operation voltage less than 14 V. This kind of device shows a good prospect for multi-level-cell memory applications.
Homogenization-based interval analysis for structural-acoustic problem involving periodical composites and multi-scale uncertain-but-bounded parameters.

PubMed

Chen, Ning; Yu, Dejie; Xia, Baizhan; Liu, Jian; Ma, Zhengdong

2017-04-01

This paper presents a homogenization-based interval analysis method for the prediction of coupled structural-acoustic systems involving periodical composites and multi-scale uncertain-but-bounded parameters. In the structural-acoustic system, the macro plate structure is assumed to be composed of a periodically uniform microstructure. The equivalent macro material properties of the microstructure are computed using the homogenization method. By integrating the first-order Taylor expansion interval analysis method with the homogenization-based finite element method, a homogenization-based interval finite element method (HIFEM) is developed to solve a periodical composite structural-acoustic system with multi-scale uncertain-but-bounded parameters. The corresponding formulations of the HIFEM are deduced. A subinterval technique is also introduced into the HIFEM for higher accuracy. Numerical examples of a hexahedral box and an automobile passenger compartment are given to demonstrate the efficiency of the presented method for a periodical composite structural-acoustic system with multi-scale uncertain-but-bounded parameters.
Electronic Structure Calculations and Adaptation Scheme in Multi-core Computing Environments

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

Seshagiri, Lakshminarasimhan; Sosonkina, Masha; Zhang, Zhao

2009-05-20

Multi-core processing environments have become the norm in the generic computing environment and are being considered for adding an extra dimension to the execution of any application. The T2 Niagara processor is a very unique environment where it consists of eight cores having a capability of running eight threads simultaneously in each of the cores. Applications like General Atomic and Molecular Electronic Structure (GAMESS), used for ab-initio molecular quantum chemistry calculations, can be good indicators of the performance of such machines and would be a guideline for both hardware designers and application programmers. In this paper we try to benchmarkmore » the GAMESS performance on a T2 Niagara processor for a couple of molecules. We also show the suitability of using a middleware based adaptation algorithm on GAMESS on such a multi-core environment.« less
Coupled multi-disciplinary composites behavior simulation

NASA Technical Reports Server (NTRS)

Singhal, Surendra N.; Murthy, Pappu L. N.; Chamis, Christos C.

1993-01-01

The capabilities of the computer code CSTEM (Coupled Structural/Thermal/Electro-Magnetic Analysis) are discussed and demonstrated. CSTEM computationally simulates the coupled response of layered multi-material composite structures subjected to simultaneous thermal, structural, vibration, acoustic, and electromagnetic loads and includes the effect of aggressive environments. The composite material behavior and structural response is determined at its various inherent scales: constituents (fiber/matrix), ply, laminate, and structural component. The thermal and mechanical properties of the constituents are considered to be nonlinearly dependent on various parameters such as temperature and moisture. The acoustic and electromagnetic properties also include dependence on vibration and electromagnetic wave frequencies, respectively. The simulation is based on a three dimensional finite element analysis in conjunction with composite mechanics and with structural tailoring codes, and with acoustic and electromagnetic analysis methods. An aircraft engine composite fan blade is selected as a typical structural component to demonstrate the CSTEM capabilities. Results of various coupled multi-disciplinary heat transfer, structural, vibration, acoustic, and electromagnetic analyses for temperature distribution, stress and displacement response, deformed shape, vibration frequencies, mode shapes, acoustic noise, and electromagnetic reflection from the fan blade are discussed for their coupled effects in hot and humid environments. Collectively, these results demonstrate the effectiveness of the CSTEM code in capturing the coupled effects on the various responses of composite structures subjected to simultaneous multiple real-life loads.
Thermal/structural Tailoring of Engine Blades (T/SEAEBL). Theoretical Manual

NASA Technical Reports Server (NTRS)

Brown, K. W.; Clevenger, W. B.

1994-01-01

The Thermal/Structural Tailoring of Engine Blades (T/STAEBL) system is a family of computer programs executed by a control program. The T/STAEBL system performs design optimizations of cooled, hollow turbine blades and vanes. This manual describes the T/STAEBL data block structure and system organization. The approximate analysis and optimization modules are detailed, and a validation test case is provided.
Thermal/structural tailoring of engine blades (T/SEAEBL). Theoretical manual

NASA Astrophysics Data System (ADS)

Brown, K. W.; Clevenger, W. B.

1994-03-01

The Thermal/Structural Tailoring of Engine Blades (T/STAEBL) system is a family of computer programs executed by a control program. The T/STAEBL system performs design optimizations of cooled, hollow turbine blades and vanes. This manual describes the T/STAEBL data block structure and system organization. The approximate analysis and optimization modules are detailed, and a validation test case is provided.
AEROELASTIC SIMULATION TOOL FOR INFLATABLE BALLUTE AEROCAPTURE

NASA Technical Reports Server (NTRS)

Liever, P. A.; Sheta, E. F.; Habchi, S. D.

2006-01-01

A multidisciplinary analysis tool is under development for predicting the impact of aeroelastic effects on the functionality of inflatable ballute aeroassist vehicles in both the continuum and rarefied flow regimes. High-fidelity modules for continuum and rarefied aerodynamics, structural dynamics, heat transfer, and computational grid deformation are coupled in an integrated multi-physics, multi-disciplinary computing environment. This flexible and extensible approach allows the integration of state-of-the-art, stand-alone NASA and industry leading continuum and rarefied flow solvers and structural analysis codes into a computing environment in which the modules can run concurrently with synchronized data transfer. Coupled fluid-structure continuum flow demonstrations were conducted on a clamped ballute configuration. The feasibility of implementing a DSMC flow solver in the simulation framework was demonstrated, and loosely coupled rarefied flow aeroelastic demonstrations were performed. A NASA and industry technology survey identified CFD, DSMC and structural analysis codes capable of modeling non-linear shape and material response of thin-film inflated aeroshells. The simulation technology will find direct and immediate applications with NASA and industry in ongoing aerocapture technology development programs.

The Ettention software package.

PubMed

Dahmen, Tim; Marsalek, Lukas; Marniok, Nico; Turoňová, Beata; Bogachev, Sviatoslav; Trampert, Patrick; Nickels, Stefan; Slusallek, Philipp

2016-02-01

We present a novel software package for the problem "reconstruction from projections" in electron microscopy. The Ettention framework consists of a set of modular building-blocks for tomographic reconstruction algorithms. The well-known block iterative reconstruction method based on Kaczmarz algorithm is implemented using these building-blocks, including adaptations specific to electron tomography. Ettention simultaneously features (1) a modular, object-oriented software design, (2) optimized access to high-performance computing (HPC) platforms such as graphic processing units (GPU) or many-core architectures like Xeon Phi, and (3) accessibility to microscopy end-users via integration in the IMOD package and eTomo user interface. We also provide developers with a clean and well-structured application programming interface (API) that allows for extending the software easily and thus makes it an ideal platform for algorithmic research while hiding most of the technical details of high-performance computing. Copyright © 2015 Elsevier B.V. All rights reserved.
Co-crystallization phase transformations in all π-conjugated block copolymers with different main-chain moieties.

PubMed

Lee, Yi-Huan; Chen, Wei-Chih; Yang, Yi-Lung; Chiang, Chi-Ju; Yokozawa, Tsutomu; Dai, Chi-An

2014-05-21

Driven by molecular affinity and balance in the crystallization kinetics, the ability to co-crystallize dissimilar yet self-crystallizable blocks of a block copolymer (BCP) into a uniform domain may strongly affect its phase diagram. In this study, we synthesize a new series of crystalline and monodisperse all-π-conjugated poly(2,5-dihexyloxy-p-phenylene)-b-poly(3-(2-ethylhexyl)thiophene) (PPP-P3EHT) BCPs and investigate this multi-crystallization effect. Despite vastly different side-chain and main-chain structures, PPP and P3EHT blocks are able to co-crystallize into a single uniform domain comprising PPP and P3EHT main-chains with mutually interdigitated side-chains spaced in-between. With increasing P3EHT fraction, PPP-P3EHTs undergo sequential phase transitions and form hierarchical superstructures including predominately PPP nanofibrils, co-crystalline nanofibrils, a bilayer co-crystalline/pure P3EHT lamellar structure, a microphase-separated bilayer PPP-P3EHT lamellar structure, and finally P3EHT nanofibrils. In particular, the presence of the new co-crystalline lamellar structure is the manifestation of the interaction balance between self-crystallization and co-crystallization of the dissimilar polymers on the resulting nanostructure of the BCP. The current study demonstrates the co-crystallization nature of all-conjugated BCPs with different main-chain moieties and may provide new guidelines for the organization of π-conjugated BCPs for future optoelectronic applications.
Computational Methods of Studying the Binding of Toxins From Venomous Animals to Biological Ion Channels: Theory and Applications

PubMed Central

Chen, Rong; Chung, Shin-Ho

2013-01-01

The discovery of new drugs that selectively block or modulate ion channels has great potential to provide new treatments for a host of conditions. One promising avenue revolves around modifying or mimicking certain naturally occurring ion channel modulator toxins. This strategy appears to offer the prospect of designing drugs that are both potent and specific. The use of computational modeling is crucial to this endeavor, as it has the potential to provide lower cost alternatives for exploring the effects of new compounds on ion channels. In addition, computational modeling can provide structural information and theoretical understanding that is not easily derivable from experimental results. In this review, we look at the theory and computational methods that are applicable to the study of ion channel modulators. The first section provides an introduction to various theoretical concepts, including force-fields and the statistical mechanics of binding. We then look at various computational techniques available to the researcher, including molecular dynamics, Brownian dynamics, and molecular docking systems. The latter section of the review explores applications of these techniques, concentrating on pore blocker and gating modifier toxins of potassium and sodium channels. After first discussing the structural features of these channels, and their modes of block, we provide an in-depth review of past computational work that has been carried out. Finally, we discuss prospects for future developments in the field. PMID:23589832
SYSTID - A flexible tool for the analysis of communication systems.

NASA Technical Reports Server (NTRS)

Dawson, C. T.; Tranter, W. H.

1972-01-01

Description of the System Time Domain Simulation (SYSTID) computer-aided analysis program which is specifically structured for communication systems analysis. The SYSTID program is user oriented so that very little knowledge of computer techniques and very little programming ability are required for proper application. The program is designed so that the user can go from a system block diagram to an accurate simulation by simply programming a single English language statement for each block in the system. The mathematical and functional models available in the SYSTID library are presented. An example problem is given which illustrates the ease of modeling communication systems. Examples of the outputs available are presented, and proposed improvements are summarized.
Data-driven train set crash dynamics simulation

NASA Astrophysics Data System (ADS)

Tang, Zhao; Zhu, Yunrui; Nie, Yinyu; Guo, Shihui; Liu, Fengjia; Chang, Jian; Zhang, Jianjun

2017-02-01

Traditional finite element (FE) methods are arguably expensive in computation/simulation of the train crash. High computational cost limits their direct applications in investigating dynamic behaviours of an entire train set for crashworthiness design and structural optimisation. On the contrary, multi-body modelling is widely used because of its low computational cost with the trade-off in accuracy. In this study, a data-driven train crash modelling method is proposed to improve the performance of a multi-body dynamics simulation of train set crash without increasing the computational burden. This is achieved by the parallel random forest algorithm, which is a machine learning approach that extracts useful patterns of force-displacement curves and predicts a force-displacement relation in a given collision condition from a collection of offline FE simulation data on various collision conditions, namely different crash velocities in our analysis. Using the FE simulation results as a benchmark, we compared our method with traditional multi-body modelling methods and the result shows that our data-driven method improves the accuracy over traditional multi-body models in train crash simulation and runs at the same level of efficiency.
Forced pitch motion of wind turbines

NASA Astrophysics Data System (ADS)

Leble, V.; Barakos, G.

2016-09-01

The possibility of a wind turbine entering vortex ring state during pitching oscillations is explored in this paper. The aerodynamic performance of the rotor was computed using the Helicopter Multi-Block flow solver. This code solves the Navier-Stokes equations in integral form using the arbitrary Lagrangian-Eulerian formulation for time-dependent domains with moving boundaries. A 10-MW wind turbine was put to perform yawing and pitching oscillations suggesting the partial vortex ring state during pitching motion. The results also show the strong effect of the frequency and amplitude of oscillations on the wind turbine performance.
Initial Mechanical Testing of Superalloy Lattice Block Structures Conducted

NASA Technical Reports Server (NTRS)

Krause, David L.; Whittenberger, J. Daniel

2002-01-01

The first mechanical tests of superalloy lattice block structures produced promising results for this exciting new lightweight material system. The testing was performed in-house at NASA Glenn Research Center's Structural Benchmark Test Facility, where small subelement-sized compression and beam specimens were loaded to observe elastic and plastic behavior, component strength levels, and fatigue resistance for hundreds of thousands of load cycles. Current lattice block construction produces a flat panel composed of thin ligaments arranged in a three-dimensional triangulated trusslike structure. Investment casting of lattice block panels has been developed and greatly expands opportunities for using this unique architecture in today's high-performance structures. In addition, advances made in NASA's Ultra-Efficient Engine Technology Program have extended the lattice block concept to superalloy materials. After a series of casting iterations, the nickel-based superalloy Inconel 718 (IN 718, Inco Alloys International, Inc., Huntington, WV) was successfully cast into lattice block panels; this combination offers light weight combined with high strength, high stiffness, and elevated-temperature durability. For tests to evaluate casting quality and configuration merit, small structural compression and bend test specimens were machined from the 5- by 12- by 0.5-in. panels. Linear elastic finite element analyses were completed for several specimen layouts to predict material stresses and deflections under proposed test conditions. The structural specimens were then subjected to room-temperature static and cyclic loads in Glenn's Life Prediction Branch's material test machine. Surprisingly, the test results exceeded analytical predictions: plastic strains greater than 5 percent were obtained, and fatigue lives did not depreciate relative to the base material. These assets were due to the formation of plastic hinges and the redundancies inherent in lattice block construction, which were not considered in the simplified computer models. The fatigue testing proved the value of redundancies since specimen strength was maintained even after the fracture of one or two ligaments. This ongoing test program is planned to continue through high-temperature testing. Also scheduled for testing are IN 718 lattice block panels with integral face sheets, as well as specimens cast from a higher temperature alloy. The initial testing suggests the value of this technology for large panels under low and moderate pressure loadings and for high-risk, damage-tolerant structures. Potential aeropropulsion uses for lattice blocks include turbine-engine actuated panels, exhaust nozzle flaps, and side panel structures.
TopMaker: A Technique for Automatic Multi-Block Topology Generation Using the Medial Axis

NASA Technical Reports Server (NTRS)

Heidmann, James D. (Technical Monitor); Rigby, David L.

2004-01-01

A two-dimensional multi-block topology generation technique has been developed. Very general configurations are addressable by the technique. A configuration is defined by a collection of non-intersecting closed curves, which will be referred to as loops. More than a single loop implies that holes exist in the domain, which poses no problem. This technique requires only the medial vertices and the touch points that define each vertex. From the information about the medial vertices, the connectivity between medial vertices is generated. The physical shape of the medial edge is not required. By applying a few simple rules to each medial edge, the multiblock topology is generated with no user intervention required. The resulting topologies contain only the level of complexity dictated by the configurations. Grid lines remain attached to the boundary except at sharp concave turns where a change in index family is introduced as would be desired. Keeping grid lines attached to the boundary is especially important in the area of computational fluid dynamics where highly clustered grids are used near no-slip boundaries. This technique is simple and robust and can easily be incorporated into the overall grid generation process.
Improved characterization, monitoring and instability assessment of high rock faces by integrating TLS and GB-InSAR

NASA Astrophysics Data System (ADS)

Bianchetti, Matteo; Agliardi, Federico; Villa, Alberto; Battista Crosta, Giovanni; Rivolta, Carlo

2015-04-01

Rockfall risk analysis require quantifying rockfall onset susceptibility and magnitude scenarios at source areas, and the expected rockfall trajectories and related dynamic quantities. Analysis efforts usually focus on the rockfall runout component, whereas rock mass characterization and block size distribution quantification, monitoring and analysis of unstable rock volumes are usually performed using simplified approaches, due to technological and site-specific issues. Nevertheless, proper quantification of rock slope stability and rockfall magnitude scenarios is key when dealing with high rock walls, where widespread rockfall sources and high variability of release mechanisms and block volumes can result in excessive modelling uncertainties and poorly constrained mitigation measures. We explored the potential of integrating field, remote sensing, structural analysis and stability modelling techniques to improve hazard assessment at the Gallivaggio sanctuary site, a XVI century heritage located along the State Road 36 in the Spluga Valley (Italian Central Alps). The site is impended by a subvertical cliff up to 600 m high, made of granitic orthogneiss of the Truzzo granitic complex (Tambo Nappe, upper Pennidic domain). The rock mass is cut by NNW and NW-trending slope-scale structural lineaments and by 5-6 fracture sets with variable spatial distribution, spacing and persistence, which bound blocks up to tens of cubic meters and control the 3D slope morphology. The area is characterised by widespread rock slope instability from rockfalls to massive failures. Although a 180 m long embankment was built to protect the site from rockfalls, concerns remain about potential large unstable rock volumes or flyrocks projected by the widely observed impact fragmentation of stiff rock blocks. Thus, the authority in charge started a series of periodical GB-InSAR monitoring surveys using LiSALabTM technology (12 surveys in 2011-2014), which outlined the occurrence of unstable spots spread over the cliff, with cm-scale cumulative displacements in the observation period. To support the interpretation and analysis of these data, we carried out multitemporal TLS surveys (5 sessions between September 2012 and October 2014) using a Riegl VZ-1000 long-range laser scanner. We performed rock mass structural analyses on dense TLS point clouds using two different approaches: 1) manual discontinuity orientation and intensity measurement from digital outcrops; 2) automatic feature extraction and intensity evaluation through the development of an original Matlab tool, suited for multi-scale applications and optimized for parallel computing. Results were validated using field discontinuity measurements and compared to evaluate advantages and limitations of different approaches, and allowed: 1) outlining the precise location, geometry and kinematics of unstable blocks and block clusters corresponding to radar moving spots; 2) performing stability analyses; 3) quantifying rockwall changes over the observation period. Our analysis provided a robust spatial characterization of rockfall sources, block size distribution and onset susceptibility as input for 3D runout modelling and quantitative risk analysis.
Inviscid and viscous flow modelling of complex aircraft configurations using the CFD simulation system sauna

NASA Astrophysics Data System (ADS)

Peace, Andrew J.; May, Nicholas E.; Pocock, Mark F.; Shaw, Jonathon A.

1994-04-01

This paper is concerned with the flow modelling capabilities of an advanced CFD simulation system known by the acronym SAUNA. This system is aimed primarily at complex aircraft configurations and possesses a unique grid generation strategy in its use of block-structured, unstructured or hybrid grids, depending on the geometric complexity of the addressed configuration. The main focus of the paper is in demonstrating the recently developed multi-grid, block-structured grid, viscous flow capability of SAUNA, through its evaluation on a number of configurations. Inviscid predictions are also presented, both as a means of interpreting the viscous results and with a view to showing more completely the capabilities of SAUNA. It is shown that accuracy and flexibility are combined in an efficient manner, thus demonstrating the value of SAUNA in aerodynamic design.
A General Sparse Tensor Framework for Electronic Structure Theory

DOE PAGES

Manzer, Samuel; Epifanovsky, Evgeny; Krylov, Anna I.; ...

2017-01-24

Linear-scaling algorithms must be developed in order to extend the domain of applicability of electronic structure theory to molecules of any desired size. But, the increasing complexity of modern linear-scaling methods makes code development and maintenance a significant challenge. A major contributor to this difficulty is the lack of robust software abstractions for handling block-sparse tensor operations. We therefore report the development of a highly efficient symbolic block-sparse tensor library in order to provide access to high-level software constructs to treat such problems. Our implementation supports arbitrary multi-dimensional sparsity in all input and output tensors. We then avoid cumbersome machine-generatedmore » code by implementing all functionality as a high-level symbolic C++ language library and demonstrate that our implementation attains very high performance for linear-scaling sparse tensor contractions.« less
Multi-heme Cytochromes in Shewanella oneidensis MR-1: Structures, functions and opportunities

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

Breuer, Marian; Rosso, Kevin M.; Blumberger, Jochen

Multi-heme cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometers. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-heme cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-heme cytochromes have attracted much interest and contributed to advances inmore » bioenergy applications and bioremediation of contaminated soils. Looking forward there are opportunities to engage multi-heme cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-heme cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-heme cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.« less
Multi-stage decoding for multi-level block modulation codes

NASA Technical Reports Server (NTRS)

Lin, Shu; Kasami, Tadao

1991-01-01

Various types of multistage decoding for multilevel block modulation codes, in which the decoding of a component code at each stage can be either soft decision or hard decision, maximum likelihood or bounded distance are discussed. Error performance for codes is analyzed for a memoryless additive channel based on various types of multi-stage decoding, and upper bounds on the probability of an incorrect decoding are derived. It was found that, if component codes of a multi-level modulation code and types of decoding at various stages are chosen properly, high spectral efficiency and large coding gain can be achieved with reduced decoding complexity. It was found that the difference in performance between the suboptimum multi-stage soft decision maximum likelihood decoding of a modulation code and the single stage optimum decoding of the overall code is very small, only a fraction of dB loss in SNR at the probability of an incorrect decoding for a block of 10(exp -6). Multi-stage decoding of multi-level modulation codes really offers a way to achieve the best of three worlds, bandwidth efficiency, coding gain, and decoding complexity.
ABINIT: Plane-Wave-Based Density-Functional Theory on High Performance Computers

NASA Astrophysics Data System (ADS)

Torrent, Marc

2014-03-01

For several years, a continuous effort has been produced to adapt electronic structure codes based on Density-Functional Theory to the future computing architectures. Among these codes, ABINIT is based on a plane-wave description of the wave functions which allows to treat systems of any kind. Porting such a code on petascale architectures pose difficulties related to the many-body nature of the DFT equations. To improve the performances of ABINIT - especially for what concerns standard LDA/GGA ground-state and response-function calculations - several strategies have been followed: A full multi-level parallelisation MPI scheme has been implemented, exploiting all possible levels and distributing both computation and memory. It allows to increase the number of distributed processes and could not be achieved without a strong restructuring of the code. The core algorithm used to solve the eigen problem (``Locally Optimal Blocked Congugate Gradient''), a Blocked-Davidson-like algorithm, is based on a distribution of processes combining plane-waves and bands. In addition to the distributed memory parallelization, a full hybrid scheme has been implemented, using standard shared-memory directives (openMP/openACC) or porting some comsuming code sections to Graphics Processing Units (GPU). As no simple performance model exists, the complexity of use has been increased; the code efficiency strongly depends on the distribution of processes among the numerous levels. ABINIT is able to predict the performances of several process distributions and automatically choose the most favourable one. On the other hand, a big effort has been carried out to analyse the performances of the code on petascale architectures, showing which sections of codes have to be improved; they all are related to Matrix Algebra (diagonalisation, orthogonalisation). The different strategies employed to improve the code scalability will be described. They are based on an exploration of new diagonalization algorithm, as well as the use of external optimized librairies. Part of this work has been supported by the european Prace project (PaRtnership for Advanced Computing in Europe) in the framework of its workpackage 8.
The multi-disciplinary design study: A life cycle cost algorithm

NASA Technical Reports Server (NTRS)

Harding, R. R.; Pichi, F. J.

1988-01-01

The approach and results of a Life Cycle Cost (LCC) analysis of the Space Station Solar Dynamic Power Subsystem (SDPS) including gimbal pointing and power output performance are documented. The Multi-Discipline Design Tool (MDDT) computer program developed during the 1986 study has been modified to include the design, performance, and cost algorithms for the SDPS as described. As with the Space Station structural and control subsystems, the LCC of the SDPS can be computed within the MDDT program as a function of the engineering design variables. Two simple examples of MDDT's capability to evaluate cost sensitivity and design based on LCC are included. MDDT was designed to accept NASA's IMAT computer program data as input so that IMAT's detailed structural and controls design capability can be assessed with expected system LCC as computed by MDDT. No changes to IMAT were required. Detailed knowledge of IMAT is not required to perform the LCC analyses as the interface with IMAT is noninteractive.
Regularized Generalized Canonical Correlation Analysis

ERIC Educational Resources Information Center

Tenenhaus, Arthur; Tenenhaus, Michel

2011-01-01

Regularized generalized canonical correlation analysis (RGCCA) is a generalization of regularized canonical correlation analysis to three or more sets of variables. It constitutes a general framework for many multi-block data analysis methods. It combines the power of multi-block data analysis methods (maximization of well identified criteria) and…
SEAWAT: A Computer Program for Simulation of Variable-Density Groundwater Flow and Multi-Species Solute and Heat Transport

USGS Publications Warehouse

Langevin, Christian D.

2009-01-01

SEAWAT is a MODFLOW-based computer program designed to simulate variable-density groundwater flow coupled with multi-species solute and heat transport. The program has been used for a wide variety of groundwater studies including saltwater intrusion in coastal aquifers, aquifer storage and recovery in brackish limestone aquifers, and brine migration within continental aquifers. SEAWAT is relatively easy to apply because it uses the familiar MODFLOW structure. Thus, most commonly used pre- and post-processors can be used to create datasets and visualize results. SEAWAT is a public domain computer program distributed free of charge by the U.S. Geological Survey.
Audio-visual perception of 3D cinematography: an fMRI study using condition-based and computation-based analyses.

PubMed

Ogawa, Akitoshi; Bordier, Cecile; Macaluso, Emiliano

2013-01-01

The use of naturalistic stimuli to probe sensory functions in the human brain is gaining increasing interest. Previous imaging studies examined brain activity associated with the processing of cinematographic material using both standard "condition-based" designs, as well as "computational" methods based on the extraction of time-varying features of the stimuli (e.g. motion). Here, we exploited both approaches to investigate the neural correlates of complex visual and auditory spatial signals in cinematography. In the first experiment, the participants watched a piece of a commercial movie presented in four blocked conditions: 3D vision with surround sounds (3D-Surround), 3D with monaural sound (3D-Mono), 2D-Surround, and 2D-Mono. In the second experiment, they watched two different segments of the movie both presented continuously in 3D-Surround. The blocked presentation served for standard condition-based analyses, while all datasets were submitted to computation-based analyses. The latter assessed where activity co-varied with visual disparity signals and the complexity of auditory multi-sources signals. The blocked analyses associated 3D viewing with the activation of the dorsal and lateral occipital cortex and superior parietal lobule, while the surround sounds activated the superior and middle temporal gyri (S/MTG). The computation-based analyses revealed the effects of absolute disparity in dorsal occipital and posterior parietal cortices and of disparity gradients in the posterior middle temporal gyrus plus the inferior frontal gyrus. The complexity of the surround sounds was associated with activity in specific sub-regions of S/MTG, even after accounting for changes of sound intensity. These results demonstrate that the processing of naturalistic audio-visual signals entails an extensive set of visual and auditory areas, and that computation-based analyses can track the contribution of complex spatial aspects characterizing such life-like stimuli.
On codes with multi-level error-correction capabilities

NASA Technical Reports Server (NTRS)

Lin, Shu

1987-01-01

In conventional coding for error control, all the information symbols of a message are regarded equally significant, and hence codes are devised to provide equal protection for each information symbol against channel errors. However, in some occasions, some information symbols in a message are more significant than the other symbols. As a result, it is desired to devise codes with multilevel error-correcting capabilities. Another situation where codes with multi-level error-correcting capabilities are desired is in broadcast communication systems. An m-user broadcast channel has one input and m outputs. The single input and each output form a component channel. The component channels may have different noise levels, and hence the messages transmitted over the component channels require different levels of protection against errors. Block codes with multi-level error-correcting capabilities are also known as unequal error protection (UEP) codes. Structural properties of these codes are derived. Based on these structural properties, two classes of UEP codes are constructed.
Adaptive Suction and Blowing for Twin-Tail Buffet Control

NASA Technical Reports Server (NTRS)

Kandil, Osama A.; Yang, Zhi

1999-01-01

Adaptive active flow control for twin-tail buffet alleviation is investigated. The concept behind this technique is to place control ports on the tail outer and inner surfaces with flow suction or blowing applied through these ports in order to minimize the pressure difference across the tail. The suction or blowing volume flow rate from each port is proportional to the pressure difference across the tail at this location. A parametric study of the effects of the number and location of these ports on the buffet response is carried out. The computational model consists of a sharp-edged delta wing of aspect ratio one and swept-back flexible twin tail with taper ratio of 0.23. This complex multidisciplinary problem is solved sequentially using three sets of equations for the fluid flow, aeroelastic response and grid deformation, using a dynamic multi-block grid structure. The computational model is pitched at 30 deg angle of attack. The freestream Mach number and Reynolds number are 0.3 and 1.25 million, respectively. The model is investigated for the inboard position of the twin tails, which corresponds to a separation distance between the twin tails of 33% of the wing span. Comparison of the time history and power spectral density responses of the tails for various distributions of the control ports are presented and discussed.

Hybrid Silicon-Based Organic/Inorganic Block Copolymers with Sol-Gel Active Moieties: Synthetic Advances, Self-Assembly and Applications in Biomedicine and Materials Science.

PubMed

Czarnecki, Sebastian; Bertin, Annabelle

2018-03-07

Hybrid silicon-based organic/inorganic (multi)block copolymers are promising polymeric precursors to create robust nano-objects and nanomaterials due to their sol-gel active moieties via self-assembly in solution or in bulk. Such nano-objects and nanomaterials have great potential in biomedicine as nanocarriers or scaffolds for bone regeneration as well as in materials science as Pickering emulsifiers, photonic crystals or coatings/films with antibiofouling, antibacterial or water- and oil-repellent properties. Thus, this Review outlines recent synthetic efforts in the preparation of these hybrid inorganic/organic block copolymers, gives an overview of their self-assembled structures and finally presents recent examples of their use in the biomedical field and material science. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
General synthesis of inorganic single-walled nanotubes

PubMed Central

Ni, Bing; Liu, Huiling; Wang, Peng-peng; He, Jie; Wang, Xun

2015-01-01

The single-walled nanotube (SWNT) is an interesting nanostructure for fundamental research and potential applications. However, very few inorganic SWNTs are available to date due to the lack of efficient fabrication methods. Here we synthesize four types of SWNT: sulfide; hydroxide; phosphate; and polyoxometalate. Each type of SWNT possesses essentially uniform diameters. Detailed studies illustrate that the formation of SWNTs is initiated by the self-coiling of the corresponding ultrathin nanostructure embryo/building blocks on the base of weak interactions between them, which is not limited to specific compounds or crystal structures. The interactions between building blocks can be modulated by varying the solvents used, thus multi-walled tubes can also be obtained. Our results reveal that the generalized synthesis of inorganic SWNTs can be achieved by the self-coiling of ultrathin building blocks under the proper weak interactions. PMID:26510862
Collapse transitions in thermosensitive multi-block copolymers: A Monte Carlo study

NASA Astrophysics Data System (ADS)

Rissanou, Anastassia N.; Tzeli, Despoina S.; Anastasiadis, Spiros H.; Bitsanis, Ioannis A.

2014-05-01

Monte Carlo simulations are performed on a simple cubic lattice to investigate the behavior of a single linear multiblock copolymer chain of various lengths N. The chain of type (AnBn)m consists of alternating A and B blocks, where A are solvophilic and B are solvophobic and N = 2nm. The conformations are classified in five cases of globule formation by the solvophobic blocks of the chain. The dependence of globule characteristics on the molecular weight and on the number of blocks, which participate in their formation, is examined. The focus is on relative high molecular weight blocks (i.e., N in the range of 500-5000 units) and very differing energetic conditions for the two blocks (very good—almost athermal solvent for A and bad solvent for B). A rich phase behavior is observed as a result of the alternating architecture of the multiblock copolymer chain. We trust that thermodynamic equilibrium has been reached for chains of N up to 2000 units; however, for longer chains kinetic entrapments are observed. The comparison among equivalent globules consisting of different number of B-blocks shows that the more the solvophobic blocks constituting the globule the bigger its radius of gyration and the looser its structure. Comparisons between globules formed by the solvophobic blocks of the multiblock copolymer chain and their homopolymer analogs highlight the important role of the solvophilic A-blocks.
MultiSETTER: web server for multiple RNA structure comparison.

PubMed

Čech, Petr; Hoksza, David; Svozil, Daniel

2015-08-12

Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.
Development of a Multi-Disciplinary Computing Environment (MDICE)

NASA Technical Reports Server (NTRS)

Kingsley, Gerry; Siegel, John M., Jr.; Harrand, Vincent J.; Lawrence, Charles; Luker, Joel J.

1999-01-01

The growing need for and importance of multi-component and multi-disciplinary engineering analysis has been understood for many years. For many applications, loose (or semi-implicit) coupling is optimal, and allows the use of various legacy codes without requiring major modifications. For this purpose, CFDRC and NASA LeRC have developed a computational environment to enable coupling between various flow analysis codes at several levels of fidelity. This has been referred to as the Visual Computing Environment (VCE), and is being successfully applied to the analysis of several aircraft engine components. Recently, CFDRC and AFRL/VAAC (WL) have extended the framework and scope of VCE to enable complex multi-disciplinary simulations. The chosen initial focus is on aeroelastic aircraft applications. The developed software is referred to as MDICE-AE, an extensible system suitable for integration of several engineering analysis disciplines. This paper describes the methodology, basic architecture, chosen software technologies, salient library modules, and the current status of and plans for MDICE. A fluid-structure interaction application is described in a separate companion paper.
A Block Iterative Finite Element Model for Nonlinear Leaky Aquifer Systems

NASA Astrophysics Data System (ADS)

Gambolati, Giuseppe; Teatini, Pietro

1996-01-01

A new quasi three-dimensional finite element model of groundwater flow is developed for highly compressible multiaquifer systems where aquitard permeability and elastic storage are dependent on hydraulic drawdown. The model is solved by a block iterative strategy, which is naturally suggested by the geological structure of the porous medium and can be shown to be mathematically equivalent to a block Gauss-Seidel procedure. As such it can be generalized into a block overrelaxation procedure and greatly accelerated by the use of the optimum overrelaxation factor. Results for both linear and nonlinear multiaquifer systems emphasize the excellent computational performance of the model and indicate that convergence in leaky systems can be improved up to as much as one order of magnitude.
Scalability of surrogate-assisted multi-objective optimization of antenna structures exploiting variable-fidelity electromagnetic simulation models

NASA Astrophysics Data System (ADS)

Koziel, Slawomir; Bekasiewicz, Adrian

2016-10-01

Multi-objective optimization of antenna structures is a challenging task owing to the high computational cost of evaluating the design objectives as well as the large number of adjustable parameters. Design speed-up can be achieved by means of surrogate-based optimization techniques. In particular, a combination of variable-fidelity electromagnetic (EM) simulations, design space reduction techniques, response surface approximation models and design refinement methods permits identification of the Pareto-optimal set of designs within a reasonable timeframe. Here, a study concerning the scalability of surrogate-assisted multi-objective antenna design is carried out based on a set of benchmark problems, with the dimensionality of the design space ranging from six to 24 and a CPU cost of the EM antenna model from 10 to 20 min per simulation. Numerical results indicate that the computational overhead of the design process increases more or less quadratically with the number of adjustable geometric parameters of the antenna structure at hand, which is a promising result from the point of view of handling even more complex problems.
Cloud computing-based TagSNP selection algorithm for human genome data.

PubMed

Hung, Che-Lun; Chen, Wen-Pei; Hua, Guan-Jie; Zheng, Huiru; Tsai, Suh-Jen Jane; Lin, Yaw-Ling

2015-01-05

Single nucleotide polymorphisms (SNPs) play a fundamental role in human genetic variation and are used in medical diagnostics, phylogeny construction, and drug design. They provide the highest-resolution genetic fingerprint for identifying disease associations and human features. Haplotypes are regions of linked genetic variants that are closely spaced on the genome and tend to be inherited together. Genetics research has revealed SNPs within certain haplotype blocks that introduce few distinct common haplotypes into most of the population. Haplotype block structures are used in association-based methods to map disease genes. In this paper, we propose an efficient algorithm for identifying haplotype blocks in the genome. In chromosomal haplotype data retrieved from the HapMap project website, the proposed algorithm identified longer haplotype blocks than an existing algorithm. To enhance its performance, we extended the proposed algorithm into a parallel algorithm that copies data in parallel via the Hadoop MapReduce framework. The proposed MapReduce-paralleled combinatorial algorithm performed well on real-world data obtained from the HapMap dataset; the improvement in computational efficiency was proportional to the number of processors used.
Efficient low-bit-rate adaptive mesh-based motion compensation technique

NASA Astrophysics Data System (ADS)

Mahmoud, Hanan A.; Bayoumi, Magdy A.

2001-08-01

This paper proposes a two-stage global motion estimation method using a novel quadtree block-based motion estimation technique and an active mesh model. In the first stage, motion parameters are estimated by fitting block-based motion vectors computed using a new efficient quadtree technique, that divides a frame into equilateral triangle blocks using the quad-tree structure. Arbitrary partition shapes are achieved by allowing 4-to-1, 3-to-1 and 2-1 merge/combine of sibling blocks having the same motion vector . In the second stage, the mesh is constructed using an adaptive triangulation procedure that places more triangles over areas with high motion content, these areas are estimated during the first stage. finally the motion compensation is achieved by using a novel algorithm that is carried by both the encoder and the decoder to determine the optimal triangulation of the resultant partitions followed by affine mapping at the encoder. Computer simulation results show that the proposed method gives better performance that the conventional ones in terms of the peak signal-to-noise ration (PSNR) and the compression ratio (CR).
Cloud Computing-Based TagSNP Selection Algorithm for Human Genome Data

PubMed Central

Hung, Che-Lun; Chen, Wen-Pei; Hua, Guan-Jie; Zheng, Huiru; Tsai, Suh-Jen Jane; Lin, Yaw-Ling

2015-01-01

Single nucleotide polymorphisms (SNPs) play a fundamental role in human genetic variation and are used in medical diagnostics, phylogeny construction, and drug design. They provide the highest-resolution genetic fingerprint for identifying disease associations and human features. Haplotypes are regions of linked genetic variants that are closely spaced on the genome and tend to be inherited together. Genetics research has revealed SNPs within certain haplotype blocks that introduce few distinct common haplotypes into most of the population. Haplotype block structures are used in association-based methods to map disease genes. In this paper, we propose an efficient algorithm for identifying haplotype blocks in the genome. In chromosomal haplotype data retrieved from the HapMap project website, the proposed algorithm identified longer haplotype blocks than an existing algorithm. To enhance its performance, we extended the proposed algorithm into a parallel algorithm that copies data in parallel via the Hadoop MapReduce framework. The proposed MapReduce-paralleled combinatorial algorithm performed well on real-world data obtained from the HapMap dataset; the improvement in computational efficiency was proportional to the number of processors used. PMID:25569088
Computational Performance of Intel MIC, Sandy Bridge, and GPU Architectures: Implementation of a 1D c++/OpenMP Electrostatic Particle-In-Cell Code

DTIC Science & Technology

2014-05-01

fusion, space and astrophysical plasmas, but still the general picture can be presented quite well with the fluid approach [6, 7]. The microscopic...purpose computing CPU for algorithms where processing of large blocks of data is done in parallel. The reason for that is the GPU’s highly effective...parallel structure. Most of the image and video processing computations involve heavy matrix and vector op- erations over large amounts of data and
A multi-populations multi-strategies differential evolution algorithm for structural optimization of metal nanoclusters

NASA Astrophysics Data System (ADS)

Fan, Tian-E.; Shao, Gui-Fang; Ji, Qing-Shuang; Zheng, Ji-Wen; Liu, Tun-dong; Wen, Yu-Hua

2016-11-01

Theoretically, the determination of the structure of a cluster is to search the global minimum on its potential energy surface. The global minimization problem is often nondeterministic-polynomial-time (NP) hard and the number of local minima grows exponentially with the cluster size. In this article, a multi-populations multi-strategies differential evolution algorithm has been proposed to search the globally stable structure of Fe and Cr nanoclusters. The algorithm combines a multi-populations differential evolution with an elite pool scheme to keep the diversity of the solutions and avoid prematurely trapping into local optima. Moreover, multi-strategies such as growing method in initialization and three differential strategies in mutation are introduced to improve the convergence speed and lower the computational cost. The accuracy and effectiveness of our algorithm have been verified by comparing the results of Fe clusters with Cambridge Cluster Database. Meanwhile, the performance of our algorithm has been analyzed by comparing the convergence rate and energy evaluations with the classical DE algorithm. The multi-populations, multi-strategies mutation and growing method in initialization in our algorithm have been considered respectively. Furthermore, the structural growth pattern of Cr clusters has been predicted by this algorithm. The results show that the lowest-energy structure of Cr clusters contains many icosahedra, and the number of the icosahedral rings rises with increasing size.
Orientation of airborne laser scanning point clouds with multi-view, multi-scale image blocks.

PubMed

Rönnholm, Petri; Hyyppä, Hannu; Hyyppä, Juha; Haggrén, Henrik

2009-01-01

Comprehensive 3D modeling of our environment requires integration of terrestrial and airborne data, which is collected, preferably, using laser scanning and photogrammetric methods. However, integration of these multi-source data requires accurate relative orientations. In this article, two methods for solving relative orientation problems are presented. The first method includes registration by minimizing the distances between of an airborne laser point cloud and a 3D model. The 3D model was derived from photogrammetric measurements and terrestrial laser scanning points. The first method was used as a reference and for validation. Having completed registration in the object space, the relative orientation between images and laser point cloud is known. The second method utilizes an interactive orientation method between a multi-scale image block and a laser point cloud. The multi-scale image block includes both aerial and terrestrial images. Experiments with the multi-scale image block revealed that the accuracy of a relative orientation increased when more images were included in the block. The orientations of the first and second methods were compared. The comparison showed that correct rotations were the most difficult to detect accurately by using the interactive method. Because the interactive method forces laser scanning data to fit with the images, inaccurate rotations cause corresponding shifts to image positions. However, in a test case, in which the orientation differences included only shifts, the interactive method could solve the relative orientation of an aerial image and airborne laser scanning data repeatedly within a couple of centimeters.
Orientation of Airborne Laser Scanning Point Clouds with Multi-View, Multi-Scale Image Blocks

PubMed Central

Rönnholm, Petri; Hyyppä, Hannu; Hyyppä, Juha; Haggrén, Henrik

2009-01-01

Comprehensive 3D modeling of our environment requires integration of terrestrial and airborne data, which is collected, preferably, using laser scanning and photogrammetric methods. However, integration of these multi-source data requires accurate relative orientations. In this article, two methods for solving relative orientation problems are presented. The first method includes registration by minimizing the distances between of an airborne laser point cloud and a 3D model. The 3D model was derived from photogrammetric measurements and terrestrial laser scanning points. The first method was used as a reference and for validation. Having completed registration in the object space, the relative orientation between images and laser point cloud is known. The second method utilizes an interactive orientation method between a multi-scale image block and a laser point cloud. The multi-scale image block includes both aerial and terrestrial images. Experiments with the multi-scale image block revealed that the accuracy of a relative orientation increased when more images were included in the block. The orientations of the first and second methods were compared. The comparison showed that correct rotations were the most difficult to detect accurately by using the interactive method. Because the interactive method forces laser scanning data to fit with the images, inaccurate rotations cause corresponding shifts to image positions. However, in a test case, in which the orientation differences included only shifts, the interactive method could solve the relative orientation of an aerial image and airborne laser scanning data repeatedly within a couple of centimeters. PMID:22454569
An object-oriented approach for parallel self adaptive mesh refinement on block structured grids

NASA Technical Reports Server (NTRS)

Lemke, Max; Witsch, Kristian; Quinlan, Daniel

1993-01-01

Self-adaptive mesh refinement dynamically matches the computational demands of a solver for partial differential equations to the activity in the application's domain. In this paper we present two C++ class libraries, P++ and AMR++, which significantly simplify the development of sophisticated adaptive mesh refinement codes on (massively) parallel distributed memory architectures. The development is based on our previous research in this area. The C++ class libraries provide abstractions to separate the issues of developing parallel adaptive mesh refinement applications into those of parallelism, abstracted by P++, and adaptive mesh refinement, abstracted by AMR++. P++ is a parallel array class library to permit efficient development of architecture independent codes for structured grid applications, and AMR++ provides support for self-adaptive mesh refinement on block-structured grids of rectangular non-overlapping blocks. Using these libraries, the application programmers' work is greatly simplified to primarily specifying the serial single grid application and obtaining the parallel and self-adaptive mesh refinement code with minimal effort. Initial results for simple singular perturbation problems solved by self-adaptive multilevel techniques (FAC, AFAC), being implemented on the basis of prototypes of the P++/AMR++ environment, are presented. Singular perturbation problems frequently arise in large applications, e.g. in the area of computational fluid dynamics. They usually have solutions with layers which require adaptive mesh refinement and fast basic solvers in order to be resolved efficiently.
Fault-tolerant computer study. [logic designs for building block circuits

NASA Technical Reports Server (NTRS)

Rennels, D. A.; Avizienis, A. A.; Ercegovac, M. D.

1981-01-01

A set of building block circuits is described which can be used with commercially available microprocessors and memories to implement fault tolerant distributed computer systems. Each building block circuit is intended for VLSI implementation as a single chip. Several building blocks and associated processor and memory chips form a self checking computer module with self contained input output and interfaces to redundant communications buses. Fault tolerance is achieved by connecting self checking computer modules into a redundant network in which backup buses and computer modules are provided to circumvent failures. The requirements and design methodology which led to the definition of the building block circuits are discussed.
Reducing power consumption while synchronizing a plurality of compute nodes during execution of a parallel application

DOEpatents

Archer, Charles J [Rochester, MN; Blocksome, Michael A [Rochester, MN; Peters, Amanda A [Rochester, MN; Ratterman, Joseph D [Rochester, MN; Smith, Brian E [Rochester, MN

2012-01-10

Methods, apparatus, and products are disclosed for reducing power consumption while synchronizing a plurality of compute nodes during execution of a parallel application that include: beginning, by each compute node, performance of a blocking operation specified by the parallel application, each compute node beginning the blocking operation asynchronously with respect to the other compute nodes; reducing, for each compute node, power to one or more hardware components of that compute node in response to that compute node beginning the performance of the blocking operation; and restoring, for each compute node, the power to the hardware components having power reduced in response to all of the compute nodes beginning the performance of the blocking operation.
Reducing power consumption while synchronizing a plurality of compute nodes during execution of a parallel application

DOEpatents

Archer, Charles J [Rochester, MN; Blocksome, Michael A [Rochester, MN; Peters, Amanda E [Cambridge, MA; Ratterman, Joseph D [Rochester, MN; Smith, Brian E [Rochester, MN

2012-04-17

Methods, apparatus, and products are disclosed for reducing power consumption while synchronizing a plurality of compute nodes during execution of a parallel application that include: beginning, by each compute node, performance of a blocking operation specified by the parallel application, each compute node beginning the blocking operation asynchronously with respect to the other compute nodes; reducing, for each compute node, power to one or more hardware components of that compute node in response to that compute node beginning the performance of the blocking operation; and restoring, for each compute node, the power to the hardware components having power reduced in response to all of the compute nodes beginning the performance of the blocking operation.
Fully automated three-dimensional microscopy system

NASA Astrophysics Data System (ADS)

Kerschmann, Russell L.

2000-04-01

Tissue-scale structures such as vessel networks are imaged at micron resolution with the Virtual Tissue System (VT System). VT System imaging of cubic millimeters of tissue and other material extends the capabilities of conventional volumetric techniques such as confocal microscopy, and allows for the first time the integrated 2D and 3D analysis of important tissue structural relationships. The VT System eliminates the need for glass slide-mounted tissue sections and instead captures images directly from the surface of a block containing a sample. Tissues are en bloc stained with fluorochrome compounds, embedded in an optically conditioned polymer that suppresses image signals form dep within the block , and serially sectioned for imaging. Thousands of fully registered 2D images are automatically captured digitally to completely convert tissue samples into blocks of high-resolution information. The resulting multi gigabyte data sets constitute the raw material for precision visualization and analysis. Cellular function may be seen in a larger anatomical context. VT System technology makes tissue metrics, accurate cell enumeration and cell cycle analyses possible while preserving full histologic setting.
Turbine Internal and Film Cooling Modeling For 3D Navier-Stokes Codes

NASA Technical Reports Server (NTRS)

DeWitt, Kenneth; Garg Vijay; Ameri, Ali

2005-01-01

The aim of this research project is to make use of NASA Glenn on-site computational facilities in order to develop, validate and apply aerodynamic, heat transfer, and turbine cooling models for use in advanced 3D Navier-Stokes Computational Fluid Dynamics (CFD) codes such as the Glenn-" code. Specific areas of effort include: Application of the Glenn-HT code to specific configurations made available under Turbine Based Combined Cycle (TBCC), and Ultra Efficient Engine Technology (UEET) projects. Validating the use of a multi-block code for the time accurate computation of the detailed flow and heat transfer of cooled turbine airfoils. The goal of the current research is to improve the predictive ability of the Glenn-HT code. This will enable one to design more efficient turbine components for both aviation and power generation. The models will be tested against specific configurations provided by NASA Glenn.

Surface Modeling and Grid Generation of Orbital Sciences X34 Vehicle. Phase 1

NASA Technical Reports Server (NTRS)

Alter, Stephen J.

1997-01-01

The surface modeling and grid generation requirements, motivations, and methods used to develop Computational Fluid Dynamic volume grids for the X34-Phase 1 are presented. The requirements set forth by the Aerothermodynamics Branch at the NASA Langley Research Center serve as the basis for the final techniques used in the construction of all volume grids, including grids for parametric studies of the X34. The Integrated Computer Engineering and Manufacturing code for Computational Fluid Dynamics (ICEM/CFD), the Grid Generation code (GRIDGEN), the Three-Dimensional Multi-block Advanced Grid Generation System (3DMAGGS) code, and Volume Grid Manipulator (VGM) code are used to enable the necessary surface modeling, surface grid generation, volume grid generation, and grid alterations, respectively. All volume grids generated for the X34, as outlined in this paper, were used for CFD simulations within the Aerothermodynamics Branch.
Interactive Terascale Particle Visualization

NASA Technical Reports Server (NTRS)

Ellsworth, David; Green, Bryan; Moran, Patrick

2004-01-01

This paper describes the methods used to produce an interactive visualization of a 2 TB computational fluid dynamics (CFD) data set using particle tracing (streaklines). We use the method introduced by Bruckschen et al. [2001] that pre-computes a large number of particles, stores them on disk using a space-filling curve ordering that minimizes seeks, and then retrieves and displays the particles according to the user's command. We describe how the particle computation can be performed using a PC cluster, how the algorithm can be adapted to work with a multi-block curvilinear mesh, and how the out-of-core visualization can be scaled to 296 billion particles while still achieving interactive performance on PG hardware. Compared to the earlier work, our data set size and total number of particles are an order of magnitude larger. We also describe a new compression technique that allows the lossless compression of the particles by 41% and speeds the particle retrieval by about 30%.
Vertical Scan (V-SCAN) for 3-D Grid Adaptive Mesh Refinement for an atmospheric Model Dynamical Core

NASA Astrophysics Data System (ADS)

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

2009-12-01

One of the major building blocks of a rigorous representation of cloud evolution in global atmospheric models is a parallel adaptive grid MPI-based communication library (an Adaptive Blocks for Locally Cartesian Topologies library -- ABLCarT), which manages the block-structured data layout, handles ghost cell updates among neighboring blocks and splits a block as refinements occur. The library has several modules that provide a layer of abstraction for adaptive refinement: blocks, which contain individual cells of user data; shells - the global geometry for the problem, including a sphere, reduced sphere, and now a 3D sphere; a load balancer for placement of blocks onto processors; and a communication support layer which encapsulates all data movement. A major performance concern with adaptive mesh refinement is how to represent calculations that have need to be sequenced in a particular order in a direction, such as calculating integrals along a specific path (e.g. atmospheric pressure or geopotential in the vertical dimension). This concern is compounded if the blocks have varying levels of refinement, or are scattered across different processors, as can be the case in parallel computing. In this paper we describe an implementation in ABLCarT of a vertical scan operation, which allows computing along vertical paths in the correct order across blocks transparent to their resolution and processor location. We test this functionality on a 2D and a 3D advection problem, which tests the performance of the model’s dynamics (transport) and physics (sources and sinks) for different model resolutions needed for inclusion of cloud formation.
Zero-block mode decision algorithm for H.264/AVC.

PubMed

Lee, Yu-Ming; Lin, Yinyi

2009-03-01

In the previous paper , we proposed a zero-block intermode decision algorithm for H.264 video coding based upon the number of zero-blocks of 4 x 4 DCT coefficients between the current macroblock and the co-located macroblock. The proposed algorithm can achieve significant improvement in computation, but the computation performance is limited for high bit-rate coding. To improve computation efficiency, in this paper, we suggest an enhanced zero-block decision algorithm, which uses an early zero-block detection method to compute the number of zero-blocks instead of direct DCT and quantization (DCT/Q) calculation and incorporates two adequate decision methods into semi-stationary and nonstationary regions of a video sequence. In addition, the zero-block decision algorithm is also applied to the intramode prediction in the P frame. The enhanced zero-block decision algorithm brings out a reduction of average 27% of total encoding time compared to the zero-block decision algorithm.
Multi-walled boron nitride nanotubes as self-excited launchers.

PubMed

Li, Yifan; Zhou, Yi; Wu, Yan; Huang, Chengchi; Wang, Long; Zhou, Xuyan; Zhao, Zhenyang; Li, Hui

2017-07-27

A self-excited launcher consisting of multi-walled boron nitride nanotubes (BNNTs) has been investigated using molecular dynamics simulation. The results show that, after a period of high frequency oscillation, the innermost BNNT can be spontaneously ejected along its central axis at a relatively fast speed. The launching is caused by the energy transfer between the nanotubes and without absorbing energy from the external environment. Most self-excited launchers could launch their innermost nanotube, although an inappropriate structure of the nanotubes contributes to a blocked or failed launch. In addition, a launch angle corrector and a nanotube receiver associated with a self-excited launcher are also manufactured to precisely control the launch angle and distance of the BNNTs. This study provides the possibility to fabricate and design self-excited launchers using multi-walled nanotubes.
The evaluation of multi-structure, multi-atlas pelvic anatomy features in a prostate MR lymphography CAD system

NASA Astrophysics Data System (ADS)

Meijs, M.; Debats, O.; Huisman, H.

2015-03-01

In prostate cancer, the detection of metastatic lymph nodes indicates progression from localized disease to metastasized cancer. The detection of positive lymph nodes is, however, a complex and time consuming task for experienced radiologists. Assistance of a two-stage Computer-Aided Detection (CAD) system in MR Lymphography (MRL) is not yet feasible due to the large number of false positives in the first stage of the system. By introducing a multi-structure, multi-atlas segmentation, using an affine transformation followed by a B-spline transformation for registration, the organ location is given by a mean density probability map. The atlas segmentation is semi-automatically drawn with ITK-SNAP, using Active Contour Segmentation. Each anatomic structure is identified by a label number. Registration is performed using Elastix, using Mutual Information and an Adaptive Stochastic Gradient optimization. The dataset consists of the MRL scans of ten patients, with lymph nodes manually annotated in consensus by two expert readers. The feature map of the CAD system consists of the Multi-Atlas and various other features (e.g. Normalized Intensity and multi-scale Blobness). The voxel-based Gentleboost classifier is evaluated using ROC analysis with cross validation. We show in a set of 10 studies that adding multi-structure, multi-atlas anatomical structure likelihood features improves the quality of the lymph node voxel likelihood map. Multiple structure anatomy maps may thus make MRL CAD more feasible.
Ring system-based chemical graph generation for de novo molecular design

NASA Astrophysics Data System (ADS)

Miyao, Tomoyuki; Kaneko, Hiromasa; Funatsu, Kimito

2016-05-01

Generating chemical graphs in silico by combining building blocks is important and fundamental in virtual combinatorial chemistry. A premise in this area is that generated structures should be irredundant as well as exhaustive. In this study, we develop structure generation algorithms regarding combining ring systems as well as atom fragments. The proposed algorithms consist of three parts. First, chemical structures are generated through a canonical construction path. During structure generation, ring systems can be treated as reduced graphs having fewer vertices than those in the original ones. Second, diversified structures are generated by a simple rule-based generation algorithm. Third, the number of structures to be generated can be estimated with adequate accuracy without actual exhaustive generation. The proposed algorithms were implemented in structure generator Molgilla. As a practical application, Molgilla generated chemical structures mimicking rosiglitazone in terms of a two dimensional pharmacophore pattern. The strength of the algorithms lies in simplicity and flexibility. Therefore, they may be applied to various computer programs regarding structure generation by combining building blocks.
Multi-Functional UV-Visible-IR Nanosensors Devices and Structures

DTIC Science & Technology

2015-04-29

Dual-Gate MOSFET System, Proceedings of the International Workshop on Computational Electronics, Nara, Japan, Society of Micro- and Nanoelectronics ...International Workshop on Computational Electronics, Nara, Japan, Society of Micro- and Nanoelectronics , 216-217 (2013); ISBN 978-3-901578-26-7 M. S...Raman Spectroscopy, Proceedings of the International Workshop on Computational Electronics, Nara, Japan, Society of Micro- and Nanoelectronics , 198
Probabilistic Structural Analysis Methods (PSAM) for select space propulsion system components, part 2

NASA Technical Reports Server (NTRS)

1991-01-01

The technical effort and computer code enhancements performed during the sixth year of the Probabilistic Structural Analysis Methods program are summarized. Various capabilities are described to probabilistically combine structural response and structural resistance to compute component reliability. A library of structural resistance models is implemented in the Numerical Evaluations of Stochastic Structures Under Stress (NESSUS) code that included fatigue, fracture, creep, multi-factor interaction, and other important effects. In addition, a user interface was developed for user-defined resistance models. An accurate and efficient reliability method was developed and was successfully implemented in the NESSUS code to compute component reliability based on user-selected response and resistance models. A risk module was developed to compute component risk with respect to cost, performance, or user-defined criteria. The new component risk assessment capabilities were validated and demonstrated using several examples. Various supporting methodologies were also developed in support of component risk assessment.
Individual-specific multi-scale finite element simulation of cortical bone of human proximal femur

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

Ascenzi, Maria-Grazia, E-mail: mgascenzi@mednet.ucla.edu; Kawas, Neal P., E-mail: nealkawas@ucla.edu; Lutz, Andre, E-mail: andre.lutz@hotmail.de

2013-07-01

We present an innovative method to perform multi-scale finite element analyses of the cortical component of the femur using the individual’s (1) computed tomography scan; and (2) a bone specimen obtained in conjunction with orthopedic surgery. The method enables study of micro-structural characteristics regulating strains and stresses under physiological loading conditions. The analysis of the micro-structural scenarios that cause variation of strain and stress is the first step in understanding the elevated strains and stresses in bone tissue, which are indicative of higher likelihood of micro-crack formation in bone, implicated in consequent remodeling or macroscopic bone fracture. Evidence that micro-structuremore » varies with clinical history and contributes in significant, but poorly understood, ways to bone function, motivates the method’s development, as does need for software tools to investigate relationships between macroscopic loading and micro-structure. Three applications – varying region of interest, bone mineral density, and orientation of collagen type I, illustrate the method. We show, in comparison between physiological loading and simple compression of a patient’s femur, that strains computed at the multi-scale model’s micro-level: (i) differ; and (ii) depend on local collagen-apatite orientation and degree of calcification. Our findings confirm the strain concentration role of osteocyte lacunae, important for mechano-transduction. We hypothesize occurrence of micro-crack formation, leading either to remodeling or macroscopic fracture, when the computed strains exceed the elastic range observed in micro-structural testing.« less
Symplectic multi-particle tracking on GPUs

NASA Astrophysics Data System (ADS)

Liu, Zhicong; Qiang, Ji

2018-05-01

A symplectic multi-particle tracking model is implemented on the Graphic Processing Units (GPUs) using the Compute Unified Device Architecture (CUDA) language. The symplectic tracking model can preserve phase space structure and reduce non-physical effects in long term simulation, which is important for beam property evaluation in particle accelerators. Though this model is computationally expensive, it is very suitable for parallelization and can be accelerated significantly by using GPUs. In this paper, we optimized the implementation of the symplectic tracking model on both single GPU and multiple GPUs. Using a single GPU processor, the code achieves a factor of 2-10 speedup for a range of problem sizes compared with the time on a single state-of-the-art Central Processing Unit (CPU) node with similar power consumption and semiconductor technology. It also shows good scalability on a multi-GPU cluster at Oak Ridge Leadership Computing Facility. In an application to beam dynamics simulation, the GPU implementation helps save more than a factor of two total computing time in comparison to the CPU implementation.
Coupled Aerodynamic and Structural Sensitivity Analysis of a High-Speed Civil Transport

NASA Technical Reports Server (NTRS)

Mason, B. H.; Walsh, J. L.

2001-01-01

An objective of the High Performance Computing and Communication Program at the NASA Langley Research Center is to demonstrate multidisciplinary shape and sizing optimization of a complete aerospace vehicle configuration by using high-fidelity, finite-element structural analysis and computational fluid dynamics aerodynamic analysis. In a previous study, a multi-disciplinary analysis system for a high-speed civil transport was formulated to integrate a set of existing discipline analysis codes, some of them computationally intensive, This paper is an extension of the previous study, in which the sensitivity analysis for the coupled aerodynamic and structural analysis problem is formulated and implemented. Uncoupled stress sensitivities computed with a constant load vector in a commercial finite element analysis code are compared to coupled aeroelastic sensitivities computed by finite differences. The computational expense of these sensitivity calculation methods is discussed.
Design search and optimization in aerospace engineering.

PubMed

Keane, A J; Scanlan, J P

2007-10-15

In this paper, we take a design-led perspective on the use of computational tools in the aerospace sector. We briefly review the current state-of-the-art in design search and optimization (DSO) as applied to problems from aerospace engineering, focusing on those problems that make heavy use of computational fluid dynamics (CFD). This ranges over issues of representation, optimization problem formulation and computational modelling. We then follow this with a multi-objective, multi-disciplinary example of DSO applied to civil aircraft wing design, an area where this kind of approach is becoming essential for companies to maintain their competitive edge. Our example considers the structure and weight of a transonic civil transport wing, its aerodynamic performance at cruise speed and its manufacturing costs. The goals are low drag and cost while holding weight and structural performance at acceptable levels. The constraints and performance metrics are modelled by a linked series of analysis codes, the most expensive of which is a CFD analysis of the aerodynamics using an Euler code with coupled boundary layer model. Structural strength and weight are assessed using semi-empirical schemes based on typical airframe company practice. Costing is carried out using a newly developed generative approach based on a hierarchical decomposition of the key structural elements of a typical machined and bolted wing-box assembly. To carry out the DSO process in the face of multiple competing goals, a recently developed multi-objective probability of improvement formulation is invoked along with stochastic process response surface models (Krigs). This approach both mitigates the significant run times involved in CFD computation and also provides an elegant way of balancing competing goals while still allowing the deployment of the whole range of single objective optimizers commonly available to design teams.
Behavior-based multi-robot collaboration for autonomous construction tasks

NASA Technical Reports Server (NTRS)

Stroupe, Ashley; Huntsberger, Terry; Okon, Avi; Aghazarian, Hrand; Robinson, Matthew

2005-01-01

The Robot Construction Crew (RCC) is a heterogeneous multi-robot system for autonomous construction of a structure through assembly of Long components. The two robot team demonstrates component placement into an existing structure in a realistic environment. The task requires component acquisition, cooperative transport, and cooperative precision manipulation. A behavior-based architecture provides adaptability. The RCC approach minimizes computation, power, communication, and sensing for applicability to space-related construction efforts, but the techniques are applicable to terrestrial construction tasks.
Behavior-Based Multi-Robot Collaboration for Autonomous Construction Tasks

NASA Technical Reports Server (NTRS)

Stroupe, Ashley; Huntsberger, Terry; Okon, Avi; Aghazarian, Hrand; Robinson, Matthew

2005-01-01

We present a heterogeneous multi-robot system for autonomous construction of a structure through assembly of long components. Placement of a component within an existing structure in a realistic environment is demonstrated on a two-robot team. The task requires component acquisition, cooperative transport, and cooperative precision manipulation. Far adaptability, the system is designed as a behavior-based architecture. Far applicability to space-related construction efforts, computation, power, communication, and sensing are minimized, though the techniques developed are also applicable to terrestrial construction tasks.
Research and application of multi-hydrogen acidizing technology of low-permeability reservoirs for increasing water injection

NASA Astrophysics Data System (ADS)

Ning, Mengmeng; Che, Hang; Kong, Weizhong; Wang, Peng; Liu, Bingxiao; Xu, Zhengdong; Wang, Xiaochao; Long, Changjun; Zhang, Bin; Wu, Youmei

2017-12-01

The physical characteristics of Xiliu 10 Block reservoir is poor, it has strong reservoir inhomogeneity between layers and high kaolinite content of the reservoir, the scaling trend of fluid is serious, causing high block injection well pressure and difficulty in achieving injection requirements. In the past acidizing process, the reaction speed with mineral is fast, the effective distance is shorter and It is also easier to lead to secondary sedimentation in conventional mud acid system. On this point, we raised multi-hydrogen acid technology, multi-hydrogen acid release hydrogen ions by multistage ionization which could react with pore blockage, fillings and skeletal effects with less secondary pollution. Multi-hydrogen acid system has advantages as moderate speed, deep penetration, clay low corrosion rate, wet water and restrains precipitation, etc. It can reach the goal of plug removal in deep stratum. The field application result shows that multi-hydrogen acid plug removal method has good effects on application in low permeability reservoir in Block Xiliu 10.
Pilot-Assisted Channel Estimation for Orthogonal Multi-Carrier DS-CDMA with Frequency-Domain Equalization

NASA Astrophysics Data System (ADS)

Shima, Tomoyuki; Tomeba, Hiromichi; Adachi, Fumiyuki

Orthogonal multi-carrier direct sequence code division multiple access (orthogonal MC DS-CDMA) is a combination of time-domain spreading and orthogonal frequency division multiplexing (OFDM). In orthogonal MC DS-CDMA, the frequency diversity gain can be obtained by applying frequency-domain equalization (FDE) based on minimum mean square error (MMSE) criterion to a block of OFDM symbols and can improve the bit error rate (BER) performance in a severe frequency-selective fading channel. FDE requires an accurate estimate of the channel gain. The channel gain can be estimated by removing the pilot modulation in the frequency domain. In this paper, we propose a pilot-assisted channel estimation suitable for orthogonal MC DS-CDMA with FDE and evaluate, by computer simulation, the BER performance in a frequency-selective Rayleigh fading channel.
The birth of quantum networks: merging remote entanglement with local multi-qubit control

NASA Astrophysics Data System (ADS)

Hanson, Ronald

The realization of a highly connected network of qubit registers is a central challenge for quantum information processing and long-distance quantum communication. Diamond spins associated with NV centers are promising building blocks for such a network: they combine a coherent spin-photon interface that has already enabled creation of spin-spin entanglement over 1km with a local register of robust and well-controlled nuclear spin qubits for information processing and error correction. We are now entering a new research stage in which we can exploit these features simultaneously and build multi-qubit networks. I will present our latest results towards the first of such experiments: entanglement distillation between remote quantum network nodes. Finally, I will discuss the challenges and opportunities ahead on the road to large-scale networks of qubit registers for quantum computation and communication.
Anti-arrhythmic strategies for atrial fibrillation

PubMed Central

Grandi, Eleonora; Maleckar, Mary M.

2016-01-01

Atrial fibrillation (AF), the most common cardiac arrhythmia, is associated with increased risk of cerebrovascular stroke, and with several other pathologies, including heart failure. Current therapies for AF are targeted at reducing risk of stroke (anticoagulation) and tachycardia-induced cardiomyopathy (rate or rhythm control). Rate control, typically achieved by atrioventricular nodal blocking drugs, is often insufficient to alleviate symptoms. Rhythm control approaches include antiarrhythmic drugs, electrical cardioversion, and ablation strategies. Here, we offer several examples of how computational modeling can provide a quantitative framework for integrating multi scale data to: (a) gain insight into multi-scale mechanisms of AF; (b) identify and test pharmacological and electrical therapy and interventions; and (c) support clinical decisions. We review how modeling approaches have evolved and contributed to the research pipeline and preclinical development and discuss future directions and challenges in the field. PMID:27612549
Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs

PubMed Central

Lin, Chun-Yuan; Wang, Chung-Hung; Hung, Che-Lun; Lin, Yu-Shiang

2015-01-01

Compound comparison is an important task for the computational chemistry. By the comparison results, potential inhibitors can be found and then used for the pharmacy experiments. The time complexity of a pairwise compound comparison is O(n 2), where n is the maximal length of compounds. In general, the length of compounds is tens to hundreds, and the computation time is small. However, more and more compounds have been synthesized and extracted now, even more than tens of millions. Therefore, it still will be time-consuming when comparing with a large amount of compounds (seen as a multiple compound comparison problem, abbreviated to MCC). The intrinsic time complexity of MCC problem is O(k 2 n 2) with k compounds of maximal length n. In this paper, we propose a GPU-based algorithm for MCC problem, called CUDA-MCC, on single- and multi-GPUs. Four LINGO-based load-balancing strategies are considered in CUDA-MCC in order to accelerate the computation speed among thread blocks on GPUs. CUDA-MCC was implemented by C+OpenMP+CUDA. CUDA-MCC achieved 45 times and 391 times faster than its CPU version on a single NVIDIA Tesla K20m GPU card and a dual-NVIDIA Tesla K20m GPU card, respectively, under the experimental results. PMID:26491652

Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs.

PubMed

Lin, Chun-Yuan; Wang, Chung-Hung; Hung, Che-Lun; Lin, Yu-Shiang

2015-01-01

Compound comparison is an important task for the computational chemistry. By the comparison results, potential inhibitors can be found and then used for the pharmacy experiments. The time complexity of a pairwise compound comparison is O(n (2)), where n is the maximal length of compounds. In general, the length of compounds is tens to hundreds, and the computation time is small. However, more and more compounds have been synthesized and extracted now, even more than tens of millions. Therefore, it still will be time-consuming when comparing with a large amount of compounds (seen as a multiple compound comparison problem, abbreviated to MCC). The intrinsic time complexity of MCC problem is O(k (2) n (2)) with k compounds of maximal length n. In this paper, we propose a GPU-based algorithm for MCC problem, called CUDA-MCC, on single- and multi-GPUs. Four LINGO-based load-balancing strategies are considered in CUDA-MCC in order to accelerate the computation speed among thread blocks on GPUs. CUDA-MCC was implemented by C+OpenMP+CUDA. CUDA-MCC achieved 45 times and 391 times faster than its CPU version on a single NVIDIA Tesla K20m GPU card and a dual-NVIDIA Tesla K20m GPU card, respectively, under the experimental results.
Zooming in: high resolution 3D reconstruction of differently stained histological whole slide images

NASA Astrophysics Data System (ADS)

Lotz, Johannes; Berger, Judith; Müller, Benedikt; Breuhahn, Kai; Grabe, Niels; Heldmann, Stefan; Homeyer, André; Lahrmann, Bernd; Laue, Hendrik; Olesch, Janine; Schwier, Michael; Sedlaczek, Oliver; Warth, Arne

2014-03-01

Much insight into metabolic interactions, tissue growth, and tissue organization can be gained by analyzing differently stained histological serial sections. One opportunity unavailable to classic histology is three-dimensional (3D) examination and computer aided analysis of tissue samples. In this case, registration is needed to reestablish spatial correspondence between adjacent slides that is lost during the sectioning process. Furthermore, the sectioning introduces various distortions like cuts, folding, tearing, and local deformations to the tissue, which need to be corrected in order to exploit the additional information arising from the analysis of neighboring slide images. In this paper we present a novel image registration based method for reconstructing a 3D tissue block implementing a zooming strategy around a user-defined point of interest. We efficiently align consecutive slides at increasingly fine resolution up to cell level. We use a two-step approach, where after a macroscopic, coarse alignment of the slides as preprocessing, a nonlinear, elastic registration is performed to correct local, non-uniform deformations. Being driven by the optimization of the normalized gradient field (NGF) distance measure, our method is suitable for differently stained and thus multi-modal slides. We applied our method to ultra thin serial sections (2 μm) of a human lung tumor. In total 170 slides, stained alternately with four different stains, have been registered. Thorough visual inspection of virtual cuts through the reconstructed block perpendicular to the cutting plane shows accurate alignment of vessels and other tissue structures. This observation is confirmed by a quantitative analysis. Using nonlinear image registration, our method is able to correct locally varying deformations in tissue structures and exceeds the limitations of globally linear transformations.
Multi-disciplinary coupling for integrated design of propulsion systems

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Singhal, S. N.

1993-01-01

Effective computational simulation procedures are described for modeling the inherent multi-disciplinary interactions for determining the true response of propulsion systems. Results are presented for propulsion system responses including multi-discipline coupling effects via (1) coupled multi-discipline tailoring, (2) an integrated system of multidisciplinary simulators, (3) coupled material-behavior/fabrication-process tailoring, (4) sensitivities using a probabilistic simulator, and (5) coupled materials/structures/fracture/probabilistic behavior simulator. The results show that the best designs can be determined if the analysis/tailoring methods account for the multi-disciplinary coupling effects. The coupling across disciplines can be used to develop an integrated interactive multi-discipline numerical propulsion system simulator.
An Overview of Spray Modeling With OpenNCC and its Application to Emissions Predictions of a LDI Combustor at High Pressure

NASA Technical Reports Server (NTRS)

Raju, M. S.

2016-01-01

The open national combustion code (Open- NCC) is developed with the aim of advancing the current multi-dimensional computational tools used in the design of advanced technology combustors. In this paper we provide an overview of the spray module, LSPRAY-V, developed as a part of this effort. The spray solver is mainly designed to predict the flow, thermal, and transport properties of a rapidly evaporating multi-component liquid spray. The modeling approach is applicable over a wide-range of evaporating conditions (normal, superheat, and supercritical). The modeling approach is based on several well-established atomization, vaporization, and wall/droplet impingement models. It facilitates large-scale combustor computations through the use of massively parallel computers with the ability to perform the computations on either structured & unstructured grids. The spray module has a multi-liquid and multi-injector capability, and can be used in the calculation of both steady and unsteady computations. We conclude the paper by providing the results for a reacting spray generated by a single injector element with 600 axially swept swirler vanes. It is a configuration based on the next-generation lean-direct injection (LDI) combustor concept. The results include comparisons for both combustor exit temperature and EINOX at three different fuel/air ratios.
Computational Analysis of a Chevron Nozzle Uniquely Tailored for Propulsion Airframe Aeroacoustics

NASA Technical Reports Server (NTRS)

Massey, Steven J.; Elmiligui, Alaa A.; Hunter, Craig A.; Thomas, Russell H.; Pao, S. Paul; Mengle, Vinod G.

2006-01-01

A computational flow field and predicted jet noise source analysis is presented for asymmetrical fan chevrons on a modern separate flow nozzle at take off conditions. The propulsion airframe aeroacoustic asymmetric fan nozzle is designed with an azimuthally varying chevron pattern with longer chevrons close to the pylon. A baseline round nozzle without chevrons and a reference nozzle with azimuthally uniform chevrons are also studied. The intent of the asymmetric fan chevron nozzle was to improve the noise reduction potential by creating a favorable propulsion airframe aeroacoustic interaction effect between the pylon and chevron nozzle. This favorable interaction and improved noise reduction was observed in model scale tests and flight test data and has been reported in other studies. The goal of this study was to identify the fundamental flow and noise source mechanisms. The flow simulation uses the asymptotically steady, compressible Reynolds averaged Navier-Stokes equations on a structured grid. Flow computations are performed using the parallel, multi-block, structured grid code PAB3D. Local noise sources were mapped and integrated computationally using the Jet3D code based upon the Lighthill Acoustic Analogy with anisotropic Reynolds stress modeling. In this study, trends of noise reduction were correctly predicted. Jet3D was also utilized to produce noise source maps that were then correlated to local flow features. The flow studies show that asymmetry of the longer fan chevrons near the pylon work to reduce the strength of the secondary flow induced by the pylon itself, such that the asymmetric merging of the fan and core shear layers is significantly delayed. The effect is to reduce the peak turbulence kinetic energy and shift it downstream, reducing overall noise production. This combined flow and noise prediction approach has yielded considerable understanding of the physics of a fan chevron nozzle designed to include propulsion airframe aeroacoustic interaction effects.
Advanced Composite Wind Turbine Blade Design Based on Durability and Damage Tolerance

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

Abumeri, Galib; Abdi, Frank

2012-02-16

The objective of the program was to demonstrate and verify Certification-by-Analysis (CBA) capability for wind turbine blades made from advanced lightweight composite materials. The approach integrated durability and damage tolerance analysis with robust design and virtual testing capabilities to deliver superior, durable, low weight, low cost, long life, and reliable wind blade design. The GENOA durability and life prediction software suite was be used as the primary simulation tool. First, a micromechanics-based computational approach was used to assess the durability of composite laminates with ply drop features commonly used in wind turbine applications. Ply drops occur in composite joints andmore » closures of wind turbine blades to reduce skin thicknesses along the blade span. They increase localized stress concentration, which may cause premature delamination failure in composite and reduced fatigue service life. Durability and damage tolerance (D&DT) were evaluated utilizing a multi-scale micro-macro progressive failure analysis (PFA) technique. PFA is finite element based and is capable of detecting all stages of material damage including initiation and propagation of delamination. It assesses multiple failure criteria and includes the effects of manufacturing anomalies (i.e., void, fiber waviness). Two different approaches have been used within PFA. The first approach is Virtual Crack Closure Technique (VCCT) PFA while the second one is strength-based. Constituent stiffness and strength properties for glass and carbon based material systems were reverse engineered for use in D&DT evaluation of coupons with ply drops under static loading. Lamina and laminate properties calculated using manufacturing and composite architecture details matched closely published test data. Similarly, resin properties were determined for fatigue life calculation. The simulation not only reproduced static strength and fatigue life as observed in the test, it also showed composite damage and fracture modes that resemble those reported in the tests. The results show that computational simulation can be relied on to enhance the design of tapered composite structures such as the ones used in turbine wind blades. A computational simulation for durability, damage tolerance (D&DT) and reliability of composite wind turbine blade structures in presence of uncertainties in material properties was performed. A composite turbine blade was first assessed with finite element based multi-scale progressive failure analysis to determine failure modes and locations as well as the fracture load. D&DT analyses were then validated with static test performed at Sandia National Laboratories. The work was followed by detailed weight analysis to identify contribution of various materials to the overall weight of the blade. The methodology ensured that certain types of failure modes, such as delamination progression, are contained to reduce risk to the structure. Probabilistic analysis indicated that composite shear strength has a great influence on the blade ultimate load under static loading. Weight was reduced by 12% with robust design without loss in reliability or D&DT. Structural benefits obtained with the use of enhanced matrix properties through nanoparticles infusion were also assessed. Thin unidirectional fiberglass layers enriched with silica nanoparticles were applied to the outer surfaces of a wind blade to improve its overall structural performance and durability. The wind blade was a 9-meter prototype structure manufactured and tested subject to three saddle static loading at Sandia National Laboratory (SNL). The blade manufacturing did not include the use of any nano-material. With silica nanoparticles in glass composite applied to the exterior surfaces of the blade, the durability and damage tolerance (D&DT) results from multi-scale PFA showed an increase in ultimate load of the blade by 9.2% as compared to baseline structural performance (without nano). The use of nanoparticles lead to a delay in the onset of delamination. Load-displacement relationships obtained from testing of the blade with baseline neat material were compared to the ones from analytical simulation using neat resin and using silica nanoparticles in the resin. Multi-scale PFA results for the neat material construction matched closely those from test for both load displacement and location and type of damage and failure. AlphaSTAR demonstrated that wind blade structures made from advanced composite materials can be certified with multi-scale progressive failure analysis by following building block verification approach.« less
Multi-paradigm simulation at nanoscale: Methodology and application to functional carbon material

NASA Astrophysics Data System (ADS)

Su, Haibin

2012-12-01

Multiparadigm methods to span the scales from quantum mechanics to practical issues of functional nanoassembly and nanofabrication are enabling first principles predictions to guide and complement the experimental developments by designing and optimizing computationally the materials compositions and structures to assemble nanoscale systems with the requisite properties. In this talk, we employ multi-paradigm approaches to investigate functional carbon materials with versatile character, including fullerene, carbon nanotube (CNT), graphene, and related hybrid structures, which have already created an enormous impact on next generation nano devices. The topics will cover the reaction dynamics of C60 dimerization and the more challenging complex tubular fullerene formation process in the peapod structures; the computational design of a new generation of peapod nano-oscillators, the predicted magnetic state in Nano Buds; opto-electronic properties of graphene nanoribbons; and disorder / vibronic effects on transport in carbonrich materials.
Vesselness propagation: a fast interactive vessel segmentation method

NASA Astrophysics Data System (ADS)

Cai, Wenli; Dachille, Frank; Harris, Gordon J.; Yoshida, Hiroyuki

2006-03-01

With the rapid development of multi-detector computed tomography (MDCT), resulting in increasing temporal and spatial resolution of data sets, clinical use of computed tomographic angiography (CTA) is rapidly increasing. Analysis of vascular structures is much needed in CTA images; however, the basis of the analysis, vessel segmentation, can still be a challenging problem. In this paper, we present a fast interactive method for CTA vessel segmentation, called vesselness propagation. This method is a two-step procedure, with a pre-processing step and an interactive step. During the pre-processing step, a vesselness volume is computed by application of a CTA transfer function followed by a multi-scale Hessian filtering. At the interactive stage, the propagation is controlled interactively in terms of the priority of the vesselness. This method was used successfully in many CTA applications such as the carotid artery, coronary artery, and peripheral arteries. It takes less than one minute for a user to segment the entire vascular structure. Thus, the proposed method provides an effective way of obtaining an overview of vascular structures.
Computational Intelligence Techniques for Tactile Sensing Systems

PubMed Central

Gastaldo, Paolo; Pinna, Luigi; Seminara, Lucia; Valle, Maurizio; Zunino, Rodolfo

2014-01-01

Tactile sensing helps robots interact with humans and objects effectively in real environments. Piezoelectric polymer sensors provide the functional building blocks of the robotic electronic skin, mainly thanks to their flexibility and suitability for detecting dynamic contact events and for recognizing the touch modality. The paper focuses on the ability of tactile sensing systems to support the challenging recognition of certain qualities/modalities of touch. The research applies novel computational intelligence techniques and a tensor-based approach for the classification of touch modalities; its main results consist in providing a procedure to enhance system generalization ability and architecture for multi-class recognition applications. An experimental campaign involving 70 participants using three different modalities in touching the upper surface of the sensor array was conducted, and confirmed the validity of the approach. PMID:24949646
Computational intelligence techniques for tactile sensing systems.

PubMed

Gastaldo, Paolo; Pinna, Luigi; Seminara, Lucia; Valle, Maurizio; Zunino, Rodolfo

2014-06-19

Tactile sensing helps robots interact with humans and objects effectively in real environments. Piezoelectric polymer sensors provide the functional building blocks of the robotic electronic skin, mainly thanks to their flexibility and suitability for detecting dynamic contact events and for recognizing the touch modality. The paper focuses on the ability of tactile sensing systems to support the challenging recognition of certain qualities/modalities of touch. The research applies novel computational intelligence techniques and a tensor-based approach for the classification of touch modalities; its main results consist in providing a procedure to enhance system generalization ability and architecture for multi-class recognition applications. An experimental campaign involving 70 participants using three different modalities in touching the upper surface of the sensor array was conducted, and confirmed the validity of the approach.
Hybrid Toffoli gate on photons and quantum spins

PubMed Central

Luo, Ming-Xing; Ma, Song-Ya; Chen, Xiu-Bo; Wang, Xiaojun

2015-01-01

Quantum computation offers potential advantages in solving a number of interesting and difficult problems. Several controlled logic gates, the elemental building blocks of quantum computer, have been realized with various physical systems. A general technique was recently proposed that significantly reduces the realization complexity of multiple-control logic gates by harnessing multi-level information carriers. We present implementations of a key quantum circuit: the three-qubit Toffoli gate. By exploring the optical selection rules of one-sided optical microcavities, a Toffoli gate may be realized on all combinations of photon and quantum spins in the QD-cavity. The three general controlled-NOT gates are involved using an auxiliary photon with two degrees of freedom. Our results show that photons and quantum spins may be used alternatively in quantum information processing. PMID:26568078
Hybrid Toffoli gate on photons and quantum spins.

PubMed

Luo, Ming-Xing; Ma, Song-Ya; Chen, Xiu-Bo; Wang, Xiaojun

2015-11-16

Quantum computation offers potential advantages in solving a number of interesting and difficult problems. Several controlled logic gates, the elemental building blocks of quantum computer, have been realized with various physical systems. A general technique was recently proposed that significantly reduces the realization complexity of multiple-control logic gates by harnessing multi-level information carriers. We present implementations of a key quantum circuit: the three-qubit Toffoli gate. By exploring the optical selection rules of one-sided optical microcavities, a Toffoli gate may be realized on all combinations of photon and quantum spins in the QD-cavity. The three general controlled-NOT gates are involved using an auxiliary photon with two degrees of freedom. Our results show that photons and quantum spins may be used alternatively in quantum information processing.
Multi-shape memory polymers achieved by the spatio-assembly of 3D printable thermoplastic building blocks.

PubMed

Li, Hongze; Gao, Xiang; Luo, Yingwu

2016-04-07

Multi-shape memory polymers were prepared by the macroscale spatio-assembly of building blocks in this work. The building blocks were methyl acrylate-co-styrene (MA-co-St) copolymers, which have the St-block-(St-random-MA)-block-St tri-block chain sequence. This design ensures that their transition temperatures can be adjusted over a wide range by varying the composition of the middle block. The two St blocks at the chain ends can generate a crosslink network in the final device to achieve strong bonding force between building blocks and the shape memory capacity. Due to their thermoplastic properties, 3D printing was employed for the spatio-assembly to build devices. This method is capable of introducing many transition phases into one device and preparing complicated shapes via 3D printing. The device can perform a complex action via a series of shape changes. Besides, this method can avoid the difficult programing of a series of temporary shapes. The control of intermediate temporary shapes was realized via programing the shapes and locations of building blocks in the final device.
Accessory oral cavity associated with duplication of the tongue and the mandible in a newborn: a rare case of Diprosopus. Multi-row detector computed tomography diagnostic role.

PubMed

Morabito, Rosa; Colonna, Michele R; Mormina, Enricomaria; Stagno d'Alcontres, Ferdinando; Salpietro, Vincenzo; Blandino, Alfredo; Longo, Marcello; Granata, Francesca

2014-12-01

Craniofacial duplication is a very rare malformation. The phenotype comprises a wide spectrum, ranging from partial duplication of few facial structures to complete dicephalus. We report the case of a newborn with an accessory oral cavity associated to duplication of the tongue and the mandible diagnosed by multi-row detector Computed Tomography, few days after her birth. Our case of partial craniofacial duplication can be considered as Type II of Gorlin classification or as an intermediate form between Type I and Type II of Sun classification. Our experience demonstrates that CT scan, using appropriate reconstruction algorithms, permits a detailed evaluation of the different structures in an anatomical region. Multi-row CT scan is also the more accurate diagnostic procedure for the pre-surgical evaluation of craniofacial malformations. Copyright © 2014 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.
InChIKey collision resistance: an experimental testing

PubMed Central

2012-01-01

InChIKey is a 27-character compacted (hashed) version of InChI which is intended for Internet and database searching/indexing and is based on an SHA-256 hash of the InChI character string. The first block of InChIKey encodes molecular skeleton while the second block represents various kinds of isomerism (stereo, tautomeric, etc.). InChIKey is designed to be a nearly unique substitute for the parent InChI. However, a single InChIKey may occasionally map to two or more InChI strings (collision). The appearance of collision itself does not compromise the signature as collision-free hashing is impossible; the only viable approach is to set and keep a reasonable level of collision resistance which is sufficient for typical applications. We tested, in computational experiments, how well the real-life InChIKey collision resistance corresponds to the theoretical estimates expected by design. For this purpose, we analyzed the statistical characteristics of InChIKey for datasets of variable size in comparison to the theoretical statistical frequencies. For the relatively short second block, an exhaustive direct testing was performed. We computed and compared to theory the numbers of collisions for the stereoisomers of Spongistatin I (using the whole set of 67,108,864 isomers and its subsets). For the longer first block, we generated, using custom-made software, InChIKeys for more than 3 × 1010 chemical structures. The statistical behavior of this block was tested by comparison of experimental and theoretical frequencies for the various four-letter sequences which may appear in the first block body. From the results of our computational experiments we conclude that the observed characteristics of InChIKey collision resistance are in good agreement with theoretical expectations. PMID:23256896
InChIKey collision resistance: an experimental testing.

PubMed

Pletnev, Igor; Erin, Andrey; McNaught, Alan; Blinov, Kirill; Tchekhovskoi, Dmitrii; Heller, Steve

2012-12-20

InChIKey is a 27-character compacted (hashed) version of InChI which is intended for Internet and database searching/indexing and is based on an SHA-256 hash of the InChI character string. The first block of InChIKey encodes molecular skeleton while the second block represents various kinds of isomerism (stereo, tautomeric, etc.). InChIKey is designed to be a nearly unique substitute for the parent InChI. However, a single InChIKey may occasionally map to two or more InChI strings (collision). The appearance of collision itself does not compromise the signature as collision-free hashing is impossible; the only viable approach is to set and keep a reasonable level of collision resistance which is sufficient for typical applications.We tested, in computational experiments, how well the real-life InChIKey collision resistance corresponds to the theoretical estimates expected by design. For this purpose, we analyzed the statistical characteristics of InChIKey for datasets of variable size in comparison to the theoretical statistical frequencies. For the relatively short second block, an exhaustive direct testing was performed. We computed and compared to theory the numbers of collisions for the stereoisomers of Spongistatin I (using the whole set of 67,108,864 isomers and its subsets). For the longer first block, we generated, using custom-made software, InChIKeys for more than 3 × 1010 chemical structures. The statistical behavior of this block was tested by comparison of experimental and theoretical frequencies for the various four-letter sequences which may appear in the first block body.From the results of our computational experiments we conclude that the observed characteristics of InChIKey collision resistance are in good agreement with theoretical expectations.
Community Seismic Network (CSN)

NASA Astrophysics Data System (ADS)

Clayton, R. W.; Heaton, T. H.; Kohler, M. D.; Chandy, M.; Krause, A.

2010-12-01

In collaboration with computer science and earthquake engineering, we are developing a dense network of low-cost accelerometers that send their data via the Internet to a cloud-based center. The goal is to make block-by-block measurements of ground shaking in urban areas, which will provide emergency response information in the case of large earthquakes, and an unprecedented high-frequency seismic array to study structure and the earthquake process with moderate shaking. When deployed in high-rise buildings they can be used to monitor the state of health of the structure. The sensors are capable of a resolution of approximately 80 micro-g, connect via USB ports to desktop computers, and cost about $100 each. The network will adapt to its environment by using network-wide machine learning to adjust the picking sensitivity. We are also looking into using other motion sensing devices such as cell phones. For a pilot project, we plan to deploy more than 1000 sensors in the greater Pasadena area. The system is easily adaptable to other seismically vulnerable urban areas.
Recent enhancements to the GRIDGEN structured grid generation system

NASA Technical Reports Server (NTRS)

Steinbrenner, John P.; Chawner, John R.

1992-01-01

Significant enhancements are being implemented into the GRIDGEN3D, multiple block, structured grid generation software. Automatic, point-to-point, interblock connectivity will be possible through the addition of the domain entity to GRIDBLOCK's block construction process. Also, the unification of GRIDGEN2D and GRIDBLOCK has begun with the addition of edge grid point distribution capability to GRIDBLOCK. The geometric accuracy of surface grids and the ease with which databases may be obtained is being improved by adding support for standard computer-aided design formats (e.g., PATRAN Neutral and IGES files). Finally, volume grid quality was improved through addition of new SOR algorithm features and the new hybrid control function type to GRIDGEN3D.
Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5

PubMed Central

Azoitei, M.L.; Ban, Y.A.; Kalyuzhny, O.; Guenaga, J.; Schroeter, A.; Porter, J.; Wyatt, R.; Schief, W.R.

2015-01-01

Rational design of proteins with novel binding specificities and increased affinity is one of the major goals of computational protein design. Epitope-scaffolds are a new class of antigens engineered by transplanting viral epitopes of pre-defined structure to protein scaffolds, or by building protein scaffolds around such epitopes. Epitope-scaffolds are of interest as vaccine components to attempt to elicit neutralizing antibodies targeting the specified epitope. In this study we developed a new computational protocol, MultiGraft Interface, that transplants epitopes but also designs additional scaffold features outside the epitope to enhance antibody-binding specificity and potentially influence the specificity of elicited antibodies. We employed MultiGraft Interface to engineer novel epitope-scaffolds that display the known epitope of HIV-1 neutralizing antibody 2F5 and that also interact with the functionally important CDR H3 antibody loop. MultiGraft Interface generated an epitope-scaffold that bound 2F5 with sub-nanomolar affinity (KD = 400 pM) and that interacted with the antibody CDR H3 loop through computationally designed contacts. Substantial structural modifications were necessary to engineer this antigen, with the 2F5 epitope replacing a helix in the native scaffold and with 15% of the native scaffold sequence being modified in the design stage. This epitope-scaffold represents a successful example of rational protein backbone engineering and protein-protein interface design and could prove useful in the field of HIV vaccine design. MultiGraft Interface can be generally applied to engineer novel binding partners with altered specificity and optimized affinity. PMID:25043744
Multi-scale structural community organisation of the human genome.

PubMed

Boulos, Rasha E; Tremblay, Nicolas; Arneodo, Alain; Borgnat, Pierre; Audit, Benjamin

2017-04-11

Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structural motifs characteristic of genome organisation. We deployed the fast multi-scale community mining algorithm based on spectral graph wavelets to characterise the networks of intra-chromosomal interactions in human cell lines. We observed that there exist structural domains of all sizes up to chromosome length and demonstrated that the set of structural communities forms a hierarchy of chromosome segments. Hence, at all scales, chromosome folding predominantly involves interactions between neighbouring sites rather than the formation of links between distant loci. Multi-scale structural decomposition of human chromosomes provides an original framework to question structural organisation and its relationship to functional regulation across the scales. By construction the proposed methodology is independent of the precise assembly of the reference genome and is thus directly applicable to genomes whose assembly is not fully determined.

Testing of a Stitched Composite Large-Scale Multi-Bay Pressure Box

NASA Technical Reports Server (NTRS)

Jegley, Dawn; Rouse, Marshall; Przekop, Adam; Lovejoy, Andrew

2016-01-01

NASA has created the Environmentally Responsible Aviation (ERA) Project to develop technologies to reduce aviation's impact on the environment. A critical aspect of this pursuit is the development of a lighter, more robust airframe to enable the introduction of unconventional aircraft configurations. NASA and The Boeing Company have worked together to develop a structural concept that is lightweight and an advancement beyond state-of-the-art composite structures. The Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS) is an integrally stiffened panel design where elements are stitched together. The PRSEUS concept is designed to maintain residual load carrying capabilities under a variety of damage scenarios. A series of building block tests were evaluated to explore the fundamental assumptions related to the capability and advantages of PRSEUS panels. The final step in the building block series is an 80%-scale pressure box representing a portion of the center section of a Hybrid Wing Body (HWB) transport aircraft. The testing of this article under maneuver load and internal pressure load conditions is the subject of this paper. The experimental evaluation of this article, along with the other building block tests and the accompanying analyses, has demonstrated the viability of a PRSEUS center body for the HWB vehicle. Additionally, much of the development effort is also applicable to traditional tube-and-wing aircraft, advanced aircraft configurations, and other structures where weight and through-the-thickness strength are design considerations.
Space Shuttle Communications Coverage Analysis for Thermal Tile Inspection

NASA Technical Reports Server (NTRS)

Kroll, Quin D.; Hwu, Shian U.; Upanavage, Matthew; Boster, John P.; Chavez, Mark A.

2009-01-01

The space shuttle ultra-high frequency Space-to-Space Communication System has to provide adequate communication coverage for astronauts who are performing thermal tile inspection and repair on the underside of the space shuttle orbiter (SSO). Careful planning and quantitative assessment are necessary to ensure successful system operations and mission safety in this work environment. This study assesses communication systems performance for astronauts who are working in the underside, non-line-of-sight shadow region on the space shuttle. All of the space shuttle and International Space Station (ISS) transmitting antennas are blocked by the SSO structure. To ensure communication coverage at planned inspection worksites, the signal strength and link margin between the SSO/ISS antennas and the extravehicular activity astronauts, whose line-of-sight is blocked by vehicle structure, was analyzed. Investigations were performed using rigorous computational electromagnetic modeling techniques. Signal strength was obtained by computing the reflected and diffracted fields along the signal propagation paths between transmitting and receiving antennas. Radio frequency (RF) coverage was determined for thermal tile inspection and repair missions using the results of this computation. Analysis results from this paper are important in formulating the limits on reliable communication range and RF coverage at planned underside inspection and repair worksites.
Biomorphic Multi-Agent Architecture for Persistent Computing

NASA Technical Reports Server (NTRS)

Lodding, Kenneth N.; Brewster, Paul

2009-01-01

A multi-agent software/hardware architecture, inspired by the multicellular nature of living organisms, has been proposed as the basis of design of a robust, reliable, persistent computing system. Just as a multicellular organism can adapt to changing environmental conditions and can survive despite the failure of individual cells, a multi-agent computing system, as envisioned, could adapt to changing hardware, software, and environmental conditions. In particular, the computing system could continue to function (perhaps at a reduced but still reasonable level of performance) if one or more component( s) of the system were to fail. One of the defining characteristics of a multicellular organism is unity of purpose. In biology, the purpose is survival of the organism. The purpose of the proposed multi-agent architecture is to provide a persistent computing environment in harsh conditions in which repair is difficult or impossible. A multi-agent, organism-like computing system would be a single entity built from agents or cells. Each agent or cell would be a discrete hardware processing unit that would include a data processor with local memory, an internal clock, and a suite of communication equipment capable of both local line-of-sight communications and global broadcast communications. Some cells, denoted specialist cells, could contain such additional hardware as sensors and emitters. Each cell would be independent in the sense that there would be no global clock, no global (shared) memory, no pre-assigned cell identifiers, no pre-defined network topology, and no centralized brain or control structure. Like each cell in a living organism, each agent or cell of the computing system would contain a full description of the system encoded as genes, but in this case, the genes would be components of a software genome.
Compressed multi-block local binary pattern for object tracking

NASA Astrophysics Data System (ADS)

Li, Tianwen; Gao, Yun; Zhao, Lei; Zhou, Hao

2018-04-01

Both robustness and real-time are very important for the application of object tracking under a real environment. The focused trackers based on deep learning are difficult to satisfy with the real-time of tracking. Compressive sensing provided a technical support for real-time tracking. In this paper, an object can be tracked via a multi-block local binary pattern feature. The feature vector was extracted based on the multi-block local binary pattern feature, which was compressed via a sparse random Gaussian matrix as the measurement matrix. The experiments showed that the proposed tracker ran in real-time and outperformed the existed compressive trackers based on Haar-like feature on many challenging video sequences in terms of accuracy and robustness.
Dynamically reassigning a connected node to a block of compute nodes for re-launching a failed job

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

Budnik, Thomas A; Knudson, Brant L; Megerian, Mark G

Methods, systems, and products for dynamically reassigning a connected node to a block of compute nodes for re-launching a failed job that include: identifying that a job failed to execute on the block of compute nodes because connectivity failed between a compute node assigned as at least one of the connected nodes for the block of compute nodes and its supporting I/O node; and re-launching the job, including selecting an alternative connected node that is actively coupled for data communications with an active I/O node; and assigning the alternative connected node as the connected node for the block of computemore » nodes running the re-launched job.« less
Structure identification methods for atomistic simulations of crystalline materials

DOE PAGES

Stukowski, Alexander

2012-05-28

Here, we discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.
Transport-aware imaging

NASA Astrophysics Data System (ADS)

Kutulakos, Kyros N.; O'Toole, Matthew

2015-03-01

Conventional cameras record all light falling on their sensor regardless of the path that light followed to get there. In this paper we give an overview of a new family of computational cameras that offers many more degrees of freedom. These cameras record just a fraction of the light coming from a controllable source, based on the actual 3D light path followed. Photos and live video captured this way offer an unconventional view of everyday scenes in which the effects of scattering, refraction and other phenomena can be selectively blocked or enhanced, visual structures that are too subtle to notice with the naked eye can become apparent, and object appearance can depend on depth. We give an overview of the basic theory behind these cameras and their DMD-based implementation, and discuss three applications: (1) live indirect-only imaging of complex everyday scenes, (2) reconstructing the 3D shape of scenes whose geometry or material properties make them hard or impossible to scan with conventional methods, and (3) acquiring time-of-flight images that are free of multi-path interference.
A versatile embedded boundary adaptive mesh method for compressible flow in complex geometry

NASA Astrophysics Data System (ADS)

Al-Marouf, M.; Samtaney, R.

2017-05-01

We present an embedded ghost fluid method for numerical solutions of the compressible Navier Stokes (CNS) equations in arbitrary complex domains. A PDE multidimensional extrapolation approach is used to reconstruct the solution in the ghost fluid regions and imposing boundary conditions on the fluid-solid interface, coupled with a multi-dimensional algebraic interpolation for freshly cleared cells. The CNS equations are numerically solved by the second order multidimensional upwind method. Block-structured adaptive mesh refinement, implemented with the Chombo framework, is utilized to reduce the computational cost while keeping high resolution mesh around the embedded boundary and regions of high gradient solutions. The versatility of the method is demonstrated via several numerical examples, in both static and moving geometry, ranging from low Mach number nearly incompressible flows to supersonic flows. Our simulation results are extensively verified against other numerical results and validated against available experimental results where applicable. The significance and advantages of our implementation, which revolve around balancing between the solution accuracy and implementation difficulties, are briefly discussed as well.
Evolution-Inspired Computational Design of Symmetric Proteins.

PubMed

Voet, Arnout R D; Simoncini, David; Tame, Jeremy R H; Zhang, Kam Y J

2017-01-01

Monomeric proteins with a number of identical repeats creating symmetrical structures are potentially very valuable building blocks with a variety of bionanotechnological applications. As such proteins do not occur naturally, the emerging field of computational protein design serves as an excellent tool to create them from nonsymmetrical templates. Existing pseudo-symmetrical proteins are believed to have evolved from oligomeric precursors by duplication and fusion of identical repeats. Here we describe a computational workflow to reverse-engineer this evolutionary process in order to create stable proteins consisting of identical sequence repeats.
Standardized Modular Power Interfaces for Future Space Explorations Missions

NASA Technical Reports Server (NTRS)

Oeftering, Richard

2015-01-01

Earlier studies show that future human explorations missions are composed of multi-vehicle assemblies with interconnected electric power systems. Some vehicles are often intended to serve as flexible multi-purpose or multi-mission platforms. This drives the need for power architectures that can be reconfigured to support this level of flexibility. Power system developmental costs can be reduced, program wide, by utilizing a common set of modular building blocks. Further, there are mission operational and logistics cost benefits of using a common set of modular spares. These benefits are the goals of the Advanced Exploration Systems (AES) Modular Power System (AMPS) project. A common set of modular blocks requires a substantial level of standardization in terms of the Electrical, Data System, and Mechanical interfaces. The AMPS project is developing a set of proposed interface standards that will provide useful guidance for modular hardware developers but not needlessly constrain technology options, or limit future growth in capability. In 2015 the AMPS project focused on standardizing the interfaces between the elements of spacecraft power distribution and energy storage. The development of the modular power standard starts with establishing mission assumptions and ground rules to define design application space. The standards are defined in terms of AMPS objectives including Commonality, Reliability-Availability, Flexibility-Configurability and Supportability-Reusability. The proposed standards are aimed at assembly and sub-assembly level building blocks. AMPS plans to adopt existing standards for spacecraft command and data, software, network interfaces, and electrical power interfaces where applicable. Other standards including structural encapsulation, heat transfer, and fluid transfer, are governed by launch and spacecraft environments and bound by practical limitations of weight and volume. Developing these mechanical interface standards is more difficult but an essential part of defining physical building blocks of modular power. This presentation describes the AMPS projects progress towards standardized modular power interfaces.
a Mini Multi-Gas Detection System Based on Infrared Principle

NASA Astrophysics Data System (ADS)

Zhijian, Xie; Qiulin, Tan

2006-12-01

To counter the problems of gas accidents in coal mines, family safety resulted from using gas, a new infrared detection system with integration and miniaturization has been developed. The infrared detection optics principle used in developing this system is mainly analyzed. The idea that multi gas detection is introduced and guided through analyzing single gas detection is got across. Through researching the design of cell structure, the cell with integration and miniaturization has been devised. The way of data transmission on Controller Area Network (CAN) bus is explained. By taking Single-Chip Microcomputer (SCM) as intelligence handling, the functional block diagram of gas detection system is designed with its hardware and software system analyzed and devised. This system designed has reached the technology requirement of lower power consumption, mini-volume, big measure range, and able to realize multi-gas detection.
Viscous flow past a collapsible channel as a model for self-excited oscillation of blood vessels.

PubMed

Tang, Chao; Zhu, Luoding; Akingba, George; Lu, Xi-Yun

2015-07-16

Motivated by collapse of blood vessels for both healthy and diseased situations under various circumstances in human body, we have performed computational studies on an incompressible viscous fluid past a rigid channel with part of its upper wall being replaced by a deformable beam. The Navier-Stokes equations governing the fluid flow are solved by a multi-block lattice Boltzmann method and the structural equation governing the elastic beam motion by a finite difference method. The mutual coupling of the fluid and solid is realized by the momentum exchange scheme. The present study focuses on the influences of the dimensionless parameters controlling the fluid-structure system on the collapse and self-excited oscillation of the beam and fluid dynamics downstream. The major conclusions obtained in this study are described as follows. The self-excited oscillation can be intrigued by application of an external pressure on the elastic portion of the channel and the part of the beam having the largest deformation tends to occur always towards the end portion of the deformable wall. The blood pressure and wall shear stress undergo significant variations near the portion of the greatest oscillation. The stretching motion has the most contribution to the total potential elastic energy of the oscillating beam. Copyright © 2015 Elsevier Ltd. All rights reserved.
Probabilistic Multi-Scale, Multi-Level, Multi-Disciplinary Analysis and Optimization of Engine Structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Abumeri, Galib H.

2000-01-01

Aircraft engines are assemblies of dynamically interacting components. Engine updates to keep present aircraft flying safely and engines for new aircraft are progressively required to operate in more demanding technological and environmental requirements. Designs to effectively meet those requirements are necessarily collections of multi-scale, multi-level, multi-disciplinary analysis and optimization methods and probabilistic methods are necessary to quantify respective uncertainties. These types of methods are the only ones that can formally evaluate advanced composite designs which satisfy those progressively demanding requirements while assuring minimum cost, maximum reliability and maximum durability. Recent research activities at NASA Glenn Research Center have focused on developing multi-scale, multi-level, multidisciplinary analysis and optimization methods. Multi-scale refers to formal methods which describe complex material behavior metal or composite; multi-level refers to integration of participating disciplines to describe a structural response at the scale of interest; multidisciplinary refers to open-ended for various existing and yet to be developed discipline constructs required to formally predict/describe a structural response in engine operating environments. For example, these include but are not limited to: multi-factor models for material behavior, multi-scale composite mechanics, general purpose structural analysis, progressive structural fracture for evaluating durability and integrity, noise and acoustic fatigue, emission requirements, hot fluid mechanics, heat-transfer and probabilistic simulations. Many of these, as well as others, are encompassed in an integrated computer code identified as Engine Structures Technology Benefits Estimator (EST/BEST) or Multi-faceted/Engine Structures Optimization (MP/ESTOP). The discipline modules integrated in MP/ESTOP include: engine cycle (thermodynamics), engine weights, internal fluid mechanics, cost, mission and coupled structural/thermal, various composite property simulators and probabilistic methods to evaluate uncertainty effects (scatter ranges) in all the design parameters. The objective of the proposed paper is to briefly describe a multi-faceted design analysis and optimization capability for coupled multi-discipline engine structures optimization. Results are presented for engine and aircraft type metrics to illustrate the versatility of that capability. Results are also presented for reliability, noise and fatigue to illustrate its inclusiveness. For example, replacing metal rotors with composites reduces the engine weight by 20 percent, 15 percent noise reduction, and an order of magnitude improvement in reliability. Composite designs exist to increase fatigue life by at least two orders of magnitude compared to state-of-the-art metals.
Multi-body Dynamic Contact Analysis Tool for Transmission Design

DTIC Science & Technology

2003-04-01

frequencies were computed in COSMIC NASTRAN, and were validated against the published experimental modal analysis [17]. • Using assumed time domain... modal superposition. • Results from the structural analysis (mode shapes or forced response) were converted into IDEAS universal format (dataset 55...ARMY RESEARCH LABORATORY Multi-body Dynamic Contact Analysis Tool for Transmission Design SBIR Phase II Final Report by
Nonlinear dynamic simulation of single- and multi-spool core engines

NASA Technical Reports Server (NTRS)

Schobeiri, T.; Lippke, C.; Abouelkheir, M.

1993-01-01

In this paper a new computational method for accurate simulation of the nonlinear dynamic behavior of single- and multi-spool core engines, turbofan engines, and power generation gas turbine engines is presented. In order to perform the simulation, a modularly structured computer code has been developed which includes individual mathematical modules representing various engine components. The generic structure of the code enables the dynamic simulation of arbitrary engine configurations ranging from single-spool thrust generation to multi-spool thrust/power generation engines under adverse dynamic operating conditions. For precise simulation of turbine and compressor components, row-by-row calculation procedures were implemented that account for the specific turbine and compressor cascade and blade geometry and characteristics. The dynamic behavior of the subject engine is calculated by solving a number of systems of partial differential equations, which describe the unsteady behavior of the individual components. In order to ensure the capability, accuracy, robustness, and reliability of the code, comprehensive critical performance assessment and validation tests were performed. As representatives, three different transient cases with single- and multi-spool thrust and power generation engines were simulated. The transient cases range from operating with a prescribed fuel schedule, to extreme load changes, to generator and turbine shut down.
Genuine multipartite entanglement of symmetric Gaussian states: Strong monogamy, unitary localization, scaling behavior, and molecular sharing structure

NASA Astrophysics Data System (ADS)

Adesso, Gerardo; Illuminati, Fabrizio

2008-10-01

We investigate the structural aspects of genuine multipartite entanglement in Gaussian states of continuous variable systems. Generalizing the results of Adesso and Illuminati [Phys. Rev. Lett. 99, 150501 (2007)], we analyze whether the entanglement shared by blocks of modes distributes according to a strong monogamy law. This property, once established, allows us to quantify the genuine N -partite entanglement not encoded into 2,…,K,…,(N-1) -partite quantum correlations. Strong monogamy is numerically verified, and the explicit expression of the measure of residual genuine multipartite entanglement is analytically derived, by a recursive formula, for a subclass of Gaussian states. These are fully symmetric (permutation-invariant) states that are multipartitioned into blocks, each consisting of an arbitrarily assigned number of modes. We compute the genuine multipartite entanglement shared by the blocks of modes and investigate its scaling properties with the number and size of the blocks, the total number of modes, the global mixedness of the state, and the squeezed resources needed for state engineering. To achieve the exact computation of the block entanglement, we introduce and prove a general result of symplectic analysis: Correlations among K blocks in N -mode multisymmetric and multipartite Gaussian states, which are locally invariant under permutation of modes within each block, can be transformed by a local (with respect to the partition) unitary operation into correlations shared by K single modes, one per block, in effective nonsymmetric states where N-K modes are completely uncorrelated. Due to this theorem, the above results, such as the derivation of the explicit expression for the residual multipartite entanglement, its nonnegativity, and its scaling properties, extend to the subclass of non-symmetric Gaussian states that are obtained by the unitary localization of the multipartite entanglement of symmetric states. These findings provide strong numerical evidence that the distributed Gaussian entanglement is strongly monogamous under and possibly beyond specific symmetry constraints, and that the residual continuous-variable tangle is a proper measure of genuine multipartite entanglement for permutation-invariant Gaussian states under any multipartition of the modes.
Effect of randomness on multi-frequency aeroelastic responses resolved by Unsteady Adaptive Stochastic Finite Elements

NASA Astrophysics Data System (ADS)

Witteveen, Jeroen A. S.; Bijl, Hester

2009-10-01

The Unsteady Adaptive Stochastic Finite Elements (UASFE) method resolves the effect of randomness in numerical simulations of single-mode aeroelastic responses with a constant accuracy in time for a constant number of samples. In this paper, the UASFE framework is extended to multi-frequency responses and continuous structures by employing a wavelet decomposition pre-processing step to decompose the sampled multi-frequency signals into single-frequency components. The effect of the randomness on the multi-frequency response is then obtained by summing the results of the UASFE interpolation at constant phase for the different frequency components. Results for multi-frequency responses and continuous structures show a three orders of magnitude reduction of computational costs compared to crude Monte Carlo simulations in a harmonically forced oscillator, a flutter panel problem, and the three-dimensional transonic AGARD 445.6 wing aeroelastic benchmark subject to random fields and random parameters with various probability distributions.
Structure-biodegradability study and computer-automated prediction of aerobic biodegradation of chemicals

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

Klopman, G.; Tu, M.

1997-09-01

It is shown that a combination of two programs, MultiCASE and META, can help assess the biodegradability of industrial organic materials in the ecosystem. MultiCASE is an artificial intelligence computer program that had been trained to identify molecular substructures believed to cause or inhibit biodegradation and META is an expert system trained to predict the aerobic biodegradation products of organic molecules. These two programs can be used to help evaluate the fate of disposed chemicals by estimating their biodegradability and the nature of their biodegradation products under conditions that may model the environment.
Audio-Visual Perception of 3D Cinematography: An fMRI Study Using Condition-Based and Computation-Based Analyses

PubMed Central

Ogawa, Akitoshi; Bordier, Cecile; Macaluso, Emiliano

2013-01-01

The use of naturalistic stimuli to probe sensory functions in the human brain is gaining increasing interest. Previous imaging studies examined brain activity associated with the processing of cinematographic material using both standard “condition-based” designs, as well as “computational” methods based on the extraction of time-varying features of the stimuli (e.g. motion). Here, we exploited both approaches to investigate the neural correlates of complex visual and auditory spatial signals in cinematography. In the first experiment, the participants watched a piece of a commercial movie presented in four blocked conditions: 3D vision with surround sounds (3D-Surround), 3D with monaural sound (3D-Mono), 2D-Surround, and 2D-Mono. In the second experiment, they watched two different segments of the movie both presented continuously in 3D-Surround. The blocked presentation served for standard condition-based analyses, while all datasets were submitted to computation-based analyses. The latter assessed where activity co-varied with visual disparity signals and the complexity of auditory multi-sources signals. The blocked analyses associated 3D viewing with the activation of the dorsal and lateral occipital cortex and superior parietal lobule, while the surround sounds activated the superior and middle temporal gyri (S/MTG). The computation-based analyses revealed the effects of absolute disparity in dorsal occipital and posterior parietal cortices and of disparity gradients in the posterior middle temporal gyrus plus the inferior frontal gyrus. The complexity of the surround sounds was associated with activity in specific sub-regions of S/MTG, even after accounting for changes of sound intensity. These results demonstrate that the processing of naturalistic audio-visual signals entails an extensive set of visual and auditory areas, and that computation-based analyses can track the contribution of complex spatial aspects characterizing such life-like stimuli. PMID:24194828
Sparse PDF Volumes for Consistent Multi-Resolution Volume Rendering.

PubMed

Sicat, Ronell; Krüger, Jens; Möller, Torsten; Hadwiger, Markus

2014-12-01

This paper presents a new multi-resolution volume representation called sparse pdf volumes, which enables consistent multi-resolution volume rendering based on probability density functions (pdfs) of voxel neighborhoods. These pdfs are defined in the 4D domain jointly comprising the 3D volume and its 1D intensity range. Crucially, the computation of sparse pdf volumes exploits data coherence in 4D, resulting in a sparse representation with surprisingly low storage requirements. At run time, we dynamically apply transfer functions to the pdfs using simple and fast convolutions. Whereas standard low-pass filtering and down-sampling incur visible differences between resolution levels, the use of pdfs facilitates consistent results independent of the resolution level used. We describe the efficient out-of-core computation of large-scale sparse pdf volumes, using a novel iterative simplification procedure of a mixture of 4D Gaussians. Finally, our data structure is optimized to facilitate interactive multi-resolution volume rendering on GPUs.

Duct flow nonuniformities: Effect of struts in SSME HGM II(+)

NASA Technical Reports Server (NTRS)

Burke, Roger

1988-01-01

A numerical study, using the INS3D flow solver, of laminar and turbulent flow around a two dimensional strut, and three dimensional flow around a strut in an annulus is presented. A multi-block procedure was used to calculate two dimensional laminar flow around two struts in parallel, with each strut represented by one computational block. Single block calculations were performed for turbulent flow around a two dimensional strut, using a Baldwin-Lomax turbulence model to parameterize the turbulent shear stresses. A modified Baldwin-Lomax model was applied to the case of a three dimensional strut in an annulus. The results displayed the essential features of wing-body flows, including the presence of a horseshoe vortex system at the junction of the strut and the lower annulus surface. A similar system was observed at the upper annulus surface. The test geometries discussed were useful in developing the capability to perform multiblock calculations, and to simulate turbulent flow around obstructions located between curved walls. Both of these skills will be necessary to model the three dimensional flow in the strut assembly of the SSME. Work is now in progress on performing a three dimensional two block turbulent calculation of the flow in the turnaround duct (TAD) and strut/fuel bowl juncture region.
Toward Transparent Data Management in Multi-layer Storage Hierarchy for HPC Systems

DOE PAGES

Wadhwa, Bharti; Byna, Suren; Butt, Ali R.

2018-04-17

Upcoming exascale high performance computing (HPC) systems are expected to comprise multi-tier storage hierarchy, and thus will necessitate innovative storage and I/O mechanisms. Traditional disk and block-based interfaces and file systems face severe challenges in utilizing capabilities of storage hierarchies due to the lack of hierarchy support and semantic interfaces. Object-based and semantically-rich data abstractions for scientific data management on large scale systems offer a sustainable solution to these challenges. Such data abstractions can also simplify users involvement in data movement. Here, we take the first steps of realizing such an object abstraction and explore storage mechanisms for these objectsmore » to enhance I/O performance, especially for scientific applications. We explore how an object-based interface can facilitate next generation scalable computing systems by presenting the mapping of data I/O from two real world HPC scientific use cases: a plasma physics simulation code (VPIC) and a cosmology simulation code (HACC). Our storage model stores data objects in different physical organizations to support data movement across layers of memory/storage hierarchy. Our implementation sclaes well to 16K parallel processes, and compared to the state of the art, such as MPI-IO and HDF5, our object-based data abstractions and data placement strategy in multi-level storage hierarchy achieves up to 7 X I/O performance improvement for scientific data.« less
Toward Transparent Data Management in Multi-layer Storage Hierarchy for HPC Systems

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

Wadhwa, Bharti; Byna, Suren; Butt, Ali R.

Upcoming exascale high performance computing (HPC) systems are expected to comprise multi-tier storage hierarchy, and thus will necessitate innovative storage and I/O mechanisms. Traditional disk and block-based interfaces and file systems face severe challenges in utilizing capabilities of storage hierarchies due to the lack of hierarchy support and semantic interfaces. Object-based and semantically-rich data abstractions for scientific data management on large scale systems offer a sustainable solution to these challenges. Such data abstractions can also simplify users involvement in data movement. Here, we take the first steps of realizing such an object abstraction and explore storage mechanisms for these objectsmore » to enhance I/O performance, especially for scientific applications. We explore how an object-based interface can facilitate next generation scalable computing systems by presenting the mapping of data I/O from two real world HPC scientific use cases: a plasma physics simulation code (VPIC) and a cosmology simulation code (HACC). Our storage model stores data objects in different physical organizations to support data movement across layers of memory/storage hierarchy. Our implementation sclaes well to 16K parallel processes, and compared to the state of the art, such as MPI-IO and HDF5, our object-based data abstractions and data placement strategy in multi-level storage hierarchy achieves up to 7 X I/O performance improvement for scientific data.« less
A multi-satellite orbit determination problem in a parallel processing environment

NASA Technical Reports Server (NTRS)

Deakyne, M. S.; Anderle, R. J.

1988-01-01

The Engineering Orbit Analysis Unit at GE Valley Forge used an Intel Hypercube Parallel Processor to investigate the performance and gain experience of parallel processors with a multi-satellite orbit determination problem. A general study was selected in which major blocks of computation for the multi-satellite orbit computations were used as units to be assigned to the various processors on the Hypercube. Problems encountered or successes achieved in addressing the orbit determination problem would be more likely to be transferable to other parallel processors. The prime objective was to study the algorithm to allow processing of observations later in time than those employed in the state update. Expertise in ephemeris determination was exploited in addressing these problems and the facility used to bring a realism to the study which would highlight the problems which may not otherwise be anticipated. Secondary objectives were to gain experience of a non-trivial problem in a parallel processor environment, to explore the necessary interplay of serial and parallel sections of the algorithm in terms of timing studies, to explore the granularity (coarse vs. fine grain) to discover the granularity limit above which there would be a risk of starvation where the majority of nodes would be idle or under the limit where the overhead associated with splitting the problem may require more work and communication time than is useful.
Parallel processors and nonlinear structural dynamics algorithms and software

NASA Technical Reports Server (NTRS)

Belytschko, Ted

1990-01-01

Techniques are discussed for the implementation and improvement of vectorization and concurrency in nonlinear explicit structural finite element codes. In explicit integration methods, the computation of the element internal force vector consumes the bulk of the computer time. The program can be efficiently vectorized by subdividing the elements into blocks and executing all computations in vector mode. The structuring of elements into blocks also provides a convenient way to implement concurrency by creating tasks which can be assigned to available processors for evaluation. The techniques were implemented in a 3-D nonlinear program with one-point quadrature shell elements. Concurrency and vectorization were first implemented in a single time step version of the program. Techniques were developed to minimize processor idle time and to select the optimal vector length. A comparison of run times between the program executed in scalar, serial mode and the fully vectorized code executed concurrently using eight processors shows speed-ups of over 25. Conjugate gradient methods for solving nonlinear algebraic equations are also readily adapted to a parallel environment. A new technique for improving convergence properties of conjugate gradients in nonlinear problems is developed in conjunction with other techniques such as diagonal scaling. A significant reduction in the number of iterations required for convergence is shown for a statically loaded rigid bar suspended by three equally spaced springs.
Magnetohydrodynamic Simulations of Black Hole Accretion Flows Using PATCHWORK, a Multi-Patch, multi-code approach

NASA Astrophysics Data System (ADS)

Avara, Mark J.; Noble, Scott; Shiokawa, Hotaka; Cheng, Roseanne; Campanelli, Manuela; Krolik, Julian H.

2017-08-01

A multi-patch approach to numerical simulations of black hole accretion flows allows one to robustly match numerical grid shape and equations solved to the natural structure of the physical system. For instance, a cartesian gridded patch can be used to cover coordinate singularities on a spherical-polar grid, increasing computational efficiency and better capturing the physical system through natural symmetries. We will present early tests, initial applications, and first results from the new MHD implementation of the PATCHWORK framework.
Beyond Low Rank + Sparse: Multi-scale Low Rank Matrix Decomposition

PubMed Central

Ong, Frank; Lustig, Michael

2016-01-01

We present a natural generalization of the recent low rank + sparse matrix decomposition and consider the decomposition of matrices into components of multiple scales. Such decomposition is well motivated in practice as data matrices often exhibit local correlations in multiple scales. Concretely, we propose a multi-scale low rank modeling that represents a data matrix as a sum of block-wise low rank matrices with increasing scales of block sizes. We then consider the inverse problem of decomposing the data matrix into its multi-scale low rank components and approach the problem via a convex formulation. Theoretically, we show that under various incoherence conditions, the convex program recovers the multi-scale low rank components either exactly or approximately. Practically, we provide guidance on selecting the regularization parameters and incorporate cycle spinning to reduce blocking artifacts. Experimentally, we show that the multi-scale low rank decomposition provides a more intuitive decomposition than conventional low rank methods and demonstrate its effectiveness in four applications, including illumination normalization for face images, motion separation for surveillance videos, multi-scale modeling of the dynamic contrast enhanced magnetic resonance imaging and collaborative filtering exploiting age information. PMID:28450978
Leveraging unsupervised training sets for multi-scale compartmentalization in renal pathology

NASA Astrophysics Data System (ADS)

Lutnick, Brendon; Tomaszewski, John E.; Sarder, Pinaki

2017-03-01

Clinical pathology relies on manual compartmentalization and quantification of biological structures, which is time consuming and often error-prone. Application of computer vision segmentation algorithms to histopathological image analysis, in contrast, can offer fast, reproducible, and accurate quantitative analysis to aid pathologists. Algorithms tunable to different biologically relevant structures can allow accurate, precise, and reproducible estimates of disease states. In this direction, we have developed a fast, unsupervised computational method for simultaneously separating all biologically relevant structures from histopathological images in multi-scale. Segmentation is achieved by solving an energy optimization problem. Representing the image as a graph, nodes (pixels) are grouped by minimizing a Potts model Hamiltonian, adopted from theoretical physics, modeling interacting electron spins. Pixel relationships (modeled as edges) are used to update the energy of the partitioned graph. By iteratively improving the clustering, the optimal number of segments is revealed. To reduce computational time, the graph is simplified using a Cantor pairing function to intelligently reduce the number of included nodes. The classified nodes are then used to train a multiclass support vector machine to apply the segmentation over the full image. Accurate segmentations of images with as many as 106 pixels can be completed only in 5 sec, allowing for attainable multi-scale visualization. To establish clinical potential, we employed our method in renal biopsies to quantitatively visualize for the first time scale variant compartments of heterogeneous intra- and extraglomerular structures simultaneously. Implications of the utility of our method extend to fields such as oncology, genomics, and non-biological problems.
THE 4-AMINOPYRIDINE IN VITRO EPILEPSY MODEL ANALYZED WITH A PERFORATED MULTI-ELECTRODE ARRAY

PubMed Central

Gonzalez-Sulser, Alfredo; Wang, Jing; Motamedi, Gholam K.; Avoli, Massimo; Vicini, Stefano; Dzakpasu, Rhonda

2010-01-01

Epileptiform discharges recorded in the 4-aminopyridine (4-AP) in vitro epilepsy model are mediated by glutamatergic and GABAergic signaling. Using a 60-channel perforated multi-electrode array (pMEA) on corticohippocampal slices from 2 to 3 week old mice we recorded interictal- and ictal-like events. When glutamatergic transmission was blocked, interictal-like events events no longer initiated in the hilus or CA3/CA1 pyramidal layers but originated from the dentate gyrus granule and molecular layers. Furthermore, frequencies of interictal-like events were reduced and durations were increased in these regions while cortical discharges were completely blocked. Following GABAA receptor blockade interictal-like events no longer propagated to the dentate gyrus while their frequency in CA3 increased; in addition, ictal-like cortical events became shorter while increasing in frequency. Lastly, drugs that affect tonic and synaptic GABAergic conductance modulate the frequency, duration, initiation and propagation of interictal-like events. These findings confirm and expand on previous studies indicating that multiple synaptic mechanisms contribute to synchronize neuronal network activity in forebrain structures. PMID:20955719
Is scaffold hopping a reliable indicator for the ability of computational methods to identify structurally diverse active compounds?

NASA Astrophysics Data System (ADS)

Dimova, Dilyana; Bajorath, Jürgen

2017-07-01

Computational scaffold hopping aims to identify core structure replacements in active compounds. To evaluate scaffold hopping potential from a principal point of view, regardless of the computational methods that are applied, a global analysis of conventional scaffolds in analog series from compound activity classes was carried out. The majority of analog series was found to contain multiple scaffolds, thus enabling the detection of intra-series scaffold hops among closely related compounds. More than 1000 activity classes were found to contain increasing proportions of multi-scaffold analog series. Thus, using such activity classes for scaffold hopping analysis is likely to overestimate the scaffold hopping (core structure replacement) potential of computational methods, due to an abundance of artificial scaffold hops that are possible within analog series.
Modeling Equity for Alternative Water Rate Structures

NASA Astrophysics Data System (ADS)

Griffin, R.; Mjelde, J.

2011-12-01

The rising popularity of increasing block rates for urban water runs counter to mainstream economic recommendations, yet decision makers in rate design forums are attracted to the notion of higher prices for larger users. Among economists, it is widely appreciated that uniform rates have stronger efficiency properties than increasing block rates, especially when volumetric prices incorporate intrinsic water value. Yet, except for regions where water market purchases have forced urban authorities to include water value in water rates, economic arguments have weakly penetrated policy. In this presentation, recent evidence will be reviewed regarding long term trends in urban rate structures while observing economic principles pertaining to these choices. The main objective is to investigate the equity of increasing block rates as contrasted to uniform rates for a representative city. Using data from four Texas cities, household water demand is established as a function of marginal price, income, weather, number of residents, and property characteristics. Two alternative rate proposals are designed on the basis of recent experiences for both water and wastewater rates. After specifying a reasonable number (~200) of diverse households populating the city and parameterizing each household's characteristics, every household's consumption selections are simulated for twelve months. This procedure is repeated for both rate systems. Monthly water and wastewater bills are also computed for each household. Most importantly, while balancing the budget of the city utility we compute the effect of switching rate structures on the welfares of households of differing types. Some of the empirical findings are as follows. Under conditions of absent water scarcity, households of opposing characters such as low versus high income do not have strong preferences regarding rate structure selection. This changes as water scarcity rises and as water's opportunity costs are allowed to influence uniform rates. The welfare results of these exercises indicate that popular conceptions about increasing block rates may be incorrect insofar as the scarcity-endogenous uniform rate favors low-income households. That is, under scarcity conditions a switch from increasing block rates to full price uniform rates redistributes welfare so as to place more of the welfare burden of conservation on high-income households. Similarly, any household characteristic that tends to accompany low water use (e.g. low property value) generates a the same rate structure preference. These results are an intriguing addition to existing knowledge pertaining to the properties of increasing block rates and uniform rates with respect to criteria such as efficiency, simplicity, effectiveness, and (now) equity.
On topological RNA interaction structures.

PubMed

Qin, Jing; Reidys, Christian M

2013-07-01

Recently a folding algorithm of topological RNA pseudoknot structures was presented in Reidys et al. (2011). This algorithm folds single-stranded γ-structures, that is, RNA structures composed by distinct motifs of bounded topological genus. In this article, we set the theoretical foundations for the folding of the two backbone analogues of γ structures: the RNA γ-interaction structures. These are RNA-RNA interaction structures that are constructed by a finite number of building blocks over two backbones having genus at most γ. Combinatorial properties of γ-interaction structures are of practical interest since they have direct implications for the folding of topological interaction structures. We compute the generating function of γ-interaction structures and show that it is algebraic, which implies that the numbers of interaction structures can be computed recursively. We obtain simple asymptotic formulas for 0- and 1-interaction structures. The simplest class of interaction structures are the 0-interaction structures, which represent the two backbone analogues of secondary structures.
A Framework for the Instructional Design of Multi-Structured Educational Applications.

ERIC Educational Resources Information Center

Buendia, F.; Diaz, P.; Benlloch, J. V.

An instructional application consists of a set of resources and activities that implement interacting, interrelated and structured experiences oriented towards achieving specific educational objectives. Computer-based instructional applications have to be looked at as any other development activity following a well defined process. With this…
Program Aids Specification Of Multiple-Block Grids

NASA Technical Reports Server (NTRS)

Sorenson, R. L.; Mccann, K. M.

1993-01-01

3DPREP computer program aids specification of multiple-block computational grids. Highly interactive graphical preprocessing program designed for use on powerful graphical scientific computer workstation. Divided into three main parts, each corresponding to principal graphical-and-alphanumerical display. Relieves user of some burden of collecting and formatting many data needed to specify blocks and grids, and prepares input data for NASA's 3DGRAPE grid-generating computer program.
2D Geodynamic models of Microcontinent Formation

NASA Astrophysics Data System (ADS)

Tetreault, Joya; Buiter, Susanne

2013-04-01

Continental fragments (microcontinents and continental ribbons) are rifted-off blocks of relatively unthinned continental crust situated among the severely thinned crust of passive margins. The existence of these large crustal blocks would suggest that the passive margin containing them either underwent simultaneous differential rifting or multi-stage rifting in order to produce continental breakup and seafloor spreading in more than one location in the span of approximately 100 km. Also, because continental fragments do not occur on every passive margin, there must be something particular about the crust and/or lithosphere that led to the production of these features. Some proposed mechanisms for microcontinent and continental ribbon formation include (1) structural inheritance, (2) strain localization by serpentinized mantle or magmatic underplating, and (3) plume interaction with an active rift. Pre-existing weakness and inherited structural fabrics in typical continental crust from past tectonic events, such as varying rheology of accreted terranes and collisional suture zones, could be reactivated and serve as foci for deformation. The second theory is that strain is localized in certain regions by large amounts of weakened material that are either serpentinized mantle or mafic bodies underplating the thinned crust. Another possible process that could lead to continental fragment formation is magmatic influence of hot plume material that focuses in various regions, producing rifts in separate areas. The Jan Mayen and Seychelles microcontinents both have geological and plate reconstruction evidence to support the plume interaction theory. We use 2-D geodynamic experiments to assess the importance of structural inheritance, strain localization by regions of weakened mantle material, and contributions to rifting from plume material on producing crustal blocks surrounded by seafloor or thinned/hyperextended crust. Our preliminary results suggest that each of these three mechanisms, working alone, cannot produce concurrent or multi-stage differential thinning and continental break-up. We infer that multistage extension produced by a combination of these mechanisms could be necessary to produce microcontinents and continental ribbons.
From Physics Model to Results: An Optimizing Framework for Cross-Architecture Code Generation

DOE PAGES

Blazewicz, Marek; Hinder, Ian; Koppelman, David M.; ...

2013-01-01

Starting from a high-level problem description in terms of partial differential equations using abstract tensor notation, the Chemora framework discretizes, optimizes, and generates complete high performance codes for a wide range of compute architectures. Chemora extends the capabilities of Cactus, facilitating the usage of large-scale CPU/GPU systems in an efficient manner for complex applications, without low-level code tuning. Chemora achieves parallelism through MPI and multi-threading, combining OpenMP and CUDA. Optimizations include high-level code transformations, efficient loop traversal strategies, dynamically selected data and instruction cache usage strategies, and JIT compilation of GPU code tailored to the problem characteristics. The discretization ismore » based on higher-order finite differences on multi-block domains. Chemora's capabilities are demonstrated by simulations of black hole collisions. This problem provides an acid test of the framework, as the Einstein equations contain hundreds of variables and thousands of terms.« less
Multi-boson block factorization of fermions

NASA Astrophysics Data System (ADS)

Giusti, Leonardo; Cè, Marco; Schaefer, Stefan

2018-03-01

The numerical computations of many quantities of theoretical and phenomenological interest are plagued by statistical errors which increase exponentially with the distance of the sources in the relevant correlators. Notable examples are baryon masses and matrix elements, the hadronic vacuum polarization and the light-by-light scattering contributions to the muon g - 2, and the form factors of semileptonic B decays. Reliable and precise determinations of these quantities are very difficult if not impractical with state-of-the-art standard Monte Carlo integration schemes. I will review a recent proposal for factorizing the fermion determinant in lattice QCD that leads to a local action in the gauge field and in the auxiliary boson fields. Once combined with the corresponding factorization of the quark propagator, it paves the way for multi-level Monte Carlo integration in the presence of fermions opening new perspectives in lattice QCD. Exploratory results on the impact on the above mentioned observables will be presented.
An efficient solution of real-time data processing for multi-GNSS network

NASA Astrophysics Data System (ADS)

Gong, Xiaopeng; Gu, Shengfeng; Lou, Yidong; Zheng, Fu; Ge, Maorong; Liu, Jingnan

2017-12-01

Global navigation satellite systems (GNSS) are acting as an indispensable tool for geodetic research and global monitoring of the Earth, and they have been rapidly developed over the past few years with abundant GNSS networks, modern constellations, and significant improvement in mathematic models of data processing. However, due to the increasing number of satellites and stations, the computational efficiency becomes a key issue and it could hamper the further development of GNSS applications. In this contribution, this problem is overcome from the aspects of both dense linear algebra algorithms and GNSS processing strategy. First, in order to fully explore the power of modern microprocessors, the square root information filter solution based on the blocked QR factorization employing as many matrix-matrix operations as possible is introduced. In addition, the algorithm complexity of GNSS data processing is further decreased by centralizing the carrier-phase observations and ambiguity parameters, as well as performing the real-time ambiguity resolution and elimination. Based on the QR factorization of the simulated matrix, we can conclude that compared to unblocked QR factorization, the blocked QR factorization can greatly improve processing efficiency with a magnitude of nearly two orders on a personal computer with four 3.30 GHz cores. Then, with 82 globally distributed stations, the processing efficiency is further validated in multi-GNSS (GPS/BDS/Galileo) satellite clock estimation. The results suggest that it will take about 31.38 s per epoch for the unblocked method. While, without any loss of accuracy, it only takes 0.50 and 0.31 s for our new algorithm per epoch for float and fixed clock solutions, respectively.
3D Voronoi grid dedicated software for modeling gas migration in deep layered sedimentary formations with TOUGH2-TMGAS

NASA Astrophysics Data System (ADS)

Bonduà, Stefano; Battistelli, Alfredo; Berry, Paolo; Bortolotti, Villiam; Consonni, Alberto; Cormio, Carlo; Geloni, Claudio; Vasini, Ester Maria

2017-11-01

As is known, a full three-dimensional (3D) unstructured grid permits a great degree of flexibility when performing accurate numerical reservoir simulations. However, when the Integral Finite Difference Method (IFDM) is used for spatial discretization, constraints (arising from the required orthogonality between the segment connecting the blocks nodes and the interface area between blocks) pose difficulties in the creation of grids with irregular shaped blocks. The full 3D Voronoi approach guarantees the respect of IFDM constraints and allows generation of grids conforming to geological formations and structural objects and at the same time higher grid resolution in volumes of interest. In this work, we present dedicated pre- and post-processing gridding software tools for the TOUGH family of numerical reservoir simulators, developed by the Geothermal Research Group of the DICAM Department, University of Bologna. VORO2MESH is a new software coded in C++, based on the voro++ library, allowing computation of the 3D Voronoi tessellation for a given domain and the creation of a ready to use TOUGH2 MESH file. If a set of geological surfaces is available, the software can directly generate the set of Voronoi seed points used for tessellation. In order to reduce the number of connections and so to decrease computation time, VORO2MESH can produce a mixed grid with regular blocks (orthogonal prisms) and irregular blocks (polyhedron Voronoi blocks) at the point of contact between different geological formations. In order to visualize 3D Voronoi grids together with the results of numerical simulations, the functionality of the TOUGH2Viewer post-processor has been extended. We describe an application of VORO2MESH and TOUGH2Viewer to validate the two tools. The case study deals with the simulation of the migration of gases in deep layered sedimentary formations at basin scale using TOUGH2-TMGAS. A comparison between the simulation performances of unstructured and structured grids is presented.
Multi-level bandwidth efficient block modulation codes

NASA Technical Reports Server (NTRS)

Lin, Shu

1989-01-01

The multilevel technique is investigated for combining block coding and modulation. There are four parts. In the first part, a formulation is presented for signal sets on which modulation codes are to be constructed. Distance measures on a signal set are defined and their properties are developed. In the second part, a general formulation is presented for multilevel modulation codes in terms of component codes with appropriate Euclidean distances. The distance properties, Euclidean weight distribution and linear structure of multilevel modulation codes are investigated. In the third part, several specific methods for constructing multilevel block modulation codes with interdependency among component codes are proposed. Given a multilevel block modulation code C with no interdependency among the binary component codes, the proposed methods give a multilevel block modulation code C which has the same rate as C, a minimum squared Euclidean distance not less than that of code C, a trellis diagram with the same number of states as that of C and a smaller number of nearest neighbor codewords than that of C. In the last part, error performance of block modulation codes is analyzed for an AWGN channel based on soft-decision maximum likelihood decoding. Error probabilities of some specific codes are evaluated based on their Euclidean weight distributions and simulation results.

Uniscale multi-view registration using double dog-leg method

NASA Astrophysics Data System (ADS)

Chen, Chao-I.; Sargent, Dusty; Tsai, Chang-Ming; Wang, Yuan-Fang; Koppel, Dan

2009-02-01

3D computer models of body anatomy can have many uses in medical research and clinical practices. This paper describes a robust method that uses videos of body anatomy to construct multiple, partial 3D structures and then fuse them to form a larger, more complete computer model using the structure-from-motion framework. We employ the Double Dog-Leg (DDL) method, a trust-region based nonlinear optimization method, to jointly optimize the camera motion parameters (rotation and translation) and determine a global scale that all partial 3D structures should agree upon. These optimized motion parameters are used for constructing local structures, and the global scale is essential for multi-view registration after all these partial structures are built. In order to provide a good initial guess of the camera movement parameters and outlier free 2D point correspondences for DDL, we also propose a two-stage scheme where multi-RANSAC with a normalized eight-point algorithm is first performed and then a few iterations of an over-determined five-point algorithm is used to polish the results. Our experimental results using colonoscopy video show that the proposed scheme always produces more accurate outputs than the standard RANSAC scheme. Furthermore, since we have obtained many reliable point correspondences, time-consuming and error-prone registration methods like the iterative closest points (ICP) based algorithms can be replaced by a simple rigid-body transformation solver when merging partial structures into a larger model.
Enhanced Mechanical Performance of Bio-Inspired Hybrid Structures Utilising Topological Interlocking Geometry.

PubMed

Djumas, Lee; Molotnikov, Andrey; Simon, George P; Estrin, Yuri

2016-05-24

Structural composites inspired by nacre have emerged as prime exemplars for guiding materials design of fracture-resistant, rigid hybrid materials. The intricate microstructure of nacre, which combines a hard majority phase with a small fraction of a soft phase, achieves superior mechanical properties compared to its constituents and has generated much interest. However, replicating the hierarchical microstructure of nacre is very challenging, not to mention improving it. In this article, we propose to alter the geometry of the hard building blocks by introducing the concept of topological interlocking. This design principle has previously been shown to provide an inherently brittle material with a remarkable flexural compliance. We now demonstrate that by combining the basic architecture of nacre with topological interlocking of discrete hard building blocks, hybrid materials of a new type can be produced. By adding a soft phase at the interfaces between topologically interlocked blocks in a single-build additive manufacturing process, further improvement of mechanical properties is achieved. The design of these fabricated hybrid structures has been guided by computational work elucidating the effect of various geometries. To our knowledge, this is the first reported study that combines the advantages of nacre-inspired structures with the benefits of topological interlocking.
Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks.

PubMed

Saravanan, Chandra; Shao, Yihan; Baer, Roi; Ross, Philip N; Head-Gordon, Martin

2003-04-15

A sparse matrix multiplication scheme with multiatom blocks is reported, a tool that can be very useful for developing linear-scaling methods with atom-centered basis functions. Compared to conventional element-by-element sparse matrix multiplication schemes, efficiency is gained by the use of the highly optimized basic linear algebra subroutines (BLAS). However, some sparsity is lost in the multiatom blocking scheme because these matrix blocks will in general contain negligible elements. As a result, an optimal block size that minimizes the CPU time by balancing these two effects is recovered. In calculations on linear alkanes, polyglycines, estane polymers, and water clusters the optimal block size is found to be between 40 and 100 basis functions, where about 55-75% of the machine peak performance was achieved on an IBM RS6000 workstation. In these calculations, the blocked sparse matrix multiplications can be 10 times faster than a standard element-by-element sparse matrix package. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 618-622, 2003
Hierarchical combinatorial deep learning architecture for pancreas segmentation of medical computed tomography cancer images.

PubMed

Fu, Min; Wu, Wenming; Hong, Xiafei; Liu, Qiuhua; Jiang, Jialin; Ou, Yaobin; Zhao, Yupei; Gong, Xinqi

2018-04-24

Efficient computational recognition and segmentation of target organ from medical images are foundational in diagnosis and treatment, especially about pancreas cancer. In practice, the diversity in appearance of pancreas and organs in abdomen, makes detailed texture information of objects important in segmentation algorithm. According to our observations, however, the structures of previous networks, such as the Richer Feature Convolutional Network (RCF), are too coarse to segment the object (pancreas) accurately, especially the edge. In this paper, we extend the RCF, proposed to the field of edge detection, for the challenging pancreas segmentation, and put forward a novel pancreas segmentation network. By employing multi-layer up-sampling structure replacing the simple up-sampling operation in all stages, the proposed network fully considers the multi-scale detailed contexture information of object (pancreas) to perform per-pixel segmentation. Additionally, using the CT scans, we supply and train our network, thus get an effective pipeline. Working with our pipeline with multi-layer up-sampling model, we achieve better performance than RCF in the task of single object (pancreas) segmentation. Besides, combining with multi scale input, we achieve the 76.36% DSC (Dice Similarity Coefficient) value in testing data. The results of our experiments show that our advanced model works better than previous networks in our dataset. On the other words, it has better ability in catching detailed contexture information. Therefore, our new single object segmentation model has practical meaning in computational automatic diagnosis.
All two-loop maximally helicity-violating amplitudes in multi-Regge kinematics from applied symbology

NASA Astrophysics Data System (ADS)

Prygarin, Alexander; Spradlin, Marcus; Vergu, Cristian; Volovich, Anastasia

2012-04-01

Recent progress on scattering amplitudes has benefited from the mathematical technology of symbols for efficiently handling the types of polylogarithm functions which frequently appear in multiloop computations. The symbol for all two-loop maximally helicity violating amplitudes in planar supersymmetric Yang-Mills theory is known, but explicit analytic formulas for the amplitudes are hard to come by except in special limits where things simplify, such as multi-Regge kinematics. By applying symbology we obtain a formula for the leading behavior of the imaginary part (the Mandelstam cut contribution) of this amplitude in multi-Regge kinematics for any number of gluons. Our result predicts a simple recursive structure which agrees with a direct Balitsky-Fadin-Kuraev-Lipatov computation carried out in a parallel publication.
Efficient high-order structure-preserving methods for the generalized Rosenau-type equation with power law nonlinearity

NASA Astrophysics Data System (ADS)

Cai, Jiaxiang; Liang, Hua; Zhang, Chun

2018-06-01

Based on the multi-symplectic Hamiltonian formula of the generalized Rosenau-type equation, a multi-symplectic scheme and an energy-preserving scheme are proposed. To improve the accuracy of the solution, we apply the composition technique to the obtained schemes to develop high-order schemes which are also multi-symplectic and energy-preserving respectively. Discrete fast Fourier transform makes a significant improvement to the computational efficiency of schemes. Numerical results verify that all the proposed schemes have satisfactory performance in providing accurate solution and preserving the discrete mass and energy invariants. Numerical results also show that although each basic time step is divided into several composition steps, the computational efficiency of the composition schemes is much higher than that of the non-composite schemes.
A novel fractal image compression scheme with block classification and sorting based on Pearson's correlation coefficient.

PubMed

Wang, Jianji; Zheng, Nanning

2013-09-01

Fractal image compression (FIC) is an image coding technology based on the local similarity of image structure. It is widely used in many fields such as image retrieval, image denoising, image authentication, and encryption. FIC, however, suffers from the high computational complexity in encoding. Although many schemes are published to speed up encoding, they do not easily satisfy the encoding time or the reconstructed image quality requirements. In this paper, a new FIC scheme is proposed based on the fact that the affine similarity between two blocks in FIC is equivalent to the absolute value of Pearson's correlation coefficient (APCC) between them. First, all blocks in the range and domain pools are chosen and classified using an APCC-based block classification method to increase the matching probability. Second, by sorting the domain blocks with respect to APCCs between these domain blocks and a preset block in each class, the matching domain block for a range block can be searched in the selected domain set in which these APCCs are closer to APCC between the range block and the preset block. Experimental results show that the proposed scheme can significantly speed up the encoding process in FIC while preserving the reconstructed image quality well.
Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5.

PubMed

Azoitei, M L; Ban, Y A; Kalyuzhny, O; Guenaga, J; Schroeter, A; Porter, J; Wyatt, R; Schief, William R

2014-10-01

Rational design of proteins with novel binding specificities and increased affinity is one of the major goals of computational protein design. Epitope-scaffolds are a new class of antigens engineered by transplanting viral epitopes of predefined structure to protein scaffolds, or by building protein scaffolds around such epitopes. Epitope-scaffolds are of interest as vaccine components to attempt to elicit neutralizing antibodies targeting the specified epitope. In this study we developed a new computational protocol, MultiGraft Interface, that transplants epitopes but also designs additional scaffold features outside the epitope to enhance antibody-binding specificity and potentially influence the specificity of elicited antibodies. We employed MultiGraft Interface to engineer novel epitope-scaffolds that display the known epitope of human immunodeficiency virus 1 (HIV-1) neutralizing antibody 2F5 and that also interact with the functionally important CDR H3 antibody loop. MultiGraft Interface generated an epitope-scaffold that bound 2F5 with subnanomolar affinity (K(D) = 400 pM) and that interacted with the antibody CDR H3 loop through computationally designed contacts. Substantial structural modifications were necessary to engineer this antigen, with the 2F5 epitope replacing a helix in the native scaffold and with 15% of the native scaffold sequence being modified in the design stage. This epitope-scaffold represents a successful example of rational protein backbone engineering and protein-protein interface design and could prove useful in the field of HIV vaccine design. MultiGraft Interface can be generally applied to engineer novel binding partners with altered specificity and optimized affinity. © 2014 Wiley Periodicals, Inc.
Effectiveness of Flow Control for Alleviation of Twin-Tail Buffet

NASA Technical Reports Server (NTRS)

Sheta, Essam F.; Kandil, Osama A.; Yang, Zhi

1998-01-01

Effectiveness of active flow control for twin- tail buffet alleviation is investigated. Tangen- tial leading-edge blowing (TLEB) and flow suction along the vortex cores (FSVC) of the lead- ing edges of the delta wing are used to delay the vortex breakdown flow upstream of the twin tail. The combined effect of the TLEB and FSVC is also investigated. A parametric study of the effects of the spanwise position of the suction tubes and volumetric suction flow rate on the twin-tail buffet response are also investigated. The TLEB moves the path of leading-edge vortices laterally towards the twin tail, which increases the aero- dynamic damping on the tails. The FSVC effectively delays the breakdown location at high angles of attack. The computational model consists of a sharp-edged delta wing of aspect ratio one and swept-back flexible twin tail with taper ratio of 0.23. This complex multidisciplinary problem is solved sequentially using three sets of equations for the fluid flow, aeroelastic response and grid deformation, on a dynamic multi-block grid structure. The computational model is pitched at 30 deg. angle of attack. The freestream Mach number and Reynolds number are 0.3 and 1.25 million, respectively. The model is investigated for the inboard position of the twin tails, which corresponds to a separation distance between the twin tails of 33% of the wing span.
Semiclassical Virasoro blocks from AdS 3 gravity

DOE PAGES

Hijano, Eliot; Kraus, Per; Perlmutter, Eric; ...

2015-12-14

We present a unified framework for the holographic computation of Virasoro conformal blocks at large central charge. In particular, we provide bulk constructions that correctly reproduce all semiclassical Virasoro blocks that are known explicitly from conformal field theory computations. The results revolve around the use of geodesic Witten diagrams, recently introduced in [1], evaluated in locally AdS 3 geometries generated by backreaction of heavy operators. We also provide an alternative computation of the heavy-light semiclassical block — in which two external operators become parametrically heavy — as a certain scattering process involving higher spin gauge fields in AdS 3; thismore » approach highlights the chiral nature of Virasoro blocks. Finally, these techniques may be systematically extended to compute corrections to these blocks and to interpolate amongst the different semiclassical regimes.« less
Thermal/structural Tailoring of Engine Blades (T/STAEBL) User's Manual

NASA Technical Reports Server (NTRS)

Brown, K. W.; Clevenger, W. B.; Arel, J. D.

1994-01-01

The Thermal/Structural Tailoring of Engine Blades (T/STAEBL) system is a family of computer programs executed by a control program. The T/STAEBL system performs design optimizations of cooled, hollow turbine blades and vanes. This manual contains an overview of the system, fundamentals of the data block structure, and detailed descriptions of the inputs required by the optimizer. Additionally, the thermal analysis input requirements are described as well as the inputs required to perform a finite element blade vibrations analysis.
Structural Optimization of a Force Balance Using a Computational Experiment Design

NASA Technical Reports Server (NTRS)

Parker, P. A.; DeLoach, R.

2002-01-01

This paper proposes a new approach to force balance structural optimization featuring a computational experiment design. Currently, this multi-dimensional design process requires the designer to perform a simplification by executing parameter studies on a small subset of design variables. This one-factor-at-a-time approach varies a single variable while holding all others at a constant level. Consequently, subtle interactions among the design variables, which can be exploited to achieve the design objectives, are undetected. The proposed method combines Modern Design of Experiments techniques to direct the exploration of the multi-dimensional design space, and a finite element analysis code to generate the experimental data. To efficiently search for an optimum combination of design variables and minimize the computational resources, a sequential design strategy was employed. Experimental results from the optimization of a non-traditional force balance measurement section are presented. An approach to overcome the unique problems associated with the simultaneous optimization of multiple response criteria is described. A quantitative single-point design procedure that reflects the designer's subjective impression of the relative importance of various design objectives, and a graphical multi-response optimization procedure that provides further insights into available tradeoffs among competing design objectives are illustrated. The proposed method enhances the intuition and experience of the designer by providing new perspectives on the relationships between the design variables and the competing design objectives providing a systematic foundation for advancements in structural design.
Label-free logic modules and two-layer cascade based on stem-loop probes containing a G-quadruplex domain.

PubMed

Guo, Yahui; Cheng, Junjie; Wang, Jine; Zhou, Xiaodong; Hu, Jiming; Pei, Renjun

2014-09-01

A simple, versatile, and label-free DNA computing strategy was designed by using toehold-mediated strand displacement and stem-loop probes. A full set of logic gates (YES, NOT, OR, NAND, AND, INHIBIT, NOR, XOR, XNOR) and a two-layer logic cascade were constructed. The probes contain a G-quadruplex domain, which was blocked or unfolded through inputs initiating strand displacement and the obviously distinguishable light-up fluorescent signal of G-quadruplex/NMM complex was used as the output readout. The inputs are the disease-specific nucleotide sequences with potential for clinic diagnosis. The developed versatile computing system based on our label-free and modular strategy might be adapted in multi-target diagnosis through DNA hybridization and aptamer-target interaction. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Multi-Body Dynamic Contact Analysis. Tool for Transmission Design SBIR Phase II Final Report

DTIC Science & Technology

2003-04-01

shapes and natural frequencies were computed in COSMIC NASTRAN, and were validated against the published experimental modal analysis [17]. • Using...COSMIC NASTRAN via modal superposition. • Results from the structural analysis (mode shapes or forced response) were converted into IDEAS universal...ARMY RESEARCH LABORATORY Multi-body Dynamic Contact Analysis Tool for Transmission Design SBIR Phase II Final Report by
Longitudinal dispersion coefficients for numerical modeling of groundwater solute transport in heterogeneous formations

NASA Astrophysics Data System (ADS)

Lee, Jonghyun; Rolle, Massimo; Kitanidis, Peter K.

2018-05-01

Most recent research on hydrodynamic dispersion in porous media has focused on whole-domain dispersion while other research is largely on laboratory-scale dispersion. This work focuses on the contribution of a single block in a numerical model to dispersion. Variability of fluid velocity and concentration within a block is not resolved and the combined spreading effect is approximated using resolved quantities and macroscopic parameters. This applies whether the formation is modeled as homogeneous or discretized into homogeneous blocks but the emphasis here being on the latter. The process of dispersion is typically described through the Fickian model, i.e., the dispersive flux is proportional to the gradient of the resolved concentration, commonly with the Scheidegger parameterization, which is a particular way to compute the dispersion coefficients utilizing dispersivity coefficients. Although such parameterization is by far the most commonly used in solute transport applications, its validity has been questioned. Here, our goal is to investigate the effects of heterogeneity and mass transfer limitations on block-scale longitudinal dispersion and to evaluate under which conditions the Scheidegger parameterization is valid. We compute the relaxation time or memory of the system; changes in time with periods larger than the relaxation time are gradually leading to a condition of local equilibrium under which dispersion is Fickian. The method we use requires the solution of a steady-state advection-dispersion equation, and thus is computationally efficient, and applicable to any heterogeneous hydraulic conductivity K field without requiring statistical or structural assumptions. The method was validated by comparing with other approaches such as the moment analysis and the first order perturbation method. We investigate the impact of heterogeneity, both in degree and structure, on the longitudinal dispersion coefficient and then discuss the role of local dispersion and mass transfer limitations, i.e., the exchange of mass between the permeable matrix and the low permeability inclusions. We illustrate the physical meaning of the method and we show how the block longitudinal dispersivity approaches, under certain conditions, the Scheidegger limit at large Péclet numbers. Lastly, we discuss the potential and limitations of the method to accurately describe dispersion in solute transport applications in heterogeneous aquifers.
Genotoxicity of multi-walled carbon nanotubes at occupationally relevant doses

PubMed Central

2014-01-01

Carbon nanotubes are commercially-important products of nanotechnology; however, their low density and small size makes carbon nanotube respiratory exposures likely during their production or processing. We have previously shown mitotic spindle aberrations in cultured primary and immortalized human airway epithelial cells exposed to single-walled carbon nanotubes (SWCNT). In this study, we examined whether multi-walled carbon nanotubes (MWCNT) cause mitotic spindle damage in cultured cells at doses equivalent to 34 years of exposure at the NIOSH Recommended Exposure Limit (REL). MWCNT induced a dose responsive increase in disrupted centrosomes, abnormal mitotic spindles and aneuploid chromosome number 24 hours after exposure to 0.024, 0.24, 2.4 and 24 μg/cm2 MWCNT. Monopolar mitotic spindles comprised 95% of disrupted mitoses. Three-dimensional reconstructions of 0.1 μm optical sections showed carbon nanotubes integrated with microtubules, DNA and within the centrosome structure. Cell cycle analysis demonstrated a greater number of cells in S-phase and fewer cells in the G2 phase in MWCNT-treated compared to diluent control, indicating a G1/S block in the cell cycle. The monopolar phenotype of the disrupted mitotic spindles and the G1/S block in the cell cycle is in sharp contrast to the multi-polar spindle and G2 block in the cell cycle previously observed following exposure to SWCNT. One month following exposure to MWCNT there was a dramatic increase in both size and number of colonies compared to diluent control cultures, indicating a potential to pass the genetic damage to daughter cells. Our results demonstrate significant disruption of the mitotic spindle by MWCNT at occupationally relevant exposure levels. PMID:24479647
Mussel-inspired nano-building block assemblies for mimicking extracellular matrix microenvironments with multiple functions.

PubMed

Wang, Zhenming; Jia, Zhanrong; Jiang, Yanan; Li, Pengfei; Han, Lu; Lu, Xiong; Ren, Fuzeng; Wang, Kefeng; Yuan, Huiping

2017-08-03

The assembly of nano-building blocks is an effective way to produce artificial extracellular matrix microenvironments with hierarchical micro/nano structures. However, it is hard to assemble different types of nano-building blocks, to form composite coatings with multiple functions, by traditional layer-by-layer (LbL) self-assembly methods. Inspired by the mussel adhesion mechanism, we developed polydopamine (PDA)-decorated bovine serum albumin microspheres (BSA-MS) and nano-hydroxyapatite (nano-HA), and assembled them to form bioactive coatings with micro/nano structures encapsulating bone morphogenetic protein-2 (BMP-2). First, PDA-decorated nano-HA (nano-pHA) was obtained by oxidative polymerization of dopamine on nano-HA. Second, BMP-2-encapsulated BSA microspheres were prepared through desolvation, and then were also decorated by PDA (pBSA-MS). Finally, the nano-pHA and pBSA-MS were assembled using the adhesive properties of PDA. Bone marrow stromal cell cultures and in vivo implantation, showed that the pHA/pBSA (BMP-2) coatings can promote cell adhesion, proliferation, and benefited for osteoinductivity. PDA decoration was also applied to assemble various functional nanoparticles, such as nano-HA, polystyrene, and Fe 3 O 4 nanoparticles. In summary, this study provides a novel strategy for the assembly of biofunctional nano-building blocks, which surpasses traditional LbL self-assembly of polyelectrolytes, and can find broad applications in bioactive agents delivery or multi-functional coatings.
Confinement factor, near and far field patterns in InGaN MQW laser diodes

NASA Astrophysics Data System (ADS)

Martín, J.; Sánchez, M.

2005-07-01

In this work the influence of the QW number in the active region on spectral characteristics in InGaN multi quamtun well lasers is analyzed. A comparison between the abrupt index step structure (Step) and a graded-index structure (GRIN) is done. The effect of the introduction of a p-AlxGa1-xN electron blocking layer, placed above the last InGaN barrier in the Step structure is also analyzed. Calculations of the confinement factor, near and far field patterns were carried out. We found that with the adequate aluminum content in this layer, the confinement factor, near and far field patterns are improved, and values similar to those obtained with GRIN structure can be reached.
A new parallel-vector finite element analysis software on distributed-memory computers

NASA Technical Reports Server (NTRS)

Qin, Jiangning; Nguyen, Duc T.

1993-01-01

A new parallel-vector finite element analysis software package MPFEA (Massively Parallel-vector Finite Element Analysis) is developed for large-scale structural analysis on massively parallel computers with distributed-memory. MPFEA is designed for parallel generation and assembly of the global finite element stiffness matrices as well as parallel solution of the simultaneous linear equations, since these are often the major time-consuming parts of a finite element analysis. Block-skyline storage scheme along with vector-unrolling techniques are used to enhance the vector performance. Communications among processors are carried out concurrently with arithmetic operations to reduce the total execution time. Numerical results on the Intel iPSC/860 computers (such as the Intel Gamma with 128 processors and the Intel Touchstone Delta with 512 processors) are presented, including an aircraft structure and some very large truss structures, to demonstrate the efficiency and accuracy of MPFEA.
Scalable software architecture for on-line multi-camera video processing

NASA Astrophysics Data System (ADS)

Camplani, Massimo; Salgado, Luis

2011-03-01

In this paper we present a scalable software architecture for on-line multi-camera video processing, that guarantees a good trade off between computational power, scalability and flexibility. The software system is modular and its main blocks are the Processing Units (PUs), and the Central Unit. The Central Unit works as a supervisor of the running PUs and each PU manages the acquisition phase and the processing phase. Furthermore, an approach to easily parallelize the desired processing application has been presented. In this paper, as case study, we apply the proposed software architecture to a multi-camera system in order to efficiently manage multiple 2D object detection modules in a real-time scenario. System performance has been evaluated under different load conditions such as number of cameras and image sizes. The results show that the software architecture scales well with the number of camera and can easily works with different image formats respecting the real time constraints. Moreover, the parallelization approach can be used in order to speed up the processing tasks with a low level of overhead.

Improving the performance of AlGaN-based deep-ultraviolet light-emitting diodes using electron blocking layer with a heart-shaped graded Al composition

NASA Astrophysics Data System (ADS)

Kwon, M. R.; Park, T. H.; Lee, T. H.; Lee, B. R.; Kim, T. G.

2018-04-01

We propose a design for highly efficient AlGaN-based deep-ultraviolet light-emitting diodes (DUV LEDs) using a heart-shaped graded Al composition electron-blocking layer (EBL). This novel structure reduced downward band bending at the interface between the last quantum barrier and the EBL and flattened the electrostatic field in the interlayer between the barriers of the multi-quantum barrier EBL. Consequently, electron leakage was significantly suppressed and hole injection efficiency was found to have improved. The parameter values of simulation were extracted from the experimental data of the reference DUV LEDs. Using the SimuLED, we compared the electrical and optical properties of three structures with different Al compositions in the active region and the EBL. The internal quantum efficiency of the proposed structure was shown to exceed those of the reference DUV LEDs by a factor of 1.9. Additionally, the output power at 20 mA was found to increase by a factor of 2.1.
Use of CAD Geometry in MDO

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

1996-01-01

The purpose of this paper is to discuss the use of Computer-Aided Design (CAD) geometry in a Multi-Disciplinary Design Optimization (MDO) environment. Two techniques are presented to facilitate the use of CAD geometry by different disciplines, such as Computational Fluid Dynamics (CFD) and Computational Structural Mechanics (CSM). One method is to transfer the load from a CFD grid to a CSM grid. The second method is to update the CAD geometry for CSM deflection.
Probabilistic Simulation of Multi-Scale Composite Behavior

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

2012-01-01

A methodology is developed to computationally assess the non-deterministic composite response at all composite scales (from micro to structural) due to the uncertainties in the constituent (fiber and matrix) properties, in the fabrication process and in structural variables (primitive variables). The methodology is computationally efficient for simulating the probability distributions of composite behavior, such as material properties, laminate and structural responses. Bi-products of the methodology are probabilistic sensitivities of the composite primitive variables. The methodology has been implemented into the computer codes PICAN (Probabilistic Integrated Composite ANalyzer) and IPACS (Integrated Probabilistic Assessment of Composite Structures). The accuracy and efficiency of this methodology are demonstrated by simulating the uncertainties in composite typical laminates and comparing the results with the Monte Carlo simulation method. Available experimental data of composite laminate behavior at all scales fall within the scatters predicted by PICAN. Multi-scaling is extended to simulate probabilistic thermo-mechanical fatigue and to simulate the probabilistic design of a composite redome in order to illustrate its versatility. Results show that probabilistic fatigue can be simulated for different temperature amplitudes and for different cyclic stress magnitudes. Results also show that laminate configurations can be selected to increase the redome reliability by several orders of magnitude without increasing the laminate thickness--a unique feature of structural composites. The old reference denotes that nothing fundamental has been done since that time.
The role of alpha-rhythm states in perceptual learning: insights from experiments and computational models

PubMed Central

Sigala, Rodrigo; Haufe, Sebastian; Roy, Dipanjan; Dinse, Hubert R.; Ritter, Petra

2014-01-01

During the past two decades growing evidence indicates that brain oscillations in the alpha band (~10 Hz) not only reflect an “idle” state of cortical activity, but also take a more active role in the generation of complex cognitive functions. A recent study shows that more than 60% of the observed inter-subject variability in perceptual learning can be ascribed to ongoing alpha activity. This evidence indicates a significant role of alpha oscillations for perceptual learning and hence motivates to explore the potential underlying mechanisms. Hence, it is the purpose of this review to highlight existent evidence that ascribes intrinsic alpha oscillations a role in shaping our ability to learn. In the review, we disentangle the alpha rhythm into different neural signatures that control information processing within individual functional building blocks of perceptual learning. We further highlight computational studies that shed light on potential mechanisms regarding how alpha oscillations may modulate information transfer and connectivity changes relevant for learning. To enable testing of those model based hypotheses, we emphasize the need for multidisciplinary approaches combining assessment of behavior and multi-scale neuronal activity, active modulation of ongoing brain states and computational modeling to reveal the mathematical principles of the complex neuronal interactions. In particular we highlight the relevance of multi-scale modeling frameworks such as the one currently being developed by “The Virtual Brain” project. PMID:24772077
Multi-level tree analysis of pulmonary artery/vein trees in non-contrast CT images

NASA Astrophysics Data System (ADS)

Gao, Zhiyun; Grout, Randall W.; Hoffman, Eric A.; Saha, Punam K.

2012-02-01

Diseases like pulmonary embolism and pulmonary hypertension are associated with vascular dystrophy. Identifying such pulmonary artery/vein (A/V) tree dystrophy in terms of quantitative measures via CT imaging significantly facilitates early detection of disease or a treatment monitoring process. A tree structure, consisting of nodes and connected arcs, linked to the volumetric representation allows multi-level geometric and volumetric analysis of A/V trees. Here, a new theory and method is presented to generate multi-level A/V tree representation of volumetric data and to compute quantitative measures of A/V tree geometry and topology at various tree hierarchies. The new method is primarily designed on arc skeleton computation followed by a tree construction based topologic and geometric analysis of the skeleton. The method starts with a volumetric A/V representation as input and generates its topologic and multi-level volumetric tree representations long with different multi-level morphometric measures. A new recursive merging and pruning algorithms are introduced to detect bad junctions and noisy branches often associated with digital geometric and topologic analysis. Also, a new notion of shortest axial path is introduced to improve the skeletal arc joining two junctions. The accuracy of the multi-level tree analysis algorithm has been evaluated using computer generated phantoms and pulmonary CT images of a pig vessel cast phantom while the reproducibility of method is evaluated using multi-user A/V separation of in vivo contrast-enhanced CT images of a pig lung at different respiratory volumes.
New Insights into Tectonics of the Saint Elias, Alaska, Region Based on Local Seismicity and Tomography

NASA Astrophysics Data System (ADS)

Ruppert, N. A.; Zabelina, I.; Freymueller, J. T.

2013-12-01

Saint Elias Mountains in southern Alaska are manifestation of ongoing tectonic processes that include collision of the Yakutat block with and subduction of the Yakutat block and Pacific plate under the North American plate. Interaction of these tectonic blocks and plates is complex and not well understood. In 2005 and 2006 a network of 22 broadband seismic sites was installed in the region as part of the SainT Elias TEctonics and Erosion Project (STEEP), a five-year multi-disciplinary study that addressed evolution of the highest coastal mountain range on Earth. High quality seismic data provides unique insights into earthquake occurrence and velocity structure of the region. Local earthquake data recorded between 2005 and 2010 became a foundation for detailed study of seismotectonic features and crustal velocities. The highest concentration of seismicity follows the Chugach-St.Elias fault, a major on land tectonic structure in the region. This fault is also delineated in tomographic images as a distinct contrast between lower velocities to the south and higher velocities to the north. The low-velocity region corresponds to the rapidly-uplifted and exhumed sediments on the south side of the range. Earthquake source parameters indicate high degree of compression and undertrusting processes along the coastal area, consistent with multiple thrust structures mapped from geological studies in the region. Tomographic inversion reveals velocity anomalies that correlate with sedimentary basins, volcanic features and subducting Yakutat block. We will present precise earthquake locations and source parameters recorded with the STEEP and regional seismic network along with the results of P- and S-wave tomographic inversion.
UNRAVELLING THE COMPONENTS OF A MULTI-THERMAL CORONAL LOOP USING MAGNETOHYDRODYNAMIC SEISMOLOGY

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

Prasad, S. Krishna; Jess, D. B.; Klimchuk, J. A.

Coronal loops, constituting the basic building blocks of the active Sun, serve as primary targets to help understand the mechanisms responsible for maintaining multi-million Kelvin temperatures in the solar and stellar coronae. Despite significant advances in observations and theory, our knowledge on the fundamental properties of these structures is limited. Here, we present unprecedented observations of accelerating slow magnetoacoustic waves along a coronal loop that show differential propagation speeds in two distinct temperature channels, revealing the multi-stranded and multithermal nature of the loop. Utilizing the observed speeds and employing nonlinear force-free magnetic field extrapolations, we derive the actual temperature variationmore » along the loop in both channels, and thus are able to resolve two individual components of the multithermal loop for the first time. The obtained positive temperature gradients indicate uniform heating along the loop, rather than isolated footpoint heating.« less
The computation of 15 deg and 10 deg equal area block terrestrial free air gravity anomalies

NASA Technical Reports Server (NTRS)

Hajela, D. P.

1973-01-01

Starting with the set of 23,355 1 deg x 1 deg mean free air gravity anomalies used in Rapp (1972) to form a 5 deg equal area block terrestrial gravity field, the computation of 15 deg equal area block mean free air gravity anomalies is described along with estimates of their standard deviations. A new scheme of an integral division of a 15 deg block into 9 component 300 n. m. blocks, and each 300 n. m. block being subdivided into 25 60 n.mi. blocks, is used. This insures that there is no loss in accuracy, which would have resulted if proportional values according to area were taken of the 5 deg equal area anomalies to form the 15 deg block anomalies. A similar scheme is used for the computation of 10 deg equal area block mean free air gravity anomalies with estimates of their standard deviations. The scheme is general enough to be used for a 30 deg equal area block terrestrial gravity field.
Real-time simulation of large-scale neural architectures for visual features computation based on GPU.

PubMed

Chessa, Manuela; Bianchi, Valentina; Zampetti, Massimo; Sabatini, Silvio P; Solari, Fabio

2012-01-01

The intrinsic parallelism of visual neural architectures based on distributed hierarchical layers is well suited to be implemented on the multi-core architectures of modern graphics cards. The design strategies that allow us to optimally take advantage of such parallelism, in order to efficiently map on GPU the hierarchy of layers and the canonical neural computations, are proposed. Speciﬁcally, the advantages of a cortical map-like representation of the data are exploited. Moreover, a GPU implementation of a novel neural architecture for the computation of binocular disparity from stereo image pairs, based on populations of binocular energy neurons, is presented. The implemented neural model achieves good performances in terms of reliability of the disparity estimates and a near real-time execution speed, thus demonstrating the effectiveness of the devised design strategies. The proposed approach is valid in general, since the neural building blocks we implemented are a common basis for the modeling of visual neural functionalities.
Learning surface molecular structures via machine vision

NASA Astrophysics Data System (ADS)

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-01

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.
Mutual information registration of multi-spectral and multi-resolution images of DigitalGlobe's WorldView-3 imaging satellite

NASA Astrophysics Data System (ADS)

Miecznik, Grzegorz; Shafer, Jeff; Baugh, William M.; Bader, Brett; Karspeck, Milan; Pacifici, Fabio

2017-05-01

WorldView-3 (WV-3) is a DigitalGlobe commercial, high resolution, push-broom imaging satellite with three instruments: visible and near-infrared VNIR consisting of panchromatic (0.3m nadir GSD) plus multi-spectral (1.2m), short-wave infrared SWIR (3.7m), and multi-spectral CAVIS (30m). Nine VNIR bands, which are on one instrument, are nearly perfectly registered to each other, whereas eight SWIR bands, belonging to the second instrument, are misaligned with respect to VNIR and to each other. Geometric calibration and ortho-rectification results in a VNIR/SWIR alignment which is accurate to approximately 0.75 SWIR pixel at 3.7m GSD, whereas inter-SWIR, band to band registration is 0.3 SWIR pixel. Numerous high resolution, spectral applications, such as object classification and material identification, require more accurate registration, which can be achieved by utilizing image processing algorithms, for example Mutual Information (MI). Although MI-based co-registration algorithms are highly accurate, implementation details for automated processing can be challenging. One particular challenge is how to compute bin widths of intensity histograms, which are fundamental building blocks of MI. We solve this problem by making the bin widths proportional to instrument shot noise. Next, we show how to take advantage of multiple VNIR bands, and improve registration sensitivity to image alignment. To meet this goal, we employ Canonical Correlation Analysis, which maximizes VNIR/SWIR correlation through an optimal linear combination of VNIR bands. Finally we explore how to register images corresponding to different spatial resolutions. We show that MI computed at a low-resolution grid is more sensitive to alignment parameters than MI computed at a high-resolution grid. The proposed modifications allow us to improve VNIR/SWIR registration to better than ¼ of a SWIR pixel, as long as terrain elevation is properly accounted for, and clouds and water are masked out.
An O([Formula: see text]) algorithm for sorting signed genomes by reversals, transpositions, transreversals and block-interchanges.

PubMed

Yu, Shuzhi; Hao, Fanchang; Leong, Hon Wai

2016-02-01

We consider the problem of sorting signed permutations by reversals, transpositions, transreversals, and block-interchanges. The problem arises in the study of species evolution via large-scale genome rearrangement operations. Recently, Hao et al. gave a 2-approximation scheme called genome sorting by bridges (GSB) for solving this problem. Their result extended and unified the results of (i) He and Chen - a 2-approximation algorithm allowing reversals, transpositions, and block-interchanges (by also allowing transversals) and (ii) Hartman and Sharan - a 1.5-approximation algorithm allowing reversals, transpositions, and transversals (by also allowing block-interchanges). The GSB result is based on introduction of three bridge structures in the breakpoint graph, the L-bridge, T-bridge, and X-bridge that models goodreversal, transposition/transreversal, and block-interchange, respectively. However, the paper by Hao et al. focused on proving the 2-approximation GSB scheme and only mention a straightforward [Formula: see text] algorithm. In this paper, we give an [Formula: see text] algorithm for implementing the GSB scheme. The key idea behind our faster GSB algorithm is to represent cycles in the breakpoint graph by their canonical sequences, which greatly simplifies the search for these bridge structures. We also give some comparison results (running time and computed distances) against the original GSB implementation.
Understanding multi-scale structural evolution in granular systems through gMEMS

NASA Astrophysics Data System (ADS)

Walker, David M.; Tordesillas, Antoinette

2013-06-01

We show how the rheological response of a material to applied loads can be systematically coded, analyzed and succinctly summarized, according to an individual grain's property (e.g. kinematics). Individual grains are considered as their own smart sensor akin to microelectromechanical systems (e.g. gyroscopes, accelerometers), each capable of recognizing their evolving role within self-organizing building block structures (e.g. contact cycles and force chains). A symbolic time series is used to represent their participation in such self-assembled building blocks and a complex network summarizing their interrelationship with other grains is constructed. In particular, relationships between grain time series are determined according to the information theory Hamming distance or the metric Euclidean distance. We then use topological distance to find network communities enabling groups of grains at remote physical metric distances in the material to share a classification. In essence grains with similar structural and functional roles at different scales are identified together. This taxonomy distills the dissipative structural rearrangements of grains down to its essential features and thus provides pointers for objective physics-based internal variable formalisms used in the construction of robust predictive continuum models.
Computer-assisted education and interdisciplinary breast cancer diagnosis

NASA Astrophysics Data System (ADS)

Whatmough, Pamela; Gale, Alastair G.; Wilson, A. R. M.

1996-04-01

The diagnosis of breast disease for screening or symptomatic women is largely arrived at by a multi-disciplinary team. We report work on the development and assessment of an inter- disciplinary computer based learning system to support the diagnosis of this disease. The diagnostic process is first modelled from different viewpoints and then appropriate knowledge structures pertinent to the domains of radiologist, pathologist and surgeon are depicted. Initially the underlying inter-relationships of the mammographic diagnostic approach were detailed which is largely considered here. Ultimately a system is envisaged which will link these specialties and act as a diagnostic aid as well as a multi-media educational system.
MIMO system identification using frequency response data

NASA Technical Reports Server (NTRS)

Medina, Enrique A.; Irwin, R. D.; Mitchell, Jerrel R.; Bukley, Angelia P.

1992-01-01

A solution to the problem of obtaining a multi-input, multi-output statespace model of a system from its individual input/output frequency responses is presented. The Residue Identification Algorithm (RID) identifies the system poles from a transfer function model of the determinant of the frequency response data matrix. Next, the residue matrices of the modes are computed guaranteeing that each input/output frequency response is fitted in the least squares sense. Finally, a realization of the system is computed. Results of the application of RID to experimental frequency responses of a large space structure ground test facility are presented and compared to those obtained via the Eigensystem Realization Algorithm.
Informatics Approaches for Predicting, Understanding, and Testing Cancer Drug Combinations.

PubMed

Tang, Jing

2017-01-01

Making cancer treatment more effective is one of the grand challenges in our health care system. However, many drugs have entered clinical trials but so far showed limited efficacy or induced rapid development of resistance. We urgently need multi-targeted drug combinations, which shall selectively inhibit the cancer cells and block the emergence of drug resistance. The book chapter focuses on mathematical and computational tools to facilitate the discovery of the most promising drug combinations to improve efficacy and prevent resistance. Data integration approaches that leverage drug-target interactions, cancer molecular features, and signaling pathways for predicting, understanding, and testing drug combinations are critically reviewed.
Malleable architecture generator for FPGA computing

NASA Astrophysics Data System (ADS)

Gokhale, Maya; Kaba, James; Marks, Aaron; Kim, Jang

1996-10-01

The malleable architecture generator (MARGE) is a tool set that translates high-level parallel C to configuration bit streams for field-programmable logic based computing systems. MARGE creates an application-specific instruction set and generates the custom hardware components required to perform exactly those computations specified by the C program. In contrast to traditional fixed-instruction processors, MARGE's dynamic instruction set creation provides for efficient use of hardware resources. MARGE processes intermediate code in which each operation is annotated by the bit lengths of the operands. Each basic block (sequence of straight line code) is mapped into a single custom instruction which contains all the operations and logic inherent in the block. A synthesis phase maps the operations comprising the instructions into register transfer level structural components and control logic which have been optimized to exploit functional parallelism and function unit reuse. As a final stage, commercial technology-specific tools are used to generate configuration bit streams for the desired target hardware. Technology- specific pre-placed, pre-routed macro blocks are utilized to implement as much of the hardware as possible. MARGE currently supports the Xilinx-based Splash-2 reconfigurable accelerator and National Semiconductor's CLAy-based parallel accelerator, MAPA. The MARGE approach has been demonstrated on systolic applications such as DNA sequence comparison.
Investigation of advanced counterrotation blade configuration concepts for high speed turboprop systems. Task 5: Unsteady counterrotation ducted propfan analysis. Computer program user's manual

NASA Technical Reports Server (NTRS)

Hall, Edward J.; Delaney, Robert A.; Adamczyk, John J.; Miller, Christopher J.; Arnone, Andrea; Swanson, Charles

1993-01-01

The primary objective of this study was the development of a time-marching three-dimensional Euler/Navier-Stokes aerodynamic analysis to predict steady and unsteady compressible transonic flows about ducted and unducted propfan propulsion systems employing multiple blade rows. The computer codes resulting from this study are referred to as ADPAC-AOACR (Advanced Ducted Propfan Analysis Codes-Angle of Attack Coupled Row). This report is intended to serve as a computer program user's manual for the ADPAC-AOACR codes developed under Task 5 of NASA Contract NAS3-25270, Unsteady Counterrotating Ducted Propfan Analysis. The ADPAC-AOACR program is based on a flexible multiple blocked grid discretization scheme permitting coupled 2-D/3-D mesh block solutions with application to a wide variety of geometries. For convenience, several standard mesh block structures are described for turbomachinery applications. Aerodynamic calculations are based on a four-stage Runge-Kutta time-marching finite volume solution technique with added numerical dissipation. Steady flow predictions are accelerated by a multigrid procedure. Numerical calculations are compared with experimental data for several test cases to demonstrate the utility of this approach for predicting the aerodynamics of modern turbomachinery configurations employing multiple blade rows.
Statistical molecular design of balanced compound libraries for QSAR modeling.

PubMed

Linusson, A; Elofsson, M; Andersson, I E; Dahlgren, M K

2010-01-01

A fundamental step in preclinical drug development is the computation of quantitative structure-activity relationship (QSAR) models, i.e. models that link chemical features of compounds with activities towards a target macromolecule associated with the initiation or progression of a disease. QSAR models are computed by combining information on the physicochemical and structural features of a library of congeneric compounds, typically assembled from two or more building blocks, and biological data from one or more in vitro assays. Since the models provide information on features affecting the compounds' biological activity they can be used as guides for further optimization. However, in order for a QSAR model to be relevant to the targeted disease, and drug development in general, the compound library used must contain molecules with balanced variation of the features spanning the chemical space believed to be important for interaction with the biological target. In addition, the assays used must be robust and deliver high quality data that are directly related to the function of the biological target and the associated disease state. In this review, we discuss and exemplify the concept of statistical molecular design (SMD) in the selection of building blocks and final synthetic targets (i.e. compounds to synthesize) to generate information-rich, balanced libraries for biological testing and computation of QSAR models.
A numerical study of mixing in supersonic combustors with hypermixing injectors

NASA Technical Reports Server (NTRS)

Lee, J.

1993-01-01

A numerical study was conducted to evaluate the performance of wall mounted fuel-injectors designed for potential Supersonic Combustion Ramjet (SCRAM-jet) engine applications. The focus of this investigation was to numerically simulate existing combustor designs for the purpose of validating the numerical technique and the physical models developed. Three different injector designs of varying complexity were studied to fully understand the computational implications involved in accurate predictions. A dual transverse injection system and two streamwise injector designs were studied. The streamwise injectors were designed with swept ramps to enhance fuel-air mixing and combustion characteristics at supersonic speeds without the large flow blockage and drag contribution of the transverse injection system. For this study, the Mass-Average Navier-Stokes equations and the chemical species continuity equations were solved. The computations were performed using a finite-volume implicit numerical technique and multiple block structured grid system. The interfaces of the multiple block structured grid systems were numerically resolved using the flux-conservative technique. Detailed comparisons between the computations and existing experimental data are presented. These comparisons show that numerical predictions are in agreement with the experimental data. These comparisons also show that a number of turbulence model improvements are needed for accurate combustor flowfield predictions.

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