Efficient control schemes with limited computation complexity for Tomographic AO systems on VLTs and ELTs

NASA Astrophysics Data System (ADS)

Petit, C.; Le Louarn, M.; Fusco, T.; Madec, P.-Y.

2011-09-01

Various tomographic control solutions have been proposed during the last decades to ensure efficient or even optimal closed-loop correction to tomographic Adaptive Optics (AO) concepts such as Laser Tomographic AO (LTAO), Multi-Conjugate AO (MCAO). The optimal solution, based on Linear Quadratic Gaussian (LQG) approach, as well as suboptimal but efficient solutions such as Pseudo-Open Loop Control (POLC) require multiple Matrix Vector Multiplications (MVM). Disregarding their respective performance, these efficient control solutions thus exhibit strong increase of on-line complexity and their implementation may become difficult in demanding cases. Among them, two cases are of particular interest. First, the system Real-Time Computer architecture and implementation is derived from past or present solutions and does not support multiple MVM. This is the case of the AO Facility which RTC architecture is derived from the SPARTA platform and inherits its simple MVM architecture, which does not fit with LTAO control solutions for instance. Second, considering future systems such as Extremely Large Telescopes, the number of degrees of freedom is twenty to one hundred times bigger than present systems. In these conditions, tomographic control solutions can hardly be used in their standard form and optimized implementation shall be considered. Single MVM tomographic control solutions represent a potential solution, and straightforward solutions such as Virtual Deformable Mirrors have been already proposed for LTAO but with tuning issues. We investigate in this paper the possibility to derive from tomographic control solutions, such as POLC or LQG, simplified control solutions ensuring simple MVM architecture and that could be thus implemented on nowadays systems or future complex systems. We theoretically derive various solutions and analyze their respective performance on various systems thanks to numerical simulation. We discuss the optimization of their performance and stability issues with respect to classic control solutions. We finally discuss off-line computation and implementation constraints.

An efficient method to compute spurious end point contributions in PO solutions. [Physical Optics

NASA Technical Reports Server (NTRS)

Gupta, Inder J.; Burnside, Walter D.; Pistorius, Carl W. I.

1987-01-01

A method is given to compute the spurious endpoint contributions in the physical optics solution for electromagnetic scattering from conducting bodies. The method is applicable to general three-dimensional structures. The only information required to use the method is the radius of curvature of the body at the shadow boundary. Thus, the method is very efficient for numerical computations. As an illustration, the method is applied to several bodies of revolution to compute the endpoint contributions for backscattering in the case of axial incidence. It is shown that in high-frequency situations, the endpoint contributions obtained using the method are equal to the true endpoint contributions.

Parallel computation using boundary elements in solid mechanics

NASA Technical Reports Server (NTRS)

Chien, L. S.; Sun, C. T.

1990-01-01

The inherent parallelism of the boundary element method is shown. The boundary element is formulated by assuming the linear variation of displacements and tractions within a line element. Moreover, MACSYMA symbolic program is employed to obtain the analytical results for influence coefficients. Three computational components are parallelized in this method to show the speedup and efficiency in computation. The global coefficient matrix is first formed concurrently. Then, the parallel Gaussian elimination solution scheme is applied to solve the resulting system of equations. Finally, and more importantly, the domain solutions of a given boundary value problem are calculated simultaneously. The linear speedups and high efficiencies are shown for solving a demonstrated problem on Sequent Symmetry S81 parallel computing system.

An unsteady aerodynamic formulation for efficient rotor tonal noise prediction

NASA Astrophysics Data System (ADS)

Gennaretti, M.; Testa, C.; Bernardini, G.

2013-12-01

An aerodynamic/aeroacoustic solution methodology for predction of tonal noise emitted by helicopter rotors and propellers is presented. It is particularly suited for configurations dominated by localized, high-frequency inflow velocity fields as those generated by blade-vortex interactions. The unsteady pressure distributions are determined by the sectional, frequency-domain Küssner-Schwarz formulation, with downwash including the wake inflow velocity predicted by a three-dimensional, unsteady, panel-method formulation suited for the analysis of rotors operating in complex aerodynamic environments. The radiated noise is predicted through solution of the Ffowcs Williams-Hawkings equation. The proposed approach yields a computationally efficient solution procedure that may be particularly useful in preliminary design/multidisciplinary optimization applications. It is validated through comparisons with solutions that apply the airloads directly evaluated by the time-marching, panel-method formulation. The results are provided in terms of blade loads, noise signatures and sound pressure level contours. An estimation of the computational efficiency of the proposed solution process is also presented.

Post-Optimality Analysis In Aerospace Vehicle Design

NASA Technical Reports Server (NTRS)

Braun, Robert D.; Kroo, Ilan M.; Gage, Peter J.

1993-01-01

This analysis pertains to the applicability of optimal sensitivity information to aerospace vehicle design. An optimal sensitivity (or post-optimality) analysis refers to computations performed once the initial optimization problem is solved. These computations may be used to characterize the design space about the present solution and infer changes in this solution as a result of constraint or parameter variations, without reoptimizing the entire system. The present analysis demonstrates that post-optimality information generated through first-order computations can be used to accurately predict the effect of constraint and parameter perturbations on the optimal solution. This assessment is based on the solution of an aircraft design problem in which the post-optimality estimates are shown to be within a few percent of the true solution over the practical range of constraint and parameter variations. Through solution of a reusable, single-stage-to-orbit, launch vehicle design problem, this optimal sensitivity information is also shown to improve the efficiency of the design process, For a hierarchically decomposed problem, this computational efficiency is realized by estimating the main-problem objective gradient through optimal sep&ivity calculations, By reducing the need for finite differentiation of a re-optimized subproblem, a significant decrease in the number of objective function evaluations required to reach the optimal solution is obtained.

Efficient self-consistent viscous-inviscid solutions for unsteady transonic flow

NASA Technical Reports Server (NTRS)

Howlett, J. T.

1985-01-01

An improved method is presented for coupling a boundary layer code with an unsteady inviscid transonic computer code in a quasi-steady fashion. At each fixed time step, the boundary layer and inviscid equations are successively solved until the process converges. An explicit coupling of the equations is described which greatly accelerates the convergence process. Computer times for converged viscous-inviscid solutions are about 1.8 times the comparable inviscid values. Comparison of the results obtained with experimental data on three airfoils are presented. These comparisons demonstrate that the explicitly coupled viscous-inviscid solutions can provide efficient predictions of pressure distributions and lift for unsteady two-dimensional transonic flows.

Efficient self-consistent viscous-inviscid solutions for unsteady transonic flow

NASA Technical Reports Server (NTRS)

Howlett, J. T.

1985-01-01

An improved method is presented for coupling a boundary layer code with an unsteady inviscid transonic computer code in a quasi-steady fashion. At each fixed time step, the boundary layer and inviscid equations are successively solved until the process converges. An explicit coupling of the equations is described which greatly accelerates the convergence process. Computer times for converged viscous-inviscid solutions are about 1.8 times the comparable inviscid values. Comparison of the results obtained with experimental data on three airfoils are presented. These comparisons demonstrate that the explicitly coupled viscous-inviscid solutions can provide efficient predictions of pressure distributions and lift for unsteady two-dimensional transonic flow.

Structural, thermodynamic, and electrical properties of polar fluids and ionic solutions on a hypersphere: Results of simulations

NASA Astrophysics Data System (ADS)

Caillol, J. M.; Levesque, D.

1992-01-01

The reliability and the efficiency of a new method suitable for the simulations of dielectric fluids and ionic solutions is established by numerical computations. The efficiency depends on the use of a simulation cell which is the surface of a four-dimensional sphere. The reliability originates from a charge-charge potential solution of the Poisson equation in this confining volume. The computation time, for systems of a few hundred molecules, is reduced by a factor of 2 or 3 compared to this of a simulation performed in a cubic volume with periodic boundary conditions and the Ewald charge-charge potential.

Implementing Parquet equations using HPX

NASA Astrophysics Data System (ADS)

Kellar, Samuel; Wagle, Bibek; Yang, Shuxiang; Tam, Ka-Ming; Kaiser, Hartmut; Moreno, Juana; Jarrell, Mark

A new C++ runtime system (HPX) enables simulations of complex systems to run more efficiently on parallel and heterogeneous systems. This increased efficiency allows for solutions to larger simulations of the parquet approximation for a system with impurities. The relevancy of the parquet equations depends upon the ability to solve systems which require long runs and large amounts of memory. These limitations, in addition to numerical complications arising from stability of the solutions, necessitate running on large distributed systems. As the computational resources trend towards the exascale and the limitations arising from computational resources vanish efficiency of large scale simulations becomes a focus. HPX facilitates efficient simulations through intelligent overlapping of computation and communication. Simulations such as the parquet equations which require the transfer of large amounts of data should benefit from HPX implementations. Supported by the the NSF EPSCoR Cooperative Agreement No. EPS-1003897 with additional support from the Louisiana Board of Regents.

Finite element analysis of transonic flows in cascades: Importance of computational grids in improving accuracy and convergence

NASA Technical Reports Server (NTRS)

Ecer, A.; Akay, H. U.

1981-01-01

The finite element method is applied for the solution of transonic potential flows through a cascade of airfoils. Convergence characteristics of the solution scheme are discussed. Accuracy of the numerical solutions is investigated for various flow regions in the transonic flow configuration. The design of an efficient finite element computational grid is discussed for improving accuracy and convergence.

A numerical method for solving systems of linear ordinary differential equations with rapidly oscillating solutions

NASA Technical Reports Server (NTRS)

Bernstein, Ira B.; Brookshaw, Leigh; Fox, Peter A.

1992-01-01

The present numerical method for accurate and efficient solution of systems of linear equations proceeds by numerically developing a set of basis solutions characterized by slowly varying dependent variables. The solutions thus obtained are shown to have a computational overhead largely independent of the small size of the scale length which characterizes the solutions; in many cases, the technique obviates series solutions near singular points, and its known sources of error can be easily controlled without a substantial increase in computational time.

An efficient computational method for solving nonlinear stochastic Itô integral equations: Application for stochastic problems in physics

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

Heydari, M.H., E-mail: heydari@stu.yazd.ac.ir; The Laboratory of Quantum Information Processing, Yazd University, Yazd; Hooshmandasl, M.R., E-mail: hooshmandasl@yazd.ac.ir

Because of the nonlinearity, closed-form solutions of many important stochastic functional equations are virtually impossible to obtain. Thus, numerical solutions are a viable alternative. In this paper, a new computational method based on the generalized hat basis functions together with their stochastic operational matrix of Itô-integration is proposed for solving nonlinear stochastic Itô integral equations in large intervals. In the proposed method, a new technique for computing nonlinear terms in such problems is presented. The main advantage of the proposed method is that it transforms problems under consideration into nonlinear systems of algebraic equations which can be simply solved. Errormore » analysis of the proposed method is investigated and also the efficiency of this method is shown on some concrete examples. The obtained results reveal that the proposed method is very accurate and efficient. As two useful applications, the proposed method is applied to obtain approximate solutions of the stochastic population growth models and stochastic pendulum problem.« less

Rapid solution of large-scale systems of equations

NASA Technical Reports Server (NTRS)

Storaasli, Olaf O.

1994-01-01

The analysis and design of complex aerospace structures requires the rapid solution of large systems of linear and nonlinear equations, eigenvalue extraction for buckling, vibration and flutter modes, structural optimization and design sensitivity calculation. Computers with multiple processors and vector capabilities can offer substantial computational advantages over traditional scalar computer for these analyses. These computers fall into two categories: shared memory computers and distributed memory computers. This presentation covers general-purpose, highly efficient algorithms for generation/assembly or element matrices, solution of systems of linear and nonlinear equations, eigenvalue and design sensitivity analysis and optimization. All algorithms are coded in FORTRAN for shared memory computers and many are adapted to distributed memory computers. The capability and numerical performance of these algorithms will be addressed.

Efficient implementation of a 3-dimensional ADI method on the iPSC/860

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

Van der Wijngaart, R.F.

1993-12-31

A comparison is made between several domain decomposition strategies for the solution of three-dimensional partial differential equations on a MIMD distributed memory parallel computer. The grids used are structured, and the numerical algorithm is ADI. Important implementation issues regarding load balancing, storage requirements, network latency, and overlap of computations and communications are discussed. Results of the solution of the three-dimensional heat equation on the Intel iPSC/860 are presented for the three most viable methods. It is found that the Bruno-Cappello decomposition delivers optimal computational speed through an almost complete elimination of processor idle time, while providing good memory efficiency.

Reduced-Order Models for the Aeroelastic Analysis of Ares Launch Vehicles

NASA Technical Reports Server (NTRS)

Silva, Walter A.; Vatsa, Veer N.; Biedron, Robert T.

2010-01-01

This document presents the development and application of unsteady aerodynamic, structural dynamic, and aeroelastic reduced-order models (ROMs) for the ascent aeroelastic analysis of the Ares I-X flight test and Ares I crew launch vehicles using the unstructured-grid, aeroelastic FUN3D computational fluid dynamics (CFD) code. The purpose of this work is to perform computationally-efficient aeroelastic response calculations that would be prohibitively expensive via computation of multiple full-order aeroelastic FUN3D solutions. These efficient aeroelastic ROM solutions provide valuable insight regarding the aeroelastic sensitivity of the vehicles to various parameters over a range of dynamic pressures.

Closed-form solutions for a class of optimal quadratic regulator problems with terminal constraints

NASA Technical Reports Server (NTRS)

Juang, J.-N.; Turner, J. D.; Chun, H. M.

1984-01-01

Closed-form solutions are derived for coupled Riccati-like matrix differential equations describing the solution of a class of optimal finite time quadratic regulator problems with terminal constraints. Analytical solutions are obtained for the feedback gains and the closed-loop response trajectory. A computational procedure is presented which introduces new variables for efficient computation of the terminal control law. Two examples are given to illustrate the validity and usefulness of the theory.

A two steps solution approach to solving large nonlinear models: application to a problem of conjunctive use.

PubMed

Vieira, J; Cunha, M C

2011-01-01

This article describes a solution method of solving large nonlinear problems in two steps. The two steps solution approach takes advantage of handling smaller and simpler models and having better starting points to improve solution efficiency. The set of nonlinear constraints (named as complicating constraints) which makes the solution of the model rather complex and time consuming is eliminated from step one. The complicating constraints are added only in the second step so that a solution of the complete model is then found. The solution method is applied to a large-scale problem of conjunctive use of surface water and groundwater resources. The results obtained are compared with solutions determined with the direct solve of the complete model in one single step. In all examples the two steps solution approach allowed a significant reduction of the computation time. This potential gain of efficiency of the two steps solution approach can be extremely important for work in progress and it can be particularly useful for cases where the computation time would be a critical factor for having an optimized solution in due time.

An efficient nonlinear finite-difference approach in the computational modeling of the dynamics of a nonlinear diffusion-reaction equation in microbial ecology.

PubMed

Macías-Díaz, J E; Macías, Siegfried; Medina-Ramírez, I E

2013-12-01

In this manuscript, we present a computational model to approximate the solutions of a partial differential equation which describes the growth dynamics of microbial films. The numerical technique reported in this work is an explicit, nonlinear finite-difference methodology which is computationally implemented using Newton's method. Our scheme is compared numerically against an implicit, linear finite-difference discretization of the same partial differential equation, whose computer coding requires an implementation of the stabilized bi-conjugate gradient method. Our numerical results evince that the nonlinear approach results in a more efficient approximation to the solutions of the biofilm model considered, and demands less computer memory. Moreover, the positivity of initial profiles is preserved in the practice by the nonlinear scheme proposed. Copyright © 2013 Elsevier Ltd. All rights reserved.

A diagonal algorithm for the method of pseudocompressibility. [for steady-state solution to incompressible Navier-Stokes equation

NASA Technical Reports Server (NTRS)

Rogers, S. E.; Kwak, D.; Chang, J. L. C.

1986-01-01

The method of pseudocompressibility has been shown to be an efficient method for obtaining a steady-state solution to the incompressible Navier-Stokes equations. Recent improvements to this method include the use of a diagonal scheme for the inversion of the equations at each iteration. The necessary transformations have been derived for the pseudocompressibility equations in generalized coordinates. The diagonal algorithm reduces the computing time necessary to obtain a steady-state solution by a factor of nearly three. Implicit viscous terms are maintained in the equations, and it has become possible to use fourth-order implicit dissipation. The steady-state solution is unchanged by the approximations resulting from the diagonalization of the equations. Computed results for flow over a two-dimensional backward-facing step and a three-dimensional cylinder mounted normal to a flat plate are presented for both the old and new algorithms. The accuracy and computing efficiency of these algorithms are compared.

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.

Inversion Of Jacobian Matrix For Robot Manipulators

NASA Technical Reports Server (NTRS)

Fijany, Amir; Bejczy, Antal K.

1989-01-01

Report discusses inversion of Jacobian matrix for class of six-degree-of-freedom arms with spherical wrist, i.e., with last three joints intersecting. Shows by taking advantage of simple geometry of such arms, closed-form solution of Q=J-1X, which represents linear transformation from task space to joint space, obtained efficiently. Presents solutions for PUMA arm, JPL/Stanford arm, and six-revolute-joint coplanar arm along with all singular points. Main contribution of paper shows simple geometry of this type of arms exploited in performing inverse transformation without any need to compute Jacobian or its inverse explicitly. Implication of this computational efficiency advanced task-space control schemes for spherical-wrist arms implemented more efficiently.

Seismic data restoration with a fast L1 norm trust region method

NASA Astrophysics Data System (ADS)

Cao, Jingjie; Wang, Yanfei

2014-08-01

Seismic data restoration is a major strategy to provide reliable wavefield when field data dissatisfy the Shannon sampling theorem. Recovery by sparsity-promoting inversion often get sparse solutions of seismic data in a transformed domains, however, most methods for sparsity-promoting inversion are line-searching methods which are efficient but are inclined to obtain local solutions. Using trust region method which can provide globally convergent solutions is a good choice to overcome this shortcoming. A trust region method for sparse inversion has been proposed, however, the efficiency should be improved to suitable for large-scale computation. In this paper, a new L1 norm trust region model is proposed for seismic data restoration and a robust gradient projection method for solving the sub-problem is utilized. Numerical results of synthetic and field data demonstrate that the proposed trust region method can get excellent computation speed and is a viable alternative for large-scale computation.

Reference interaction site model with hydrophobicity induced density inhomogeneity: An analytical theory to compute solvation properties of large hydrophobic solutes in the mixture of polyatomic solvent molecules.

PubMed

Cao, Siqin; Sheong, Fu Kit; Huang, Xuhui

2015-08-07

Reference interaction site model (RISM) has recently become a popular approach in the study of thermodynamical and structural properties of the solvent around macromolecules. On the other hand, it was widely suggested that there exists water density depletion around large hydrophobic solutes (>1 nm), and this may pose a great challenge to the RISM theory. In this paper, we develop a new analytical theory, the Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity (RISM-HI), to compute solvent radial distribution function (RDF) around large hydrophobic solute in water as well as its mixture with other polyatomic organic solvents. To achieve this, we have explicitly considered the density inhomogeneity at the solute-solvent interface using the framework of the Yvon-Born-Green hierarchy, and the RISM theory is used to obtain the solute-solvent pair correlation. In order to efficiently solve the relevant equations while maintaining reasonable accuracy, we have also developed a new closure called the D2 closure. With this new theory, the solvent RDFs around a large hydrophobic particle in water and different water-acetonitrile mixtures could be computed, which agree well with the results of the molecular dynamics simulations. Furthermore, we show that our RISM-HI theory can also efficiently compute the solvation free energy of solute with a wide range of hydrophobicity in various water-acetonitrile solvent mixtures with a reasonable accuracy. We anticipate that our theory could be widely applied to compute the thermodynamic and structural properties for the solvation of hydrophobic solute.

FPGA-Based High-Performance Embedded Systems for Adaptive Edge Computing in Cyber-Physical Systems: The ARTICo³ Framework.

PubMed

Rodríguez, Alfonso; Valverde, Juan; Portilla, Jorge; Otero, Andrés; Riesgo, Teresa; de la Torre, Eduardo

2018-06-08

Cyber-Physical Systems are experiencing a paradigm shift in which processing has been relocated to the distributed sensing layer and is no longer performed in a centralized manner. This approach, usually referred to as Edge Computing, demands the use of hardware platforms that are able to manage the steadily increasing requirements in computing performance, while keeping energy efficiency and the adaptability imposed by the interaction with the physical world. In this context, SRAM-based FPGAs and their inherent run-time reconfigurability, when coupled with smart power management strategies, are a suitable solution. However, they usually fail in user accessibility and ease of development. In this paper, an integrated framework to develop FPGA-based high-performance embedded systems for Edge Computing in Cyber-Physical Systems is presented. This framework provides a hardware-based processing architecture, an automated toolchain, and a runtime to transparently generate and manage reconfigurable systems from high-level system descriptions without additional user intervention. Moreover, it provides users with support for dynamically adapting the available computing resources to switch the working point of the architecture in a solution space defined by computing performance, energy consumption and fault tolerance. Results show that it is indeed possible to explore this solution space at run time and prove that the proposed framework is a competitive alternative to software-based edge computing platforms, being able to provide not only faster solutions, but also higher energy efficiency for computing-intensive algorithms with significant levels of data-level parallelism.

A Simple and Resource-efficient Setup for the Computer-aided Drug Design Laboratory.

PubMed

Moretti, Loris; Sartori, Luca

2016-10-01

Undertaking modelling investigations for Computer-Aided Drug Design (CADD) requires a proper environment. In principle, this could be done on a single computer, but the reality of a drug discovery program requires robustness and high-throughput computing (HTC) to efficiently support the research. Therefore, a more capable alternative is needed but its implementation has no widespread solution. Here, the realization of such a computing facility is discussed, from general layout to technical details all aspects are covered. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Secure Multiparty Quantum Computation for Summation and Multiplication.

PubMed

Shi, Run-hua; Mu, Yi; Zhong, Hong; Cui, Jie; Zhang, Shun

2016-01-21

As a fundamental primitive, Secure Multiparty Summation and Multiplication can be used to build complex secure protocols for other multiparty computations, specially, numerical computations. However, there is still lack of systematical and efficient quantum methods to compute Secure Multiparty Summation and Multiplication. In this paper, we present a novel and efficient quantum approach to securely compute the summation and multiplication of multiparty private inputs, respectively. Compared to classical solutions, our proposed approach can ensure the unconditional security and the perfect privacy protection based on the physical principle of quantum mechanics.

Secure Multiparty Quantum Computation for Summation and Multiplication

PubMed Central

Shi, Run-hua; Mu, Yi; Zhong, Hong; Cui, Jie; Zhang, Shun

2016-01-01

As a fundamental primitive, Secure Multiparty Summation and Multiplication can be used to build complex secure protocols for other multiparty computations, specially, numerical computations. However, there is still lack of systematical and efficient quantum methods to compute Secure Multiparty Summation and Multiplication. In this paper, we present a novel and efficient quantum approach to securely compute the summation and multiplication of multiparty private inputs, respectively. Compared to classical solutions, our proposed approach can ensure the unconditional security and the perfect privacy protection based on the physical principle of quantum mechanics. PMID:26792197

SCOTCH: Secure Counting Of encrypTed genomiC data using a Hybrid approach.

PubMed

Chenghong, Wang; Jiang, Yichen; Mohammed, Noman; Chen, Feng; Jiang, Xiaoqian; Al Aziz, Md Momin; Sadat, Md Nazmus; Wang, Shuang

2017-01-01

As genomic data are usually at large scale and highly sensitive, it is essential to enable both efficient and secure analysis, by which the data owner can securely delegate both computation and storage on untrusted public cloud. Counting query of genotypes is a basic function for many downstream applications in biomedical research (e.g., computing allele frequency, calculating chi-squared statistics, etc.). Previous solutions show promise on secure counting of outsourced data but the efficiency is still a big limitation for real world applications. In this paper, we propose a novel hybrid solution to combine a rigorous theoretical model (homomorphic encryption) and the latest hardware-based infrastructure (i.e., Software Guard Extensions) to speed up the computation while preserving the privacy of both data owners and data users. Our results demonstrated efficiency by using the real data from the personal genome project.

SCOTCH: Secure Counting Of encrypTed genomiC data using a Hybrid approach

PubMed Central

Chenghong, Wang; Jiang, Yichen; Mohammed, Noman; Chen, Feng; Jiang, Xiaoqian; Al Aziz, Md Momin; Sadat, Md Nazmus; Wang, Shuang

2017-01-01

As genomic data are usually at large scale and highly sensitive, it is essential to enable both efficient and secure analysis, by which the data owner can securely delegate both computation and storage on untrusted public cloud. Counting query of genotypes is a basic function for many downstream applications in biomedical research (e.g., computing allele frequency, calculating chi-squared statistics, etc.). Previous solutions show promise on secure counting of outsourced data but the efficiency is still a big limitation for real world applications. In this paper, we propose a novel hybrid solution to combine a rigorous theoretical model (homomorphic encryption) and the latest hardware-based infrastructure (i.e., Software Guard Extensions) to speed up the computation while preserving the privacy of both data owners and data users. Our results demonstrated efficiency by using the real data from the personal genome project. PMID:29854245

A non-local computational boundary condition for duct acoustics

NASA Technical Reports Server (NTRS)

Zorumski, William E.; Watson, Willie R.; Hodge, Steve L.

1994-01-01

A non-local boundary condition is formulated for acoustic waves in ducts without flow. The ducts are two dimensional with constant area, but with variable impedance wall lining. Extension of the formulation to three dimensional and variable area ducts is straightforward in principle, but requires significantly more computation. The boundary condition simulates a nonreflecting wave field in an infinite duct. It is implemented by a constant matrix operator which is applied at the boundary of the computational domain. An efficient computational solution scheme is developed which allows calculations for high frequencies and long duct lengths. This computational solution utilizes the boundary condition to limit the computational space while preserving the radiation boundary condition. The boundary condition is tested for several sources. It is demonstrated that the boundary condition can be applied close to the sound sources, rendering the computational domain small. Computational solutions with the new non-local boundary condition are shown to be consistent with the known solutions for nonreflecting wavefields in an infinite uniform duct.

Higher-order adaptive finite-element methods for Kohn–Sham density functional theory

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

Motamarri, P.; Nowak, M.R.; Leiter, K.

2013-11-15

We present an efficient computational approach to perform real-space electronic structure calculations using an adaptive higher-order finite-element discretization of Kohn–Sham density-functional theory (DFT). To this end, we develop an a priori mesh-adaption technique to construct a close to optimal finite-element discretization of the problem. We further propose an efficient solution strategy for solving the discrete eigenvalue problem by using spectral finite-elements in conjunction with Gauss–Lobatto quadrature, and a Chebyshev acceleration technique for computing the occupied eigenspace. The proposed approach has been observed to provide a staggering 100–200-fold computational advantage over the solution of a generalized eigenvalue problem. Using the proposedmore » solution procedure, we investigate the computational efficiency afforded by higher-order finite-element discretizations of the Kohn–Sham DFT problem. Our studies suggest that staggering computational savings—of the order of 1000-fold—relative to linear finite-elements can be realized, for both all-electron and local pseudopotential calculations, by using higher-order finite-element discretizations. On all the benchmark systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemical accuracy, suggesting that the hexic spectral-element may be an optimal choice for the finite-element discretization of the Kohn–Sham DFT problem. A comparative study of the computational efficiency of the proposed higher-order finite-element discretizations suggests that the performance of finite-element basis is competing with the plane-wave discretization for non-periodic local pseudopotential calculations, and compares to the Gaussian basis for all-electron calculations to within an order of magnitude. Further, we demonstrate the capability of the proposed approach to compute the electronic structure of a metallic system containing 1688 atoms using modest computational resources, and good scalability of the present implementation up to 192 processors.« less

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.

High-Performance Computing Data Center Warm-Water Liquid Cooling |

Science.gov Websites

Computational Science | NREL Warm-Water Liquid Cooling High-Performance Computing Data Center Warm-Water Liquid Cooling NREL's High-Performance Computing Data Center (HPC Data Center) is liquid water Liquid cooling technologies offer a more energy-efficient solution that also allows for effective

Efficient Solution of Three-Dimensional Problems of Acoustic and Electromagnetic Scattering by Open Surfaces

NASA Technical Reports Server (NTRS)

Turc, Catalin; Anand, Akash; Bruno, Oscar; Chaubell, Julian

2011-01-01

We present a computational methodology (a novel Nystrom approach based on use of a non-overlapping patch technique and Chebyshev discretizations) for efficient solution of problems of acoustic and electromagnetic scattering by open surfaces. Our integral equation formulations (1) Incorporate, as ansatz, the singular nature of open-surface integral-equation solutions, and (2) For the Electric Field Integral Equation (EFIE), use analytical regularizes that effectively reduce the number of iterations required by iterative linear-algebra solution based on Krylov-subspace iterative solvers.

Parallel, adaptive finite element methods for conservation laws

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Devine, Karen D.; Flaherty, Joseph E.

1994-01-01

We construct parallel finite element methods for the solution of hyperbolic conservation laws in one and two dimensions. Spatial discretization is performed by a discontinuous Galerkin finite element method using a basis of piecewise Legendre polynomials. Temporal discretization utilizes a Runge-Kutta method. Dissipative fluxes and projection limiting prevent oscillations near solution discontinuities. A posteriori estimates of spatial errors are obtained by a p-refinement technique using superconvergence at Radau points. The resulting method is of high order and may be parallelized efficiently on MIMD computers. We compare results using different limiting schemes and demonstrate parallel efficiency through computations on an NCUBE/2 hypercube. We also present results using adaptive h- and p-refinement to reduce the computational cost of the method.

Algorithms for the computation of solutions of the Ornstein-Zernike equation.

PubMed

Peplow, A T; Beardmore, R E; Bresme, F

2006-10-01

We introduce a robust and efficient methodology to solve the Ornstein-Zernike integral equation using the pseudoarc length (PAL) continuation method that reformulates the integral equation in an equivalent but nonstandard form. This enables the computation of solutions in regions where the compressibility experiences large changes or where the existence of multiple solutions and so-called branch points prevents Newton's method from converging. We illustrate the use of the algorithm with a difficult problem that arises in the numerical solution of integral equations, namely the evaluation of the so-called no-solution line of the Ornstein-Zernike hypernetted chain (HNC) integral equation for the Lennard-Jones potential. We are able to use the PAL algorithm to solve the integral equation along this line and to connect physical and nonphysical solution branches (both isotherms and isochores) where appropriate. We also show that PAL continuation can compute solutions within the no-solution region that cannot be computed when Newton and Picard methods are applied directly to the integral equation. While many solutions that we find are new, some correspond to states with negative compressibility and consequently are not physical.

Aerodynamic optimization by simultaneously updating flow variables and design parameters

NASA Technical Reports Server (NTRS)

Rizk, M. H.

1990-01-01

The application of conventional optimization schemes to aerodynamic design problems leads to inner-outer iterative procedures that are very costly. An alternative approach is presented based on the idea of updating the flow variable iterative solutions and the design parameter iterative solutions simultaneously. Two schemes based on this idea are applied to problems of correcting wind tunnel wall interference and optimizing advanced propeller designs. The first of these schemes is applicable to a limited class of two-design-parameter problems with an equality constraint. It requires the computation of a single flow solution. The second scheme is suitable for application to general aerodynamic problems. It requires the computation of several flow solutions in parallel. In both schemes, the design parameters are updated as the iterative flow solutions evolve. Computations are performed to test the schemes' efficiency, accuracy, and sensitivity to variations in the computational parameters.

CORDIC-based digital signal processing (DSP) element for adaptive signal processing

NASA Astrophysics Data System (ADS)

Bolstad, Gregory D.; Neeld, Kenneth B.

1995-04-01

The High Performance Adaptive Weight Computation (HAWC) processing element is a CORDIC based application specific DSP element that, when connected in a linear array, can perform extremely high throughput (100s of GFLOPS) matrix arithmetic operations on linear systems of equations in real time. In particular, it very efficiently performs the numerically intense computation of optimal least squares solutions for large, over-determined linear systems. Most techniques for computing solutions to these types of problems have used either a hard-wired, non-programmable systolic array approach, or more commonly, programmable DSP or microprocessor approaches. The custom logic methods can be efficient, but are generally inflexible. Approaches using multiple programmable generic DSP devices are very flexible, but suffer from poor efficiency and high computation latencies, primarily due to the large number of DSP devices that must be utilized to achieve the necessary arithmetic throughput. The HAWC processor is implemented as a highly optimized systolic array, yet retains some of the flexibility of a programmable data-flow system, allowing efficient implementation of algorithm variations. This provides flexible matrix processing capabilities that are one to three orders of magnitude less expensive and more dense than the current state of the art, and more importantly, allows a realizable solution to matrix processing problems that were previously considered impractical to physically implement. HAWC has direct applications in RADAR, SONAR, communications, and image processing, as well as in many other types of systems.

Efficient computation of the Grünwald-Letnikov fractional diffusion derivative using adaptive time step memory

NASA Astrophysics Data System (ADS)

MacDonald, Christopher L.; Bhattacharya, Nirupama; Sprouse, Brian P.; Silva, Gabriel A.

2015-09-01

Computing numerical solutions to fractional differential equations can be computationally intensive due to the effect of non-local derivatives in which all previous time points contribute to the current iteration. In general, numerical approaches that depend on truncating part of the system history while efficient, can suffer from high degrees of error and inaccuracy. Here we present an adaptive time step memory method for smooth functions applied to the Grünwald-Letnikov fractional diffusion derivative. This method is computationally efficient and results in smaller errors during numerical simulations. Sampled points along the system's history at progressively longer intervals are assumed to reflect the values of neighboring time points. By including progressively fewer points backward in time, a temporally 'weighted' history is computed that includes contributions from the entire past of the system, maintaining accuracy, but with fewer points actually calculated, greatly improving computational efficiency.

Computing Interactions Of Free-Space Radiation With Matter

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Cucinotta, F. A.; Shinn, J. L.; Townsend, L. W.; Badavi, F. F.; Tripathi, R. K.; Silberberg, R.; Tsao, C. H.; Badwar, G. D.

1995-01-01

High Charge and Energy Transport (HZETRN) computer program computationally efficient, user-friendly package of software adressing problem of transport of, and shielding against, radiation in free space. Designed as "black box" for design engineers not concerned with physics of underlying atomic and nuclear radiation processes in free-space environment, but rather primarily interested in obtaining fast and accurate dosimetric information for design and construction of modules and devices for use in free space. Computational efficiency achieved by unique algorithm based on deterministic approach to solution of Boltzmann equation rather than computationally intensive statistical Monte Carlo method. Written in FORTRAN.

Discrete-time neural network for fast solving large linear L1 estimation problems and its application to image restoration.

PubMed

Xia, Youshen; Sun, Changyin; Zheng, Wei Xing

2012-05-01

There is growing interest in solving linear L1 estimation problems for sparsity of the solution and robustness against non-Gaussian noise. This paper proposes a discrete-time neural network which can calculate large linear L1 estimation problems fast. The proposed neural network has a fixed computational step length and is proved to be globally convergent to an optimal solution. Then, the proposed neural network is efficiently applied to image restoration. Numerical results show that the proposed neural network is not only efficient in solving degenerate problems resulting from the nonunique solutions of the linear L1 estimation problems but also needs much less computational time than the related algorithms in solving both linear L1 estimation and image restoration problems.

Flowing partially penetrating well: solution to a mixed-type boundary value problem

NASA Astrophysics Data System (ADS)

Cassiani, G.; Kabala, Z. J.; Medina, M. A.

A new semi-analytic solution to the mixed-type boundary value problem for a flowing partially penetrating well with infinitesimal skin situated in an anisotropic aquifer is developed. The solution is suited to aquifers having a semi-infinite vertical extent or to packer tests with aquifer horizontal boundaries far enough from the tested area. The problem reduces to a system of dual integral equations (DE) and further to a deconvolution problem. Unlike the analogous Dagan's steady-state solution [Water Resour. Res. 1978; 14:929-34], our DE solution does not suffer from numerical oscillations. The new solution is validated by matching the corresponding finite-difference solution and is computationally much more efficient. An automated (Newton-Raphson) parameter identification algorithm is proposed for field test inversion, utilizing the DE solution for the forward model. The procedure is computationally efficient and converges to correct parameter values. A solution for the partially penetrating flowing well with no skin and a drawdown-drawdown discontinuous boundary condition, analogous to that by Novakowski [Can. Geotech. J. 1993; 30:600-6], is compared to the DE solution. The D-D solution leads to physically inconsistent infinite total flow rate to the well, when no skin effect is considered. The DE solution, on the other hand, produces accurate results.

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

Cao, Siqin; Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon; Sheong, Fu Kit

Reference interaction site model (RISM) has recently become a popular approach in the study of thermodynamical and structural properties of the solvent around macromolecules. On the other hand, it was widely suggested that there exists water density depletion around large hydrophobic solutes (>1 nm), and this may pose a great challenge to the RISM theory. In this paper, we develop a new analytical theory, the Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity (RISM-HI), to compute solvent radial distribution function (RDF) around large hydrophobic solute in water as well as its mixture with other polyatomic organic solvents. To achievemore » this, we have explicitly considered the density inhomogeneity at the solute-solvent interface using the framework of the Yvon-Born-Green hierarchy, and the RISM theory is used to obtain the solute-solvent pair correlation. In order to efficiently solve the relevant equations while maintaining reasonable accuracy, we have also developed a new closure called the D2 closure. With this new theory, the solvent RDFs around a large hydrophobic particle in water and different water-acetonitrile mixtures could be computed, which agree well with the results of the molecular dynamics simulations. Furthermore, we show that our RISM-HI theory can also efficiently compute the solvation free energy of solute with a wide range of hydrophobicity in various water-acetonitrile solvent mixtures with a reasonable accuracy. We anticipate that our theory could be widely applied to compute the thermodynamic and structural properties for the solvation of hydrophobic solute.« less

Research related to improved computer aided design software package. [comparative efficiency of finite, boundary, and hybrid element methods in elastostatics

NASA Technical Reports Server (NTRS)

Walston, W. H., Jr.

1986-01-01

The comparative computational efficiencies of the finite element (FEM), boundary element (BEM), and hybrid boundary element-finite element (HVFEM) analysis techniques are evaluated for representative bounded domain interior and unbounded domain exterior problems in elastostatics. Computational efficiency is carefully defined in this study as the computer time required to attain a specified level of solution accuracy. The study found the FEM superior to the BEM for the interior problem, while the reverse was true for the exterior problem. The hybrid analysis technique was found to be comparable or superior to both the FEM and BEM for both the interior and exterior problems.

SAGE: The Self-Adaptive Grid Code. 3

NASA Technical Reports Server (NTRS)

Davies, Carol B.; Venkatapathy, Ethiraj

1999-01-01

The multi-dimensional self-adaptive grid code, SAGE, is an important tool in the field of computational fluid dynamics (CFD). It provides an efficient method to improve the accuracy of flow solutions while simultaneously reducing computer processing time. Briefly, SAGE enhances an initial computational grid by redistributing the mesh points into more appropriate locations. The movement of these points is driven by an equal-error-distribution algorithm that utilizes the relationship between high flow gradients and excessive solution errors. The method also provides a balance between clustering points in the high gradient regions and maintaining the smoothness and continuity of the adapted grid, The latest version, Version 3, includes the ability to change the boundaries of a given grid to more efficiently enclose flow structures and provides alternative redistribution algorithms.

An imperialist competitive algorithm for virtual machine placement in cloud computing

NASA Astrophysics Data System (ADS)

Jamali, Shahram; Malektaji, Sepideh; Analoui, Morteza

2017-05-01

Cloud computing, the recently emerged revolution in IT industry, is empowered by virtualisation technology. In this paradigm, the user's applications run over some virtual machines (VMs). The process of selecting proper physical machines to host these virtual machines is called virtual machine placement. It plays an important role on resource utilisation and power efficiency of cloud computing environment. In this paper, we propose an imperialist competitive-based algorithm for the virtual machine placement problem called ICA-VMPLC. The base optimisation algorithm is chosen to be ICA because of its ease in neighbourhood movement, good convergence rate and suitable terminology. The proposed algorithm investigates search space in a unique manner to efficiently obtain optimal placement solution that simultaneously minimises power consumption and total resource wastage. Its final solution performance is compared with several existing methods such as grouping genetic and ant colony-based algorithms as well as bin packing heuristic. The simulation results show that the proposed method is superior to other tested algorithms in terms of power consumption, resource wastage, CPU usage efficiency and memory usage efficiency.

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.

Sensitivity analysis of dynamic biological systems with time-delays.

PubMed

Wu, Wu Hsiung; Wang, Feng Sheng; Chang, Maw Shang

2010-10-15

Mathematical modeling has been applied to the study and analysis of complex biological systems for a long time. Some processes in biological systems, such as the gene expression and feedback control in signal transduction networks, involve a time delay. These systems are represented as delay differential equation (DDE) models. Numerical sensitivity analysis of a DDE model by the direct method requires the solutions of model and sensitivity equations with time-delays. The major effort is the computation of Jacobian matrix when computing the solution of sensitivity equations. The computation of partial derivatives of complex equations either by the analytic method or by symbolic manipulation is time consuming, inconvenient, and prone to introduce human errors. To address this problem, an automatic approach to obtain the derivatives of complex functions efficiently and accurately is necessary. We have proposed an efficient algorithm with an adaptive step size control to compute the solution and dynamic sensitivities of biological systems described by ordinal differential equations (ODEs). The adaptive direct-decoupled algorithm is extended to solve the solution and dynamic sensitivities of time-delay systems describing by DDEs. To save the human effort and avoid the human errors in the computation of partial derivatives, an automatic differentiation technique is embedded in the extended algorithm to evaluate the Jacobian matrix. The extended algorithm is implemented and applied to two realistic models with time-delays: the cardiovascular control system and the TNF-α signal transduction network. The results show that the extended algorithm is a good tool for dynamic sensitivity analysis on DDE models with less user intervention. By comparing with direct-coupled methods in theory, the extended algorithm is efficient, accurate, and easy to use for end users without programming background to do dynamic sensitivity analysis on complex biological systems with time-delays.

Developing eThread pipeline using SAGA-pilot abstraction for large-scale structural bioinformatics.

PubMed

Ragothaman, Anjani; Boddu, Sairam Chowdary; Kim, Nayong; Feinstein, Wei; Brylinski, Michal; Jha, Shantenu; Kim, Joohyun

2014-01-01

While most of computational annotation approaches are sequence-based, threading methods are becoming increasingly attractive because of predicted structural information that could uncover the underlying function. However, threading tools are generally compute-intensive and the number of protein sequences from even small genomes such as prokaryotes is large typically containing many thousands, prohibiting their application as a genome-wide structural systems biology tool. To leverage its utility, we have developed a pipeline for eThread--a meta-threading protein structure modeling tool, that can use computational resources efficiently and effectively. We employ a pilot-based approach that supports seamless data and task-level parallelism and manages large variation in workload and computational requirements. Our scalable pipeline is deployed on Amazon EC2 and can efficiently select resources based upon task requirements. We present runtime analysis to characterize computational complexity of eThread and EC2 infrastructure. Based on results, we suggest a pathway to an optimized solution with respect to metrics such as time-to-solution or cost-to-solution. Our eThread pipeline can scale to support a large number of sequences and is expected to be a viable solution for genome-scale structural bioinformatics and structure-based annotation, particularly, amenable for small genomes such as prokaryotes. The developed pipeline is easily extensible to other types of distributed cyberinfrastructure.

Developing eThread Pipeline Using SAGA-Pilot Abstraction for Large-Scale Structural Bioinformatics

PubMed Central

Ragothaman, Anjani; Feinstein, Wei; Jha, Shantenu; Kim, Joohyun

2014-01-01

While most of computational annotation approaches are sequence-based, threading methods are becoming increasingly attractive because of predicted structural information that could uncover the underlying function. However, threading tools are generally compute-intensive and the number of protein sequences from even small genomes such as prokaryotes is large typically containing many thousands, prohibiting their application as a genome-wide structural systems biology tool. To leverage its utility, we have developed a pipeline for eThread—a meta-threading protein structure modeling tool, that can use computational resources efficiently and effectively. We employ a pilot-based approach that supports seamless data and task-level parallelism and manages large variation in workload and computational requirements. Our scalable pipeline is deployed on Amazon EC2 and can efficiently select resources based upon task requirements. We present runtime analysis to characterize computational complexity of eThread and EC2 infrastructure. Based on results, we suggest a pathway to an optimized solution with respect to metrics such as time-to-solution or cost-to-solution. Our eThread pipeline can scale to support a large number of sequences and is expected to be a viable solution for genome-scale structural bioinformatics and structure-based annotation, particularly, amenable for small genomes such as prokaryotes. The developed pipeline is easily extensible to other types of distributed cyberinfrastructure. PMID:24995285

A Formal Algorithm for Routing Traces on a Printed Circuit Board

NASA Technical Reports Server (NTRS)

Hedgley, David R., Jr.

1996-01-01

This paper addresses the classical problem of printed circuit board routing: that is, the problem of automatic routing by a computer other than by brute force that causes the execution time to grow exponentially as a function of the complexity. Most of the present solutions are either inexpensive but not efficient and fast, or efficient and fast but very costly. Many solutions are proprietary, so not much is written or known about the actual algorithms upon which these solutions are based. This paper presents a formal algorithm for routing traces on a print- ed circuit board. The solution presented is very fast and efficient and for the first time speaks to the question eloquently by way of symbolic statements.

Parallel CE/SE Computations via Domain Decomposition

NASA Technical Reports Server (NTRS)

Himansu, Ananda; Jorgenson, Philip C. E.; Wang, Xiao-Yen; Chang, Sin-Chung

2000-01-01

This paper describes the parallelization strategy and achieved parallel efficiency of an explicit time-marching algorithm for solving conservation laws. The Space-Time Conservation Element and Solution Element (CE/SE) algorithm for solving the 2D and 3D Euler equations is parallelized with the aid of domain decomposition. The parallel efficiency of the resultant algorithm on a Silicon Graphics Origin 2000 parallel computer is checked.

A Comparison of Solver Performance for Complex Gastric Electrophysiology Models

PubMed Central

Sathar, Shameer; Cheng, Leo K.; Trew, Mark L.

2016-01-01

Computational techniques for solving systems of equations arising in gastric electrophysiology have not been studied for efficient solution process. We present a computationally challenging problem of simulating gastric electrophysiology in anatomically realistic stomach geometries with multiple intracellular and extracellular domains. The multiscale nature of the problem and mesh resolution required to capture geometric and functional features necessitates efficient solution methods if the problem is to be tractable. In this study, we investigated and compared several parallel preconditioners for the linear systems arising from tetrahedral discretisation of electrically isotropic and anisotropic problems, with and without stimuli. The results showed that the isotropic problem was computationally less challenging than the anisotropic problem and that the application of extracellular stimuli increased workload considerably. Preconditioning based on block Jacobi and algebraic multigrid solvers were found to have the best overall solution times and least iteration counts, respectively. The algebraic multigrid preconditioner would be expected to perform better on large problems. PMID:26736543

Conjugate Gradient Algorithms For Manipulator Simulation

NASA Technical Reports Server (NTRS)

Fijany, Amir; Scheid, Robert E.

1991-01-01

Report discusses applicability of conjugate-gradient algorithms to computation of forward dynamics of robotic manipulators. Rapid computation of forward dynamics essential to teleoperation and other advanced robotic applications. Part of continuing effort to find algorithms meeting requirements for increased computational efficiency and speed. Method used for iterative solution of systems of linear equations.

An efficient algorithm using matrix methods to solve wind tunnel force-balance equations

NASA Technical Reports Server (NTRS)

Smith, D. L.

1972-01-01

An iterative procedure applying matrix methods to accomplish an efficient algorithm for automatic computer reduction of wind-tunnel force-balance data has been developed. Balance equations are expressed in a matrix form that is convenient for storing balance sensitivities and interaction coefficient values for online or offline batch data reduction. The convergence of the iterative values to a unique solution of this system of equations is investigated, and it is shown that for balances which satisfy the criteria discussed, this type of solution does occur. Methods for making sensitivity adjustments and initial load effect considerations in wind-tunnel applications are also discussed, and the logic for determining the convergence accuracy limits for the iterative solution is given. This more efficient data reduction program is compared with the technique presently in use at the NASA Langley Research Center, and computational times on the order of one-third or less are demonstrated by use of this new program.

Perspective: Memcomputing: Leveraging memory and physics to compute efficiently

NASA Astrophysics Data System (ADS)

Di Ventra, Massimiliano; Traversa, Fabio L.

2018-05-01

It is well known that physical phenomena may be of great help in computing some difficult problems efficiently. A typical example is prime factorization that may be solved in polynomial time by exploiting quantum entanglement on a quantum computer. There are, however, other types of (non-quantum) physical properties that one may leverage to compute efficiently a wide range of hard problems. In this perspective, we discuss how to employ one such property, memory (time non-locality), in a novel physics-based approach to computation: Memcomputing. In particular, we focus on digital memcomputing machines (DMMs) that are scalable. DMMs can be realized with non-linear dynamical systems with memory. The latter property allows the realization of a new type of Boolean logic, one that is self-organizing. Self-organizing logic gates are "terminal-agnostic," namely, they do not distinguish between the input and output terminals. When appropriately assembled to represent a given combinatorial/optimization problem, the corresponding self-organizing circuit converges to the equilibrium points that express the solutions of the problem at hand. In doing so, DMMs take advantage of the long-range order that develops during the transient dynamics. This collective dynamical behavior, reminiscent of a phase transition, or even the "edge of chaos," is mediated by families of classical trajectories (instantons) that connect critical points of increasing stability in the system's phase space. The topological character of the solution search renders DMMs robust against noise and structural disorder. Since DMMs are non-quantum systems described by ordinary differential equations, not only can they be built in hardware with the available technology, they can also be simulated efficiently on modern classical computers. As an example, we will show the polynomial-time solution of the subset-sum problem for the worst cases, and point to other types of hard problems where simulations of DMMs' equations of motion on classical computers have already demonstrated substantial advantages over traditional approaches. We conclude this article by outlining further directions of study.

Parallel goal-oriented adaptive finite element modeling for 3D electromagnetic exploration

NASA Astrophysics Data System (ADS)

Zhang, Y.; Key, K.; Ovall, J.; Holst, M.

2014-12-01

We present a parallel goal-oriented adaptive finite element method for accurate and efficient electromagnetic (EM) modeling of complex 3D structures. An unstructured tetrahedral mesh allows this approach to accommodate arbitrarily complex 3D conductivity variations and a priori known boundaries. The total electric field is approximated by the lowest order linear curl-conforming shape functions and the discretized finite element equations are solved by a sparse LU factorization. Accuracy of the finite element solution is achieved through adaptive mesh refinement that is performed iteratively until the solution converges to the desired accuracy tolerance. Refinement is guided by a goal-oriented error estimator that uses a dual-weighted residual method to optimize the mesh for accurate EM responses at the locations of the EM receivers. As a result, the mesh refinement is highly efficient since it only targets the elements where the inaccuracy of the solution corrupts the response at the possibly distant locations of the EM receivers. We compare the accuracy and efficiency of two approaches for estimating the primary residual error required at the core of this method: one uses local element and inter-element residuals and the other relies on solving a global residual system using a hierarchical basis. For computational efficiency our method follows the Bank-Holst algorithm for parallelization, where solutions are computed in subdomains of the original model. To resolve the load-balancing problem, this approach applies a spectral bisection method to divide the entire model into subdomains that have approximately equal error and the same number of receivers. The finite element solutions are then computed in parallel with each subdomain carrying out goal-oriented adaptive mesh refinement independently. We validate the newly developed algorithm by comparison with controlled-source EM solutions for 1D layered models and with 2D results from our earlier 2D goal oriented adaptive refinement code named MARE2DEM. We demonstrate the performance and parallel scaling of this algorithm on a medium-scale computing cluster with a marine controlled-source EM example that includes a 3D array of receivers located over a 3D model that includes significant seafloor bathymetry variations and a heterogeneous subsurface.

The symbolic computation of series solutions to ordinary differential equations using trees (extended abstract)

NASA Technical Reports Server (NTRS)

Grossman, Robert

1991-01-01

Algorithms previously developed by the author give formulas which can be used for the efficient symbolic computation of series expansions to solutions of nonlinear systems of ordinary differential equations. As a by product of this analysis, formulas are derived which relate to trees to the coefficients of the series expansions, similar to the work of Leroux and Viennot, and Lamnabhi, Leroux and Viennot.

The use of methods of structural optimization at the stage of designing high-rise buildings with steel construction

NASA Astrophysics Data System (ADS)

Vasilkin, Andrey

2018-03-01

The more designing solutions at the search stage for design for high-rise buildings can be synthesized by the engineer, the more likely that the final adopted version will be the most efficient and economical. However, in modern market conditions, taking into account the complexity and responsibility of high-rise buildings the designer does not have the necessary time to develop, analyze and compare any significant number of options. To solve this problem, it is expedient to use the high potential of computer-aided designing. To implement automated search for design solutions, it is proposed to develop the computing facilities, the application of which will significantly increase the productivity of the designer and reduce the complexity of designing. Methods of structural and parametric optimization have been adopted as the basis of the computing facilities. Their efficiency in the synthesis of design solutions is shown, also the schemes, that illustrate and explain the introduction of structural optimization in the traditional design of steel frames, are constructed. To solve the problem of synthesis and comparison of design solutions for steel frames, it is proposed to develop the computing facilities that significantly reduces the complexity of search designing and based on the use of methods of structural and parametric optimization.

Parallel Computing Strategies for Irregular Algorithms

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Oliker, Leonid; Shan, Hongzhang; Biegel, Bryan (Technical Monitor)

2002-01-01

Parallel computing promises several orders of magnitude increase in our ability to solve realistic computationally-intensive problems, but relies on their efficient mapping and execution on large-scale multiprocessor architectures. Unfortunately, many important applications are irregular and dynamic in nature, making their effective parallel implementation a daunting task. Moreover, with the proliferation of parallel architectures and programming paradigms, the typical scientist is faced with a plethora of questions that must be answered in order to obtain an acceptable parallel implementation of the solution algorithm. In this paper, we consider three representative irregular applications: unstructured remeshing, sparse matrix computations, and N-body problems, and parallelize them using various popular programming paradigms on a wide spectrum of computer platforms ranging from state-of-the-art supercomputers to PC clusters. We present the underlying problems, the solution algorithms, and the parallel implementation strategies. Smart load-balancing, partitioning, and ordering techniques are used to enhance parallel performance. Overall results demonstrate the complexity of efficiently parallelizing irregular algorithms.

Encapsulation Efficiency and Micellar Structure of Solute-Carrying Block Copolymer Nanoparticles

PubMed Central

Woodhead, Jeffrey L.; Hall, Carol K.

2011-01-01

We use discontinuous molecular dynamics (DMD) computer simulation to investigate the encapsulation efficiency and micellar structure of solute-carrying block copolymer nanoparticles as a function of packing fraction, polymer volume fraction, solute mole fraction, and the interaction parameters between the hydrophobic head blocks and between the head and the solute. The encapsulation efficiency increases with increasing polymer volume fraction and packing fraction but decreases with increasing head-head interaction strength. The latter is due to an increased tendency for the solute to remain on the micelle surface. We compared two different nanoparticle assembly methods, one in which the solute and copolymer co-associate and the other in which the copolymer micelle is formed before the introduction of solute. The assembly method does not affect the encapsulation efficiency but does affect the solute uptake kinetics. Both head-solute interaction strength and head-head interaction strength affect the density profile of the micelles; increases in the former cause the solute to distribute more evenly throughout the micelle, while increases in the latter cause the solute to concentrate further from the center of the micelle. We explain our results in the context of a model of drug insertion into micelles formulated by Kumar and Prud’homme; as conditions become more conducive to micelle formation, a stronger energy barrier to solute insertion forms which in turn decreases the encapsulation efficiency of the system. PMID:21918582

Efficient Jacobian inversion for the control of simple robot manipulators

NASA Technical Reports Server (NTRS)

Fijany, Amir; Bejczy, Antal K.

1988-01-01

Symbolic inversion of the Jacobian matrix for spherical wrist arms is investigated. It is shown that, taking advantage of the simple geometry of these arms, the closed-form solution of the system Q = J-1X, representing a transformation from task space to joint space, can be obtained very efficiently. The solutions for PUMA, Stanford, and a six-revolute-joint coplanar arm, along with all singular points, are presented. The solution for each joint variable is found as an explicit function of the singular points which provides a better insight into the effect of different singular points on the motion and force exertion of each individual joint. For the above arms, the computation cost of the solution is on the same order as the cost of forward kinematic solution and it is significantly reduced if forward kinematic solution is already obtained. A comparison with previous methods shows that this method is the most efficient to date.

An efficient and general numerical method to compute steady uniform vortices

NASA Astrophysics Data System (ADS)

Luzzatto-Fegiz, Paolo; Williamson, Charles H. K.

2011-07-01

Steady uniform vortices are widely used to represent high Reynolds number flows, yet their efficient computation still presents some challenges. Existing Newton iteration methods become inefficient as the vortices develop fine-scale features; in addition, these methods cannot, in general, find solutions with specified Casimir invariants. On the other hand, available relaxation approaches are computationally inexpensive, but can fail to converge to a solution. In this paper, we overcome these limitations by introducing a new discretization, based on an inverse-velocity map, which radically increases the efficiency of Newton iteration methods. In addition, we introduce a procedure to prescribe Casimirs and remove the degeneracies in the steady vorticity equation, thus ensuring convergence for general vortex configurations. We illustrate our methodology by considering several unbounded flows involving one or two vortices. Our method enables the computation, for the first time, of steady vortices that do not exhibit any geometric symmetry. In addition, we discover that, as the limiting vortex state for each flow is approached, each family of solutions traces a clockwise spiral in a bifurcation plot consisting of a velocity-impulse diagram. By the recently introduced "IVI diagram" stability approach [Phys. Rev. Lett. 104 (2010) 044504], each turn of this spiral is associated with a loss of stability for the steady flows. Such spiral structure is suggested to be a universal feature of steady, uniform-vorticity flows.

News on Seeking Gaia's Astrometric Core Solution with AGIS

NASA Astrophysics Data System (ADS)

Lammers, U.; Lindegren, L.

We report on recent new developments around the Astrometric Global Iterative Solution system. This includes the availability of an efficient Conjugate Gradient solver and the Generic Astrometric Calibration scheme that had been proposed a while ago. The number of primary stars to be included in the core solution is now believed to be significantly higher than the 100 Million that served as baseline until now. Cloud computing services are being studied as a possible cost-effective alternative to running AGIS on dedicated computing hardware at ESAC during the operational phase.

Managing Laboratory Data Using Cloud Computing as an Organizational Tool

ERIC Educational Resources Information Center

Bennett, Jacqueline; Pence, Harry E.

2011-01-01

One of the most significant difficulties encountered when directing undergraduate research and developing new laboratory experiments is how to efficiently manage the data generated by a number of students. Cloud computing, where both software and computer files reside online, offers a solution to this data-management problem and allows researchers…

Development and application of unified algorithms for problems in computational science

NASA Technical Reports Server (NTRS)

Shankar, Vijaya; Chakravarthy, Sukumar

1987-01-01

A framework is presented for developing computationally unified numerical algorithms for solving nonlinear equations that arise in modeling various problems in mathematical physics. The concept of computational unification is an attempt to encompass efficient solution procedures for computing various nonlinear phenomena that may occur in a given problem. For example, in Computational Fluid Dynamics (CFD), a unified algorithm will be one that allows for solutions to subsonic (elliptic), transonic (mixed elliptic-hyperbolic), and supersonic (hyperbolic) flows for both steady and unsteady problems. The objectives are: development of superior unified algorithms emphasizing accuracy and efficiency aspects; development of codes based on selected algorithms leading to validation; application of mature codes to realistic problems; and extension/application of CFD-based algorithms to problems in other areas of mathematical physics. The ultimate objective is to achieve integration of multidisciplinary technologies to enhance synergism in the design process through computational simulation. Specific unified algorithms for a hierarchy of gas dynamics equations and their applications to two other areas: electromagnetic scattering, and laser-materials interaction accounting for melting.

Parallel processing for scientific computations

NASA Technical Reports Server (NTRS)

Alkhatib, Hasan S.

1991-01-01

The main contribution of the effort in the last two years is the introduction of the MOPPS system. After doing extensive literature search, we introduced the system which is described next. MOPPS employs a new solution to the problem of managing programs which solve scientific and engineering applications on a distributed processing environment. Autonomous computers cooperate efficiently in solving large scientific problems with this solution. MOPPS has the advantage of not assuming the presence of any particular network topology or configuration, computer architecture, or operating system. It imposes little overhead on network and processor resources while efficiently managing programs concurrently. The core of MOPPS is an intelligent program manager that builds a knowledge base of the execution performance of the parallel programs it is managing under various conditions. The manager applies this knowledge to improve the performance of future runs. The program manager learns from experience.

Computation of unsteady transonic aerodynamics with steady state fixed by truncation error injection

NASA Technical Reports Server (NTRS)

Fung, K.-Y.; Fu, J.-K.

1985-01-01

A novel technique is introduced for efficient computations of unsteady transonic aerodynamics. The steady flow corresponding to body shape is maintained by truncation error injection while the perturbed unsteady flows corresponding to unsteady body motions are being computed. This allows the use of different grids comparable to the characteristic length scales of the steady and unsteady flows and, hence, allows efficient computation of the unsteady perturbations. An example of typical unsteady computation of flow over a supercritical airfoil shows that substantial savings in computation time and storage without loss of solution accuracy can easily be achieved. This technique is easy to apply and requires very few changes to existing codes.

Fuel Injector Design Optimization for an Annular Scramjet Geometry

NASA Technical Reports Server (NTRS)

Steffen, Christopher J., Jr.

2003-01-01

A four-parameter, three-level, central composite experiment design has been used to optimize the configuration of an annular scramjet injector geometry using computational fluid dynamics. The computational fluid dynamic solutions played the role of computer experiments, and response surface methodology was used to capture the simulation results for mixing efficiency and total pressure recovery within the scramjet flowpath. An optimization procedure, based upon the response surface results of mixing efficiency, was used to compare the optimal design configuration against the target efficiency value of 92.5%. The results of three different optimization procedures are presented and all point to the need to look outside the current design space for different injector geometries that can meet or exceed the stated mixing efficiency target.

CFD studies on biomass thermochemical conversion.

PubMed

Wang, Yiqun; Yan, Lifeng

2008-06-01

Thermochemical conversion of biomass offers an efficient and economically process to provide gaseous, liquid and solid fuels and prepare chemicals derived from biomass. Computational fluid dynamic (CFD) modeling applications on biomass thermochemical processes help to optimize the design and operation of thermochemical reactors. Recent progression in numerical techniques and computing efficacy has advanced CFD as a widely used approach to provide efficient design solutions in industry. This paper introduces the fundamentals involved in developing a CFD solution. Mathematical equations governing the fluid flow, heat and mass transfer and chemical reactions in thermochemical systems are described and sub-models for individual processes are presented. It provides a review of various applications of CFD in the biomass thermochemical process field.

CFD Studies on Biomass Thermochemical Conversion

PubMed Central

Wang, Yiqun; Yan, Lifeng

2008-01-01

Thermochemical conversion of biomass offers an efficient and economically process to provide gaseous, liquid and solid fuels and prepare chemicals derived from biomass. Computational fluid dynamic (CFD) modeling applications on biomass thermochemical processes help to optimize the design and operation of thermochemical reactors. Recent progression in numerical techniques and computing efficacy has advanced CFD as a widely used approach to provide efficient design solutions in industry. This paper introduces the fundamentals involved in developing a CFD solution. Mathematical equations governing the fluid flow, heat and mass transfer and chemical reactions in thermochemical systems are described and sub-models for individual processes are presented. It provides a review of various applications of CFD in the biomass thermochemical process field. PMID:19325848

Computational Efficiency of the Simplex Embedding Method in Convex Nondifferentiable Optimization

NASA Astrophysics Data System (ADS)

Kolosnitsyn, A. V.

2018-02-01

The simplex embedding method for solving convex nondifferentiable optimization problems is considered. A description of modifications of this method based on a shift of the cutting plane intended for cutting off the maximum number of simplex vertices is given. These modification speed up the problem solution. A numerical comparison of the efficiency of the proposed modifications based on the numerical solution of benchmark convex nondifferentiable optimization problems is presented.

A general solution to the hidden-line problem. [to graphically represent aerodynamic stability derivatives

NASA Technical Reports Server (NTRS)

Hedgley, D. R., Jr.

1982-01-01

The requirements for computer-generated perspective projections of three dimensional objects has escalated. A general solution was developed. The theoretical solution to this problem is presented. The method is very efficient as it minimizes the selection of points and comparison of line segments and hence avoids the devastation of square-law growth.

Aerodynamic optimization studies on advanced architecture computers

NASA Technical Reports Server (NTRS)

Chawla, Kalpana

1995-01-01

The approach to carrying out multi-discipline aerospace design studies in the future, especially in massively parallel computing environments, comprises of choosing (1) suitable solvers to compute solutions to equations characterizing a discipline, and (2) efficient optimization methods. In addition, for aerodynamic optimization problems, (3) smart methodologies must be selected to modify the surface shape. In this research effort, a 'direct' optimization method is implemented on the Cray C-90 to improve aerodynamic design. It is coupled with an existing implicit Navier-Stokes solver, OVERFLOW, to compute flow solutions. The optimization method is chosen such that it can accomodate multi-discipline optimization in future computations. In the work , however, only single discipline aerodynamic optimization will be included.

An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions

NASA Astrophysics Data System (ADS)

Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Xu, Zhenli; Jacobs, Donald; Cai, Wei

2009-10-01

In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed.

Analysis of Algorithms: Coping with Hard Problems

ERIC Educational Resources Information Center

Kolata, Gina Bari

1974-01-01

Although today's computers can perform as many as one million operations per second, there are many problems that are still too large to be solved in a straightforward manner. Recent work indicates that many approximate solutions are useful and more efficient than exact solutions. (Author/RH)

Fast sweeping methods for hyperbolic systems of conservation laws at steady state II

NASA Astrophysics Data System (ADS)

Engquist, Björn; Froese, Brittany D.; Tsai, Yen-Hsi Richard

2015-04-01

The idea of using fast sweeping methods for solving stationary systems of conservation laws has previously been proposed for efficiently computing solutions with sharp shocks. We further develop these methods to allow for a more challenging class of problems including problems with sonic points, shocks originating in the interior of the domain, rarefaction waves, and two-dimensional systems. We show that fast sweeping methods can produce higher-order accuracy. Computational results validate the claims of accuracy, sharp shock curves, and optimal computational efficiency.

Efficient algorithms for single-axis attitude estimation

NASA Technical Reports Server (NTRS)

Shuster, M. D.

1981-01-01

The computationally efficient algorithms determine attitude from the measurement of art lengths and dihedral angles. The dependence of these algorithms on the solution of trigonometric equations was reduced. Both single time and batch estimators are presented along with the covariance analysis of each algorithm.

Projected role of advanced computational aerodynamic methods at the Lockheed-Georgia company

NASA Technical Reports Server (NTRS)

Lores, M. E.

1978-01-01

Experience with advanced computational methods being used at the Lockheed-Georgia Company to aid in the evaluation and design of new and modified aircraft indicates that large and specialized computers will be needed to make advanced three-dimensional viscous aerodynamic computations practical. The Numerical Aerodynamic Simulation Facility should be used to provide a tool for designing better aerospace vehicles while at the same time reducing development costs by performing computations using Navier-Stokes equations solution algorithms and permitting less sophisticated but nevertheless complex calculations to be made efficiently. Configuration definition procedures and data output formats can probably best be defined in cooperation with industry, therefore, the computer should handle many remote terminals efficiently. The capability of transferring data to and from other computers needs to be provided. Because of the significant amount of input and output associated with 3-D viscous flow calculations and because of the exceedingly fast computation speed envisioned for the computer, special attention should be paid to providing rapid, diversified, and efficient input and output.

Desired Precision in Multi-Objective Optimization: Epsilon Archiving or Rounding Objectives?

NASA Astrophysics Data System (ADS)

Asadzadeh, M.; Sahraei, S.

2016-12-01

Multi-objective optimization (MO) aids in supporting the decision making process in water resources engineering and design problems. One of the main goals of solving a MO problem is to archive a set of solutions that is well-distributed across a wide range of all the design objectives. Modern MO algorithms use the epsilon dominance concept to define a mesh with pre-defined grid-cell size (often called epsilon) in the objective space and archive at most one solution at each grid-cell. Epsilon can be set to the desired precision level of each objective function to make sure that the difference between each pair of archived solutions is meaningful. This epsilon archiving process is computationally expensive in problems that have quick-to-evaluate objective functions. This research explores the applicability of a similar but computationally more efficient approach to respect the desired precision level of all objectives in the solution archiving process. In this alternative approach each objective function is rounded to the desired precision level before comparing any new solution to the set of archived solutions that already have rounded objective function values. This alternative solution archiving approach is compared to the epsilon archiving approach in terms of efficiency and quality of archived solutions for solving mathematical test problems and hydrologic model calibration problems.

Privacy-preserving genome-wide association studies on cloud environment using fully homomorphic encryption.

PubMed

Lu, Wen-Jie; Yamada, Yoshiji; Sakuma, Jun

2015-01-01

Developed sequencing techniques are yielding large-scale genomic data at low cost. A genome-wide association study (GWAS) targeting genetic variations that are significantly associated with a particular disease offers great potential for medical improvement. However, subjects who volunteer their genomic data expose themselves to the risk of privacy invasion; these privacy concerns prevent efficient genomic data sharing. Our goal is to presents a cryptographic solution to this problem. To maintain the privacy of subjects, we propose encryption of all genotype and phenotype data. To allow the cloud to perform meaningful computation in relation to the encrypted data, we use a fully homomorphic encryption scheme. Noting that we can evaluate typical statistics for GWAS from a frequency table, our solution evaluates frequency tables with encrypted genomic and clinical data as input. We propose to use a packing technique for efficient evaluation of these frequency tables. Our solution supports evaluation of the D' measure of linkage disequilibrium, the Hardy-Weinberg Equilibrium, the χ2 test, etc. In this paper, we take χ2 test and linkage disequilibrium as examples and demonstrate how we can conduct these algorithms securely and efficiently in an outsourcing setting. We demonstrate with experimentation that secure outsourcing computation of one χ2 test with 10, 000 subjects requires about 35 ms and evaluation of one linkage disequilibrium with 10, 000 subjects requires about 80 ms. With appropriate encoding and packing technique, cryptographic solutions based on fully homomorphic encryption for secure computations of GWAS can be practical.

A comparison of detection efficiency on an air traffic control monitoring task with and without computer aiding.

DOT National Transportation Integrated Search

1989-01-01

Future levels of air traffic control automation plan to incorporate computer aiding features designed to alert the controller to upcoming problem situations by displaying information that will identify the situation and suggest possible solutions. Co...

Automated lettuce nutrient solution management using an array of ion-selective electrodes

USDA-ARS?s Scientific Manuscript database

Automated sensing and control of macronutrients in hydroponic solutions would allow more efficient management of nutrients for crop growth in closed systems. This paper describes the development and evaluation of a computer-controlled nutrient management system with an array of ion-selective electro...

Iterative solution of the inverse Cauchy problem for an elliptic equation by the conjugate gradient method

NASA Astrophysics Data System (ADS)

Vasil'ev, V. I.; Kardashevsky, A. M.; Popov, V. V.; Prokopev, G. A.

2017-10-01

This article presents results of computational experiment carried out using a finite-difference method for solving the inverse Cauchy problem for a two-dimensional elliptic equation. The computational algorithm involves an iterative determination of the missing boundary condition from the override condition using the conjugate gradient method. The results of calculations are carried out on the examples with exact solutions as well as at specifying an additional condition with random errors are presented. Results showed a high efficiency of the iterative method of conjugate gradients for numerical solution

Orientation of doubly rotated quartz plates.

PubMed

Sherman, J R

1989-01-01

A derivation from classical spherical trigonometry of equations to compute the orientation of doubly-rotated quartz blanks from Bragg X-ray data is discussed. These are usually derived by compact and efficient vector methods, which are reviewed briefly. They are solved by generating a quadratic equation with numerical coefficients. Two methods exist for performing the computation from measurements against two planes: a direct solution by a quadratic equation and a process of convergent iteration. Both have a spurious solution. Measurement against three lattice planes yields a set of three linear equations the solution of which is an unambiguous result.

Computation of Reacting Flows in Combustion Processes

NASA Technical Reports Server (NTRS)

Keith, Theo G., Jr.; Chen, Kuo-Huey

1997-01-01

The main objective of this research was to develop an efficient three-dimensional computer code for chemically reacting flows. The main computer code developed is ALLSPD-3D. The ALLSPD-3D computer program is developed for the calculation of three-dimensional, chemically reacting flows with sprays. The ALL-SPD code employs a coupled, strongly implicit solution procedure for turbulent spray combustion flows. A stochastic droplet model and an efficient method for treatment of the spray source terms in the gas-phase equations are used to calculate the evaporating liquid sprays. The chemistry treatment in the code is general enough that an arbitrary number of reaction and species can be defined by the users. Also, it is written in generalized curvilinear coordinates with both multi-block and flexible internal blockage capabilities to handle complex geometries. In addition, for general industrial combustion applications, the code provides both dilution and transpiration cooling capabilities. The ALLSPD algorithm, which employs the preconditioning and eigenvalue rescaling techniques, is capable of providing efficient solution for flows with a wide range of Mach numbers. Although written for three-dimensional flows in general, the code can be used for two-dimensional and axisymmetric flow computations as well. The code is written in such a way that it can be run in various computer platforms (supercomputers, workstations and parallel processors) and the GUI (Graphical User Interface) should provide a user-friendly tool in setting up and running the code.

Dual Solutions for Nonlinear Flow Using Lie Group Analysis

PubMed Central

Awais, Muhammad; Hayat, Tasawar; Irum, Sania; Saleem, Salman

2015-01-01

`The aim of this analysis is to investigate the existence of the dual solutions for magnetohydrodynamic (MHD) flow of an upper-convected Maxwell (UCM) fluid over a porous shrinking wall. We have employed the Lie group analysis for the simplification of the nonlinear differential system and computed the absolute invariants explicitly. An efficient numerical technique namely the shooting method has been employed for the constructions of solutions. Dual solutions are computed for velocity profile of an upper-convected Maxwell (UCM) fluid flow. Plots reflecting the impact of dual solutions for the variations of Deborah number, Hartman number, wall mass transfer are presented and analyzed. Streamlines are also plotted for the wall mass transfer effects when suction and blowing situations are considered. PMID:26575996

Evaluation of solution procedures for material and/or geometrically nonlinear structural analysis by the direct stiffness method.

NASA Technical Reports Server (NTRS)

Stricklin, J. A.; Haisler, W. E.; Von Riesemann, W. A.

1972-01-01

This paper presents an assessment of the solution procedures available for the analysis of inelastic and/or large deflection structural behavior. A literature survey is given which summarized the contribution of other researchers in the analysis of structural problems exhibiting material nonlinearities and combined geometric-material nonlinearities. Attention is focused at evaluating the available computation and solution techniques. Each of the solution techniques is developed from a common equation of equilibrium in terms of pseudo forces. The solution procedures are applied to circular plates and shells of revolution in an attempt to compare and evaluate each with respect to computational accuracy, economy, and efficiency. Based on the numerical studies, observations and comments are made with regard to the accuracy and economy of each solution technique.

An implicit scheme with memory reduction technique for steady state solutions of DVBE in all flow regimes

NASA Astrophysics Data System (ADS)

Yang, L. M.; Shu, C.; Yang, W. M.; Wu, J.

2018-04-01

High consumption of memory and computational effort is the major barrier to prevent the widespread use of the discrete velocity method (DVM) in the simulation of flows in all flow regimes. To overcome this drawback, an implicit DVM with a memory reduction technique for solving a steady discrete velocity Boltzmann equation (DVBE) is presented in this work. In the method, the distribution functions in the whole discrete velocity space do not need to be stored, and they are calculated from the macroscopic flow variables. As a result, its memory requirement is in the same order as the conventional Euler/Navier-Stokes solver. In the meantime, it is more efficient than the explicit DVM for the simulation of various flows. To make the method efficient for solving flow problems in all flow regimes, a prediction step is introduced to estimate the local equilibrium state of the DVBE. In the prediction step, the distribution function at the cell interface is calculated by the local solution of DVBE. For the flow simulation, when the cell size is less than the mean free path, the prediction step has almost no effect on the solution. However, when the cell size is much larger than the mean free path, the prediction step dominates the solution so as to provide reasonable results in such a flow regime. In addition, to further improve the computational efficiency of the developed scheme in the continuum flow regime, the implicit technique is also introduced into the prediction step. Numerical results showed that the proposed implicit scheme can provide reasonable results in all flow regimes and increase significantly the computational efficiency in the continuum flow regime as compared with the existing DVM solvers.

An approximate solution to improve computational efficiency of impedance-type payload load prediction

NASA Technical Reports Server (NTRS)

White, C. W.

1981-01-01

The computational efficiency of the impedance type loads prediction method was studied. Three goals were addressed: devise a method to make the impedance method operate more efficiently in the computer; assess the accuracy and convenience of the method for determining the effect of design changes; and investigate the use of the method to identify design changes for reduction of payload loads. The method is suitable for calculation of dynamic response in either the frequency or time domain. It is concluded that: the choice of an orthogonal coordinate system will allow the impedance method to operate more efficiently in the computer; the approximate mode impedance technique is adequate for determining the effect of design changes, and is applicable for both statically determinate and statically indeterminate payload attachments; and beneficial design changes to reduce payload loads can be identified by the combined application of impedance techniques and energy distribution review techniques.

Flow through three-dimensional arrangements of cylinders with alternating streamwise planar tilt

NASA Astrophysics Data System (ADS)

Sahraoui, M.; Marshall, H.; Kaviany, M.

1993-09-01

In this report, fluid flow through a three-dimensional model for the fibrous filters is examined. In this model, the three-dimensional Stokes equation with the appropriate periodic boundary conditions is solved using the finite volume method. In addition to the numerical solution, we attempt to model this flow analytically by using the two-dimensional extended analytic solution in each of the unit cells of the three-dimensional structure. Particle trajectories computed using the superimposed analytic solution of the flow field are closed to those computed using the numerical solution of the flow field. The numerical results show that the pressure drop is not affected significantly by the relative angle of rotation of the cylinders for the high porosity used in this study (epsilon = 0.8 and epsilon = 0.95). The numerical solution and the superimposed analytic solution are also compared in terms of the particle capture efficiency. The results show that the efficiency predictions using the two methods are within 10% for St = 0.01 and 5% for St = 100. As the the porosity decreases, the three-dimensional effect becomes more significant and a difference of 35% is obtained for epsilon = 0.8.

Efficient and robust model-to-image alignment using 3D scale-invariant features.

PubMed

Toews, Matthew; Wells, William M

2013-04-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. Copyright © 2012 Elsevier B.V. All rights reserved.

Efficient and Robust Model-to-Image Alignment using 3D Scale-Invariant Features

PubMed Central

Toews, Matthew; Wells, William M.

2013-01-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a-posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. PMID:23265799

Eigenproblem solution by a combined Sturm sequence and inverse iteration technique.

NASA Technical Reports Server (NTRS)

Gupta, K. K.

1973-01-01

Description of an efficient and numerically stable algorithm, along with a complete listing of the associated computer program, developed for the accurate computation of specified roots and associated vectors of the eigenvalue problem Aq = lambda Bq with band symmetric A and B, B being also positive-definite. The desired roots are first isolated by the Sturm sequence procedure; then a special variant of the inverse iteration technique is applied for the individual determination of each root along with its vector. The algorithm fully exploits the banded form of relevant matrices, and the associated program written in FORTRAN V for the JPL UNIVAC 1108 computer proves to be most significantly economical in comparison to similar existing procedures. The program may be conveniently utilized for the efficient solution of practical engineering problems, involving free vibration and buckling analysis of structures. Results of such analyses are presented for representative structures.

Finite volume model for two-dimensional shallow environmental flow

USGS Publications Warehouse

Simoes, F.J.M.

2011-01-01

This paper presents the development of a two-dimensional, depth integrated, unsteady, free-surface model based on the shallow water equations. The development was motivated by the desire of balancing computational efficiency and accuracy by selective and conjunctive use of different numerical techniques. The base framework of the discrete model uses Godunov methods on unstructured triangular grids, but the solution technique emphasizes the use of a high-resolution Riemann solver where needed, switching to a simpler and computationally more efficient upwind finite volume technique in the smooth regions of the flow. Explicit time marching is accomplished with strong stability preserving Runge-Kutta methods, with additional acceleration techniques for steady-state computations. A simplified mass-preserving algorithm is used to deal with wet/dry fronts. Application of the model is made to several benchmark cases that show the interplay of the diverse solution techniques.

Partitioning problems in parallel, pipelined and distributed computing

NASA Technical Reports Server (NTRS)

Bokhari, S.

1985-01-01

The problem of optimally assigning the modules of a parallel program over the processors of a multiple computer system is addressed. A Sum-Bottleneck path algorithm is developed that permits the efficient solution of many variants of this problem under some constraints on the structure of the partitions. In particular, the following problems are solved optimally for a single-host, multiple satellite system: partitioning multiple chain structured parallel programs, multiple arbitrarily structured serial programs and single tree structured parallel programs. In addition, the problems of partitioning chain structured parallel programs across chain connected systems and across shared memory (or shared bus) systems are also solved under certain constraints. All solutions for parallel programs are equally applicable to pipelined programs. These results extend prior research in this area by explicitly taking concurrency into account and permit the efficient utilization of multiple computer architectures for a wide range of problems of practical interest.

Krylov subspace methods on supercomputers

NASA Technical Reports Server (NTRS)

Saad, Youcef

1988-01-01

A short survey of recent research on Krylov subspace methods with emphasis on implementation on vector and parallel computers is presented. Conjugate gradient methods have proven very useful on traditional scalar computers, and their popularity is likely to increase as three-dimensional models gain importance. A conservative approach to derive effective iterative techniques for supercomputers has been to find efficient parallel/vector implementations of the standard algorithms. The main source of difficulty in the incomplete factorization preconditionings is in the solution of the triangular systems at each step. A few approaches consisting of implementing efficient forward and backward triangular solutions are described in detail. Polynomial preconditioning as an alternative to standard incomplete factorization techniques is also discussed. Another efficient approach is to reorder the equations so as to improve the structure of the matrix to achieve better parallelism or vectorization. An overview of these and other ideas and their effectiveness or potential for different types of architectures is given.

Determinants of the efficiency of photon upconversion by triplet-triplet annihilation in the solid state: zinc porphyrin derivatives in PVA.

PubMed

Rautela, Ranjana; Joshi, Neeraj K; Novakovic, Sacha; Wong, Wallace W H; White, Jonathan M; Ghiggino, Kenneth P; Paige, Matthew F; Steer, Ronald P

2017-08-30

Spectroscopic, photophysical and computational studies designed to expose and explain the differences in the efficiencies of non-coherent photon upconversion (NCPU) by triplet-triplet annihilation (TTA) have been carried out for a new series of alkyl-substituted diphenyl and tetraphenyl zinc porphyrins, both in fluid solution and in solid films. Systematic variations in the alkyl-substitution of the phenyl groups in both the di- and tetraphenyl porphyrins introduces small, but well-understood changes in their spectroscopic and photophysical properties and in their TTA efficiencies. In degassed toluene solution TTA occurs for all derivatives and produces the fluorescent S 2 product states in all cases. In PVA matrices, however, none of the di-phenylporphyrins exhibit measurable NCPU whereas all the tetraphenyl-substituted compounds remain upconversion-active. In PVA the NCPU efficiencies of the zinc tetraphenylporphyrins vary significantly with their steric characteristics; the most sterically crowded tetraphenyl derivative exhibits the greatest efficiency. DFT-D computations have been undertaken and help reveal the sources of these differences.

Exploratory High-Fidelity Aerostructural Optimization Using an Efficient Monolithic Solution Method

NASA Astrophysics Data System (ADS)

Zhang, Jenmy Zimi

This thesis is motivated by the desire to discover fuel efficient aircraft concepts through exploratory design. An optimization methodology based on tightly integrated high-fidelity aerostructural analysis is proposed, which has the flexibility, robustness, and efficiency to contribute to this goal. The present aerostructural optimization methodology uses an integrated geometry parameterization and mesh movement strategy, which was initially proposed for aerodynamic shape optimization. This integrated approach provides the optimizer with a large amount of geometric freedom for conducting exploratory design, while allowing for efficient and robust mesh movement in the presence of substantial shape changes. In extending this approach to aerostructural optimization, this thesis has addressed a number of important challenges. A structural mesh deformation strategy has been introduced to translate consistently the shape changes described by the geometry parameterization to the structural model. A three-field formulation of the discrete steady aerostructural residual couples the mesh movement equations with the three-dimensional Euler equations and a linear structural analysis. Gradients needed for optimization are computed with a three-field coupled adjoint approach. A number of investigations have been conducted to demonstrate the suitability and accuracy of the present methodology for use in aerostructural optimization involving substantial shape changes. Robustness and efficiency in the coupled solution algorithms is crucial to the success of an exploratory optimization. This thesis therefore also focuses on the design of an effective monolithic solution algorithm for the proposed methodology. This involves using a Newton-Krylov method for the aerostructural analysis and a preconditioned Krylov subspace method for the coupled adjoint solution. Several aspects of the monolithic solution method have been investigated. These include appropriate strategies for scaling and matrix-vector product evaluation, as well as block preconditioning techniques that preserve the modularity between subproblems. The monolithic solution method is applied to problems with varying degrees of fluid-structural coupling, as well as a wing span optimization study. The monolithic solution algorithm typically requires 20%-70% less computing time than its partitioned counterpart. This advantage increases with increasing wing flexibility. The performance of the monolithic solution method is also much less sensitive to the choice of the solution parameter.

Computationally Efficient Power Allocation Algorithm in Multicarrier-Based Cognitive Radio Networks: OFDM and FBMC Systems

NASA Astrophysics Data System (ADS)

Shaat, Musbah; Bader, Faouzi

2010-12-01

Cognitive Radio (CR) systems have been proposed to increase the spectrum utilization by opportunistically access the unused spectrum. Multicarrier communication systems are promising candidates for CR systems. Due to its high spectral efficiency, filter bank multicarrier (FBMC) can be considered as an alternative to conventional orthogonal frequency division multiplexing (OFDM) for transmission over the CR networks. This paper addresses the problem of resource allocation in multicarrier-based CR networks. The objective is to maximize the downlink capacity of the network under both total power and interference introduced to the primary users (PUs) constraints. The optimal solution has high computational complexity which makes it unsuitable for practical applications and hence a low complexity suboptimal solution is proposed. The proposed algorithm utilizes the spectrum holes in PUs bands as well as active PU bands. The performance of the proposed algorithm is investigated for OFDM and FBMC based CR systems. Simulation results illustrate that the proposed resource allocation algorithm with low computational complexity achieves near optimal performance and proves the efficiency of using FBMC in CR context.

Dynamic graph cuts for efficient inference in Markov Random Fields.

PubMed

Kohli, Pushmeet; Torr, Philip H S

2007-12-01

Abstract-In this paper we present a fast new fully dynamic algorithm for the st-mincut/max-flow problem. We show how this algorithm can be used to efficiently compute MAP solutions for certain dynamically changing MRF models in computer vision such as image segmentation. Specifically, given the solution of the max-flow problem on a graph, the dynamic algorithm efficiently computes the maximum flow in a modified version of the graph. The time taken by it is roughly proportional to the total amount of change in the edge weights of the graph. Our experiments show that, when the number of changes in the graph is small, the dynamic algorithm is significantly faster than the best known static graph cut algorithm. We test the performance of our algorithm on one particular problem: the object-background segmentation problem for video. It should be noted that the application of our algorithm is not limited to the above problem, the algorithm is generic and can be used to yield similar improvements in many other cases that involve dynamic change.

Efficient mapping algorithms for scheduling robot inverse dynamics computation on a multiprocessor system

NASA Technical Reports Server (NTRS)

Lee, C. S. G.; Chen, C. L.

1989-01-01

Two efficient mapping algorithms for scheduling the robot inverse dynamics computation consisting of m computational modules with precedence relationship to be executed on a multiprocessor system consisting of p identical homogeneous processors with processor and communication costs to achieve minimum computation time are presented. An objective function is defined in terms of the sum of the processor finishing time and the interprocessor communication time. The minimax optimization is performed on the objective function to obtain the best mapping. This mapping problem can be formulated as a combination of the graph partitioning and the scheduling problems; both have been known to be NP-complete. Thus, to speed up the searching for a solution, two heuristic algorithms were proposed to obtain fast but suboptimal mapping solutions. The first algorithm utilizes the level and the communication intensity of the task modules to construct an ordered priority list of ready modules and the module assignment is performed by a weighted bipartite matching algorithm. For a near-optimal mapping solution, the problem can be solved by the heuristic algorithm with simulated annealing. These proposed optimization algorithms can solve various large-scale problems within a reasonable time. Computer simulations were performed to evaluate and verify the performance and the validity of the proposed mapping algorithms. Finally, experiments for computing the inverse dynamics of a six-jointed PUMA-like manipulator based on the Newton-Euler dynamic equations were implemented on an NCUBE/ten hypercube computer to verify the proposed mapping algorithms. Computer simulation and experimental results are compared and discussed.

Modified Method of Adaptive Artificial Viscosity for Solution of Gas Dynamics Problems on Parallel Computer Systems

NASA Astrophysics Data System (ADS)

Popov, Igor; Sukov, Sergey

2018-02-01

A modification of the adaptive artificial viscosity (AAV) method is considered. This modification is based on one stage time approximation and is adopted to calculation of gasdynamics problems on unstructured grids with an arbitrary type of grid elements. The proposed numerical method has simplified logic, better performance and parallel efficiency compared to the implementation of the original AAV method. Computer experiments evidence the robustness and convergence of the method to difference solution.

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.

An efficient and guaranteed stable numerical method for continuous modeling of infiltration and redistribution with a shallow dynamic water table

NASA Astrophysics Data System (ADS)

Lai, Wencong; Ogden, Fred L.; Steinke, Robert C.; Talbot, Cary A.

2015-03-01

We have developed a one-dimensional numerical method to simulate infiltration and redistribution in the presence of a shallow dynamic water table. This method builds upon the Green-Ampt infiltration with Redistribution (GAR) model and incorporates features from the Talbot-Ogden (T-O) infiltration and redistribution method in a discretized moisture content domain. The redistribution scheme is more physically meaningful than the capillary weighted redistribution scheme in the T-O method. Groundwater dynamics are considered in this new method instead of hydrostatic groundwater front. It is also computationally more efficient than the T-O method. Motion of water in the vadose zone due to infiltration, redistribution, and interactions with capillary groundwater are described by ordinary differential equations. Numerical solutions to these equations are computationally less expensive than solutions of the highly nonlinear Richards' (1931) partial differential equation. We present results from numerical tests on 11 soil types using multiple rain pulses with different boundary conditions, with and without a shallow water table and compare against the numerical solution of Richards' equation (RE). Results from the new method are in satisfactory agreement with RE solutions in term of ponding time, deponding time, infiltration rate, and cumulative infiltrated depth. The new method, which we call "GARTO" can be used as an alternative to the RE for 1-D coupled surface and groundwater models in general situations with homogeneous soils with dynamic water table. The GARTO method represents a significant advance in simulating groundwater surface water interactions because it very closely matches the RE solution while being computationally efficient, with guaranteed mass conservation, and no stability limitations that can affect RE solvers in the case of a near-surface water table.

Efficient option valuation of single and double barrier options

NASA Astrophysics Data System (ADS)

Kabaivanov, Stanimir; Milev, Mariyan; Koleva-Petkova, Dessislava; Vladev, Veselin

2017-12-01

In this paper we present an implementation of pricing algorithm for single and double barrier options using Mellin transformation with Maximum Entropy Inversion and its suitability for real-world applications. A detailed analysis of the applied algorithm is accompanied by implementation in C++ that is then compared to existing solutions in terms of efficiency and computational power. We then compare the applied method with existing closed-form solutions and well known methods of pricing barrier options that are based on finite differences.

Automatic computation and solution of generalized harmonic balance equations

NASA Astrophysics Data System (ADS)

Peyton Jones, J. C.; Yaser, K. S. A.; Stevenson, J.

2018-02-01

Generalized methods are presented for generating and solving the harmonic balance equations for a broad class of nonlinear differential or difference equations and for a general set of harmonics chosen by the user. In particular, a new algorithm for automatically generating the Jacobian of the balance equations enables efficient solution of these equations using continuation methods. Efficient numeric validation techniques are also presented, and the combined algorithm is applied to the analysis of dc, fundamental, second and third harmonic response of a nonlinear automotive damper.

An implicit higher-order spatially accurate scheme for solving time dependent flows on unstructured meshes

NASA Astrophysics Data System (ADS)

Tomaro, Robert F.

1998-07-01

The present research is aimed at developing a higher-order, spatially accurate scheme for both steady and unsteady flow simulations using unstructured meshes. The resulting scheme must work on a variety of general problems to ensure the creation of a flexible, reliable and accurate aerodynamic analysis tool. To calculate the flow around complex configurations, unstructured grids and the associated flow solvers have been developed. Efficient simulations require the minimum use of computer memory and computational times. Unstructured flow solvers typically require more computer memory than a structured flow solver due to the indirect addressing of the cells. The approach taken in the present research was to modify an existing three-dimensional unstructured flow solver to first decrease the computational time required for a solution and then to increase the spatial accuracy. The terms required to simulate flow involving non-stationary grids were also implemented. First, an implicit solution algorithm was implemented to replace the existing explicit procedure. Several test cases, including internal and external, inviscid and viscous, two-dimensional, three-dimensional and axi-symmetric problems, were simulated for comparison between the explicit and implicit solution procedures. The increased efficiency and robustness of modified code due to the implicit algorithm was demonstrated. Two unsteady test cases, a plunging airfoil and a wing undergoing bending and torsion, were simulated using the implicit algorithm modified to include the terms required for a moving and/or deforming grid. Secondly, a higher than second-order spatially accurate scheme was developed and implemented into the baseline code. Third- and fourth-order spatially accurate schemes were implemented and tested. The original dissipation was modified to include higher-order terms and modified near shock waves to limit pre- and post-shock oscillations. The unsteady cases were repeated using the higher-order spatially accurate code. The new solutions were compared with those obtained using the second-order spatially accurate scheme. Finally, the increased efficiency of using an implicit solution algorithm in a production Computational Fluid Dynamics flow solver was demonstrated for steady and unsteady flows. A third- and fourth-order spatially accurate scheme has been implemented creating a basis for a state-of-the-art aerodynamic analysis tool.

A mixed analog/digital chaotic neuro-computer system for quadratic assignment problems.

PubMed

Horio, Yoshihiko; Ikeguchi, Tohru; Aihara, Kazuyuki

2005-01-01

We construct a mixed analog/digital chaotic neuro-computer prototype system for quadratic assignment problems (QAPs). The QAP is one of the difficult NP-hard problems, and includes several real-world applications. Chaotic neural networks have been used to solve combinatorial optimization problems through chaotic search dynamics, which efficiently searches optimal or near optimal solutions. However, preliminary experiments have shown that, although it obtained good feasible solutions, the Hopfield-type chaotic neuro-computer hardware system could not obtain the optimal solution of the QAP. Therefore, in the present study, we improve the system performance by adopting a solution construction method, which constructs a feasible solution using the analog internal state values of the chaotic neurons at each iteration. In order to include the construction method into our hardware, we install a multi-channel analog-to-digital conversion system to observe the internal states of the chaotic neurons. We show experimentally that a great improvement in the system performance over the original Hopfield-type chaotic neuro-computer is obtained. That is, we obtain the optimal solution for the size-10 QAP in less than 1000 iterations. In addition, we propose a guideline for parameter tuning of the chaotic neuro-computer system according to the observation of the internal states of several chaotic neurons in the network.

Semi-implicit finite difference methods for three-dimensional shallow water flow

USGS Publications Warehouse

Casulli, Vincenzo; Cheng, Ralph T.

1992-01-01

A semi-implicit finite difference method for the numerical solution of three-dimensional shallow water flows is presented and discussed. The governing equations are the primitive three-dimensional turbulent mean flow equations where the pressure distribution in the vertical has been assumed to be hydrostatic. In the method of solution a minimal degree of implicitness has been adopted in such a fashion that the resulting algorithm is stable and gives a maximal computational efficiency at a minimal computational cost. At each time step the numerical method requires the solution of one large linear system which can be formally decomposed into a set of small three-diagonal systems coupled with one five-diagonal system. All these linear systems are symmetric and positive definite. Thus the existence and uniquencess of the numerical solution are assured. When only one vertical layer is specified, this method reduces as a special case to a semi-implicit scheme for solving the corresponding two-dimensional shallow water equations. The resulting two- and three-dimensional algorithm has been shown to be fast, accurate and mass-conservative and can also be applied to simulate flooding and drying of tidal mud-flats in conjunction with three-dimensional flows. Furthermore, the resulting algorithm is fully vectorizable for an efficient implementation on modern vector computers.

Semiannual Report October 1, 1999 through March 31, 2000

DTIC Science & Technology

2000-04-01

Mark Carpenter (NASA Langley). Textbook Multigrid Efficiency for the Navier-Stokes Equations Boris Diskin A typical modern Reynolds-Averaged...defined as textbook multigrid efficiency (TME), meaning the solutions to the governing system of equations are attained in a computational work...basic elements of the barriers to be overcome in extending textbook efficiencies to the compressible RANS equations, namely entering flows, far wake

A comparison between state-specific and linear-response formalisms for the calculation of vertical electronic transition energy in solution with the CCSD-PCM method.

PubMed

Caricato, Marco

2013-07-28

The calculation of vertical electronic transition energies of molecular systems in solution with accurate quantum mechanical methods requires the use of approximate and yet reliable models to describe the effect of the solvent on the electronic structure of the solute. The polarizable continuum model (PCM) of solvation represents a computationally efficient way to describe this effect, especially when combined with coupled cluster (CC) methods. Two formalisms are available to compute transition energies within the PCM framework: State-Specific (SS) and Linear-Response (LR). The former provides a more complete account of the solute-solvent polarization in the excited states, while the latter is computationally very efficient (i.e., comparable to gas phase) and transition properties are well defined. In this work, I review the theory for the two formalisms within CC theory with a focus on their computational requirements, and present the first implementation of the LR-PCM formalism with the coupled cluster singles and doubles method (CCSD). Transition energies computed with LR- and SS-CCSD-PCM are presented, as well as a comparison between solvation models in the LR approach. The numerical results show that the two formalisms provide different absolute values of transition energy, but similar relative solvatochromic shifts (from nonpolar to polar solvents). The LR formalism may then be used to explore the solvent effect on multiple states and evaluate transition probabilities, while the SS formalism may be used to refine the description of specific states and for the exploration of excited state potential energy surfaces of solvated systems.

Heterogeneous High Throughput Scientific Computing with APM X-Gene and Intel Xeon Phi

NASA Astrophysics Data System (ADS)

Abdurachmanov, David; Bockelman, Brian; Elmer, Peter; Eulisse, Giulio; Knight, Robert; Muzaffar, Shahzad

2015-05-01

Electrical power requirements will be a constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics. Performance-per-watt is a critical metric for the evaluation of computer architectures for cost- efficient computing. Additionally, future performance growth will come from heterogeneous, many-core, and high computing density platforms with specialized processors. In this paper, we examine the Intel Xeon Phi Many Integrated Cores (MIC) co-processor and Applied Micro X-Gene ARMv8 64-bit low-power server system-on-a-chip (SoC) solutions for scientific computing applications. We report our experience on software porting, performance and energy efficiency and evaluate the potential for use of such technologies in the context of distributed computing systems such as the Worldwide LHC Computing Grid (WLCG).

An Exact Dual Adjoint Solution Method for Turbulent Flows on Unstructured Grids

NASA Technical Reports Server (NTRS)

Nielsen, Eric J.; Lu, James; Park, Michael A.; Darmofal, David L.

2003-01-01

An algorithm for solving the discrete adjoint system based on an unstructured-grid discretization of the Navier-Stokes equations is presented. The method is constructed such that an adjoint solution exactly dual to a direct differentiation approach is recovered at each time step, yielding a convergence rate which is asymptotically equivalent to that of the primal system. The new approach is implemented within a three-dimensional unstructured-grid framework and results are presented for inviscid, laminar, and turbulent flows. Improvements to the baseline solution algorithm, such as line-implicit relaxation and a tight coupling of the turbulence model, are also presented. By storing nearest-neighbor terms in the residual computation, the dual scheme is computationally efficient, while requiring twice the memory of the flow solution. The scheme is expected to have a broad impact on computational problems related to design optimization as well as error estimation and grid adaptation efforts.

Constrained Total Generalized p-Variation Minimization for Few-View X-Ray Computed Tomography Image Reconstruction.

PubMed

Zhang, Hanming; Wang, Linyuan; Yan, Bin; Li, Lei; Cai, Ailong; Hu, Guoen

2016-01-01

Total generalized variation (TGV)-based computed tomography (CT) image reconstruction, which utilizes high-order image derivatives, is superior to total variation-based methods in terms of the preservation of edge information and the suppression of unfavorable staircase effects. However, conventional TGV regularization employs l1-based form, which is not the most direct method for maximizing sparsity prior. In this study, we propose a total generalized p-variation (TGpV) regularization model to improve the sparsity exploitation of TGV and offer efficient solutions to few-view CT image reconstruction problems. To solve the nonconvex optimization problem of the TGpV minimization model, we then present an efficient iterative algorithm based on the alternating minimization of augmented Lagrangian function. All of the resulting subproblems decoupled by variable splitting admit explicit solutions by applying alternating minimization method and generalized p-shrinkage mapping. In addition, approximate solutions that can be easily performed and quickly calculated through fast Fourier transform are derived using the proximal point method to reduce the cost of inner subproblems. The accuracy and efficiency of the simulated and real data are qualitatively and quantitatively evaluated to validate the efficiency and feasibility of the proposed method. Overall, the proposed method exhibits reasonable performance and outperforms the original TGV-based method when applied to few-view problems.

Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists

PubMed Central

Visser, Marco D.; McMahon, Sean M.; Merow, Cory; Dixon, Philip M.; Record, Sydne; Jongejans, Eelke

2015-01-01

Computation has become a critical component of research in biology. A risk has emerged that computational and programming challenges may limit research scope, depth, and quality. We review various solutions to common computational efficiency problems in ecological and evolutionary research. Our review pulls together material that is currently scattered across many sources and emphasizes those techniques that are especially effective for typical ecological and environmental problems. We demonstrate how straightforward it can be to write efficient code and implement techniques such as profiling or parallel computing. We supply a newly developed R package (aprof) that helps to identify computational bottlenecks in R code and determine whether optimization can be effective. Our review is complemented by a practical set of examples and detailed Supporting Information material (S1–S3 Texts) that demonstrate large improvements in computational speed (ranging from 10.5 times to 14,000 times faster). By improving computational efficiency, biologists can feasibly solve more complex tasks, ask more ambitious questions, and include more sophisticated analyses in their research. PMID:25811842

Seeding the initial population with feasible solutions in metaheuristic optimization of steel trusses

NASA Astrophysics Data System (ADS)

Kazemzadeh Azad, Saeid

2018-01-01

In spite of considerable research work on the development of efficient algorithms for discrete sizing optimization of steel truss structures, only a few studies have addressed non-algorithmic issues affecting the general performance of algorithms. For instance, an important question is whether starting the design optimization from a feasible solution is fruitful or not. This study is an attempt to investigate the effect of seeding the initial population with feasible solutions on the general performance of metaheuristic techniques. To this end, the sensitivity of recently proposed metaheuristic algorithms to the feasibility of initial candidate designs is evaluated through practical discrete sizing of real-size steel truss structures. The numerical experiments indicate that seeding the initial population with feasible solutions can improve the computational efficiency of metaheuristic structural optimization algorithms, especially in the early stages of the optimization. This paves the way for efficient metaheuristic optimization of large-scale structural systems.

International Conference on Stiff Computation Held at Park City, Utah on April 12, 13 and 14, 1982.

DTIC Science & Technology

1983-05-31

algorithm should be designed which can analyse a system description and find out for the user ~to which class of problems his system belongs... Dove...processors designed to implement aspecific solution process. yrne: IEE floating point chip design " used by INE and others is an example (Xahan)...the...hardware speciaList has designed his computer such that the paraL#L features can be addressed convenientLy and !! ’) efficientLy, and 4;) the software

A Computer Program for the Calculation of Three-Dimensional Transonic Nacelle/Inlet Flowfields

NASA Technical Reports Server (NTRS)

Vadyak, J.; Atta, E. H.

1983-01-01

A highly efficient computer analysis was developed for predicting transonic nacelle/inlet flowfields. This algorithm can compute the three dimensional transonic flowfield about axisymmetric (or asymmetric) nacelle/inlet configurations at zero or nonzero incidence. The flowfield is determined by solving the full-potential equation in conservative form on a body-fitted curvilinear computational mesh. The difference equations are solved using the AF2 approximate factorization scheme. This report presents a discussion of the computational methods used to both generate the body-fitted curvilinear mesh and to obtain the inviscid flow solution. Computed results and correlations with existing methods and experiment are presented. Also presented are discussions on the organization of the grid generation (NGRIDA) computer program and the flow solution (NACELLE) computer program, descriptions of the respective subroutines, definitions of the required input parameters for both algorithms, a brief discussion on interpretation of the output, and sample cases to illustrate application of the analysis.

Multiple-grid convergence acceleration of viscous and inviscid flow computations

NASA Technical Reports Server (NTRS)

Johnson, G. M.

1983-01-01

A multiple-grid algorithm for use in efficiently obtaining steady solution to the Euler and Navier-Stokes equations is presented. The convergence of a simple, explicit fine-grid solution procedure is accelerated on a sequence of successively coarser grids by a coarse-grid information propagation method which rapidly eliminates transients from the computational domain. This use of multiple-gridding to increase the convergence rate results in substantially reduced work requirements for the numerical solution of a wide range of flow problems. Computational results are presented for subsonic and transonic inviscid flows and for laminar and turbulent, attached and separated, subsonic viscous flows. Work reduction factors as large as eight, in comparison to the basic fine-grid algorithm, were obtained. Possibilities for further performance improvement are discussed.

A Stochastic Total Least Squares Solution of Adaptive Filtering Problem

PubMed Central

Ahmad, Noor Atinah

2014-01-01

An efficient and computationally linear algorithm is derived for total least squares solution of adaptive filtering problem, when both input and output signals are contaminated by noise. The proposed total least mean squares (TLMS) algorithm is designed by recursively computing an optimal solution of adaptive TLS problem by minimizing instantaneous value of weighted cost function. Convergence analysis of the algorithm is given to show the global convergence of the proposed algorithm, provided that the stepsize parameter is appropriately chosen. The TLMS algorithm is computationally simpler than the other TLS algorithms and demonstrates a better performance as compared with the least mean square (LMS) and normalized least mean square (NLMS) algorithms. It provides minimum mean square deviation by exhibiting better convergence in misalignment for unknown system identification under noisy inputs. PMID:24688412

Privacy-preserving genome-wide association studies on cloud environment using fully homomorphic encryption

PubMed Central

2015-01-01

Objective Developed sequencing techniques are yielding large-scale genomic data at low cost. A genome-wide association study (GWAS) targeting genetic variations that are significantly associated with a particular disease offers great potential for medical improvement. However, subjects who volunteer their genomic data expose themselves to the risk of privacy invasion; these privacy concerns prevent efficient genomic data sharing. Our goal is to presents a cryptographic solution to this problem. Methods To maintain the privacy of subjects, we propose encryption of all genotype and phenotype data. To allow the cloud to perform meaningful computation in relation to the encrypted data, we use a fully homomorphic encryption scheme. Noting that we can evaluate typical statistics for GWAS from a frequency table, our solution evaluates frequency tables with encrypted genomic and clinical data as input. We propose to use a packing technique for efficient evaluation of these frequency tables. Results Our solution supports evaluation of the D′ measure of linkage disequilibrium, the Hardy-Weinberg Equilibrium, the χ2 test, etc. In this paper, we take χ2 test and linkage disequilibrium as examples and demonstrate how we can conduct these algorithms securely and efficiently in an outsourcing setting. We demonstrate with experimentation that secure outsourcing computation of one χ2 test with 10, 000 subjects requires about 35 ms and evaluation of one linkage disequilibrium with 10, 000 subjects requires about 80 ms. Conclusions With appropriate encoding and packing technique, cryptographic solutions based on fully homomorphic encryption for secure computations of GWAS can be practical. PMID:26732892

A pertinent approach to solve nonlinear fuzzy integro-differential equations.

PubMed

Narayanamoorthy, S; Sathiyapriya, S P

2016-01-01

Fuzzy integro-differential equations is one of the important parts of fuzzy analysis theory that holds theoretical as well as applicable values in analytical dynamics and so an appropriate computational algorithm to solve them is in essence. In this article, we use parametric forms of fuzzy numbers and suggest an applicable approach for solving nonlinear fuzzy integro-differential equations using homotopy perturbation method. A clear and detailed description of the proposed method is provided. Our main objective is to illustrate that the construction of appropriate convex homotopy in a proper way leads to highly accurate solutions with less computational work. The efficiency of the approximation technique is expressed via stability and convergence analysis so as to guarantee the efficiency and performance of the methodology. Numerical examples are demonstrated to verify the convergence and it reveals the validity of the presented numerical technique. Numerical results are tabulated and examined by comparing the obtained approximate solutions with the known exact solutions. Graphical representations of the exact and acquired approximate fuzzy solutions clarify the accuracy of the approach.

A direct numerical method for predicting concentration profiles in a turbulent boundary layer over a flat plate. M.S. Thesis

NASA Technical Reports Server (NTRS)

Dow, J. W.

1972-01-01

A numerical solution of the turbulent mass transport equation utilizing the concept of eddy diffusivity is presented as an efficient method of investigating turbulent mass transport in boundary layer type flows. A FORTRAN computer program is used to study the two-dimensional diffusion of ammonia, from a line source on the surface, into a turbulent boundary layer over a flat plate. The results of the numerical solution are compared with experimental data to verify the results of the solution. Several other solutions to diffusion problems are presented to illustrate the versatility of the computer program and to provide some insight into the problem of mass diffusion as a whole.

Computational strategies for three-dimensional flow simulations on distributed computer systems. Ph.D. Thesis Semiannual Status Report, 15 Aug. 1993 - 15 Feb. 1994

NASA Technical Reports Server (NTRS)

Weed, Richard Allen; Sankar, L. N.

1994-01-01

An increasing amount of research activity in computational fluid dynamics has been devoted to the development of efficient algorithms for parallel computing systems. The increasing performance to price ratio of engineering workstations has led to research to development procedures for implementing a parallel computing system composed of distributed workstations. This thesis proposal outlines an ongoing research program to develop efficient strategies for performing three-dimensional flow analysis on distributed computing systems. The PVM parallel programming interface was used to modify an existing three-dimensional flow solver, the TEAM code developed by Lockheed for the Air Force, to function as a parallel flow solver on clusters of workstations. Steady flow solutions were generated for three different wing and body geometries to validate the code and evaluate code performance. The proposed research will extend the parallel code development to determine the most efficient strategies for unsteady flow simulations.

FWT2D: A massively parallel program for frequency-domain full-waveform tomography of wide-aperture seismic data—Part 1: Algorithm

NASA Astrophysics Data System (ADS)

Sourbier, Florent; Operto, Stéphane; Virieux, Jean; Amestoy, Patrick; L'Excellent, Jean-Yves

2009-03-01

This is the first paper in a two-part series that describes a massively parallel code that performs 2D frequency-domain full-waveform inversion of wide-aperture seismic data for imaging complex structures. Full-waveform inversion methods, namely quantitative seismic imaging methods based on the resolution of the full wave equation, are computationally expensive. Therefore, designing efficient algorithms which take advantage of parallel computing facilities is critical for the appraisal of these approaches when applied to representative case studies and for further improvements. Full-waveform modelling requires the resolution of a large sparse system of linear equations which is performed with the massively parallel direct solver MUMPS for efficient multiple-shot simulations. Efficiency of the multiple-shot solution phase (forward/backward substitutions) is improved by using the BLAS3 library. The inverse problem relies on a classic local optimization approach implemented with a gradient method. The direct solver returns the multiple-shot wavefield solutions distributed over the processors according to a domain decomposition driven by the distribution of the LU factors. The domain decomposition of the wavefield solutions is used to compute in parallel the gradient of the objective function and the diagonal Hessian, this latter providing a suitable scaling of the gradient. The algorithm allows one to test different strategies for multiscale frequency inversion ranging from successive mono-frequency inversion to simultaneous multifrequency inversion. These different inversion strategies will be illustrated in the following companion paper. The parallel efficiency and the scalability of the code will also be quantified.

Computation of incompressible viscous flows through artificial heart devices with moving boundaries

NASA Technical Reports Server (NTRS)

Kiris, Cetin; Rogers, Stuart; Kwak, Dochan; Chang, I.-DEE

1991-01-01

The extension of computational fluid dynamics techniques to artificial heart flow simulations is illustrated. Unsteady incompressible Navier-Stokes equations written in 3-D generalized curvilinear coordinates are solved iteratively at each physical time step until the incompressibility condition is satisfied. The solution method is based on the pseudo compressibility approach and uses an implicit upwind differencing scheme together with the Gauss-Seidel line relaxation method. The efficiency and robustness of the time accurate formulation of the algorithm are tested by computing the flow through model geometries. A channel flow with a moving indentation is computed and validated with experimental measurements and other numerical solutions. In order to handle the geometric complexity and the moving boundary problems, a zonal method and an overlapping grid embedding scheme are used, respectively. Steady state solutions for the flow through a tilting disk heart valve was compared against experimental measurements. Good agreement was obtained. The flow computation during the valve opening and closing is carried out to illustrate the moving boundary capability.

Computational structures for robotic computations

NASA Technical Reports Server (NTRS)

Lee, C. S. G.; Chang, P. R.

1987-01-01

The computational problem of inverse kinematics and inverse dynamics of robot manipulators by taking advantage of parallelism and pipelining architectures is discussed. For the computation of inverse kinematic position solution, a maximum pipelined CORDIC architecture has been designed based on a functional decomposition of the closed-form joint equations. For the inverse dynamics computation, an efficient p-fold parallel algorithm to overcome the recurrence problem of the Newton-Euler equations of motion to achieve the time lower bound of O(log sub 2 n) has also been developed.

Efficient Optimization of Low-Thrust Spacecraft Trajectories

NASA Technical Reports Server (NTRS)

Lee, Seungwon; Fink, Wolfgang; Russell, Ryan; Terrile, Richard; Petropoulos, Anastassios; vonAllmen, Paul

2007-01-01

A paper describes a computationally efficient method of optimizing trajectories of spacecraft driven by propulsion systems that generate low thrusts and, hence, must be operated for long times. A common goal in trajectory-optimization problems is to find minimum-time, minimum-fuel, or Pareto-optimal trajectories (here, Pareto-optimality signifies that no other solutions are superior with respect to both flight time and fuel consumption). The present method utilizes genetic and simulated-annealing algorithms to search for globally Pareto-optimal solutions. These algorithms are implemented in parallel form to reduce computation time. These algorithms are coupled with either of two traditional trajectory- design approaches called "direct" and "indirect." In the direct approach, thrust control is discretized in either arc time or arc length, and the resulting discrete thrust vectors are optimized. The indirect approach involves the primer-vector theory (introduced in 1963), in which the thrust control problem is transformed into a co-state control problem and the initial values of the co-state vector are optimized. In application to two example orbit-transfer problems, this method was found to generate solutions comparable to those of other state-of-the-art trajectory-optimization methods while requiring much less computation time.

Approximate Algorithms for Computing Spatial Distance Histograms with Accuracy Guarantees

PubMed Central

Grupcev, Vladimir; Yuan, Yongke; Tu, Yi-Cheng; Huang, Jin; Chen, Shaoping; Pandit, Sagar; Weng, Michael

2014-01-01

Particle simulation has become an important research tool in many scientific and engineering fields. Data generated by such simulations impose great challenges to database storage and query processing. One of the queries against particle simulation data, the spatial distance histogram (SDH) query, is the building block of many high-level analytics, and requires quadratic time to compute using a straightforward algorithm. Previous work has developed efficient algorithms that compute exact SDHs. While beating the naive solution, such algorithms are still not practical in processing SDH queries against large-scale simulation data. In this paper, we take a different path to tackle this problem by focusing on approximate algorithms with provable error bounds. We first present a solution derived from the aforementioned exact SDH algorithm, and this solution has running time that is unrelated to the system size N. We also develop a mathematical model to analyze the mechanism that leads to errors in the basic approximate algorithm. Our model provides insights on how the algorithm can be improved to achieve higher accuracy and efficiency. Such insights give rise to a new approximate algorithm with improved time/accuracy tradeoff. Experimental results confirm our analysis. PMID:24693210

A filtering approach to edge preserving MAP estimation of images.

PubMed

Humphrey, David; Taubman, David

2011-05-01

The authors present a computationally efficient technique for maximum a posteriori (MAP) estimation of images in the presence of both blur and noise. The image is divided into statistically independent regions. Each region is modelled with a WSS Gaussian prior. Classical Wiener filter theory is used to generate a set of convex sets in the solution space, with the solution to the MAP estimation problem lying at the intersection of these sets. The proposed algorithm uses an underlying segmentation of the image, and a means of determining the segmentation and refining it are described. The algorithm is suitable for a range of image restoration problems, as it provides a computationally efficient means to deal with the shortcomings of Wiener filtering without sacrificing the computational simplicity of the filtering approach. The algorithm is also of interest from a theoretical viewpoint as it provides a continuum of solutions between Wiener filtering and Inverse filtering depending upon the segmentation used. We do not attempt to show here that the proposed method is the best general approach to the image reconstruction problem. However, related work referenced herein shows excellent performance in the specific problem of demosaicing.

Heterogeneous high throughput scientific computing with APM X-Gene and Intel Xeon Phi

DOE PAGES

Abdurachmanov, David; Bockelman, Brian; Elmer, Peter; ...

2015-05-22

Electrical power requirements will be a constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics. Performance-per-watt is a critical metric for the evaluation of computer architectures for cost- efficient computing. Additionally, future performance growth will come from heterogeneous, many-core, and high computing density platforms with specialized processors. In this paper, we examine the Intel Xeon Phi Many Integrated Cores (MIC) co-processor and Applied Micro X-Gene ARMv8 64-bit low-power server system-on-a-chip (SoC) solutions for scientific computing applications. As a result, we report our experience on software porting, performance and energy efficiency and evaluatemore » the potential for use of such technologies in the context of distributed computing systems such as the Worldwide LHC Computing Grid (WLCG).« less

Overview of the NASA Glenn Flux Reconstruction Based High-Order Unstructured Grid Code

NASA Technical Reports Server (NTRS)

Spiegel, Seth C.; DeBonis, James R.; Huynh, H. T.

2016-01-01

A computational fluid dynamics code based on the flux reconstruction (FR) method is currently being developed at NASA Glenn Research Center to ultimately provide a large- eddy simulation capability that is both accurate and efficient for complex aeropropulsion flows. The FR approach offers a simple and efficient method that is easy to implement and accurate to an arbitrary order on common grid cell geometries. The governing compressible Navier-Stokes equations are discretized in time using various explicit Runge-Kutta schemes, with the default being the 3-stage/3rd-order strong stability preserving scheme. The code is written in modern Fortran (i.e., Fortran 2008) and parallelization is attained through MPI for execution on distributed-memory high-performance computing systems. An h- refinement study of the isentropic Euler vortex problem is able to empirically demonstrate the capability of the FR method to achieve super-accuracy for inviscid flows. Additionally, the code is applied to the Taylor-Green vortex problem, performing numerous implicit large-eddy simulations across a range of grid resolutions and solution orders. The solution found by a pseudo-spectral code is commonly used as a reference solution to this problem, and the FR code is able to reproduce this solution using approximately the same grid resolution. Finally, an examination of the code's performance demonstrates good parallel scaling, as well as an implementation of the FR method with a computational cost/degree- of-freedom/time-step that is essentially independent of the solution order of accuracy for structured geometries.

Approximate Analysis for Interlaminar Stresses in Composite Structures with Thickness Discontinuities

NASA Technical Reports Server (NTRS)

Rose, Cheryl A.; Starnes, James H., Jr.

1996-01-01

An efficient, approximate analysis for calculating complete three-dimensional stress fields near regions of geometric discontinuities in laminated composite structures is presented. An approximate three-dimensional local analysis is used to determine the detailed local response due to far-field stresses obtained from a global two-dimensional analysis. The stress results from the global analysis are used as traction boundary conditions for the local analysis. A generalized plane deformation assumption is made in the local analysis to reduce the solution domain to two dimensions. This assumption allows out-of-plane deformation to occur. The local analysis is based on the principle of minimum complementary energy and uses statically admissible stress functions that have an assumed through-the-thickness distribution. Examples are presented to illustrate the accuracy and computational efficiency of the local analysis. Comparisons of the results of the present local analysis with the corresponding results obtained from a finite element analysis and from an elasticity solution are presented. These results indicate that the present local analysis predicts the stress field accurately. Computer execution-times are also presented. The demonstrated accuracy and computational efficiency of the analysis make it well suited for parametric and design studies.

X-ray solution scattering combined with computation characterizing protein folds and multiple conformational states : computation and application.

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

Yang, S.; Park, S.; Makowski, L.

Small angle X-ray scattering (SAXS) is an increasingly powerful technique to characterize the structure of biomolecules in solution. We present a computational method for accurately and efficiently computing the solution scattering curve from a protein with dynamical fluctuations. The method is built upon a coarse-grained (CG) representation of the protein. This CG approach takes advantage of the low-resolution character of solution scattering. It allows rapid determination of the scattering pattern from conformations extracted from CG simulations to obtain scattering characterization of the protein conformational landscapes. Important elements incorporated in the method include an effective residue-based structure factor for each aminomore » acid, an explicit treatment of the hydration layer at the surface of the protein, and an ensemble average of scattering from all accessible conformations to account for macromolecular flexibility. The CG model is calibrated and illustrated to accurately reproduce the experimental scattering curve of Hen egg white lysozyme. We then illustrate the computational method by calculating the solution scattering pattern of several representative protein folds and multiple conformational states. The results suggest that solution scattering data, when combined with a reliable computational method, have great potential for a better structural description of multi-domain complexes in different functional states, and for recognizing structural folds when sequence similarity to a protein of known structure is low. Possible applications of the method are discussed.« less

Numerical algorithm comparison for the accurate and efficient computation of high-incidence vortical flow

NASA Technical Reports Server (NTRS)

Chaderjian, Neal M.

1991-01-01

Computations from two Navier-Stokes codes, NSS and F3D, are presented for a tangent-ogive-cylinder body at high angle of attack. Features of this steady flow include a pair of primary vortices on the leeward side of the body as well as secondary vortices. The topological and physical plausibility of this vortical structure is discussed. The accuracy of these codes are assessed by comparison of the numerical solutions with experimental data. The effects of turbulence model, numerical dissipation, and grid refinement are presented. The overall efficiency of these codes are also assessed by examining their convergence rates, computational time per time step, and maximum allowable time step for time-accurate computations. Overall, the numerical results from both codes compared equally well with experimental data, however, the NSS code was found to be significantly more efficient than the F3D code.

An efficient method for hybrid density functional calculation with spin-orbit coupling

NASA Astrophysics Data System (ADS)

Wang, Maoyuan; Liu, Gui-Bin; Guo, Hong; Yao, Yugui

2018-03-01

In first-principles calculations, hybrid functional is often used to improve accuracy from local exchange correlation functionals. A drawback is that evaluating the hybrid functional needs significantly more computing effort. When spin-orbit coupling (SOC) is taken into account, the non-collinear spin structure increases computing effort by at least eight times. As a result, hybrid functional calculations with SOC are intractable in most cases. In this paper, we present an approximate solution to this problem by developing an efficient method based on a mixed linear combination of atomic orbital (LCAO) scheme. We demonstrate the power of this method using several examples and we show that the results compare very well with those of direct hybrid functional calculations with SOC, yet the method only requires a computing effort similar to that without SOC. The presented technique provides a good balance between computing efficiency and accuracy, and it can be extended to magnetic materials.

Spatial adaption procedures on unstructured meshes for accurate unsteady aerodynamic flow computation

NASA Technical Reports Server (NTRS)

Rausch, Russ D.; Batina, John T.; Yang, Henry T. Y.

1991-01-01

Spatial adaption procedures for the accurate and efficient solution of steady and unsteady inviscid flow problems are described. The adaption procedures were developed and implemented within a two-dimensional unstructured-grid upwind-type Euler code. These procedures involve mesh enrichment and mesh coarsening to either add points in a high gradient region or the flow or remove points where they are not needed, respectively, to produce solutions of high spatial accuracy at minimal computational costs. A detailed description is given of the enrichment and coarsening procedures and comparisons with alternative results and experimental data are presented to provide an assessment of the accuracy and efficiency of the capability. Steady and unsteady transonic results, obtained using spatial adaption for the NACA 0012 airfoil, are shown to be of high spatial accuracy, primarily in that the shock waves are very sharply captured. The results were obtained with a computational savings of a factor of approximately fifty-three for a steady case and as much as twenty-five for the unsteady cases.

Use of the parameterised finite element method to robustly and efficiently evolve the edge of a moving cell.

PubMed

Neilson, Matthew P; Mackenzie, John A; Webb, Steven D; Insall, Robert H

2010-11-01

In this paper we present a computational tool that enables the simulation of mathematical models of cell migration and chemotaxis on an evolving cell membrane. Recent models require the numerical solution of systems of reaction-diffusion equations on the evolving cell membrane and then the solution state is used to drive the evolution of the cell edge. Previous work involved moving the cell edge using a level set method (LSM). However, the LSM is computationally very expensive, which severely limits the practical usefulness of the algorithm. To address this issue, we have employed the parameterised finite element method (PFEM) as an alternative method for evolving a cell boundary. We show that the PFEM is far more efficient and robust than the LSM. We therefore suggest that the PFEM potentially has an essential role to play in computational modelling efforts towards the understanding of many of the complex issues related to chemotaxis.

Solution of nonlinear time-dependent PDEs through componentwise approximation of matrix functions

NASA Astrophysics Data System (ADS)

Cibotarica, Alexandru; Lambers, James V.; Palchak, Elisabeth M.

2016-09-01

Exponential propagation iterative (EPI) methods provide an efficient approach to the solution of large stiff systems of ODEs, compared to standard integrators. However, the bulk of the computational effort in these methods is due to products of matrix functions and vectors, which can become very costly at high resolution due to an increase in the number of Krylov projection steps needed to maintain accuracy. In this paper, it is proposed to modify EPI methods by using Krylov subspace spectral (KSS) methods, instead of standard Krylov projection methods, to compute products of matrix functions and vectors. Numerical experiments demonstrate that this modification causes the number of Krylov projection steps to become bounded independently of the grid size, thus dramatically improving efficiency and scalability. As a result, for each test problem featured, as the total number of grid points increases, the growth in computation time is just below linear, while other methods achieved this only on selected test problems or not at all.

A multigrid nonoscillatory method for computing high speed flows

NASA Technical Reports Server (NTRS)

Li, C. P.; Shieh, T. H.

1993-01-01

A multigrid method using different smoothers has been developed to solve the Euler equations discretized by a nonoscillatory scheme up to fourth order accuracy. The best smoothing property is provided by a five-stage Runge-Kutta technique with optimized coefficients, yet the most efficient smoother is a backward Euler technique in factored and diagonalized form. The singlegrid solution for a hypersonic, viscous conic flow is in excellent agreement with the solution obtained by the third order MUSCL and Roe's method. Mach 8 inviscid flow computations for a complete entry probe have shown that the accuracy is at least as good as the symmetric TVD scheme of Yee and Harten. The implicit multigrid method is four times more efficient than the explicit multigrid technique and 3.5 times faster than the single-grid implicit technique. For a Mach 8.7 inviscid flow over a blunt delta wing at 30 deg incidence, the CPU reduction factor from the three-level multigrid computation is 2.2 on a grid of 37 x 41 x 73 nodes.

Spatial adaption procedures on unstructured meshes for accurate unsteady aerodynamic flow computation

NASA Technical Reports Server (NTRS)

Rausch, Russ D.; Yang, Henry T. Y.; Batina, John T.

1991-01-01

Spatial adaption procedures for the accurate and efficient solution of steady and unsteady inviscid flow problems are described. The adaption procedures were developed and implemented within a two-dimensional unstructured-grid upwind-type Euler code. These procedures involve mesh enrichment and mesh coarsening to either add points in high gradient regions of the flow or remove points where they are not needed, respectively, to produce solutions of high spatial accuracy at minimal computational cost. The paper gives a detailed description of the enrichment and coarsening procedures and presents comparisons with alternative results and experimental data to provide an assessment of the accuracy and efficiency of the capability. Steady and unsteady transonic results, obtained using spatial adaption for the NACA 0012 airfoil, are shown to be of high spatial accuracy, primarily in that the shock waves are very sharply captured. The results were obtained with a computational savings of a factor of approximately fifty-three for a steady case and as much as twenty-five for the unsteady cases.

Parameterized Algorithmics for Finding Exact Solutions of NP-Hard Biological Problems.

PubMed

Hüffner, Falk; Komusiewicz, Christian; Niedermeier, Rolf; Wernicke, Sebastian

2017-01-01

Fixed-parameter algorithms are designed to efficiently find optimal solutions to some computationally hard (NP-hard) problems by identifying and exploiting "small" problem-specific parameters. We survey practical techniques to develop such algorithms. Each technique is introduced and supported by case studies of applications to biological problems, with additional pointers to experimental results.

Hybrid Symbiotic Organisms Search Optimization Algorithm for Scheduling of Tasks on Cloud Computing Environment.

PubMed

Abdullahi, Mohammed; Ngadi, Md Asri

2016-01-01

Cloud computing has attracted significant attention from research community because of rapid migration rate of Information Technology services to its domain. Advances in virtualization technology has made cloud computing very popular as a result of easier deployment of application services. Tasks are submitted to cloud datacenters to be processed on pay as you go fashion. Task scheduling is one the significant research challenges in cloud computing environment. The current formulation of task scheduling problems has been shown to be NP-complete, hence finding the exact solution especially for large problem sizes is intractable. The heterogeneous and dynamic feature of cloud resources makes optimum task scheduling non-trivial. Therefore, efficient task scheduling algorithms are required for optimum resource utilization. Symbiotic Organisms Search (SOS) has been shown to perform competitively with Particle Swarm Optimization (PSO). The aim of this study is to optimize task scheduling in cloud computing environment based on a proposed Simulated Annealing (SA) based SOS (SASOS) in order to improve the convergence rate and quality of solution of SOS. The SOS algorithm has a strong global exploration capability and uses fewer parameters. The systematic reasoning ability of SA is employed to find better solutions on local solution regions, hence, adding exploration ability to SOS. Also, a fitness function is proposed which takes into account the utilization level of virtual machines (VMs) which reduced makespan and degree of imbalance among VMs. CloudSim toolkit was used to evaluate the efficiency of the proposed method using both synthetic and standard workload. Results of simulation showed that hybrid SOS performs better than SOS in terms of convergence speed, response time, degree of imbalance, and makespan.

Hybrid Symbiotic Organisms Search Optimization Algorithm for Scheduling of Tasks on Cloud Computing Environment

PubMed Central

Abdullahi, Mohammed; Ngadi, Md Asri

2016-01-01

Cloud computing has attracted significant attention from research community because of rapid migration rate of Information Technology services to its domain. Advances in virtualization technology has made cloud computing very popular as a result of easier deployment of application services. Tasks are submitted to cloud datacenters to be processed on pay as you go fashion. Task scheduling is one the significant research challenges in cloud computing environment. The current formulation of task scheduling problems has been shown to be NP-complete, hence finding the exact solution especially for large problem sizes is intractable. The heterogeneous and dynamic feature of cloud resources makes optimum task scheduling non-trivial. Therefore, efficient task scheduling algorithms are required for optimum resource utilization. Symbiotic Organisms Search (SOS) has been shown to perform competitively with Particle Swarm Optimization (PSO). The aim of this study is to optimize task scheduling in cloud computing environment based on a proposed Simulated Annealing (SA) based SOS (SASOS) in order to improve the convergence rate and quality of solution of SOS. The SOS algorithm has a strong global exploration capability and uses fewer parameters. The systematic reasoning ability of SA is employed to find better solutions on local solution regions, hence, adding exploration ability to SOS. Also, a fitness function is proposed which takes into account the utilization level of virtual machines (VMs) which reduced makespan and degree of imbalance among VMs. CloudSim toolkit was used to evaluate the efficiency of the proposed method using both synthetic and standard workload. Results of simulation showed that hybrid SOS performs better than SOS in terms of convergence speed, response time, degree of imbalance, and makespan. PMID:27348127

Enabling smart personalized healthcare: a hybrid mobile-cloud approach for ECG telemonitoring.

PubMed

Wang, Xiaoliang; Gui, Qiong; Liu, Bingwei; Jin, Zhanpeng; Chen, Yu

2014-05-01

The severe challenges of the skyrocketing healthcare expenditure and the fast aging population highlight the needs for innovative solutions supporting more accurate, affordable, flexible, and personalized medical diagnosis and treatment. Recent advances of mobile technologies have made mobile devices a promising tool to manage patients' own health status through services like telemedicine. However, the inherent limitations of mobile devices make them less effective in computation- or data-intensive tasks such as medical monitoring. In this study, we propose a new hybrid mobile-cloud computational solution to enable more effective personalized medical monitoring. To demonstrate the efficacy and efficiency of the proposed approach, we present a case study of mobile-cloud based electrocardiograph monitoring and analysis and develop a mobile-cloud prototype. The experimental results show that the proposed approach can significantly enhance the conventional mobile-based medical monitoring in terms of diagnostic accuracy, execution efficiency, and energy efficiency, and holds the potential in addressing future large-scale data analysis in personalized healthcare.

Efficient parallel implicit methods for rotary-wing aerodynamics calculations

NASA Astrophysics Data System (ADS)

Wissink, Andrew M.

Euler/Navier-Stokes Computational Fluid Dynamics (CFD) methods are commonly used for prediction of the aerodynamics and aeroacoustics of modern rotary-wing aircraft. However, their widespread application to large complex problems is limited lack of adequate computing power. Parallel processing offers the potential for dramatic increases in computing power, but most conventional implicit solution methods are inefficient in parallel and new techniques must be adopted to realize its potential. This work proposes alternative implicit schemes for Euler/Navier-Stokes rotary-wing calculations which are robust and efficient in parallel. The first part of this work proposes an efficient parallelizable modification of the Lower Upper-Symmetric Gauss Seidel (LU-SGS) implicit operator used in the well-known Transonic Unsteady Rotor Navier Stokes (TURNS) code. The new hybrid LU-SGS scheme couples a point-relaxation approach of the Data Parallel-Lower Upper Relaxation (DP-LUR) algorithm for inter-processor communication with the Symmetric Gauss Seidel algorithm of LU-SGS for on-processor computations. With the modified operator, TURNS is implemented in parallel using Message Passing Interface (MPI) for communication. Numerical performance and parallel efficiency are evaluated on the IBM SP2 and Thinking Machines CM-5 multi-processors for a variety of steady-state and unsteady test cases. The hybrid LU-SGS scheme maintains the numerical performance of the original LU-SGS algorithm in all cases and shows a good degree of parallel efficiency. It experiences a higher degree of robustness than DP-LUR for third-order upwind solutions. The second part of this work examines use of Krylov subspace iterative solvers for the nonlinear CFD solutions. The hybrid LU-SGS scheme is used as a parallelizable preconditioner. Two iterative methods are tested, Generalized Minimum Residual (GMRES) and Orthogonal s-Step Generalized Conjugate Residual (OSGCR). The Newton method demonstrates good parallel performance on the IBM SP2, with OS-GCR giving slightly better performance than GMRES on large numbers of processors. For steady and quasi-steady calculations, the convergence rate is accelerated but the overall solution time remains about the same as the standard hybrid LU-SGS scheme. For unsteady calculations, however, the Newton method maintains a higher degree of time-accuracy which allows tbe use of larger timesteps and results in CPU savings of 20-35%.

Fast inverse scattering solutions using the distorted Born iterative method and the multilevel fast multipole algorithm

PubMed Central

Hesford, Andrew J.; Chew, Weng C.

2010-01-01

The distorted Born iterative method (DBIM) computes iterative solutions to nonlinear inverse scattering problems through successive linear approximations. By decomposing the scattered field into a superposition of scattering by an inhomogeneous background and by a material perturbation, large or high-contrast variations in medium properties can be imaged through iterations that are each subject to the distorted Born approximation. However, the need to repeatedly compute forward solutions still imposes a very heavy computational burden. To ameliorate this problem, the multilevel fast multipole algorithm (MLFMA) has been applied as a forward solver within the DBIM. The MLFMA computes forward solutions in linear time for volumetric scatterers. The typically regular distribution and shape of scattering elements in the inverse scattering problem allow the method to take advantage of data redundancy and reduce the computational demands of the normally expensive MLFMA setup. Additional benefits are gained by employing Kaczmarz-like iterations, where partial measurements are used to accelerate convergence. Numerical results demonstrate both the efficiency of the forward solver and the successful application of the inverse method to imaging problems with dimensions in the neighborhood of ten wavelengths. PMID:20707438

Paramaterization of a coarse-grained model for linear alkylbenzene sulfonate surfactants and molecular dynamics studies of their self-assembly in aqueous solution

NASA Astrophysics Data System (ADS)

He, Xibing; Shinoda, Wataru; DeVane, Russell; Anderson, Kelly L.; Klein, Michael L.

2010-02-01

A coarse-grained (CG) forcefield for linear alkylbenzene sulfonates (LAS) was systematically parameterized. Thermodynamic data from experiments and structural data obtained from all-atom molecular dynamics were used as targets to parameterize CG potentials for the bonded and non-bonded interactions. The added computational efficiency permits one to employ computer simulation to probe the self-assembly of LAS aqueous solutions into different morphologies starting from a random configuration. The present CG model is shown to accurately reproduce the phase behavior of solutions of pure isomers of sodium dodecylbenzene sulfonate, despite the fact that phase behavior was not directly taken into account in the forcefield parameterization.

MHOST: An efficient finite element program for inelastic analysis of solids and structures

NASA Technical Reports Server (NTRS)

Nakazawa, S.

1988-01-01

An efficient finite element program for 3-D inelastic analysis of gas turbine hot section components was constructed and validated. A novel mixed iterative solution strategy is derived from the augmented Hu-Washizu variational principle in order to nodally interpolate coordinates, displacements, deformation, strains, stresses and material properties. A series of increasingly sophisticated material models incorporated in MHOST include elasticity, secant plasticity, infinitesimal and finite deformation plasticity, creep and unified viscoplastic constitutive model proposed by Walker. A library of high performance elements is built into this computer program utilizing the concepts of selective reduced integrations and independent strain interpolations. A family of efficient solution algorithms is implemented in MHOST for linear and nonlinear equation solution including the classical Newton-Raphson, modified, quasi and secant Newton methods with optional line search and the conjugate gradient method.

Efficient solution of ordinary differential equations modeling electrical activity in cardiac cells.

PubMed

Sundnes, J; Lines, G T; Tveito, A

2001-08-01

The contraction of the heart is preceded and caused by a cellular electro-chemical reaction, causing an electrical field to be generated. Performing realistic computer simulations of this process involves solving a set of partial differential equations, as well as a large number of ordinary differential equations (ODEs) characterizing the reactive behavior of the cardiac tissue. Experiments have shown that the solution of the ODEs contribute significantly to the total work of a simulation, and there is thus a strong need to utilize efficient solution methods for this part of the problem. This paper presents how an efficient implicit Runge-Kutta method may be adapted to solve a complicated cardiac cell model consisting of 31 ODEs, and how this solver may be coupled to a set of PDE solvers to provide complete simulations of the electrical activity.

Efficient and secure outsourcing of genomic data storage.

PubMed

Sousa, João Sá; Lefebvre, Cédric; Huang, Zhicong; Raisaro, Jean Louis; Aguilar-Melchor, Carlos; Killijian, Marc-Olivier; Hubaux, Jean-Pierre

2017-07-26

Cloud computing is becoming the preferred solution for efficiently dealing with the increasing amount of genomic data. Yet, outsourcing storage and processing sensitive information, such as genomic data, comes with important concerns related to privacy and security. This calls for new sophisticated techniques that ensure data protection from untrusted cloud providers and that still enable researchers to obtain useful information. We present a novel privacy-preserving algorithm for fully outsourcing the storage of large genomic data files to a public cloud and enabling researchers to efficiently search for variants of interest. In order to protect data and query confidentiality from possible leakage, our solution exploits optimal encoding for genomic variants and combines it with homomorphic encryption and private information retrieval. Our proposed algorithm is implemented in C++ and was evaluated on real data as part of the 2016 iDash Genome Privacy-Protection Challenge. Results show that our solution outperforms the state-of-the-art solutions and enables researchers to search over millions of encrypted variants in a few seconds. As opposed to prior beliefs that sophisticated privacy-enhancing technologies (PETs) are unpractical for real operational settings, our solution demonstrates that, in the case of genomic data, PETs are very efficient enablers.

Numerical solution of the Saint-Venant equations by an efficient hybrid finite-volume/finite-difference method

NASA Astrophysics Data System (ADS)

Lai, Wencong; Khan, Abdul A.

2018-04-01

A computationally efficient hybrid finite-volume/finite-difference method is proposed for the numerical solution of Saint-Venant equations in one-dimensional open channel flows. The method adopts a mass-conservative finite volume discretization for the continuity equation and a semi-implicit finite difference discretization for the dynamic-wave momentum equation. The spatial discretization of the convective flux term in the momentum equation employs an upwind scheme and the water-surface gradient term is discretized using three different schemes. The performance of the numerical method is investigated in terms of efficiency and accuracy using various examples, including steady flow over a bump, dam-break flow over wet and dry downstream channels, wetting and drying in a parabolic bowl, and dam-break floods in laboratory physical models. Numerical solutions from the hybrid method are compared with solutions from a finite volume method along with analytic solutions or experimental measurements. Comparisons demonstrates that the hybrid method is efficient, accurate, and robust in modeling various flow scenarios, including subcritical, supercritical, and transcritical flows. In this method, the QUICK scheme for the surface slope discretization is more accurate and less diffusive than the center difference and the weighted average schemes.

Software Surface Modeling and Grid Generation Steering Committee

NASA Technical Reports Server (NTRS)

Smith, Robert E. (Editor)

1992-01-01

It is a NASA objective to promote improvements in the capability and efficiency of computational fluid dynamics. Grid generation, the creation of a discrete representation of the solution domain, is an essential part of computational fluid dynamics. However, grid generation about complex boundaries requires sophisticated surface-model descriptions of the boundaries. The surface modeling and the associated computation of surface grids consume an extremely large percentage of the total time required for volume grid generation. Efficient and user friendly software systems for surface modeling and grid generation are critical for computational fluid dynamics to reach its potential. The papers presented here represent the state-of-the-art in software systems for surface modeling and grid generation. Several papers describe improved techniques for grid generation.

Star adaptation for two-algorithms used on serial computers

NASA Technical Reports Server (NTRS)

Howser, L. M.; Lambiotte, J. J., Jr.

1974-01-01

Two representative algorithms used on a serial computer and presently executed on the Control Data Corporation 6000 computer were adapted to execute efficiently on the Control Data STAR-100 computer. Gaussian elimination for the solution of simultaneous linear equations and the Gauss-Legendre quadrature formula for the approximation of an integral are the two algorithms discussed. A description is given of how the programs were adapted for STAR and why these adaptations were necessary to obtain an efficient STAR program. Some points to consider when adapting an algorithm for STAR are discussed. Program listings of the 6000 version coded in 6000 FORTRAN, the adapted STAR version coded in 6000 FORTRAN, and the STAR version coded in STAR FORTRAN are presented in the appendices.

Unified treatment of microscopic boundary conditions and efficient algorithms for estimating tangent operators of the homogenized behavior in the computational homogenization method

NASA Astrophysics Data System (ADS)

Nguyen, Van-Dung; Wu, Ling; Noels, Ludovic

2017-03-01

This work provides a unified treatment of arbitrary kinds of microscopic boundary conditions usually considered in the multi-scale computational homogenization method for nonlinear multi-physics problems. An efficient procedure is developed to enforce the multi-point linear constraints arising from the microscopic boundary condition either by the direct constraint elimination or by the Lagrange multiplier elimination methods. The macroscopic tangent operators are computed in an efficient way from a multiple right hand sides linear system whose left hand side matrix is the stiffness matrix of the microscopic linearized system at the converged solution. The number of vectors at the right hand side is equal to the number of the macroscopic kinematic variables used to formulate the microscopic boundary condition. As the resolution of the microscopic linearized system often follows a direct factorization procedure, the computation of the macroscopic tangent operators is then performed using this factorized matrix at a reduced computational time.

Accurate Monotonicity - Preserving Schemes With Runge-Kutta Time Stepping

NASA Technical Reports Server (NTRS)

Suresh, A.; Huynh, H. T.

1997-01-01

A new class of high-order monotonicity-preserving schemes for the numerical solution of conservation laws is presented. The interface value in these schemes is obtained by limiting a higher-order polynominal reconstruction. The limiting is designed to preserve accuracy near extrema and to work well with Runge-Kutta time stepping. Computational efficiency is enhanced by a simple test that determines whether the limiting procedure is needed. For linear advection in one dimension, these schemes are shown as well as the Euler equations also confirm their high accuracy, good shock resolution, and computational efficiency.

Compiling for Application Specific Computational Acceleration in Reconfigurable Architectures Final Report CRADA No. TSB-2033-01

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

De Supinski, B.; Caliga, D.

2017-09-28

The primary objective of this project was to develop memory optimization technology to efficiently deliver data to, and distribute data within, the SRC-6's Field Programmable Gate Array- ("FPGA") based Multi-Adaptive Processors (MAPs). The hardware/software approach was to explore efficient MAP configurations and generate the compiler technology to exploit those configurations. This memory accessing technology represents an important step towards making reconfigurable symmetric multi-processor (SMP) architectures that will be a costeffective solution for large-scale scientific computing.

An Analysis of Performance Enhancement Techniques for Overset Grid Applications

NASA Technical Reports Server (NTRS)

Djomehri, J. J.; Biswas, R.; Potsdam, M.; Strawn, R. C.; Biegel, Bryan (Technical Monitor)

2002-01-01

The overset grid methodology has significantly reduced time-to-solution of high-fidelity 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 techniques on the parallel efficiency of an overset grid Navier-Stokes CFD application running on an SGI Origin2000 machine. Specifically, the role of asynchronous communication, grid splitting, and grid grouping strategies are presented and discussed. Results indicate that performance depends critically on the level of latency hiding and the quality of load balancing across the processors.

Illustrative Computer Programming for Libraries; Selected Examples for Information Specialists. Contributions in Librarianship and Information Science, No. 12.

ERIC Educational Resources Information Center

Davis, Charles H.

Intended for teaching applications programing for libraries and information centers, this volume is a graded workbook or text supplement containing typical practice problems, suggested solutions, and brief analyses which emphasize programing efficiency. The computer language used is Programing Language/One (PL/1) because it adapts readily to…

Hybrid-dual-fourier tomographic algorithm for a fast three-dimensionial optical image reconstruction in turbid media

NASA Technical Reports Server (NTRS)

Alfano, Robert R. (Inventor); Cai, Wei (Inventor)

2007-01-01

A reconstruction technique for reducing computation burden in the 3D image processes, wherein the reconstruction procedure comprises an inverse and a forward model. The inverse model uses a hybrid dual Fourier algorithm that combines a 2D Fourier inversion with a 1D matrix inversion to thereby provide high-speed inverse computations. The inverse algorithm uses a hybrid transfer to provide fast Fourier inversion for data of multiple sources and multiple detectors. The forward model is based on an analytical cumulant solution of a radiative transfer equation. The accurate analytical form of the solution to the radiative transfer equation provides an efficient formalism for fast computation of the forward model.

A computer program for calculating laminar and turbulent boundary layers for two-dimensional time-dependent flows

NASA Technical Reports Server (NTRS)

Cebeci, T.; Carr, L. W.

1978-01-01

A computer program is described which provides solutions of two dimensional equations appropriate to laminar and turbulent boundary layers for boundary conditions with an external flow which fluctuates in magnitude. The program is based on the numerical solution of the governing boundary layer equations by an efficient two point finite difference method. An eddy viscosity formulation was used to model the Reynolds shear stress term. The main features of the method are briefly described and instructions for the computer program with a listing are provided. Sample calculations to demonstrate its usage and capabilities for laminar and turbulent unsteady boundary layers with an external flow which fluctuated in magnitude are presented.

Solution of quadratic matrix equations for free vibration analysis of structures.

NASA Technical Reports Server (NTRS)

Gupta, K. K.

1973-01-01

An efficient digital computer procedure and the related numerical algorithm are presented herein for the solution of quadratic matrix equations associated with free vibration analysis of structures. Such a procedure enables accurate and economical analysis of natural frequencies and associated modes of discretized structures. The numerically stable algorithm is based on the Sturm sequence method, which fully exploits the banded form of associated stiffness and mass matrices. The related computer program written in FORTRAN V for the JPL UNIVAC 1108 computer proves to be substantially more accurate and economical than other existing procedures of such analysis. Numerical examples are presented for two structures - a cantilever beam and a semicircular arch.

Constrained Total Generalized p-Variation Minimization for Few-View X-Ray Computed Tomography Image Reconstruction

PubMed Central

Zhang, Hanming; Wang, Linyuan; Yan, Bin; Li, Lei; Cai, Ailong; Hu, Guoen

2016-01-01

Total generalized variation (TGV)-based computed tomography (CT) image reconstruction, which utilizes high-order image derivatives, is superior to total variation-based methods in terms of the preservation of edge information and the suppression of unfavorable staircase effects. However, conventional TGV regularization employs l1-based form, which is not the most direct method for maximizing sparsity prior. In this study, we propose a total generalized p-variation (TGpV) regularization model to improve the sparsity exploitation of TGV and offer efficient solutions to few-view CT image reconstruction problems. To solve the nonconvex optimization problem of the TGpV minimization model, we then present an efficient iterative algorithm based on the alternating minimization of augmented Lagrangian function. All of the resulting subproblems decoupled by variable splitting admit explicit solutions by applying alternating minimization method and generalized p-shrinkage mapping. In addition, approximate solutions that can be easily performed and quickly calculated through fast Fourier transform are derived using the proximal point method to reduce the cost of inner subproblems. The accuracy and efficiency of the simulated and real data are qualitatively and quantitatively evaluated to validate the efficiency and feasibility of the proposed method. Overall, the proposed method exhibits reasonable performance and outperforms the original TGV-based method when applied to few-view problems. PMID:26901410

Resource allocation in shared spectrum access communications for operators with diverse service requirements

NASA Astrophysics Data System (ADS)

Kibria, Mirza Golam; Villardi, Gabriel Porto; Ishizu, Kentaro; Kojima, Fumihide; Yano, Hiroyuki

2016-12-01

In this paper, we study inter-operator spectrum sharing and intra-operator resource allocation in shared spectrum access communication systems and propose efficient dynamic solutions to address both inter-operator and intra-operator resource allocation optimization problems. For inter-operator spectrum sharing, we present two competent approaches, namely the subcarrier gain-based sharing and fragmentation-based sharing, which carry out fair and flexible allocation of the available shareable spectrum among the operators subject to certain well-defined sharing rules, traffic demands, and channel propagation characteristics. The subcarrier gain-based spectrum sharing scheme has been found to be more efficient in terms of achieved throughput. However, the fragmentation-based sharing is more attractive in terms of computational complexity. For intra-operator resource allocation, we consider resource allocation problem with users' dissimilar service requirements, where the operator supports users with delay constraint and non-delay constraint service requirements, simultaneously. This optimization problem is a mixed-integer non-linear programming problem and non-convex, which is computationally very expensive, and the complexity grows exponentially with the number of integer variables. We propose less-complex and efficient suboptimal solution based on formulating exact linearization, linear approximation, and convexification techniques for the non-linear and/or non-convex objective functions and constraints. Extensive simulation performance analysis has been carried out that validates the efficiency of the proposed solution.

A GPU-accelerated implicit meshless method for compressible flows

NASA Astrophysics Data System (ADS)

Zhang, Jia-Le; Ma, Zhi-Hua; Chen, Hong-Quan; Cao, Cheng

2018-05-01

This paper develops a recently proposed GPU based two-dimensional explicit meshless method (Ma et al., 2014) by devising and implementing an efficient parallel LU-SGS implicit algorithm to further improve the computational efficiency. The capability of the original 2D meshless code is extended to deal with 3D complex compressible flow problems. To resolve the inherent data dependency of the standard LU-SGS method, which causes thread-racing conditions destabilizing numerical computation, a generic rainbow coloring method is presented and applied to organize the computational points into different groups by painting neighboring points with different colors. The original LU-SGS method is modified and parallelized accordingly to perform calculations in a color-by-color manner. The CUDA Fortran programming model is employed to develop the key kernel functions to apply boundary conditions, calculate time steps, evaluate residuals as well as advance and update the solution in the temporal space. A series of two- and three-dimensional test cases including compressible flows over single- and multi-element airfoils and a M6 wing are carried out to verify the developed code. The obtained solutions agree well with experimental data and other computational results reported in the literature. Detailed analysis on the performance of the developed code reveals that the developed CPU based implicit meshless method is at least four to eight times faster than its explicit counterpart. The computational efficiency of the implicit method could be further improved by ten to fifteen times on the GPU.

Status and future prospects of using numerical methods to study complex flows at High Reynolds numbers

NASA Technical Reports Server (NTRS)

Maccormack, R. W.

1978-01-01

The calculation of flow fields past aircraft configuration at flight Reynolds numbers is considered. Progress in devising accurate and efficient numerical methods, in understanding and modeling the physics of turbulence, and in developing reliable and powerful computer hardware is discussed. Emphasis is placed on efficient solutions to the Navier-Stokes equations.

Securing SIFT: Privacy-preserving Outsourcing Computation of Feature Extractions Over Encrypted Image Data.

PubMed

Hu, Shengshan; Wang, Qian; Wang, Jingjun; Qin, Zhan; Ren, Kui

2016-05-13

Advances in cloud computing have greatly motivated data owners to outsource their huge amount of personal multimedia data and/or computationally expensive tasks onto the cloud by leveraging its abundant resources for cost saving and flexibility. Despite the tremendous benefits, the outsourced multimedia data and its originated applications may reveal the data owner's private information, such as the personal identity, locations or even financial profiles. This observation has recently aroused new research interest on privacy-preserving computations over outsourced multimedia data. In this paper, we propose an effective and practical privacy-preserving computation outsourcing protocol for the prevailing scale-invariant feature transform (SIFT) over massive encrypted image data. We first show that previous solutions to this problem have either efficiency/security or practicality issues, and none can well preserve the important characteristics of the original SIFT in terms of distinctiveness and robustness. We then present a new scheme design that achieves efficiency and security requirements simultaneously with the preservation of its key characteristics, by randomly splitting the original image data, designing two novel efficient protocols for secure multiplication and comparison, and carefully distributing the feature extraction computations onto two independent cloud servers. We both carefully analyze and extensively evaluate the security and effectiveness of our design. The results show that our solution is practically secure, outperforms the state-of-theart, and performs comparably to the original SIFT in terms of various characteristics, including rotation invariance, image scale invariance, robust matching across affine distortion, addition of noise and change in 3D viewpoint and illumination.

SecSIFT: Privacy-preserving Outsourcing Computation of Feature Extractions Over Encrypted Image Data.

PubMed

Hu, Shengshan; Wang, Qian; Wang, Jingjun; Qin, Zhan; Ren, Kui

2016-05-13

Advances in cloud computing have greatly motivated data owners to outsource their huge amount of personal multimedia data and/or computationally expensive tasks onto the cloud by leveraging its abundant resources for cost saving and flexibility. Despite the tremendous benefits, the outsourced multimedia data and its originated applications may reveal the data owner's private information, such as the personal identity, locations or even financial profiles. This observation has recently aroused new research interest on privacy-preserving computations over outsourced multimedia data. In this paper, we propose an effective and practical privacy-preserving computation outsourcing protocol for the prevailing scale-invariant feature transform (SIFT) over massive encrypted image data. We first show that previous solutions to this problem have either efficiency/security or practicality issues, and none can well preserve the important characteristics of the original SIFT in terms of distinctiveness and robustness. We then present a new scheme design that achieves efficiency and security requirements simultaneously with the preservation of its key characteristics, by randomly splitting the original image data, designing two novel efficient protocols for secure multiplication and comparison, and carefully distributing the feature extraction computations onto two independent cloud servers. We both carefully analyze and extensively evaluate the security and effectiveness of our design. The results show that our solution is practically secure, outperforms the state-of-theart, and performs comparably to the original SIFT in terms of various characteristics, including rotation invariance, image scale invariance, robust matching across affine distortion, addition of noise and change in 3D viewpoint and illumination.

An efficient implementation of a high-order filter for a cubed-sphere spectral element model

NASA Astrophysics Data System (ADS)

Kang, Hyun-Gyu; Cheong, Hyeong-Bin

2017-03-01

A parallel-scalable, isotropic, scale-selective spatial filter was developed for the cubed-sphere spectral element model on the sphere. The filter equation is a high-order elliptic (Helmholtz) equation based on the spherical Laplacian operator, which is transformed into cubed-sphere local coordinates. The Laplacian operator is discretized on the computational domain, i.e., on each cell, by the spectral element method with Gauss-Lobatto Lagrange interpolating polynomials (GLLIPs) as the orthogonal basis functions. On the global domain, the discrete filter equation yielded a linear system represented by a highly sparse matrix. The density of this matrix increases quadratically (linearly) with the order of GLLIP (order of the filter), and the linear system is solved in only O (Ng) operations, where Ng is the total number of grid points. The solution, obtained by a row reduction method, demonstrated the typical accuracy and convergence rate of the cubed-sphere spectral element method. To achieve computational efficiency on parallel computers, the linear system was treated by an inverse matrix method (a sparse matrix-vector multiplication). The density of the inverse matrix was lowered to only a few times of the original sparse matrix without degrading the accuracy of the solution. For better computational efficiency, a local-domain high-order filter was introduced: The filter equation is applied to multiple cells, and then the central cell was only used to reconstruct the filtered field. The parallel efficiency of applying the inverse matrix method to the global- and local-domain filter was evaluated by the scalability on a distributed-memory parallel computer. The scale-selective performance of the filter was demonstrated on Earth topography. The usefulness of the filter as a hyper-viscosity for the vorticity equation was also demonstrated.

Plant Aquaporins: Genome-Wide Identification, Transcriptomics, Proteomics, and Advanced Analytical Tools.

PubMed

Deshmukh, Rupesh K; Sonah, Humira; Bélanger, Richard R

2016-01-01

Aquaporins (AQPs) are channel-forming integral membrane proteins that facilitate the movement of water and many other small molecules. Compared to animals, plants contain a much higher number of AQPs in their genome. Homology-based identification of AQPs in sequenced species is feasible because of the high level of conservation of protein sequences across plant species. Genome-wide characterization of AQPs has highlighted several important aspects such as distribution, genetic organization, evolution and conserved features governing solute specificity. From a functional point of view, the understanding of AQP transport system has expanded rapidly with the help of transcriptomics and proteomics data. The efficient analysis of enormous amounts of data generated through omic scale studies has been facilitated through computational advancements. Prediction of protein tertiary structures, pore architecture, cavities, phosphorylation sites, heterodimerization, and co-expression networks has become more sophisticated and accurate with increasing computational tools and pipelines. However, the effectiveness of computational approaches is based on the understanding of physiological and biochemical properties, transport kinetics, solute specificity, molecular interactions, sequence variations, phylogeny and evolution of aquaporins. For this purpose, tools like Xenopus oocyte assays, yeast expression systems, artificial proteoliposomes, and lipid membranes have been efficiently exploited to study the many facets that influence solute transport by AQPs. In the present review, we discuss genome-wide identification of AQPs in plants in relation with recent advancements in analytical tools, and their availability and technological challenges as they apply to AQPs. An exhaustive review of omics resources available for AQP research is also provided in order to optimize their efficient utilization. Finally, a detailed catalog of computational tools and analytical pipelines is offered as a resource for AQP research.

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs.

PubMed

Blazewicz, Jacek; Frohmberg, Wojciech; Kierzynka, Michal; Pesch, Erwin; Wojciechowski, Pawel

2011-05-20

Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest future. To overcome this challenge several GPU (Graphics Processing Unit) computing approaches have been proposed lately. These solutions show a great potential of a GPU platform but in most cases address the problem of sequence database scanning and computing only the alignment score whereas the alignment itself is omitted. Thus, the need arose to implement the global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment. In this paper we present the solution that performs the alignment of every given sequence pair, which is a required step for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Performed tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions. Moreover, multiple GPUs support with load balancing makes the application very scalable. The article shows that the backtracking procedure of the sequence alignment algorithms may be designed to fit in with the GPU architecture. Therefore, our algorithm, apart from scores, is able to compute pairwise alignments. This opens a wide range of new possibilities, allowing other methods from the area of molecular biology to take advantage of the new computational architecture. Performed tests show that the efficiency of the implementation is excellent. Moreover, the speed of our GPU-based algorithms can be almost linearly increased when using more than one graphics card.

Plant Aquaporins: Genome-Wide Identification, Transcriptomics, Proteomics, and Advanced Analytical Tools

PubMed Central

Deshmukh, Rupesh K.; Sonah, Humira; Bélanger, Richard R.

2016-01-01

Aquaporins (AQPs) are channel-forming integral membrane proteins that facilitate the movement of water and many other small molecules. Compared to animals, plants contain a much higher number of AQPs in their genome. Homology-based identification of AQPs in sequenced species is feasible because of the high level of conservation of protein sequences across plant species. Genome-wide characterization of AQPs has highlighted several important aspects such as distribution, genetic organization, evolution and conserved features governing solute specificity. From a functional point of view, the understanding of AQP transport system has expanded rapidly with the help of transcriptomics and proteomics data. The efficient analysis of enormous amounts of data generated through omic scale studies has been facilitated through computational advancements. Prediction of protein tertiary structures, pore architecture, cavities, phosphorylation sites, heterodimerization, and co-expression networks has become more sophisticated and accurate with increasing computational tools and pipelines. However, the effectiveness of computational approaches is based on the understanding of physiological and biochemical properties, transport kinetics, solute specificity, molecular interactions, sequence variations, phylogeny and evolution of aquaporins. For this purpose, tools like Xenopus oocyte assays, yeast expression systems, artificial proteoliposomes, and lipid membranes have been efficiently exploited to study the many facets that influence solute transport by AQPs. In the present review, we discuss genome-wide identification of AQPs in plants in relation with recent advancements in analytical tools, and their availability and technological challenges as they apply to AQPs. An exhaustive review of omics resources available for AQP research is also provided in order to optimize their efficient utilization. Finally, a detailed catalog of computational tools and analytical pipelines is offered as a resource for AQP research. PMID:28066459

Computationally efficient algorithms for Brownian dynamics simulation of long flexible macromolecules modeled as bead-rod chains

NASA Astrophysics Data System (ADS)

Moghani, Mahdy Malekzadeh; Khomami, Bamin

2017-02-01

The computational efficiency of Brownian dynamics (BD) simulation of the constrained model of a polymeric chain (bead-rod) with n beads and in the presence of hydrodynamic interaction (HI) is reduced to the order of n2 via an efficient algorithm which utilizes the conjugate-gradient (CG) method within a Picard iteration scheme. Moreover, the utility of the Barnes and Hut (BH) multipole method in BD simulation of polymeric solutions in the presence of HI, with regard to computational cost, scaling, and accuracy, is discussed. Overall, it is determined that this approach leads to a scaling of O (n1.2) . Furthermore, a stress algorithm is developed which accurately captures the transient stress growth in the startup of flow for the bead-rod model with HI and excluded volume (EV) interaction. Rheological properties of the chains up to n =350 in the presence of EV and HI are computed via the former algorithm. The result depicts qualitative differences in shear thinning behavior of the polymeric solutions in the intermediate values of the Weissenburg number (10

Development of numerical methods for overset grids with applications for the integrated Space Shuttle vehicle

NASA Technical Reports Server (NTRS)

Chan, William M.

1995-01-01

Algorithms and computer code developments were performed for the overset grid approach to solving computational fluid dynamics problems. The techniques developed are applicable to compressible Navier-Stokes flow for any general complex configurations. The computer codes developed were tested on different complex configurations with the Space Shuttle launch vehicle configuration as the primary test bed. General, efficient and user-friendly codes were produced for grid generation, flow solution and force and moment computation.

Radiation Tolerant, FPGA-Based SmallSat Computer System

NASA Technical Reports Server (NTRS)

LaMeres, Brock J.; Crum, Gary A.; Martinez, Andres; Petro, Andrew

2015-01-01

The Radiation Tolerant, FPGA-based SmallSat Computer System (RadSat) computing platform exploits a commercial off-the-shelf (COTS) Field Programmable Gate Array (FPGA) with real-time partial reconfiguration to provide increased performance, power efficiency and radiation tolerance at a fraction of the cost of existing radiation hardened computing solutions. This technology is ideal for small spacecraft that require state-of-the-art on-board processing in harsh radiation environments but where using radiation hardened processors is cost prohibitive.

The reduced basis method for the electric field integral equation

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

Fares, M., E-mail: fares@cerfacs.f; Hesthaven, J.S., E-mail: Jan_Hesthaven@Brown.ed; Maday, Y., E-mail: maday@ann.jussieu.f

We introduce the reduced basis method (RBM) as an efficient tool for parametrized scattering problems in computational electromagnetics for problems where field solutions are computed using a standard Boundary Element Method (BEM) for the parametrized electric field integral equation (EFIE). This combination enables an algorithmic cooperation which results in a two step procedure. The first step consists of a computationally intense assembling of the reduced basis, that needs to be effected only once. In the second step, we compute output functionals of the solution, such as the Radar Cross Section (RCS), independently of the dimension of the discretization space, formore » many different parameter values in a many-query context at very little cost. Parameters include the wavenumber, the angle of the incident plane wave and its polarization.« less

Euler Technology Assessment for Preliminary Aircraft Design-Unstructured/Structured Grid NASTD Application for Aerodynamic Analysis of an Advanced Fighter/Tailless Configuration

NASA Technical Reports Server (NTRS)

Michal, Todd R.

1998-01-01

This study supports the NASA Langley sponsored project aimed at determining the viability of using Euler technology for preliminary design use. The primary objective of this study was to assess the accuracy and efficiency of the Boeing, St. Louis unstructured grid flow field analysis system, consisting of the MACGS grid generation and NASTD flow solver codes. Euler solutions about the Aero Configuration/Weapons Fighter Technology (ACWFT) 1204 aircraft configuration were generated. Several variations of the geometry were investigated including a standard wing, cambered wing, deflected elevon, and deflected body flap. A wide range of flow conditions, most of which were in the non-linear regimes of the flight envelope, including variations in speed (subsonic, transonic, supersonic), angles of attack, and sideslip were investigated. Several flowfield non-linearities were present in these solutions including shock waves, vortical flows and the resulting interactions. The accuracy of this method was evaluated by comparing solutions with test data and Navier-Stokes solutions. The ability to accurately predict lateral-directional characteristics and control effectiveness was investigated by computing solutions with sideslip, and with deflected control surfaces. Problem set up times and computational resource requirements were documented and used to evaluate the efficiency of this approach for use in the fast paced preliminary design environment.

Towards New Metrics for High-Performance Computing Resilience

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

Hukerikar, Saurabh; Ashraf, Rizwan A; Engelmann, Christian

Ensuring the reliability of applications is becoming an increasingly important challenge as high-performance computing (HPC) systems experience an ever-growing number of faults, errors and failures. While the HPC community has made substantial progress in developing various resilience solutions, it continues to rely on platform-based metrics to quantify application resiliency improvements. The resilience of an HPC application is concerned with the reliability of the application outcome as well as the fault handling efficiency. To understand the scope of impact, effective coverage and performance efficiency of existing and emerging resilience solutions, there is a need for new metrics. In this paper, wemore » develop new ways to quantify resilience that consider both the reliability and the performance characteristics of the solutions from the perspective of HPC applications. As HPC systems continue to evolve in terms of scale and complexity, it is expected that applications will experience various types of faults, errors and failures, which will require applications to apply multiple resilience solutions across the system stack. The proposed metrics are intended to be useful for understanding the combined impact of these solutions on an application's ability to produce correct results and to evaluate their overall impact on an application's performance in the presence of various modes of faults.« less

HPC on Competitive Cloud Resources

NASA Astrophysics Data System (ADS)

Bientinesi, Paolo; Iakymchuk, Roman; Napper, Jeff

Computing as a utility has reached the mainstream. Scientists can now easily rent time on large commercial clusters that can be expanded and reduced on-demand in real-time. However, current commercial cloud computing performance falls short of systems specifically designed for scientific applications. Scientific computing needs are quite different from those of the web applications that have been the focus of cloud computing vendors. In this chapter we demonstrate through empirical evaluation the computational efficiency of high-performance numerical applications in a commercial cloud environment when resources are shared under high contention. Using the Linpack benchmark as a case study, we show that cache utilization becomes highly unpredictable and similarly affects computation time. For some problems, not only is it more efficient to underutilize resources, but the solution can be reached sooner in realtime (wall-time). We also show that the smallest, cheapest (64-bit) instance on the studied environment is the best for price to performance ration. In light of the high-contention we witness, we believe that alternative definitions of efficiency for commercial cloud environments should be introduced where strong performance guarantees do not exist. Concepts like average, expected performance and execution time, expected cost to completion, and variance measures--traditionally ignored in the high-performance computing context--now should complement or even substitute the standard definitions of efficiency.

Combinatorial solutions to integrable hierarchies

NASA Astrophysics Data System (ADS)

Kazarian, M. E.; Lando, S. K.

2015-06-01

This paper reviews modern approaches to the construction of formal solutions to integrable hierarchies of mathematical physics whose coefficients are answers to various enumerative problems. The relationship between these approaches and the combinatorics of symmetric groups and their representations is explained. Applications of the results to the construction of efficient computations in problems related to models of quantum field theories are described. Bibliography: 34 titles.

Solute segregation kinetics and dislocation depinning in a binary alloy

NASA Astrophysics Data System (ADS)

Dontsova, E.; Rottler, J.; Sinclair, C. W.

2015-06-01

Static strain aging, a phenomenon caused by diffusion of solute atoms to dislocations, is an important contributor to the strength of substitutional alloys. Accurate modeling of this complex process requires both atomic spatial resolution and diffusional time scales, which is very challenging to achieve with commonly used atomistic computational methods. In this paper, we use the recently developed "diffusive molecular dynamics" (DMD) method that is capable of describing the kinetics of the solute segregation process at the atomic level while operating on diffusive time scales in a computationally efficient way. We study static strain aging in the Al-Mg system and calculate the depinning shear stress between edge and screw dislocations and their solute atmospheres formed for various waiting times with different solute content and for a range of temperatures. A simple phenomenological model is also proposed that describes the observed behavior of the critical shear stress as a function of segregation level.

A method to approximate a closest loadability limit using multiple load flow solutions

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

Yorino, Naoto; Harada, Shigemi; Cheng, Haozhong

A new method is proposed to approximate a closest loadability limit (CLL), or closest saddle node bifurcation point, using a pair of multiple load flow solutions. More strictly, the obtainable points by the method are the stationary points including not only CLL but also farthest and saddle points. An operating solution and a low voltage load flow solution are used to efficiently estimate the node injections at a CLL as well as the left and right eigenvectors corresponding to the zero eigenvalue of the load flow Jacobian. They can be used in monitoring loadability margin, in identification of weak spotsmore » in a power system and in the examination of an optimal control against voltage collapse. Most of the computation time of the proposed method is taken in calculating the load flow solution pair. The remaining computation time is less than that of an ordinary load flow.« less

A forward-advancing wave expansion method for numerical solution of large-scale sound propagation problems

NASA Astrophysics Data System (ADS)

Rolla, L. Barrera; Rice, H. J.

2006-09-01

In this paper a "forward-advancing" field discretization method suitable for solving the Helmholtz equation in large-scale problems is proposed. The forward wave expansion method (FWEM) is derived from a highly efficient discretization procedure based on interpolation of wave functions known as the wave expansion method (WEM). The FWEM computes the propagated sound field by means of an exclusively forward advancing solution, neglecting the backscattered field. It is thus analogous to methods such as the (one way) parabolic equation method (PEM) (usually discretized using standard finite difference or finite element methods). These techniques do not require the inversion of large system matrices and thus enable the solution of large-scale acoustic problems where backscatter is not of interest. Calculations using FWEM are presented for two propagation problems and comparisons to data computed with analytical and theoretical solutions and show this forward approximation to be highly accurate. Examples of sound propagation over a screen in upwind and downwind refracting atmospheric conditions at low nodal spacings (0.2 per wavelength in the propagation direction) are also included to demonstrate the flexibility and efficiency of the method.

Ray convergence in a flux-like propagation formulation.

PubMed

Harrison, Chris H

2013-06-01

The energy flux formulation of waveguide propagation is closely related to the incoherent mode sum, and its simplicity has led to development of efficient computational algorithms for reverberation and target echo strength, but it lacks the effects of convergence or modal interference. By starting with the coherent mode sum and rejecting the most rapid interference but retaining beats on a scale of a ray cycle distance it is shown that convergence can be included in a hybrid formulation requiring minimal extra computation. Three solutions are offered by evaluating the modal intensity cross terms using Taylor expansions. In the most efficient approach the double summation of the cross terms is reduced to a single numerical sum by solving the other summation analytically. The other two solutions are a local range average and a local depth average. Favorable comparisons are made between these three solutions and the wave model Orca with, and without, spatial averaging in an upward refracting duct. As a by-product, it is shown that the running range average is very close to the mode solution excluding its fringes, given a relation between averaging window size and effective number of modes which, in turn, is related to the waveguide invariant.

Computational methods for aerodynamic design using numerical optimization

NASA Technical Reports Server (NTRS)

Peeters, M. F.

1983-01-01

Five methods to increase the computational efficiency of aerodynamic design using numerical optimization, by reducing the computer time required to perform gradient calculations, are examined. The most promising method consists of drastically reducing the size of the computational domain on which aerodynamic calculations are made during gradient calculations. Since a gradient calculation requires the solution of the flow about an airfoil whose geometry was slightly perturbed from a base airfoil, the flow about the base airfoil is used to determine boundary conditions on the reduced computational domain. This method worked well in subcritical flow.

Quantified Event Automata: Towards Expressive and Efficient Runtime Monitors

NASA Technical Reports Server (NTRS)

Barringer, Howard; Falcone, Ylies; Havelund, Klaus; Reger, Giles; Rydeheard, David

2012-01-01

Runtime verification is the process of checking a property on a trace of events produced by the execution of a computational system. Runtime verification techniques have recently focused on parametric specifications where events take data values as parameters. These techniques exist on a spectrum inhabited by both efficient and expressive techniques. These characteristics are usually shown to be conflicting - in state-of-the-art solutions, efficiency is obtained at the cost of loss of expressiveness and vice-versa. To seek a solution to this conflict we explore a new point on the spectrum by defining an alternative runtime verification approach.We introduce a new formalism for concisely capturing expressive specifications with parameters. Our technique is more expressive than the currently most efficient techniques while at the same time allowing for optimizations.

Towards efficient backward-in-time adjoint computations using data compression techniques

DOE PAGES

Cyr, E. C.; Shadid, J. N.; Wildey, T.

2014-12-16

In the context of a posteriori error estimation for nonlinear time-dependent partial differential equations, the state-of-the-practice is to use adjoint approaches which require the solution of a backward-in-time problem defined by a linearization of the forward problem. One of the major obstacles in the practical application of these approaches, we found, is the need to store, or recompute, the forward solution to define the adjoint problem and to evaluate the error representation. Our study considers the use of data compression techniques to approximate forward solutions employed in the backward-in-time integration. The development derives an error representation that accounts for themore » difference between the standard-approach and the compressed approximation of the forward solution. This representation is algorithmically similar to the standard representation and only requires the computation of the quantity of interest for the forward solution and the data-compressed reconstructed solution (i.e. scalar quantities that can be evaluated as the forward problem is integrated). This approach is then compared with existing techniques, such as checkpointing and time-averaged adjoints. Lastly, we provide numerical results indicating the potential efficiency of our approach on a transient diffusion–reaction equation and on the Navier–Stokes equations. These results demonstrate memory compression ratios up to 450×450× while maintaining reasonable accuracy in the error-estimates.« less

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

Bolding, Simon R.; Cleveland, Mathew Allen; Morel, Jim E.

In this paper, we have implemented a new high-order low-order (HOLO) algorithm for solving thermal radiative transfer problems. The low-order (LO) system is based on the spatial and angular moments of the transport equation and a linear-discontinuous finite-element spatial representation, producing equations similar to the standard S 2 equations. The LO solver is fully implicit in time and efficiently resolves the nonlinear temperature dependence at each time step. The high-order (HO) solver utilizes exponentially convergent Monte Carlo (ECMC) to give a globally accurate solution for the angular intensity to a fixed-source pure-absorber transport problem. This global solution is used tomore » compute consistency terms, which require the HO and LO solutions to converge toward the same solution. The use of ECMC allows for the efficient reduction of statistical noise in the Monte Carlo solution, reducing inaccuracies introduced through the LO consistency terms. Finally, we compare results with an implicit Monte Carlo code for one-dimensional gray test problems and demonstrate the efficiency of ECMC over standard Monte Carlo in this HOLO algorithm.« less

A High-Order Low-Order Algorithm with Exponentially Convergent Monte Carlo for Thermal Radiative Transfer

DOE PAGES

Bolding, Simon R.; Cleveland, Mathew Allen; Morel, Jim E.

2016-10-21

In this paper, we have implemented a new high-order low-order (HOLO) algorithm for solving thermal radiative transfer problems. The low-order (LO) system is based on the spatial and angular moments of the transport equation and a linear-discontinuous finite-element spatial representation, producing equations similar to the standard S 2 equations. The LO solver is fully implicit in time and efficiently resolves the nonlinear temperature dependence at each time step. The high-order (HO) solver utilizes exponentially convergent Monte Carlo (ECMC) to give a globally accurate solution for the angular intensity to a fixed-source pure-absorber transport problem. This global solution is used tomore » compute consistency terms, which require the HO and LO solutions to converge toward the same solution. The use of ECMC allows for the efficient reduction of statistical noise in the Monte Carlo solution, reducing inaccuracies introduced through the LO consistency terms. Finally, we compare results with an implicit Monte Carlo code for one-dimensional gray test problems and demonstrate the efficiency of ECMC over standard Monte Carlo in this HOLO algorithm.« less

WEBSLIDE: A "Virtual" Slide Projector Based on World Wide Web.

ERIC Educational Resources Information Center

Barra, Maria; Ferrandino, Salvatore; Scarano, Vittorio

1999-01-01

Presents the key design concepts of a software project whose objective is to provide a simple, cheap, and efficient solution for showing slides during lessons in computer labs. Contains 26 references. (DDR)

Low-Energy Truly Random Number Generation with Superparamagnetic Tunnel Junctions for Unconventional Computing

NASA Astrophysics Data System (ADS)

Vodenicarevic, D.; Locatelli, N.; Mizrahi, A.; Friedman, J. S.; Vincent, A. F.; Romera, M.; Fukushima, A.; Yakushiji, K.; Kubota, H.; Yuasa, S.; Tiwari, S.; Grollier, J.; Querlioz, D.

2017-11-01

Low-energy random number generation is critical for many emerging computing schemes proposed to complement or replace von Neumann architectures. However, current random number generators are always associated with an energy cost that is prohibitive for these computing schemes. We introduce random number bit generation based on specific nanodevices: superparamagnetic tunnel junctions. We experimentally demonstrate high-quality random bit generation that represents an orders-of-magnitude improvement in energy efficiency over current solutions. We show that the random generation speed improves with nanodevice scaling, and we investigate the impact of temperature, magnetic field, and cross talk. Finally, we show how alternative computing schemes can be implemented using superparamagentic tunnel junctions as random number generators. These results open the way for fabricating efficient hardware computing devices leveraging stochasticity, and they highlight an alternative use for emerging nanodevices.

Parallel discontinuous Galerkin FEM for computing hyperbolic conservation law on unstructured grids

NASA Astrophysics Data System (ADS)

Ma, Xinrong; Duan, Zhijian

2018-04-01

High-order resolution Discontinuous Galerkin finite element methods (DGFEM) has been known as a good method for solving Euler equations and Navier-Stokes equations on unstructured grid, but it costs too much computational resources. An efficient parallel algorithm was presented for solving the compressible Euler equations. Moreover, the multigrid strategy based on three-stage three-order TVD Runge-Kutta scheme was used in order to improve the computational efficiency of DGFEM and accelerate the convergence of the solution of unsteady compressible Euler equations. In order to make each processor maintain load balancing, the domain decomposition method was employed. Numerical experiment performed for the inviscid transonic flow fluid problems around NACA0012 airfoil and M6 wing. The results indicated that our parallel algorithm can improve acceleration and efficiency significantly, which is suitable for calculating the complex flow fluid.

Recursive Newton-Euler formulation of manipulator dynamics

NASA Technical Reports Server (NTRS)

Nasser, M. G.

1989-01-01

A recursive Newton-Euler procedure is presented for the formulation and solution of manipulator dynamical equations. The procedure includes rotational and translational joints and a topological tree. This model was verified analytically using a planar two-link manipulator. Also, the model was tested numerically against the Walker-Orin model using the Shuttle Remote Manipulator System data. The hinge accelerations obtained from both models were identical. The computational requirements of the model vary linearly with the number of joints. The computational efficiency of this method exceeds that of Walker-Orin methods. This procedure may be viewed as a considerable generalization of Armstrong's method. A six-by-six formulation is adopted which enhances both the computational efficiency and simplicity of the model.

AN EFFICIENT HIGHER-ORDER FAST MULTIPOLE BOUNDARY ELEMENT SOLUTION FOR POISSON-BOLTZMANN BASED MOLECULAR ELECTROSTATICS

PubMed Central

Bajaj, Chandrajit; Chen, Shun-Chuan; Rand, Alexander

2011-01-01

In order to compute polarization energy of biomolecules, we describe a boundary element approach to solving the linearized Poisson-Boltzmann equation. Our approach combines several important features including the derivative boundary formulation of the problem and a smooth approximation of the molecular surface based on the algebraic spline molecular surface. State of the art software for numerical linear algebra and the kernel independent fast multipole method is used for both simplicity and efficiency of our implementation. We perform a variety of computational experiments, testing our method on a number of actual proteins involved in molecular docking and demonstrating the effectiveness of our solver for computing molecular polarization energy. PMID:21660123

Modeling weakly-ionized plasmas in magnetic field: A new computationally-efficient approach

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

Parent, Bernard, E-mail: parent@pusan.ac.kr; Macheret, Sergey O.; Shneider, Mikhail N.

2015-11-01

Despite its success at simulating accurately both non-neutral and quasi-neutral weakly-ionized plasmas, the drift-diffusion model has been observed to be a particularly stiff set of equations. Recently, it was demonstrated that the stiffness of the system could be relieved by rewriting the equations such that the potential is obtained from Ohm's law rather than Gauss's law while adding some source terms to the ion transport equation to ensure that Gauss's law is satisfied in non-neutral regions. Although the latter was applicable to multicomponent and multidimensional plasmas, it could not be used for plasmas in which the magnetic field was significant.more » This paper hence proposes a new computationally-efficient set of electron and ion transport equations that can be used not only for a plasma with multiple types of positive and negative ions, but also for a plasma in magnetic field. Because the proposed set of equations is obtained from the same physical model as the conventional drift-diffusion equations without introducing new assumptions or simplifications, it results in the same exact solution when the grid is refined sufficiently while being more computationally efficient: not only is the proposed approach considerably less stiff and hence requires fewer iterations to reach convergence but it yields a converged solution that exhibits a significantly higher resolution. The combined faster convergence and higher resolution is shown to result in a hundredfold increase in computational efficiency for some typical steady and unsteady plasma problems including non-neutral cathode and anode sheaths as well as quasi-neutral regions.« less

Time-Accurate Solutions of Incompressible Navier-Stokes Equations for Potential Turbopump Applications

NASA Technical Reports Server (NTRS)

Kiris, Cetin; Kwak, Dochan

2001-01-01

Two numerical procedures, one based on artificial compressibility method and the other pressure projection method, are outlined for obtaining time-accurate solutions of the incompressible Navier-Stokes equations. The performance of the two method are compared by obtaining unsteady solutions for the evolution of twin vortices behind a at plate. Calculated results are compared with experimental and other numerical results. For an un- steady ow which requires small physical time step, pressure projection method was found to be computationally efficient since it does not require any subiterations procedure. It was observed that the artificial compressibility method requires a fast convergence scheme at each physical time step in order to satisfy incompressibility condition. This was obtained by using a GMRES-ILU(0) solver in our computations. When a line-relaxation scheme was used, the time accuracy was degraded and time-accurate computations became very expensive.

Optimizing Integrated Terminal Airspace Operations Under Uncertainty

NASA Technical Reports Server (NTRS)

Bosson, Christabelle; Xue, Min; Zelinski, Shannon

2014-01-01

In the terminal airspace, integrated departures and arrivals have the potential to increase operations efficiency. Recent research has developed geneticalgorithm- based schedulers for integrated arrival and departure operations under uncertainty. This paper presents an alternate method using a machine jobshop scheduling formulation to model the integrated airspace operations. A multistage stochastic programming approach is chosen to formulate the problem and candidate solutions are obtained by solving sample average approximation problems with finite sample size. Because approximate solutions are computed, the proposed algorithm incorporates the computation of statistical bounds to estimate the optimality of the candidate solutions. A proof-ofconcept study is conducted on a baseline implementation of a simple problem considering a fleet mix of 14 aircraft evolving in a model of the Los Angeles terminal airspace. A more thorough statistical analysis is also performed to evaluate the impact of the number of scenarios considered in the sampled problem. To handle extensive sampling computations, a multithreading technique is introduced.

Efficient ICCG on a shared memory multiprocessor

NASA Technical Reports Server (NTRS)

Hammond, Steven W.; Schreiber, Robert

1989-01-01

Different approaches are discussed for exploiting parallelism in the ICCG (Incomplete Cholesky Conjugate Gradient) method for solving large sparse symmetric positive definite systems of equations on a shared memory parallel computer. Techniques for efficiently solving triangular systems and computing sparse matrix-vector products are explored. Three methods for scheduling the tasks in solving triangular systems are implemented on the Sequent Balance 21000. Sample problems that are representative of a large class of problems solved using iterative methods are used. We show that a static analysis to determine data dependences in the triangular solve can greatly improve its parallel efficiency. We also show that ignoring symmetry and storing the whole matrix can reduce solution time substantially.

ACCURATE CHEMICAL MASTER EQUATION SOLUTION USING MULTI-FINITE BUFFERS

PubMed Central

Cao, Youfang; Terebus, Anna; Liang, Jie

2016-01-01

The discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multi-scale nature of many networks where reaction rates have large disparity, directly solving dCMEs is intractable due to the exploding size of the state space. It is important to truncate the state space effectively with quantified errors, so accurate solutions can be computed. It is also important to know if all major probabilistic peaks have been computed. Here we introduce the Accurate CME (ACME) algorithm for obtaining direct solutions to dCMEs. With multi-finite buffers for reducing the state space by O(n!), exact steady-state and time-evolving network probability landscapes can be computed. We further describe a theoretical framework of aggregating microstates into a smaller number of macrostates by decomposing a network into independent aggregated birth and death processes, and give an a priori method for rapidly determining steady-state truncation errors. The maximal sizes of the finite buffers for a given error tolerance can also be pre-computed without costly trial solutions of dCMEs. We show exactly computed probability landscapes of three multi-scale networks, namely, a 6-node toggle switch, 11-node phage-lambda epigenetic circuit, and 16-node MAPK cascade network, the latter two with no known solutions. We also show how probabilities of rare events can be computed from first-passage times, another class of unsolved problems challenging for simulation-based techniques due to large separations in time scales. Overall, the ACME method enables accurate and efficient solutions of the dCME for a large class of networks. PMID:27761104

Finding all solutions of nonlinear equations using the dual simplex method

NASA Astrophysics Data System (ADS)

Yamamura, Kiyotaka; Fujioka, Tsuyoshi

2003-03-01

Recently, an efficient algorithm has been proposed for finding all solutions of systems of nonlinear equations using linear programming. This algorithm is based on a simple test (termed the LP test) for nonexistence of a solution to a system of nonlinear equations using the dual simplex method. In this letter, an improved version of the LP test algorithm is proposed. By numerical examples, it is shown that the proposed algorithm could find all solutions of a system of 300 nonlinear equations in practical computation time.

Beamforming strategy of ULA and UCA sensor configuration in multistatic passive radar

NASA Astrophysics Data System (ADS)

Hossa, Robert

2009-06-01

A Beamforming Network (BN) concept of Uniform Linear Array (ULA) and Uniform Circular Array (UCA) dipole configuration designed to multistatic passive radar is considered in details. In the case of UCA configuration, computationally efficient procedure of beamspace transformation from UCA to virtual ULA configuration with omnidirectional coverage is utilized. If effect, the idea of the proposed solution is equivalent to the techniques of antenna array factor shaping dedicated to ULA structure. Finally, exemplary results from the computer software simulations of elaborated spatial filtering solutions to reference and surveillance channels are provided and discussed.

Forward Period Analysis Method of the Periodic Hamiltonian System.

PubMed

Wang, Pengfei

2016-01-01

Using the forward period analysis (FPA), we obtain the period of a Morse oscillator and mathematical pendulum system, with the accuracy of 100 significant digits. From these results, the long-term [0, 1060] (time unit) solutions, ranging from the Planck time to the age of the universe, are computed reliably and quickly with a parallel multiple-precision Taylor series (PMT) scheme. The application of FPA to periodic systems can greatly reduce the computation time of long-term reliable simulations. This scheme provides an efficient way to generate reference solutions, against which long-term simulations using other schemes can be tested.

Manipulation of oligonucleotides immobilized on solid supports - DNA computations on surfaces

NASA Astrophysics Data System (ADS)

Liu, Qinghua

The manipulation of DNA oligonucleotides immobilized on various solid supports has been studied intensively, especially in the area of surface hybridization. Recently, surface-based biotechnology has been applied to the area of molecular computing. These surface-based methods have advantages with regard to ease of handling, facile purification, and less interference when compared to solution methodologies. This dissertation describes the investigation of molecular approaches to DNA computing. The feasibility of encoding a bit (0 or 1) of information for DNA-based computations at the single nucleotide level was studied, particularly with regard to the efficiency and specificity of hybridization discrimination. Both gold and glass surfaces, with addressed arrays of 32 oligonucleotides, were employed with similar hybridization results. Although single-base discrimination may be achieved in the system, it is at the cost of a severe decrease in the efficiency of hybridization to perfectly matched sequences. This compromises the utility of single nucleotide encoding for DNA computing applications in the absence of some additional mechanism for increasing specificity. Several methods are suggested including a multiple-base encoding strategy. The multiple-base encoding strategy was employed to develop a prototype DNA computer. The approach was demonstrated by solving a small example of the Satisfiability (SAT) problem, an NP-complete problem in Boolean logic. 16 distinct DNA oligonucleotides, encoding all candidate solutions to the 4-variable-4-clause-3-SAT problem, were immobilized on a gold surface in the non-addressed format. Four cycles of MARK (hybridization), DESTROY (enzymatic destruction) and UNMARK (denaturation) were performed, which identified and eliminated members of the set which were not solutions to the problem. Determination of the answer was accomplished in the READOUT (sequence identification) operation by PCR amplification of the remaining molecules and hybridization to an addressed array. Four answers were determined and the S/N ratio between correct and incorrect solutions ranged from 10 to 777, making discrimination between correct and incorrect solutions to the problem straightforward. Additionally, studies of enzymatic manipulations of DNA molecules on surfaces suggested the use of E. coli Exonuclease I (Exo I) and perhaps EarI in the DESTROY operation.

Direct numerical simulation of particulate flows with an overset grid method

NASA Astrophysics Data System (ADS)

Koblitz, A. R.; Lovett, S.; Nikiforakis, N.; Henshaw, W. D.

2017-08-01

We evaluate an efficient overset grid method for two-dimensional and three-dimensional particulate flows for small numbers of particles at finite Reynolds number. The rigid particles are discretised using moving overset grids overlaid on a Cartesian background grid. This allows for strongly-enforced boundary conditions and local grid refinement at particle surfaces, thereby accurately capturing the viscous boundary layer at modest computational cost. The incompressible Navier-Stokes equations are solved with a fractional-step scheme which is second-order-accurate in space and time, while the fluid-solid coupling is achieved with a partitioned approach including multiple sub-iterations to increase stability for light, rigid bodies. Through a series of benchmark studies we demonstrate the accuracy and efficiency of this approach compared to other boundary conformal and static grid methods in the literature. In particular, we find that fully resolving boundary layers at particle surfaces is crucial to obtain accurate solutions to many common test cases. With our approach we are able to compute accurate solutions using as little as one third the number of grid points as uniform grid computations in the literature. A detailed convergence study shows a 13-fold decrease in CPU time over a uniform grid test case whilst maintaining comparable solution accuracy.

Hierarchical Poly Tree Configurations for the Solution of Dynamically Refined Finte Element Models

NASA Technical Reports Server (NTRS)

Gute, G. D.; Padovan, J.

1993-01-01

This paper demonstrates how a multilevel substructuring technique, called the Hierarchical Poly Tree (HPT), can be used to integrate a localized mesh refinement into the original finite element model more efficiently. The optimal HPT configurations for solving isoparametrically square h-, p-, and hp-extensions on single and multiprocessor computers is derived. In addition, the reduced number of stiffness matrix elements that must be stored when employing this type of solution strategy is quantified. Moreover, the HPT inherently provides localize 'error-trapping' and a logical, efficient means with which to isolate physically anomalous and analytically singular behavior.

Ship Trim Optimization: Assessment of Influence of Trim on Resistance of MOERI Container Ship

PubMed Central

Duan, Wenyang

2014-01-01

Environmental issues and rising fuel prices necessitate better energy efficiency in all sectors. Shipping industry is a stakeholder in environmental issues. Shipping industry is responsible for approximately 3% of global CO2 emissions, 14-15% of global NOX emissions, and 16% of global SOX emissions. Ship trim optimization has gained enormous momentum in recent years being an effective operational measure for better energy efficiency to reduce emissions. Ship trim optimization analysis has traditionally been done through tow-tank testing for a specific hullform. Computational techniques are increasingly popular in ship hydrodynamics applications. The purpose of this study is to present MOERI container ship (KCS) hull trim optimization by employing computational methods. KCS hull total resistances and trim and sinkage computed values, in even keel condition, are compared with experimental values and found in reasonable agreement. The agreement validates that mesh, boundary conditions, and solution techniques are correct. The same mesh, boundary conditions, and solution techniques are used to obtain resistance values in different trim conditions at Fn = 0.2274. Based on attained results, optimum trim is suggested. This research serves as foundation for employing computational techniques for ship trim optimization. PMID:24578649

Solving Constraint Satisfaction Problems with Networks of Spiking Neurons

PubMed Central

Jonke, Zeno; Habenschuss, Stefan; Maass, Wolfgang

2016-01-01

Network of neurons in the brain apply—unlike processors in our current generation of computer hardware—an event-based processing strategy, where short pulses (spikes) are emitted sparsely by neurons to signal the occurrence of an event at a particular point in time. Such spike-based computations promise to be substantially more power-efficient than traditional clocked processing schemes. However, it turns out to be surprisingly difficult to design networks of spiking neurons that can solve difficult computational problems on the level of single spikes, rather than rates of spikes. We present here a new method for designing networks of spiking neurons via an energy function. Furthermore, we show how the energy function of a network of stochastically firing neurons can be shaped in a transparent manner by composing the networks of simple stereotypical network motifs. We show that this design approach enables networks of spiking neurons to produce approximate solutions to difficult (NP-hard) constraint satisfaction problems from the domains of planning/optimization and verification/logical inference. The resulting networks employ noise as a computational resource. Nevertheless, the timing of spikes plays an essential role in their computations. Furthermore, networks of spiking neurons carry out for the Traveling Salesman Problem a more efficient stochastic search for good solutions compared with stochastic artificial neural networks (Boltzmann machines) and Gibbs sampling. PMID:27065785

Resource Constrained Planning of Multiple Projects with Separable Activities

NASA Astrophysics Data System (ADS)

Fujii, Susumu; Morita, Hiroshi; Kanawa, Takuya

In this study we consider a resource constrained planning problem of multiple projects with separable activities. This problem provides a plan to process the activities considering a resource availability with time window. We propose a solution algorithm based on the branch and bound method to obtain the optimal solution minimizing the completion time of all projects. We develop three methods for improvement of computational efficiency, that is, to obtain initial solution with minimum slack time rule, to estimate lower bound considering both time and resource constraints and to introduce an equivalence relation for bounding operation. The effectiveness of the proposed methods is demonstrated by numerical examples. Especially as the number of planning projects increases, the average computational time and the number of searched nodes are reduced.

Computational System For Rapid CFD Analysis In Engineering

NASA Technical Reports Server (NTRS)

Barson, Steven L.; Ascoli, Edward P.; Decroix, Michelle E.; Sindir, Munir M.

1995-01-01

Computational system comprising modular hardware and software sub-systems developed to accelerate and facilitate use of techniques of computational fluid dynamics (CFD) in engineering environment. Addresses integration of all aspects of CFD analysis process, including definition of hardware surfaces, generation of computational grids, CFD flow solution, and postprocessing. Incorporates interfaces for integration of all hardware and software tools needed to perform complete CFD analysis. Includes tools for efficient definition of flow geometry, generation of computational grids, computation of flows on grids, and postprocessing of flow data. System accepts geometric input from any of three basic sources: computer-aided design (CAD), computer-aided engineering (CAE), or definition by user.

Numerical methods for engine-airframe integration

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

Murthy, S.N.B.; Paynter, G.C.

1986-01-01

Various papers on numerical methods for engine-airframe integration are presented. The individual topics considered include: scientific computing environment for the 1980s, overview of prediction of complex turbulent flows, numerical solutions of the compressible Navier-Stokes equations, elements of computational engine/airframe integrations, computational requirements for efficient engine installation, application of CAE and CFD techniques to complete tactical missile design, CFD applications to engine/airframe integration, and application of a second-generation low-order panel methods to powerplant installation studies. Also addressed are: three-dimensional flow analysis of turboprop inlet and nacelle configurations, application of computational methods to the design of large turbofan engine nacelles, comparison ofmore » full potential and Euler solution algorithms for aeropropulsive flow field computations, subsonic/transonic, supersonic nozzle flows and nozzle integration, subsonic/transonic prediction capabilities for nozzle/afterbody configurations, three-dimensional viscous design methodology of supersonic inlet systems for advanced technology aircraft, and a user's technology assessment.« less

Edge-Based Efficient Search over Encrypted Data Mobile Cloud Storage

PubMed Central

Liu, Fang; Cai, Zhiping; Xiao, Nong; Zhao, Ziming

2018-01-01

Smart sensor-equipped mobile devices sense, collect, and process data generated by the edge network to achieve intelligent control, but such mobile devices usually have limited storage and computing resources. Mobile cloud storage provides a promising solution owing to its rich storage resources, great accessibility, and low cost. But it also brings a risk of information leakage. The encryption of sensitive data is the basic step to resist the risk. However, deploying a high complexity encryption and decryption algorithm on mobile devices will greatly increase the burden of terminal operation and the difficulty to implement the necessary privacy protection algorithm. In this paper, we propose ENSURE (EfficieNt and SecURE), an efficient and secure encrypted search architecture over mobile cloud storage. ENSURE is inspired by edge computing. It allows mobile devices to offload the computation intensive task onto the edge server to achieve a high efficiency. Besides, to protect data security, it reduces the information acquisition of untrusted cloud by hiding the relevance between query keyword and search results from the cloud. Experiments on a real data set show that ENSURE reduces the computation time by 15% to 49% and saves the energy consumption by 38% to 69% per query. PMID:29652810

Edge-Based Efficient Search over Encrypted Data Mobile Cloud Storage.

PubMed

Guo, Yeting; Liu, Fang; Cai, Zhiping; Xiao, Nong; Zhao, Ziming

2018-04-13

Smart sensor-equipped mobile devices sense, collect, and process data generated by the edge network to achieve intelligent control, but such mobile devices usually have limited storage and computing resources. Mobile cloud storage provides a promising solution owing to its rich storage resources, great accessibility, and low cost. But it also brings a risk of information leakage. The encryption of sensitive data is the basic step to resist the risk. However, deploying a high complexity encryption and decryption algorithm on mobile devices will greatly increase the burden of terminal operation and the difficulty to implement the necessary privacy protection algorithm. In this paper, we propose ENSURE (EfficieNt and SecURE), an efficient and secure encrypted search architecture over mobile cloud storage. ENSURE is inspired by edge computing. It allows mobile devices to offload the computation intensive task onto the edge server to achieve a high efficiency. Besides, to protect data security, it reduces the information acquisition of untrusted cloud by hiding the relevance between query keyword and search results from the cloud. Experiments on a real data set show that ENSURE reduces the computation time by 15% to 49% and saves the energy consumption by 38% to 69% per query.

Dynamical analysis of the avian-human influenza epidemic model using the semi-analytical method

NASA Astrophysics Data System (ADS)

Jabbari, Azizeh; Kheiri, Hossein; Bekir, Ahmet

2015-03-01

In this work, we present a dynamic behavior of the avian-human influenza epidemic model by using efficient computational algorithm, namely the multistage differential transform method(MsDTM). The MsDTM is used here as an algorithm for approximating the solutions of the avian-human influenza epidemic model in a sequence of time intervals. In order to show the efficiency of the method, the obtained numerical results are compared with the fourth-order Runge-Kutta method (RK4M) and differential transform method(DTM) solutions. It is shown that the MsDTM has the advantage of giving an analytical form of the solution within each time interval which is not possible in purely numerical techniques like RK4M.

Constraint treatment techniques and parallel algorithms for multibody dynamic analysis. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Chiou, Jin-Chern

1990-01-01

Computational procedures for kinematic and dynamic analysis of three-dimensional multibody dynamic (MBD) systems are developed from the differential-algebraic equations (DAE's) viewpoint. Constraint violations during the time integration process are minimized and penalty constraint stabilization techniques and partitioning schemes are developed. The governing equations of motion, a two-stage staggered explicit-implicit numerical algorithm, are treated which takes advantage of a partitioned solution procedure. A robust and parallelizable integration algorithm is developed. This algorithm uses a two-stage staggered central difference algorithm to integrate the translational coordinates and the angular velocities. The angular orientations of bodies in MBD systems are then obtained by using an implicit algorithm via the kinematic relationship between Euler parameters and angular velocities. It is shown that the combination of the present solution procedures yields a computationally more accurate solution. To speed up the computational procedures, parallel implementation of the present constraint treatment techniques, the two-stage staggered explicit-implicit numerical algorithm was efficiently carried out. The DAE's and the constraint treatment techniques were transformed into arrowhead matrices to which Schur complement form was derived. By fully exploiting the sparse matrix structural analysis techniques, a parallel preconditioned conjugate gradient numerical algorithm is used to solve the systems equations written in Schur complement form. A software testbed was designed and implemented in both sequential and parallel computers. This testbed was used to demonstrate the robustness and efficiency of the constraint treatment techniques, the accuracy of the two-stage staggered explicit-implicit numerical algorithm, and the speed up of the Schur-complement-based parallel preconditioned conjugate gradient algorithm on a parallel computer.

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.

Efficient computation paths for the systematic analysis of sensitivities

NASA Astrophysics Data System (ADS)

Greppi, Paolo; Arato, Elisabetta

2013-01-01

A systematic sensitivity analysis requires computing the model on all points of a multi-dimensional grid covering the domain of interest, defined by the ranges of variability of the inputs. The issues to efficiently perform such analyses on algebraic models are handling solution failures within and close to the feasible region and minimizing the total iteration count. Scanning the domain in the obvious order is sub-optimal in terms of total iterations and is likely to cause many solution failures. The problem of choosing a better order can be translated geometrically into finding Hamiltonian paths on certain grid graphs. This work proposes two paths, one based on a mixed-radix Gray code and the other, a quasi-spiral path, produced by a novel heuristic algorithm. Some simple, easy-to-visualize examples are presented, followed by performance results for the quasi-spiral algorithm and the practical application of the different paths in a process simulation tool.

On Using Surrogates with Genetic Programming.

PubMed

Hildebrandt, Torsten; Branke, Jürgen

2015-01-01

One way to accelerate evolutionary algorithms with expensive fitness evaluations is to combine them with surrogate models. Surrogate models are efficiently computable approximations of the fitness function, derived by means of statistical or machine learning techniques from samples of fully evaluated solutions. But these models usually require a numerical representation, and therefore cannot be used with the tree representation of genetic programming (GP). In this paper, we present a new way to use surrogate models with GP. Rather than using the genotype directly as input to the surrogate model, we propose using a phenotypic characterization. This phenotypic characterization can be computed efficiently and allows us to define approximate measures of equivalence and similarity. Using a stochastic, dynamic job shop scenario as an example of simulation-based GP with an expensive fitness evaluation, we show how these ideas can be used to construct surrogate models and improve the convergence speed and solution quality of GP.

Linear homotopy solution of nonlinear systems of equations in geodesy

NASA Astrophysics Data System (ADS)

Paláncz, Béla; Awange, Joseph L.; Zaletnyik, Piroska; Lewis, Robert H.

2010-01-01

A fundamental task in geodesy is solving systems of equations. Many geodetic problems are represented as systems of multivariate polynomials. A common problem in solving such systems is improper initial starting values for iterative methods, leading to convergence to solutions with no physical meaning, or to convergence that requires global methods. Though symbolic methods such as Groebner bases or resultants have been shown to be very efficient, i.e., providing solutions for determined systems such as 3-point problem of 3D affine transformation, the symbolic algebra can be very time consuming, even with special Computer Algebra Systems (CAS). This study proposes the Linear Homotopy method that can be implemented easily in high-level computer languages like C++ and Fortran that are faster than CAS by at least two orders of magnitude. Using Mathematica, the power of Homotopy is demonstrated in solving three nonlinear geodetic problems: resection, GPS positioning, and affine transformation. The method enlarging the domain of convergence is found to be efficient, less sensitive to rounding of numbers, and has lower complexity compared to other local methods like Newton-Raphson.

A solid reactor core thermal model for nuclear thermal rockets

NASA Astrophysics Data System (ADS)

Rider, William J.; Cappiello, Michael W.; Liles, Dennis R.

1991-01-01

A Helium/Hydrogen Cooled Reactor Analysis (HERA) computer code has been developed. HERA has the ability to model arbitrary geometries in three dimensions, which allows the user to easily analyze reactor cores constructed of prismatic graphite elements. The code accounts for heat generation in the fuel, control rods, and other structures; conduction and radiation across gaps; convection to the coolant; and a variety of boundary conditions. The numerical solution scheme has been optimized for vector computers, making long transient analyses economical. Time integration is either explicit or implicit, which allows the use of the model to accurately calculate both short- or long-term transients with an efficient use of computer time. Both the basic spatial and temporal integration schemes have been benchmarked against analytical solutions.

Time-dependent jet flow and noise computations

NASA Technical Reports Server (NTRS)

Berman, C. H.; Ramos, J. I.; Karniadakis, G. E.; Orszag, S. A.

1990-01-01

Methods for computing jet turbulence noise based on the time-dependent solution of Lighthill's (1952) differential equation are demonstrated. A key element in this approach is a flow code for solving the time-dependent Navier-Stokes equations at relatively high Reynolds numbers. Jet flow results at Re = 10,000 are presented here. This code combines a computationally efficient spectral element technique and a new self-consistent turbulence subgrid model to supply values for Lighthill's turbulence noise source tensor.

Newton-like methods for Navier-Stokes solution

NASA Astrophysics Data System (ADS)

Qin, N.; Xu, X.; Richards, B. E.

1992-12-01

The paper reports on Newton-like methods called SFDN-alpha-GMRES and SQN-alpha-GMRES methods that have been devised and proven as powerful schemes for large nonlinear problems typical of viscous compressible Navier-Stokes solutions. They can be applied using a partially converged solution from a conventional explicit or approximate implicit method. Developments have included the efficient parallelization of the schemes on a distributed memory parallel computer. The methods are illustrated using a RISC workstation and a transputer parallel system respectively to solve a hypersonic vortical flow.

Aerodynamic optimization by simultaneously updating flow variables and design parameters with application to advanced propeller designs

NASA Technical Reports Server (NTRS)

Rizk, Magdi H.

1988-01-01

A scheme is developed for solving constrained optimization problems in which the objective function and the constraint function are dependent on the solution of the nonlinear flow equations. The scheme updates the design parameter iterative solutions and the flow variable iterative solutions simultaneously. It is applied to an advanced propeller design problem with the Euler equations used as the flow governing equations. The scheme's accuracy, efficiency and sensitivity to the computational parameters are tested.

An efficient graph theory based method to identify every minimal reaction set in a metabolic network

PubMed Central

2014-01-01

Background Development of cells with minimal metabolic functionality is gaining importance due to their efficiency in producing chemicals and fuels. Existing computational methods to identify minimal reaction sets in metabolic networks are computationally expensive. Further, they identify only one of the several possible minimal reaction sets. Results In this paper, we propose an efficient graph theory based recursive optimization approach to identify all minimal reaction sets. Graph theoretical insights offer systematic methods to not only reduce the number of variables in math programming and increase its computational efficiency, but also provide efficient ways to find multiple optimal solutions. The efficacy of the proposed approach is demonstrated using case studies from Escherichia coli and Saccharomyces cerevisiae. In case study 1, the proposed method identified three minimal reaction sets each containing 38 reactions in Escherichia coli central metabolic network with 77 reactions. Analysis of these three minimal reaction sets revealed that one of them is more suitable for developing minimal metabolism cell compared to other two due to practically achievable internal flux distribution. In case study 2, the proposed method identified 256 minimal reaction sets from the Saccharomyces cerevisiae genome scale metabolic network with 620 reactions. The proposed method required only 4.5 hours to identify all the 256 minimal reaction sets and has shown a significant reduction (approximately 80%) in the solution time when compared to the existing methods for finding minimal reaction set. Conclusions Identification of all minimal reactions sets in metabolic networks is essential since different minimal reaction sets have different properties that effect the bioprocess development. The proposed method correctly identified all minimal reaction sets in a both the case studies. The proposed method is computationally efficient compared to other methods for finding minimal reaction sets and useful to employ with genome-scale metabolic networks. PMID:24594118

Robust optimization with transiently chaotic dynamical systems

NASA Astrophysics Data System (ADS)

Sumi, R.; Molnár, B.; Ercsey-Ravasz, M.

2014-05-01

Efficiently solving hard optimization problems has been a strong motivation for progress in analog computing. In a recent study we presented a continuous-time dynamical system for solving the NP-complete Boolean satisfiability (SAT) problem, with a one-to-one correspondence between its stable attractors and the SAT solutions. While physical implementations could offer great efficiency, the transiently chaotic dynamics raises the question of operability in the presence of noise, unavoidable on analog devices. Here we show that the probability of finding solutions is robust to noise intensities well above those present on real hardware. We also developed a cellular neural network model realizable with analog circuits, which tolerates even larger noise intensities. These methods represent an opportunity for robust and efficient physical implementations.

Improved numerical methods for turbulent viscous flows aerothermal modeling program, phase 2

NASA Technical Reports Server (NTRS)

Karki, K. C.; Patankar, S. V.; Runchal, A. K.; Mongia, H. C.

1988-01-01

The details of a study to develop accurate and efficient numerical schemes to predict complex flows are described. In this program, several discretization schemes were evaluated using simple test cases. This assessment led to the selection of three schemes for an in-depth evaluation based on two-dimensional flows. The scheme with the superior overall performance was incorporated in a computer program for three-dimensional flows. To improve the computational efficiency, the selected discretization scheme was combined with a direct solution approach in which the fluid flow equations are solved simultaneously rather than sequentially.

Exponential Methods for the Time Integration of Schroedinger Equation

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

Cano, B.; Gonzalez-Pachon, A.

2010-09-30

We consider exponential methods of second order in time in order to integrate the cubic nonlinear Schroedinger equation. We are interested in taking profit of the special structure of this equation. Therefore, we look at symmetry, symplecticity and approximation of invariants of the proposed methods. That will allow to integrate till long times with reasonable accuracy. Computational efficiency is also our aim. Therefore, we make numerical computations in order to compare the methods considered and so as to conclude that explicit Lawson schemes projected on the norm of the solution are an efficient tool to integrate this equation.

An efficient solution technique for shockwave-boundary layer interactions with flow separation and slot suction effects

NASA Technical Reports Server (NTRS)

Edwards, Jack R.; Mcrae, D. Scott

1991-01-01

An efficient method for computing two-dimensional compressible Navier-Stokes flow fields is presented. The solution algorithm is a fully-implicit approximate factorization technique based on an unsymmetric line Gauss-Seidel splitting of the equation system Jacobian matrix. Convergence characteristics are improved by the addition of acceleration techniques based on Shamanskii's method for nonlinear equations and Broyden's quasi-Newton update. Characteristic-based differencing of the equations is provided by means of Van Leer's flux vector splitting. In this investigation, emphasis is placed on the fast and accurate computation of shock-wave-boundary layer interactions with and without slot suction effects. In the latter context, a set of numerical boundary conditions for simulating the transpiration flow in an open slot is devised. Both laminar and turbulent cases are considered, with turbulent closure provided by a modified Cebeci-Smith algebraic model. Comparisons with computational and experimental data sets are presented for a variety of interactions, and a fully-coupled simulation of a plenum chamber/inlet flowfield with shock interaction and suction is also shown and discussed.

Spectral-based propagation schemes for time-dependent quantum systems with application to carbon nanotubes

NASA Astrophysics Data System (ADS)

Chen, Zuojing; Polizzi, Eric

2010-11-01

Effective modeling and numerical spectral-based propagation schemes are proposed for addressing the challenges in time-dependent quantum simulations of systems ranging from atoms, molecules, and nanostructures to emerging nanoelectronic devices. While time-dependent Hamiltonian problems can be formally solved by propagating the solutions along tiny simulation time steps, a direct numerical treatment is often considered too computationally demanding. In this paper, however, we propose to go beyond these limitations by introducing high-performance numerical propagation schemes to compute the solution of the time-ordered evolution operator. In addition to the direct Hamiltonian diagonalizations that can be efficiently performed using the new eigenvalue solver FEAST, we have designed a Gaussian propagation scheme and a basis-transformed propagation scheme (BTPS) which allow to reduce considerably the simulation times needed by time intervals. It is outlined that BTPS offers the best computational efficiency allowing new perspectives in time-dependent simulations. Finally, these numerical schemes are applied to study the ac response of a (5,5) carbon nanotube within a three-dimensional real-space mesh framework.

Efficient and accurate two-scale FE-FFT-based prediction of the effective material behavior of elasto-viscoplastic polycrystals

NASA Astrophysics Data System (ADS)

Kochmann, Julian; Wulfinghoff, Stephan; Ehle, Lisa; Mayer, Joachim; Svendsen, Bob; Reese, Stefanie

2018-06-01

Recently, two-scale FE-FFT-based methods (e.g., Spahn et al. in Comput Methods Appl Mech Eng 268:871-883, 2014; Kochmann et al. in Comput Methods Appl Mech Eng 305:89-110, 2016) have been proposed to predict the microscopic and overall mechanical behavior of heterogeneous materials. The purpose of this work is the extension to elasto-viscoplastic polycrystals, efficient and robust Fourier solvers and the prediction of micromechanical fields during macroscopic deformation processes. Assuming scale separation, the macroscopic problem is solved using the finite element method. The solution of the microscopic problem, which is embedded as a periodic unit cell (UC) in each macroscopic integration point, is found by employing fast Fourier transforms, fixed-point and Newton-Krylov methods. The overall material behavior is defined by the mean UC response. In order to ensure spatially converged micromechanical fields as well as feasible overall CPU times, an efficient but simple solution strategy for two-scale simulations is proposed. As an example, the constitutive behavior of 42CrMo4 steel is predicted during macroscopic three-point bending tests.

Efficient and Robust Optimization for Building Energy Simulation

PubMed Central

Pourarian, Shokouh; Kearsley, Anthony; Wen, Jin; Pertzborn, Amanda

2016-01-01

Efficiently, robustly and accurately solving large sets of structured, non-linear algebraic and differential equations is one of the most computationally expensive steps in the dynamic simulation of building energy systems. Here, the efficiency, robustness and accuracy of two commonly employed solution methods are compared. The comparison is conducted using the HVACSIM+ software package, a component based building system simulation tool. The HVACSIM+ software presently employs Powell’s Hybrid method to solve systems of nonlinear algebraic equations that model the dynamics of energy states and interactions within buildings. It is shown here that the Powell’s method does not always converge to a solution. Since a myriad of other numerical methods are available, the question arises as to which method is most appropriate for building energy simulation. This paper finds considerable computational benefits result from replacing the Powell’s Hybrid method solver in HVACSIM+ with a solver more appropriate for the challenges particular to numerical simulations of buildings. Evidence is provided that a variant of the Levenberg-Marquardt solver has superior accuracy and robustness compared to the Powell’s Hybrid method presently used in HVACSIM+. PMID:27325907

Efficient and Robust Optimization for Building Energy Simulation.

PubMed

Pourarian, Shokouh; Kearsley, Anthony; Wen, Jin; Pertzborn, Amanda

2016-06-15

Efficiently, robustly and accurately solving large sets of structured, non-linear algebraic and differential equations is one of the most computationally expensive steps in the dynamic simulation of building energy systems. Here, the efficiency, robustness and accuracy of two commonly employed solution methods are compared. The comparison is conducted using the HVACSIM+ software package, a component based building system simulation tool. The HVACSIM+ software presently employs Powell's Hybrid method to solve systems of nonlinear algebraic equations that model the dynamics of energy states and interactions within buildings. It is shown here that the Powell's method does not always converge to a solution. Since a myriad of other numerical methods are available, the question arises as to which method is most appropriate for building energy simulation. This paper finds considerable computational benefits result from replacing the Powell's Hybrid method solver in HVACSIM+ with a solver more appropriate for the challenges particular to numerical simulations of buildings. Evidence is provided that a variant of the Levenberg-Marquardt solver has superior accuracy and robustness compared to the Powell's Hybrid method presently used in HVACSIM+.

Efficient and accurate two-scale FE-FFT-based prediction of the effective material behavior of elasto-viscoplastic polycrystals

NASA Astrophysics Data System (ADS)

Kochmann, Julian; Wulfinghoff, Stephan; Ehle, Lisa; Mayer, Joachim; Svendsen, Bob; Reese, Stefanie

2017-09-01

Recently, two-scale FE-FFT-based methods (e.g., Spahn et al. in Comput Methods Appl Mech Eng 268:871-883, 2014; Kochmann et al. in Comput Methods Appl Mech Eng 305:89-110, 2016) have been proposed to predict the microscopic and overall mechanical behavior of heterogeneous materials. The purpose of this work is the extension to elasto-viscoplastic polycrystals, efficient and robust Fourier solvers and the prediction of micromechanical fields during macroscopic deformation processes. Assuming scale separation, the macroscopic problem is solved using the finite element method. The solution of the microscopic problem, which is embedded as a periodic unit cell (UC) in each macroscopic integration point, is found by employing fast Fourier transforms, fixed-point and Newton-Krylov methods. The overall material behavior is defined by the mean UC response. In order to ensure spatially converged micromechanical fields as well as feasible overall CPU times, an efficient but simple solution strategy for two-scale simulations is proposed. As an example, the constitutive behavior of 42CrMo4 steel is predicted during macroscopic three-point bending tests.

Efficient analytical implementation of the DOT Riemann solver for the de Saint Venant-Exner morphodynamic model

NASA Astrophysics Data System (ADS)

Carraro, F.; Valiani, A.; Caleffi, V.

2018-03-01

Within the framework of the de Saint Venant equations coupled with the Exner equation for morphodynamic evolution, this work presents a new efficient implementation of the Dumbser-Osher-Toro (DOT) scheme for non-conservative problems. The DOT path-conservative scheme is a robust upwind method based on a complete Riemann solver, but it has the drawback of requiring expensive numerical computations. Indeed, to compute the non-linear time evolution in each time step, the DOT scheme requires numerical computation of the flux matrix eigenstructure (the totality of eigenvalues and eigenvectors) several times at each cell edge. In this work, an analytical and compact formulation of the eigenstructure for the de Saint Venant-Exner (dSVE) model is introduced and tested in terms of numerical efficiency and stability. Using the original DOT and PRICE-C (a very efficient FORCE-type method) as reference methods, we present a convergence analysis (error against CPU time) to study the performance of the DOT method with our new analytical implementation of eigenstructure calculations (A-DOT). In particular, the numerical performance of the three methods is tested in three test cases: a movable bed Riemann problem with analytical solution; a problem with smooth analytical solution; a test in which the water flow is characterised by subcritical and supercritical regions. For a given target error, the A-DOT method is always the most efficient choice. Finally, two experimental data sets and different transport formulae are considered to test the A-DOT model in more practical case studies.

Additional development of the XTRAN3S computer program

NASA Technical Reports Server (NTRS)

Borland, C. J.

1989-01-01

Additional developments and enhancements to the XTRAN3S computer program, a code for calculation of steady and unsteady aerodynamics, and associated aeroelastic solutions, for 3-D wings in the transonic flow regime are described. Algorithm improvements for the XTRAN3S program were provided including an implicit finite difference scheme to enhance the allowable time step and vectorization for improved computational efficiency. The code was modified to treat configurations with a fuselage, multiple stores/nacelles/pylons, and winglets. Computer program changes (updates) for error corrections and updates for version control are provided.

Solving search problems by strongly simulating quantum circuits

PubMed Central

Johnson, T. H.; Biamonte, J. D.; Clark, S. R.; Jaksch, D.

2013-01-01

Simulating quantum circuits using classical computers lets us analyse the inner workings of quantum algorithms. The most complete type of simulation, strong simulation, is believed to be generally inefficient. Nevertheless, several efficient strong simulation techniques are known for restricted families of quantum circuits and we develop an additional technique in this article. Further, we show that strong simulation algorithms perform another fundamental task: solving search problems. Efficient strong simulation techniques allow solutions to a class of search problems to be counted and found efficiently. This enhances the utility of strong simulation methods, known or yet to be discovered, and extends the class of search problems known to be efficiently simulable. Relating strong simulation to search problems also bounds the computational power of efficiently strongly simulable circuits; if they could solve all problems in P this would imply that all problems in NP and #P could be solved in polynomial time. PMID:23390585

Efficient classical simulation of the Deutsch-Jozsa and Simon's algorithms

NASA Astrophysics Data System (ADS)

Johansson, Niklas; Larsson, Jan-Åke

2017-09-01

A long-standing aim of quantum information research is to understand what gives quantum computers their advantage. This requires separating problems that need genuinely quantum resources from those for which classical resources are enough. Two examples of quantum speed-up are the Deutsch-Jozsa and Simon's problem, both efficiently solvable on a quantum Turing machine, and both believed to lack efficient classical solutions. Here we present a framework that can simulate both quantum algorithms efficiently, solving the Deutsch-Jozsa problem with probability 1 using only one oracle query, and Simon's problem using linearly many oracle queries, just as expected of an ideal quantum computer. The presented simulation framework is in turn efficiently simulatable in a classical probabilistic Turing machine. This shows that the Deutsch-Jozsa and Simon's problem do not require any genuinely quantum resources, and that the quantum algorithms show no speed-up when compared with their corresponding classical simulation. Finally, this gives insight into what properties are needed in the two algorithms and calls for further study of oracle separation between quantum and classical computation.

Teaching Ionic Solvation Structure with a Monte Carlo Liquid Simulation Program

ERIC Educational Resources Information Center

Serrano, Agostinho; Santos, Flavia M. T.; Greca, Ileana M.

2004-01-01

The use of molecular dynamics and Monte Carlo methods has provided efficient means to stimulate the behavior of molecular liquids and solutions. A Monte Carlo simulation program is used to compute the structure of liquid water and of water as a solvent to Na(super +), Cl(super -), and Ar on a personal computer to show that it is easily feasible to…

Evolving binary classifiers through parallel computation of multiple fitness cases.

PubMed

Cagnoni, Stefano; Bergenti, Federico; Mordonini, Monica; Adorni, Giovanni

2005-06-01

This paper describes two versions of a novel approach to developing binary classifiers, based on two evolutionary computation paradigms: cellular programming and genetic programming. Such an approach achieves high computation efficiency both during evolution and at runtime. Evolution speed is optimized by allowing multiple solutions to be computed in parallel. Runtime performance is optimized explicitly using parallel computation in the case of cellular programming or implicitly taking advantage of the intrinsic parallelism of bitwise operators on standard sequential architectures in the case of genetic programming. The approach was tested on a digit recognition problem and compared with a reference classifier.

Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads.

PubMed

Stone, John E; Hallock, Michael J; Phillips, James C; Peterson, Joseph R; Luthey-Schulten, Zaida; Schulten, Klaus

2016-05-01

Many of the continuing scientific advances achieved through computational biology are predicated on the availability of ongoing increases in computational power required for detailed simulation and analysis of cellular processes on biologically-relevant timescales. A critical challenge facing the development of future exascale supercomputer systems is the development of new computing hardware and associated scientific applications that dramatically improve upon the energy efficiency of existing solutions, while providing increased simulation, analysis, and visualization performance. Mobile computing platforms have recently become powerful enough to support interactive molecular visualization tasks that were previously only possible on laptops and workstations, creating future opportunities for their convenient use for meetings, remote collaboration, and as head mounted displays for immersive stereoscopic viewing. We describe early experiences adapting several biomolecular simulation and analysis applications for emerging heterogeneous computing platforms that combine power-efficient system-on-chip multi-core CPUs with high-performance massively parallel GPUs. We present low-cost power monitoring instrumentation that provides sufficient temporal resolution to evaluate the power consumption of individual CPU algorithms and GPU kernels. We compare the performance and energy efficiency of scientific applications running on emerging platforms with results obtained on traditional platforms, identify hardware and algorithmic performance bottlenecks that affect the usability of these platforms, and describe avenues for improving both the hardware and applications in pursuit of the needs of molecular modeling tasks on mobile devices and future exascale computers.

Computational Aerothermodynamic Design Issues for Hypersonic Vehicles

NASA Technical Reports Server (NTRS)

Gnoffo, Peter A.; Weilmuenster, K. James; Hamilton, H. Harris, II; Olynick, David R.; Venkatapathy, Ethiraj

1997-01-01

A brief review of the evolutionary progress in computational aerothermodynamics is presented. The current status of computational aerothermodynamics is then discussed, with emphasis on its capabilities and limitations for contributions to the design process of hypersonic vehicles. Some topics to be highlighted include: (1) aerodynamic coefficient predictions with emphasis on high temperature gas effects; (2) surface heating and temperature predictions for thermal protection system (TPS) design in a high temperature, thermochemical nonequilibrium environment; (3) methods for extracting and extending computational fluid dynamic (CFD) solutions for efficient utilization by all members of a multidisciplinary design team; (4) physical models; (5) validation process and error estimation; and (6) gridding and solution generation strategies. Recent experiences in the design of X-33 will be featured. Computational aerothermodynamic contributions to Mars Pathfinder, METEOR, and Stardust (Comet Sample return) will also provide context for this discussion. Some of the barriers that currently limit computational aerothermodynamics to a predominantly reactive mode in the design process will also be discussed, with the goal of providing focus for future research.

Computational Aerothermodynamic Design Issues for Hypersonic Vehicles

NASA Technical Reports Server (NTRS)

Gnoffo, Peter A.; Weilmuenster, K. James; Hamilton, H. Harris, II; Olynick, David R.; Venkatapathy, Ethiraj

2005-01-01

A brief review of the evolutionary progress in computational aerothermodynamics is presented. The current status of computational aerothermodynamics is then discussed, with emphasis on its capabilities and limitations for contributions to the design process of hypersonic vehicles. Some topics to be highlighted include: (1) aerodynamic coefficient predictions with emphasis on high temperature gas effects; (2) surface heating and temperature predictions for thermal protection system (TPS) design in a high temperature, thermochemical nonequilibrium environment; (3) methods for extracting and extending computational fluid dynamic (CFD) solutions for efficient utilization by all members of a multidisciplinary design team; (4) physical models; (5) validation process and error estimation; and (6) gridding and solution generation strategies. Recent experiences in the design of X-33 will be featured. Computational aerothermodynamic contributions to Mars Path finder, METEOR, and Stardust (Comet Sample return) will also provide context for this discussion. Some of the barriers that currently limit computational aerothermodynamics to a predominantly reactive mode in the design process will also be discussed, with the goal of providing focus for future research.

Computational Aerothermodynamic Design Issues for Hypersonic Vehicles

NASA Technical Reports Server (NTRS)

Olynick, David R.; Venkatapathy, Ethiraj

2004-01-01

A brief review of the evolutionary progress in computational aerothermodynamics is presented. The current status of computational aerothermodynamics is then discussed, with emphasis on its capabilities and limitations for contributions to the design process of hypersonic vehicles. Some topics to be highlighted include: (1) aerodynamic coefficient predictions with emphasis on high temperature gas effects; (2) surface heating and temperature predictions for thermal protection system (TPS) design in a high temperature, thermochemical nonequilibrium environment; (3) methods for extracting and extending computational fluid dynamic (CFD) solutions for efficient utilization by all members of a multidisciplinary design team; (4) physical models; (5) validation process and error estimation; and (6) gridding and solution generation strategies. Recent experiences in the design of X-33 will be featured. Computational aerothermodynamic contributions to Mars Pathfinder, METEOR, and Stardust (Comet Sample return) will also provide context for this discussion. Some of the barriers that currently limit computational aerothermodynamics to a predominantly reactive mode in the design process will also be discussed, with the goal of providing focus for future research.

Computational complexities and storage requirements of some Riccati equation solvers

NASA Technical Reports Server (NTRS)

Utku, Senol; Garba, John A.; Ramesh, A. V.

1989-01-01

The linear optimal control problem of an nth-order time-invariant dynamic system with a quadratic performance functional is usually solved by the Hamilton-Jacobi approach. This leads to the solution of the differential matrix Riccati equation with a terminal condition. The bulk of the computation for the optimal control problem is related to the solution of this equation. There are various algorithms in the literature for solving the matrix Riccati equation. However, computational complexities and storage requirements as a function of numbers of state variables, control variables, and sensors are not available for all these algorithms. In this work, the computational complexities and storage requirements for some of these algorithms are given. These expressions show the immensity of the computational requirements of the algorithms in solving the Riccati equation for large-order systems such as the control of highly flexible space structures. The expressions are also needed to compute the speedup and efficiency of any implementation of these algorithms on concurrent machines.

A grid-embedding transonic flow analysis computer program for wing/nacelle configurations

NASA Technical Reports Server (NTRS)

Atta, E. H.; Vadyak, J.

1983-01-01

An efficient grid-interfacing zonal algorithm was developed for computing the three-dimensional transonic flow field about wing/nacelle configurations. the algorithm uses the full-potential formulation and the AF2 approximate factorization scheme. The flow field solution is computed using a component-adaptive grid approach in which separate grids are employed for the individual components in the multi-component configuration, where each component grid is optimized for a particular geometry such as the wing or nacelle. The wing and nacelle component grids are allowed to overlap, and flow field information is transmitted from one grid to another through the overlap region using trivariate interpolation. This report represents a discussion of the computational methods used to generate both the wing and nacelle component grids, the technique used to interface the component grids, and the method used to obtain the inviscid flow solution. Computed results and correlations with experiment are presented. also presented are discussions on the organization of the wing grid generation (GRGEN3) and nacelle grid generation (NGRIDA) computer programs, the grid interface (LK) computer program, and the wing/nacelle flow solution (TWN) computer program. Descriptions of the respective subroutines, definitions of the required input parameters, a discussion on interpretation of the output, and the sample cases illustrating application of the analysis are provided for each of the four computer programs.

A boundary element alternating method for two-dimensional mixed-mode fracture problems

NASA Technical Reports Server (NTRS)

Raju, I. S.; Krishnamurthy, T.

1992-01-01

A boundary element alternating method, denoted herein as BEAM, is presented for two dimensional fracture problems. This is an iterative method which alternates between two solutions. An analytical solution for arbitrary polynomial normal and tangential pressure distributions applied to the crack faces of an embedded crack in an infinite plate is used as the fundamental solution in the alternating method. A boundary element method for an uncracked finite plate is the second solution. For problems of edge cracks a technique of utilizing finite elements with BEAM is presented to overcome the inherent singularity in boundary element stress calculation near the boundaries. Several computational aspects that make the algorithm efficient are presented. Finally, the BEAM is applied to a variety of two dimensional crack problems with different configurations and loadings to assess the validity of the method. The method gives accurate stress intensity factors with minimal computing effort.

Computational screening of biomolecular adsorption and self-assembly on nanoscale surfaces.

PubMed

Heinz, Hendrik

2010-05-01

The quantification of binding properties of ions, surfactants, biopolymers, and other macromolecules to nanometer-scale surfaces is often difficult experimentally and a recurring challenge in molecular simulation. A simple and computationally efficient method is introduced to compute quantitatively the energy of adsorption of solute molecules on a given surface. Highly accurate summation of Coulomb energies as well as precise control of temperature and pressure is required to extract the small energy differences in complex environments characterized by a large total energy. The method involves the simulation of four systems, the surface-solute-solvent system, the solute-solvent system, the solvent system, and the surface-solvent system under consideration of equal molecular volumes of each component under NVT conditions using standard molecular dynamics or Monte Carlo algorithms. Particularly in chemically detailed systems including thousands of explicit solvent molecules and specific concentrations of ions and organic solutes, the method takes into account the effect of complex nonbond interactions and rotational isomeric states on the adsorption behavior on surfaces. As a numerical example, the adsorption of a dodecapeptide on the Au {111} and mica {001} surfaces is described in aqueous solution. Copyright 2009 Wiley Periodicals, Inc.

Asymptotic co- and post-seismic displacements in a homogeneous Maxwell sphere

NASA Astrophysics Data System (ADS)

Tang, He; Sun, Wenke

2018-07-01

The deformations of the Earth caused by internal and external forces are usually expressed through Green's functions or the superposition of normal modes, that is, via numerical methods, which are applicable for computing both co- and post-seismic deformations. It is difficult to express these deformations in an analytical form, even for a uniform viscoelastic sphere. In this study, we present a set of asymptotic solutions for computing co- and post-seismic displacements; these solutions can be further applied to solving co- and post-seismic geoid, gravity and strain changes. Expressions are derived for a uniform Maxwell Earth by combining the reciprocity theorem, which links earthquake, tidal, shear and loading deformations, with the asymptotic solutions of these three external forces (tidal, shear and loading) and analytical inverse Laplace transformation formulae. Since the asymptotic solutions are given in a purely analytical form without series summations or extra convergence skills, they can be practically applied in an efficient way, especially when computing post-seismic deformations and glacial isotactic adjustments of the Earth over long timescales.

Asymptotic Co- and Post-seismic displacements in a homogeneous Maxwell sphere

NASA Astrophysics Data System (ADS)

Tang, He; Sun, Wenke

2018-05-01

The deformations of the Earth caused by internal and external forces are usually expressed through Green's functions or the superposition of normal modes, i.e. via numerical methods, which are applicable for computing both co- and post-seismic deformations. It is difficult to express these deformations in an analytical form, even for a uniform viscoelastic sphere. In this study, we present a set of asymptotic solutions for computing co- and post-seismic displacements; these solutions can be further applied to solving co- and post-seismic geoid, gravity, and strain changes. Expressions are derived for a uniform Maxwell Earth by combining the reciprocity theorem, which links earthquake, tidal, shear and loading deformations, with the asymptotic solutions of these three external forces (tidal, shear and loading) and analytical inverse Laplace transformation formulae. Since the asymptotic solutions are given in a purely analytical form without series summations or extra convergence skills, they can be practically applied in an efficient way, especially when computing post-seismic deformations and glacial isotactic adjustments of the Earth over long timescales.

Implementing direct, spatially isolated problems on transputer networks

NASA Technical Reports Server (NTRS)

Ellis, Graham K.

1988-01-01

Parametric studies were performed on transputer networks of up to 40 processors to determine how to implement and maximize the performance of the solution of problems where no processor-to-processor data transfer is required for the problem solution (spatially isolated). Two types of problems are investigated a computationally intensive problem where the solution required the transmission of 160 bytes of data through the parallel network, and a communication intensive example that required the transmission of 3 Mbytes of data through the network. This data consists of solutions being sent back to the host processor and not intermediate results for another processor to work on. Studies were performed on both integer and floating-point transputers. The latter features an on-chip floating-point math unit and offers approximately an order of magnitude performance increase over the integer transputer on real valued computations. The results indicate that a minimum amount of work is required on each node per communication to achieve high network speedups (efficiencies). The floating-point processor requires approximately an order of magnitude more work per communication than the integer processor because of the floating-point unit's increased computing capacity.

Multiobjective Optimization of Low-Energy Trajectories Using Optimal Control on Dynamical Channels

NASA Technical Reports Server (NTRS)

Coffee, Thomas M.; Anderson, Rodney L.; Lo, Martin W.

2011-01-01

We introduce a computational method to design efficient low-energy trajectories by extracting initial solutions from dynamical channels formed by invariant manifolds, and improving these solutions through variational optimal control. We consider trajectories connecting two unstable periodic orbits in the circular restricted 3-body problem (CR3BP). Our method leverages dynamical channels to generate a range of solutions, and approximates the areto front for impulse and time of flight through a multiobjective optimization of these solutions based on primer vector theory. We demonstrate the application of our method to a libration orbit transfer in the Earth-Moon system.

A comparison of the Method of Lines to finite difference techniques in solving time-dependent partial differential equations. [with applications to Burger equation and stream function-vorticity problem

NASA Technical Reports Server (NTRS)

Kurtz, L. A.; Smith, R. E.; Parks, C. L.; Boney, L. R.

1978-01-01

Steady state solutions to two time dependent partial differential systems have been obtained by the Method of Lines (MOL) and compared to those obtained by efficient standard finite difference methods: (1) Burger's equation over a finite space domain by a forward time central space explicit method, and (2) the stream function - vorticity form of viscous incompressible fluid flow in a square cavity by an alternating direction implicit (ADI) method. The standard techniques were far more computationally efficient when applicable. In the second example, converged solutions at very high Reynolds numbers were obtained by MOL, whereas solution by ADI was either unattainable or impractical. With regard to 'set up' time, solution by MOL is an attractive alternative to techniques with complicated algorithms, as much of the programming difficulty is eliminated.

Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids

NASA Astrophysics Data System (ADS)

Nguyen, Hung T.; Pabit, Suzette A.; Meisburger, Steve P.; Pollack, Lois; Case, David A.

2014-12-01

A new method is introduced to compute X-ray solution scattering profiles from atomic models of macromolecules. The three-dimensional version of the Reference Interaction Site Model (RISM) from liquid-state statistical mechanics is employed to compute the solvent distribution around the solute, including both water and ions. X-ray scattering profiles are computed from this distribution together with the solute geometry. We describe an efficient procedure for performing this calculation employing a Lebedev grid for the angular averaging. The intensity profiles (which involve no adjustable parameters) match experiment and molecular dynamics simulations up to wide angle for two proteins (lysozyme and myoglobin) in water, as well as the small-angle profiles for a dozen biomolecules taken from the BioIsis.net database. The RISM model is especially well-suited for studies of nucleic acids in salt solution. Use of fiber-diffraction models for the structure of duplex DNA in solution yields close agreement with the observed scattering profiles in both the small and wide angle scattering (SAXS and WAXS) regimes. In addition, computed profiles of anomalous SAXS signals (for Rb+ and Sr2+) emphasize the ionic contribution to scattering and are in reasonable agreement with experiment. In cases where an absolute calibration of the experimental data at q = 0 is available, one can extract a count of the excess number of waters and ions; computed values depend on the closure that is assumed in the solution of the Ornstein-Zernike equations, with results from the Kovalenko-Hirata closure being closest to experiment for the cases studied here.

OGS#PETSc approach for robust and efficient simulations of strongly coupled hydrothermal processes in EGS reservoirs

NASA Astrophysics Data System (ADS)

Watanabe, Norihiro; Blucher, Guido; Cacace, Mauro; Kolditz, Olaf

2016-04-01

A robust and computationally efficient solution is important for 3D modelling of EGS reservoirs. This is particularly the case when the reservoir model includes hydraulic conduits such as induced or natural fractures, fault zones, and wellbore open-hole sections. The existence of such hydraulic conduits results in heterogeneous flow fields and in a strengthened coupling between fluid flow and heat transport processes via temperature dependent fluid properties (e.g. density and viscosity). A commonly employed partitioned solution (or operator-splitting solution) may not robustly work for such strongly coupled problems its applicability being limited by small time step sizes (e.g. 5-10 days) whereas the processes have to be simulated for 10-100 years. To overcome this limitation, an alternative approach is desired which can guarantee a robust solution of the coupled problem with minor constraints on time step sizes. In this work, we present a Newton-Raphson based monolithic coupling approach implemented in the OpenGeoSys simulator (OGS) combined with the Portable, Extensible Toolkit for Scientific Computation (PETSc) library. The PETSc library is used for both linear and nonlinear solvers as well as MPI-based parallel computations. The suggested method has been tested by application to the 3D reservoir site of Groß Schönebeck, in northern Germany. Results show that the exact Newton-Raphson approach can also be limited to small time step sizes (e.g. one day) due to slight oscillations in the temperature field. The usage of a line search technique and modification of the Jacobian matrix were necessary to achieve robust convergence of the nonlinear solution. For the studied example, the proposed monolithic approach worked even with a very large time step size of 3.5 years.

A CFD Study on the Prediction of Cyclone Collection Efficiency

NASA Astrophysics Data System (ADS)

Gimbun, Jolius; Chuah, T. G.; Choong, Thomas S. Y.; Fakhru'L-Razi, A.

2005-09-01

This work presents a Computational Fluid Dynamics calculation to predict and to evaluate the effects of temperature, operating pressure and inlet velocity on the collection efficiency of gas cyclones. The numerical solutions were carried out using spreadsheet and commercial CFD code FLUENT 6.0. This paper also reviews four empirical models for the prediction of cyclone collection efficiency, namely Lapple [1], Koch and Licht [2], Li and Wang [3], and Iozia and Leith [4]. All the predictions proved to be satisfactory when compared with the presented experimental data. The CFD simulations predict the cyclone cut-off size for all operating conditions with a deviation of 3.7% from the experimental data. Specifically, results obtained from the computer modelling exercise have demonstrated that CFD model is the best method of modelling the cyclones collection efficiency.

Three-Dimensional Shallow Water Acoustics

DTIC Science & Technology

2015-09-30

converts the Helmholtz wave equation of elliptic type to a one-way wave equation of parabolic type. The conversion allows efficient marching solution ...algorithms for 2 solving the boundary value problem posed by the Helmholtz equation . This can reduce significantly the requirement for computational...Fourier parabolic- equation sound propagation solution scheme," J. Acoust. Soc. Am, vol. 132, pp. EL61-EL67 (2012). [6] Y.-T. Lin, J.M. Collis and T.F

Efficient QR sequential least square algorithm for high frequency GNSS precise point positioning seismic application

NASA Astrophysics Data System (ADS)

Barbu, Alina L.; Laurent-Varin, Julien; Perosanz, Felix; Mercier, Flavien; Marty, Jean-Charles

2018-01-01

The implementation into the GINS CNES geodetic software of a more efficient filter was needed to satisfy the users who wanted to compute high-rate GNSS PPP solutions. We selected the SRI approach and a QR factorization technique including an innovative algorithm which optimizes the matrix reduction step. A full description of this algorithm is given for future users. The new capacities of the software have been tested using a set of 1 Hz data from the Japanese GEONET network including the Mw 9.0 2011 Tohoku earthquake. Station coordinates solution agreed at a sub-decimeter level with previous publications as well as with solutions we computed with the National Resource Canada software. An additional benefit from the implementation of the SRI filter is the capability to estimate high-rate tropospheric parameters too. As the CPU time to estimate a 1 Hz kinematic solution from 1 h of data is now less than 1 min we could produced series of coordinates for the full 1300 stations of the Japanese network. The corresponding movie shows the impressive co-seismic deformation as well as the wave propagation along the island. The processing was straightforward using a cluster of PCs which illustrates the new potentiality of the GINS software for massive network high rate PPP processing.

Elastic Cloud Computing Architecture and System for Heterogeneous Spatiotemporal Computing

NASA Astrophysics Data System (ADS)

Shi, X.

2017-10-01

Spatiotemporal computation implements a variety of different algorithms. When big data are involved, desktop computer or standalone application may not be able to complete the computation task due to limited memory and computing power. Now that a variety of hardware accelerators and computing platforms are available to improve the performance of geocomputation, different algorithms may have different behavior on different computing infrastructure and platforms. Some are perfect for implementation on a cluster of graphics processing units (GPUs), while GPUs may not be useful on certain kind of spatiotemporal computation. This is the same situation in utilizing a cluster of Intel's many-integrated-core (MIC) or Xeon Phi, as well as Hadoop or Spark platforms, to handle big spatiotemporal data. Furthermore, considering the energy efficiency requirement in general computation, Field Programmable Gate Array (FPGA) may be a better solution for better energy efficiency when the performance of computation could be similar or better than GPUs and MICs. It is expected that an elastic cloud computing architecture and system that integrates all of GPUs, MICs, and FPGAs could be developed and deployed to support spatiotemporal computing over heterogeneous data types and computational problems.

On the efficient and reliable numerical solution of rate-and-state friction problems

NASA Astrophysics Data System (ADS)

Pipping, Elias; Kornhuber, Ralf; Rosenau, Matthias; Oncken, Onno

2016-03-01

We present a mathematically consistent numerical algorithm for the simulation of earthquake rupture with rate-and-state friction. Its main features are adaptive time stepping, a novel algebraic solution algorithm involving nonlinear multigrid and a fixed point iteration for the rate-and-state decoupling. The algorithm is applied to a laboratory scale subduction zone which allows us to compare our simulations with experimental results. Using physical parameters from the experiment, we find a good fit of recurrence time of slip events as well as their rupture width and peak slip. Computations in 3-D confirm efficiency and robustness of our algorithm.

No programming required. Mobile PCs can help physicians work more efficiently, especially when the application is designed to fit the practice.

PubMed

Campbell, J

2000-09-01

The Jacobson Medical Group San Antonio Jacobson Medical Group (JMG) needed a way to effectively and efficiently coordinate referral information between their hospitalist physicians and specialists. JMG decided to replace paper-based binders with something more convenient and easily updated. The organization chose to implement a mobile solution that would provide its physicians with convenient access to a database of information via a hand-held computer. The hand-held solution provides physicians with full demographic profiles of primary care givers for each area where the group operates. The database includes multiple profiles based on different healthcare plans, along with details about preferred and authorized specialists. JMG adopted a user-friendly solution that the hospitalists and specialists would embrace and actually use.

Efficient estimation of diffusion during dendritic solidification

NASA Technical Reports Server (NTRS)

Yeum, K. S.; Poirier, D. R.; Laxmanan, V.

1989-01-01

A very efficient finite difference method has been developed to estimate the solute redistribution during solidification with diffusion in the solid. This method is validated by comparing the computed results with the results of an analytical solution derived by Kobayashi (1988) for the assumptions of a constant diffusion coefficient, a constant equilibrium partition ratio, and a parabolic rate of the advancement of the solid/liquid interface. The flexibility of the method is demonstrated by applying it to the dendritic solidification of a Pb-15 wt pct Sn alloy, for which the equilibrium partition ratio and diffusion coefficient vary substantially during solidification. The fraction eutectic at the end of solidification is also obtained by estimating the fraction solid, in greater resolution, where the concentration of solute in the interdendritic liquid reaches the eutectic composition of the alloy.

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

Wu, Qishi; Zhu, Mengxia; Rao, Nageswara S

We propose an intelligent decision support system based on sensor and computer networks that incorporates various component techniques for sensor deployment, data routing, distributed computing, and information fusion. The integrated system is deployed in a distributed environment composed of both wireless sensor networks for data collection and wired computer networks for data processing in support of homeland security defense. We present the system framework and formulate the analytical problems and develop approximate or exact solutions for the subtasks: (i) sensor deployment strategy based on a two-dimensional genetic algorithm to achieve maximum coverage with cost constraints; (ii) data routing scheme tomore » achieve maximum signal strength with minimum path loss, high energy efficiency, and effective fault tolerance; (iii) network mapping method to assign computing modules to network nodes for high-performance distributed data processing; and (iv) binary decision fusion rule that derive threshold bounds to improve system hit rate and false alarm rate. These component solutions are implemented and evaluated through either experiments or simulations in various application scenarios. The extensive results demonstrate that these component solutions imbue the integrated system with the desirable and useful quality of intelligence in decision making.« less

Domain decomposition methods for the parallel computation of reacting flows

NASA Technical Reports Server (NTRS)

Keyes, David E.

1988-01-01

Domain decomposition is a natural route to parallel computing for partial differential equation solvers. Subdomains of which the original domain of definition is comprised are assigned to independent processors at the price of periodic coordination between processors to compute global parameters and maintain the requisite degree of continuity of the solution at the subdomain interfaces. In the domain-decomposed solution of steady multidimensional systems of PDEs by finite difference methods using a pseudo-transient version of Newton iteration, the only portion of the computation which generally stands in the way of efficient parallelization is the solution of the large, sparse linear systems arising at each Newton step. For some Jacobian matrices drawn from an actual two-dimensional reacting flow problem, comparisons are made between relaxation-based linear solvers and also preconditioned iterative methods of Conjugate Gradient and Chebyshev type, focusing attention on both iteration count and global inner product count. The generalized minimum residual method with block-ILU preconditioning is judged the best serial method among those considered, and parallel numerical experiments on the Encore Multimax demonstrate for it approximately 10-fold speedup on 16 processors.

The ELPA library: scalable parallel eigenvalue solutions for electronic structure theory and computational science.

PubMed

Marek, A; Blum, V; Johanni, R; Havu, V; Lang, B; Auckenthaler, T; Heinecke, A; Bungartz, H-J; Lederer, H

2014-05-28

Obtaining the eigenvalues and eigenvectors of large matrices is a key problem in electronic structure theory and many other areas of computational science. The computational effort formally scales as O(N(3)) with the size of the investigated problem, N (e.g. the electron count in electronic structure theory), and thus often defines the system size limit that practical calculations cannot overcome. In many cases, more than just a small fraction of the possible eigenvalue/eigenvector pairs is needed, so that iterative solution strategies that focus only on a few eigenvalues become ineffective. Likewise, it is not always desirable or practical to circumvent the eigenvalue solution entirely. We here review some current developments regarding dense eigenvalue solvers and then focus on the Eigenvalue soLvers for Petascale Applications (ELPA) library, which facilitates the efficient algebraic solution of symmetric and Hermitian eigenvalue problems for dense matrices that have real-valued and complex-valued matrix entries, respectively, on parallel computer platforms. ELPA addresses standard as well as generalized eigenvalue problems, relying on the well documented matrix layout of the Scalable Linear Algebra PACKage (ScaLAPACK) library but replacing all actual parallel solution steps with subroutines of its own. For these steps, ELPA significantly outperforms the corresponding ScaLAPACK routines and proprietary libraries that implement the ScaLAPACK interface (e.g. Intel's MKL). The most time-critical step is the reduction of the matrix to tridiagonal form and the corresponding backtransformation of the eigenvectors. ELPA offers both a one-step tridiagonalization (successive Householder transformations) and a two-step transformation that is more efficient especially towards larger matrices and larger numbers of CPU cores. ELPA is based on the MPI standard, with an early hybrid MPI-OpenMPI implementation available as well. Scalability beyond 10,000 CPU cores for problem sizes arising in the field of electronic structure theory is demonstrated for current high-performance computer architectures such as Cray or Intel/Infiniband. For a matrix of dimension 260,000, scalability up to 295,000 CPU cores has been shown on BlueGene/P.

Efficient implementation of three-dimensional reference interaction site model self-consistent-field method: Application to solvatochromic shift calculations

NASA Astrophysics Data System (ADS)

Minezawa, Noriyuki; Kato, Shigeki

2007-02-01

The authors present an implementation of the three-dimensional reference interaction site model self-consistent-field (3D-RISM-SCF) method. First, they introduce a robust and efficient algorithm for solving the 3D-RISM equation. The algorithm is a hybrid of the Newton-Raphson and Picard methods. The Jacobian matrix is analytically expressed in a computationally useful form. Second, they discuss the solute-solvent electrostatic interaction. For the solute to solvent route, the electrostatic potential (ESP) map on a 3D grid is constructed directly from the electron density. The charge fitting procedure is not required to determine the ESP. For the solvent to solute route, the ESP acting on the solute molecule is derived from the solvent charge distribution obtained by solving the 3D-RISM equation. Matrix elements of the solute-solvent interaction are evaluated by the direct numerical integration. A remarkable reduction in the computational time is observed in both routes. Finally, the authors implement the first derivatives of the free energy with respect to the solute nuclear coordinates. They apply the present method to "solute" water and formaldehyde in aqueous solvent using the simple point charge model, and the results are compared with those from other methods: the six-dimensional molecular Ornstein-Zernike SCF, the one-dimensional site-site RISM-SCF, and the polarizable continuum model. The authors also calculate the solvatochromic shifts of acetone, benzonitrile, and nitrobenzene using the present method and compare them with the experimental and other theoretical results.

Efficient implementation of three-dimensional reference interaction site model self-consistent-field method: application to solvatochromic shift calculations.

PubMed

Minezawa, Noriyuki; Kato, Shigeki

2007-02-07

The authors present an implementation of the three-dimensional reference interaction site model self-consistent-field (3D-RISM-SCF) method. First, they introduce a robust and efficient algorithm for solving the 3D-RISM equation. The algorithm is a hybrid of the Newton-Raphson and Picard methods. The Jacobian matrix is analytically expressed in a computationally useful form. Second, they discuss the solute-solvent electrostatic interaction. For the solute to solvent route, the electrostatic potential (ESP) map on a 3D grid is constructed directly from the electron density. The charge fitting procedure is not required to determine the ESP. For the solvent to solute route, the ESP acting on the solute molecule is derived from the solvent charge distribution obtained by solving the 3D-RISM equation. Matrix elements of the solute-solvent interaction are evaluated by the direct numerical integration. A remarkable reduction in the computational time is observed in both routes. Finally, the authors implement the first derivatives of the free energy with respect to the solute nuclear coordinates. They apply the present method to "solute" water and formaldehyde in aqueous solvent using the simple point charge model, and the results are compared with those from other methods: the six-dimensional molecular Ornstein-Zernike SCF, the one-dimensional site-site RISM-SCF, and the polarizable continuum model. The authors also calculate the solvatochromic shifts of acetone, benzonitrile, and nitrobenzene using the present method and compare them with the experimental and other theoretical results.

Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul

2015-03-01

Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 103-105 molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.

A Benders based rolling horizon algorithm for a dynamic facility location problem

DOE PAGES

Marufuzzaman,, Mohammad; Gedik, Ridvan; Roni, Mohammad S.

2016-06-28

This study presents a well-known capacitated dynamic facility location problem (DFLP) that satisfies the customer demand at a minimum cost by determining the time period for opening, closing, or retaining an existing facility in a given location. To solve this challenging NP-hard problem, this paper develops a unique hybrid solution algorithm that combines a rolling horizon algorithm with an accelerated Benders decomposition algorithm. Extensive computational experiments are performed on benchmark test instances to evaluate the hybrid algorithm’s efficiency and robustness in solving the DFLP problem. Computational results indicate that the hybrid Benders based rolling horizon algorithm consistently offers high qualitymore » feasible solutions in a much shorter computational time period than the standalone rolling horizon and accelerated Benders decomposition algorithms in the experimental range.« less

Estimation of Faults in DC Electrical Power System

NASA Technical Reports Server (NTRS)

Gorinevsky, Dimitry; Boyd, Stephen; Poll, Scott

2009-01-01

This paper demonstrates a novel optimization-based approach to estimating fault states in a DC power system. Potential faults changing the circuit topology are included along with faulty measurements. Our approach can be considered as a relaxation of the mixed estimation problem. We develop a linear model of the circuit and pose a convex problem for estimating the faults and other hidden states. A sparse fault vector solution is computed by using 11 regularization. The solution is computed reliably and efficiently, and gives accurate diagnostics on the faults. We demonstrate a real-time implementation of the approach for an instrumented electrical power system testbed, the ADAPT testbed at NASA ARC. The estimates are computed in milliseconds on a PC. The approach performs well despite unmodeled transients and other modeling uncertainties present in the system.

IBM system/360 assembly language interval arithmetic software

NASA Technical Reports Server (NTRS)

Phillips, E. J.

1972-01-01

Computer software designed to perform interval arithmetic is described. An interval is defined as the set of all real numbers between two given numbers including or excluding one or both endpoints. Interval arithmetic consists of the various elementary arithmetic operations defined on the set of all intervals, such as interval addition, subtraction, union, etc. One of the main applications of interval arithmetic is in the area of error analysis of computer calculations. For example, it has been used sucessfully to compute bounds on sounding errors in the solution of linear algebraic systems, error bounds in numerical solutions of ordinary differential equations, as well as integral equations and boundary value problems. The described software enables users to implement algorithms of the type described in references efficiently on the IBM 360 system.

New analytical exact solutions of time fractional KdV-KZK equation by Kudryashov methods

NASA Astrophysics Data System (ADS)

S Saha, Ray

2016-04-01

In this paper, new exact solutions of the time fractional KdV-Khokhlov-Zabolotskaya-Kuznetsov (KdV-KZK) equation are obtained by the classical Kudryashov method and modified Kudryashov method respectively. For this purpose, the modified Riemann-Liouville derivative is used to convert the nonlinear time fractional KdV-KZK equation into the nonlinear ordinary differential equation. In the present analysis, the classical Kudryashov method and modified Kudryashov method are both used successively to compute the analytical solutions of the time fractional KdV-KZK equation. As a result, new exact solutions involving the symmetrical Fibonacci function, hyperbolic function and exponential function are obtained for the first time. The methods under consideration are reliable and efficient, and can be used as an alternative to establish new exact solutions of different types of fractional differential equations arising from mathematical physics. The obtained results are exhibited graphically in order to demonstrate the efficiencies and applicabilities of these proposed methods of solving the nonlinear time fractional KdV-KZK equation.

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

DOE PAGES

Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.; ...

2017-01-18

Currently, Constraint-Based Reconstruction and Analysis (COBRA) is the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many orders of magnitude. Data values also have greatly varying magnitudes. Furthermore, standard double-precision solvers may return inaccurate solutions or report that no solution exists. Exact simplex solvers based on rational arithmetic require a near-optimal warm start to be practical on large problems (current ME models have 70,000 constraints and variables and will grow larger). We also developed a quadrupleprecision version of ourmore » linear and nonlinear optimizer MINOS, and a solution procedure (DQQ) involving Double and Quad MINOS that achieves reliability and efficiency for ME models and other challenging problems tested here. DQQ will enable extensive use of large linear and nonlinear models in systems biology and other applications involving multiscale data.« less

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

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

Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.

Currently, Constraint-Based Reconstruction and Analysis (COBRA) is the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many orders of magnitude. Data values also have greatly varying magnitudes. Furthermore, standard double-precision solvers may return inaccurate solutions or report that no solution exists. Exact simplex solvers based on rational arithmetic require a near-optimal warm start to be practical on large problems (current ME models have 70,000 constraints and variables and will grow larger). We also developed a quadrupleprecision version of ourmore » linear and nonlinear optimizer MINOS, and a solution procedure (DQQ) involving Double and Quad MINOS that achieves reliability and efficiency for ME models and other challenging problems tested here. DQQ will enable extensive use of large linear and nonlinear models in systems biology and other applications involving multiscale data.« less

Multiobjective evolutionary optimization of water distribution systems: Exploiting diversity with infeasible solutions.

PubMed

Tanyimboh, Tiku T; Seyoum, Alemtsehay G

2016-12-01

This article investigates the computational efficiency of constraint handling in multi-objective evolutionary optimization algorithms for water distribution systems. The methodology investigated here encourages the co-existence and simultaneous development including crossbreeding of subpopulations of cost-effective feasible and infeasible solutions based on Pareto dominance. This yields a boundary search approach that also promotes diversity in the gene pool throughout the progress of the optimization by exploiting the full spectrum of non-dominated infeasible solutions. The relative effectiveness of small and moderate population sizes with respect to the number of decision variables is investigated also. The results reveal the optimization algorithm to be efficient, stable and robust. It found optimal and near-optimal solutions reliably and efficiently. The real-world system based optimization problem involved multiple variable head supply nodes, 29 fire-fighting flows, extended period simulation and multiple demand categories including water loss. The least cost solutions found satisfied the flow and pressure requirements consistently. The best solutions achieved indicative savings of 48.1% and 48.2% based on the cost of the pipes in the existing network, for populations of 200 and 1000, respectively. The population of 1000 achieved slightly better results overall. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Parallelization of interpolation, solar radiation and water flow simulation modules in GRASS GIS using OpenMP

NASA Astrophysics Data System (ADS)

Hofierka, Jaroslav; Lacko, Michal; Zubal, Stanislav

2017-10-01

In this paper, we describe the parallelization of three complex and computationally intensive modules of GRASS GIS using the OpenMP application programming interface for multi-core computers. These include the v.surf.rst module for spatial interpolation, the r.sun module for solar radiation modeling and the r.sim.water module for water flow simulation. We briefly describe the functionality of the modules and parallelization approaches used in the modules. Our approach includes the analysis of the module's functionality, identification of source code segments suitable for parallelization and proper application of OpenMP parallelization code to create efficient threads processing the subtasks. We document the efficiency of the solutions using the airborne laser scanning data representing land surface in the test area and derived high-resolution digital terrain model grids. We discuss the performance speed-up and parallelization efficiency depending on the number of processor threads. The study showed a substantial increase in computation speeds on a standard multi-core computer while maintaining the accuracy of results in comparison to the output from original modules. The presented parallelization approach showed the simplicity and efficiency of the parallelization of open-source GRASS GIS modules using OpenMP, leading to an increased performance of this geospatial software on standard multi-core computers.

Unstructured mesh methods for CFD

NASA Technical Reports Server (NTRS)

Peraire, J.; Morgan, K.; Peiro, J.

1990-01-01

Mesh generation methods for Computational Fluid Dynamics (CFD) are outlined. Geometric modeling is discussed. An advancing front method is described. Flow past a two engine Falcon aeroplane is studied. An algorithm and associated data structure called the alternating digital tree, which efficiently solves the geometric searching problem is described. The computation of an initial approximation to the steady state solution of a given poblem is described. Mesh generation for transient flows is described.

Efficient electromagnetic source imaging with adaptive standardized LORETA/FOCUSS.

PubMed

Schimpf, Paul H; Liu, Hesheng; Ramon, Ceon; Haueisen, Jens

2005-05-01

Functional brain imaging and source localization based on the scalp's potential field require a solution to an ill-posed inverse problem with many solutions. This makes it necessary to incorporate a priori knowledge in order to select a particular solution. A computational challenge for some subject-specific head models is that many inverse algorithms require a comprehensive sampling of the candidate source space at the desired resolution. In this study, we present an algorithm that can accurately reconstruct details of localized source activity from a sparse sampling of the candidate source space. Forward computations are minimized through an adaptive procedure that increases source resolution as the spatial extent is reduced. With this algorithm, we were able to compute inverses using only 6% to 11% of the full resolution lead-field, with a localization accuracy that was not significantly different than an exhaustive search through a fully-sampled source space. The technique is, therefore, applicable for use with anatomically-realistic, subject-specific forward models for applications with spatially concentrated source activity.

An all-at-once reduced Hessian SQP scheme for aerodynamic design optimization

NASA Technical Reports Server (NTRS)

Feng, Dan; Pulliam, Thomas H.

1995-01-01

This paper introduces a computational scheme for solving a class of aerodynamic design problems that can be posed as nonlinear equality constrained optimizations. The scheme treats the flow and design variables as independent variables, and solves the constrained optimization problem via reduced Hessian successive quadratic programming. It updates the design and flow variables simultaneously at each iteration and allows flow variables to be infeasible before convergence. The solution of an adjoint flow equation is never needed. In addition, a range space basis is chosen so that in a certain sense the 'cross term' ignored in reduced Hessian SQP methods is minimized. Numerical results for a nozzle design using the quasi-one-dimensional Euler equations show that this scheme is computationally efficient and robust. The computational cost of a typical nozzle design is only a fraction more than that of the corresponding analysis flow calculation. Superlinear convergence is also observed, which agrees with the theoretical properties of this scheme. All optimal solutions are obtained by starting far away from the final solution.

Conformational free energies of methyl-α-L-iduronic and methyl-β-D-glucuronic acids in water

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Sagui, Celeste

2010-03-01

We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a nonequilibrium umbrella sampling method, in this case, the recently developed adaptively biased molecular dynamics method, to compute an approximate free energy for the slow modes of the solute in explicit solvent. This approximate free energy is then used to set up a Hamiltonian replica exchange scheme that samples both from biased and unbiased distributions. The final accurate free energy is recovered via the weighted histogram analysis technique applied to all the replicas, and equilibrium properties of the solute are computed from the unbiased trajectory. We illustrate the approach by applying it to the study of the puckering landscapes of the methyl glycosides of α-L-iduronic acid and its C5 epimer β-D-glucuronic acid in water. Big savings in computational resources are gained in comparison to the standard parallel tempering method.

Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water.

PubMed

Babin, Volodymyr; Sagui, Celeste

2010-03-14

We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a nonequilibrium umbrella sampling method, in this case, the recently developed adaptively biased molecular dynamics method, to compute an approximate free energy for the slow modes of the solute in explicit solvent. This approximate free energy is then used to set up a Hamiltonian replica exchange scheme that samples both from biased and unbiased distributions. The final accurate free energy is recovered via the weighted histogram analysis technique applied to all the replicas, and equilibrium properties of the solute are computed from the unbiased trajectory. We illustrate the approach by applying it to the study of the puckering landscapes of the methyl glycosides of alpha-L-iduronic acid and its C5 epimer beta-D-glucuronic acid in water. Big savings in computational resources are gained in comparison to the standard parallel tempering method.

A three-dimensional parabolic equation model of sound propagation using higher-order operator splitting and Padé approximants.

PubMed

Lin, Ying-Tsong; Collis, Jon M; Duda, Timothy F

2012-11-01

An alternating direction implicit (ADI) three-dimensional fluid parabolic equation solution method with enhanced accuracy is presented. The method uses a square-root Helmholtz operator splitting algorithm that retains cross-multiplied operator terms that have been previously neglected. With these higher-order cross terms, the valid angular range of the parabolic equation solution is improved. The method is tested for accuracy against an image solution in an idealized wedge problem. Computational efficiency improvements resulting from the ADI discretization are also discussed.

Furniture for the Future.

ERIC Educational Resources Information Center

Roskos, Bob

1999-01-01

Discusses key planning tips prior to purchasing computer-lab furniture to help ensure the furniture is stylish yet able to deliver efficient, cost-effective technology support. Discusses one school's solutions to wire management and finding furniture that was durable, easy to maintain, and competitively priced. (GR)

Solving Hard Computational Problems Efficiently: Asymptotic Parametric Complexity 3-Coloring Algorithm

PubMed Central

Martín H., José Antonio

2013-01-01

Many practical problems in almost all scientific and technological disciplines have been classified as computationally hard (NP-hard or even NP-complete). In life sciences, combinatorial optimization problems frequently arise in molecular biology, e.g., genome sequencing; global alignment of multiple genomes; identifying siblings or discovery of dysregulated pathways. In almost all of these problems, there is the need for proving a hypothesis about certain property of an object that can be present if and only if it adopts some particular admissible structure (an NP-certificate) or be absent (no admissible structure), however, none of the standard approaches can discard the hypothesis when no solution can be found, since none can provide a proof that there is no admissible structure. This article presents an algorithm that introduces a novel type of solution method to “efficiently” solve the graph 3-coloring problem; an NP-complete problem. The proposed method provides certificates (proofs) in both cases: present or absent, so it is possible to accept or reject the hypothesis on the basis of a rigorous proof. It provides exact solutions and is polynomial-time (i.e., efficient) however parametric. The only requirement is sufficient computational power, which is controlled by the parameter . Nevertheless, here it is proved that the probability of requiring a value of to obtain a solution for a random graph decreases exponentially: , making tractable almost all problem instances. Thorough experimental analyses were performed. The algorithm was tested on random graphs, planar graphs and 4-regular planar graphs. The obtained experimental results are in accordance with the theoretical expected results. PMID:23349711

Permeability Sensitivity Functions and Rapid Simulation of Hydraulic-Testing Measurements Using Perturbation Theory

NASA Astrophysics Data System (ADS)

Escobar Gómez, J. D.; Torres-Verdín, C.

2018-03-01

Single-well pressure-diffusion simulators enable improved quantitative understanding of hydraulic-testing measurements in the presence of arbitrary spatial variations of rock properties. Simulators of this type implement robust numerical algorithms which are often computationally expensive, thereby making the solution of the forward modeling problem onerous and inefficient. We introduce a time-domain perturbation theory for anisotropic permeable media to efficiently and accurately approximate the transient pressure response of spatially complex aquifers. Although theoretically valid for any spatially dependent rock/fluid property, our single-phase flow study emphasizes arbitrary spatial variations of permeability and anisotropy, which constitute key objectives of hydraulic-testing operations. Contrary to time-honored techniques, the perturbation method invokes pressure-flow deconvolution to compute the background medium's permeability sensitivity function (PSF) with a single numerical simulation run. Subsequently, the first-order term of the perturbed solution is obtained by solving an integral equation that weighs the spatial variations of permeability with the spatial-dependent and time-dependent PSF. Finally, discrete convolution transforms the constant-flow approximation to arbitrary multirate conditions. Multidimensional numerical simulation studies for a wide range of single-well field conditions indicate that perturbed solutions can be computed in less than a few CPU seconds with relative errors in pressure of <5%, corresponding to perturbations in background permeability of up to two orders of magnitude. Our work confirms that the proposed joint perturbation-convolution (JPC) method is an efficient alternative to analytical and numerical solutions for accurate modeling of pressure-diffusion phenomena induced by Neumann or Dirichlet boundary conditions.

Improved Discrete Ordinate Solutions in the Presence of an Anisotropically Reflecting Lower Boundary: Upgrades of the DISORT Computational Tool

NASA Technical Reports Server (NTRS)

Lin, Z.; Stamnes, S.; Jin, Z.; Laszlo, I.; Tsay, S. C.; Wiscombe, W. J.; Stamnes, K.

2015-01-01

A successor version 3 of DISORT (DISORT3) is presented with important upgrades that improve the accuracy, efficiency, and stability of the algorithm. Compared with version 2 (DISORT2 released in 2000) these upgrades include (a) a redesigned BRDF computation that improves both speed and accuracy, (b) a revised treatment of the single scattering correction, and (c) additional efficiency and stability upgrades for beam sources. In DISORT3 the BRDF computation is improved in the following three ways: (i) the Fourier decomposition is prepared "off-line", thus avoiding the repeated internal computations done in DISORT2; (ii) a large enough number of terms in the Fourier expansion of the BRDF is employed to guarantee accurate values of the expansion coefficients (default is 200 instead of 50 in DISORT2); (iii) in the post processing step the reflection of the direct attenuated beam from the lower boundary is included resulting in a more accurate single scattering correction. These improvements in the treatment of the BRDF have led to improved accuracy and a several-fold increase in speed. In addition, the stability of beam sources has been improved by removing a singularity occurring when the cosine of the incident beam angle is too close to the reciprocal of any of the eigenvalues. The efficiency for beam sources has been further improved from reducing by a factor of 2 (compared to DISORT2) the dimension of the linear system of equations that must be solved to obtain the particular solutions, and by replacing the LINPAK routines used in DISORT2 by LAPACK 3.5 in DISORT3. These beam source stability and efficiency upgrades bring enhanced stability and an additional 5-7% improvement in speed. Numerical results are provided to demonstrate and quantify the improvements in accuracy and efficiency of DISORT3 compared to DISORT2.

Vectorization of transport and diffusion computations on the CDC Cyber 205

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

Abu-Shumays, I.K.

1986-01-01

The development and testing of alternative numerical methods and computational algorithms specifically designed for the vectorization of transport and diffusion computations on a Control Data Corporation (CDC) Cyber 205 vector computer are described. Two solution methods for the discrete ordinates approximation to the transport equation are summarized and compared. Factors of 4 to 7 reduction in run times for certain large transport problems were achieved on a Cyber 205 as compared with run times on a CDC-7600. The solution of tridiagonal systems of linear equations, central to several efficient numerical methods for multidimensional diffusion computations and essential for fluid flowmore » and other physics and engineering problems, is also dealt with. Among the methods tested, a combined odd-even cyclic reduction and modified Cholesky factorization algorithm for solving linear symmetric positive definite tridiagonal systems is found to be the most effective for these systems on a Cyber 205. For large tridiagonal systems, computation with this algorithm is an order of magnitude faster on a Cyber 205 than computation with the best algorithm for tridiagonal systems on a CDC-7600.« less

Combined Numerical/Analytical Perturbation Solutions of the Navier-Stokes Equations for Aerodynamic Ejector/Mixer Nozzle Flows

NASA Technical Reports Server (NTRS)

DeChant, Lawrence Justin

1998-01-01

In spite of rapid advances in both scalar and parallel computational tools, the large number of variables involved in both design and inverse problems make the use of sophisticated fluid flow models impractical, With this restriction, it is concluded that an important family of methods for mathematical/computational development are reduced or approximate fluid flow models. In this study a combined perturbation/numerical modeling methodology is developed which provides a rigorously derived family of solutions. The mathematical model is computationally more efficient than classical boundary layer but provides important two-dimensional information not available using quasi-1-d approaches. An additional strength of the current methodology is its ability to locally predict static pressure fields in a manner analogous to more sophisticated parabolized Navier Stokes (PNS) formulations. To resolve singular behavior, the model utilizes classical analytical solution techniques. Hence, analytical methods have been combined with efficient numerical methods to yield an efficient hybrid fluid flow model. In particular, the main objective of this research has been to develop a system of analytical and numerical ejector/mixer nozzle models, which require minimal empirical input. A computer code, DREA Differential Reduced Ejector/mixer Analysis has been developed with the ability to run sufficiently fast so that it may be used either as a subroutine or called by an design optimization routine. Models are of direct use to the High Speed Civil Transport Program (a joint government/industry project seeking to develop an economically.viable U.S. commercial supersonic transport vehicle) and are currently being adopted by both NASA and industry. Experimental validation of these models is provided by comparison to results obtained from open literature and Limited Exclusive Right Distribution (LERD) sources, as well as dedicated experiments performed at Texas A&M. These experiments have been performed using a hydraulic/gas flow analog. Results of comparisons of DREA computations with experimental data, which include entrainment, thrust, and local profile information, are overall good. Computational time studies indicate that DREA provides considerably more information at a lower computational cost than contemporary ejector nozzle design models. Finally. physical limitations of the method, deviations from experimental data, potential improvements and alternative formulations are described. This report represents closure to the NASA Graduate Researchers Program. Versions of the DREA code and a user's guide may be obtained from the NASA Lewis Research Center.

A CLASS OF RECONSTRUCTED DISCONTINUOUS GALERKIN METHODS IN COMPUTATIONAL FLUID DYNAMICS

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

Hong Luo; Yidong Xia; Robert Nourgaliev

2011-05-01

A class of reconstructed discontinuous Galerkin (DG) methods is presented to solve compressible flow problems on arbitrary grids. The idea is to combine the efficiency of the reconstruction methods in finite volume methods and the accuracy of the DG methods to obtain a better numerical algorithm in computational fluid dynamics. The beauty of the resulting reconstructed discontinuous Galerkin (RDG) methods is that they provide a unified formulation for both finite volume and DG methods, and contain both classical finite volume and standard DG methods as two special cases of the RDG methods, and thus allow for a direct efficiency comparison.more » Both Green-Gauss and least-squares reconstruction methods and a least-squares recovery method are presented to obtain a quadratic polynomial representation of the underlying linear discontinuous Galerkin solution on each cell via a so-called in-cell reconstruction process. The devised in-cell reconstruction is aimed to augment the accuracy of the discontinuous Galerkin method by increasing the order of the underlying polynomial solution. These three reconstructed discontinuous Galerkin methods are used to compute a variety of compressible flow problems on arbitrary meshes to assess their accuracy. The numerical experiments demonstrate that all three reconstructed discontinuous Galerkin methods can significantly improve the accuracy of the underlying second-order DG method, although the least-squares reconstructed DG method provides the best performance in terms of both accuracy, efficiency, and robustness.« less

MC-GenomeKey: a multicloud system for the detection and annotation of genomic variants.

PubMed

Elshazly, Hatem; Souilmi, Yassine; Tonellato, Peter J; Wall, Dennis P; Abouelhoda, Mohamed

2017-01-20

Next Generation Genome sequencing techniques became affordable for massive sequencing efforts devoted to clinical characterization of human diseases. However, the cost of providing cloud-based data analysis of the mounting datasets remains a concerning bottleneck for providing cost-effective clinical services. To address this computational problem, it is important to optimize the variant analysis workflow and the used analysis tools to reduce the overall computational processing time, and concomitantly reduce the processing cost. Furthermore, it is important to capitalize on the use of the recent development in the cloud computing market, which have witnessed more providers competing in terms of products and prices. In this paper, we present a new package called MC-GenomeKey (Multi-Cloud GenomeKey) that efficiently executes the variant analysis workflow for detecting and annotating mutations using cloud resources from different commercial cloud providers. Our package supports Amazon, Google, and Azure clouds, as well as, any other cloud platform based on OpenStack. Our package allows different scenarios of execution with different levels of sophistication, up to the one where a workflow can be executed using a cluster whose nodes come from different clouds. MC-GenomeKey also supports scenarios to exploit the spot instance model of Amazon in combination with the use of other cloud platforms to provide significant cost reduction. To the best of our knowledge, this is the first solution that optimizes the execution of the workflow using computational resources from different cloud providers. MC-GenomeKey provides an efficient multicloud based solution to detect and annotate mutations. The package can run in different commercial cloud platforms, which enables the user to seize the best offers. The package also provides a reliable means to make use of the low-cost spot instance model of Amazon, as it provides an efficient solution to the sudden termination of spot machines as a result of a sudden price increase. The package has a web-interface and it is available for free for academic use.

A fast marching algorithm for the factored eikonal equation

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

Treister, Eran, E-mail: erantreister@gmail.com; Haber, Eldad, E-mail: haber@math.ubc.ca; Department of Mathematics, The University of British Columbia, Vancouver, BC

The eikonal equation is instrumental in many applications in several fields ranging from computer vision to geoscience. This equation can be efficiently solved using the iterative Fast Sweeping (FS) methods and the direct Fast Marching (FM) methods. However, when used for a point source, the original eikonal equation is known to yield inaccurate numerical solutions, because of a singularity at the source. In this case, the factored eikonal equation is often preferred, and is known to yield a more accurate numerical solution. One application that requires the solution of the eikonal equation for point sources is travel time tomography. Thismore » inverse problem may be formulated using the eikonal equation as a forward problem. While this problem has been solved using FS in the past, the more recent choice for applying it involves FM methods because of the efficiency in which sensitivities can be obtained using them. However, while several FS methods are available for solving the factored equation, the FM method is available only for the original eikonal equation. In this paper we develop a Fast Marching algorithm for the factored eikonal equation, using both first and second order finite-difference schemes. Our algorithm follows the same lines as the original FM algorithm and requires the same computational effort. In addition, we show how to obtain sensitivities using this FM method and apply travel time tomography, formulated as an inverse factored eikonal equation. Numerical results in two and three dimensions show that our algorithm solves the factored eikonal equation efficiently, and demonstrate the achieved accuracy for computing the travel time. We also demonstrate a recovery of a 2D and 3D heterogeneous medium by travel time tomography using the eikonal equation for forward modeling and inversion by Gauss–Newton.« less

Unstructured Mesh Methods for the Simulation of Hypersonic Flows

NASA Technical Reports Server (NTRS)

Peraire, Jaime; Bibb, K. L. (Technical Monitor)

2001-01-01

This report describes the research work undertaken at the Massachusetts Institute of Technology. The aim of this research is to identify effective algorithms and methodologies for the efficient and routine solution of hypersonic viscous flows about re-entry vehicles. For over ten years we have received support from NASA to develop unstructured mesh methods for Computational Fluid Dynamics. As a result of this effort a methodology based on the use, of unstructured adapted meshes of tetrahedra and finite volume flow solvers has been developed. A number of gridding algorithms flow solvers, and adaptive strategies have been proposed. The most successful algorithms developed from the basis of the unstructured mesh system FELISA. The FELISA system has been extensively for the analysis of transonic and hypersonic flows about complete vehicle configurations. The system is highly automatic and allows for the routine aerodynamic analysis of complex configurations starting from CAD data. The code has been parallelized and utilizes efficient solution algorithms. For hypersonic flows, a version of the, code which incorporates real gas effects, has been produced. One of the latest developments before the start of this grant was to extend the system to include viscous effects. This required the development of viscous generators, capable of generating the anisotropic grids required to represent boundary layers, and viscous flow solvers. In figures I and 2, we show some sample hypersonic viscous computations using the developed viscous generators and solvers. Although these initial results were encouraging, it became apparent that in order to develop a fully functional capability for viscous flows, several advances in gridding, solution accuracy, robustness and efficiency were required. As part of this research we have developed: 1) automatic meshing techniques and the corresponding computer codes have been delivered to NASA and implemented into the GridEx system, 2) a finite element algorithm for the solution of the viscous compressible flow equations which can solve flows all the way down to the incompressible limit and that can use higher order (quadratic) approximations leading to highly accurate answers, and 3) and iterative algebraic multigrid solution techniques.

Rapid optimization of multiple-burn rocket flights.

NASA Technical Reports Server (NTRS)

Brown, K. R.; Harrold, E. F.; Johnson, G. W.

1972-01-01

Different formulations of the fuel optimization problem for multiple burn trajectories are considered. It is shown that certain customary idealizing assumptions lead to an ill-posed optimization problem for which no solution exists. Several ways are discussed for avoiding such difficulties by more realistic problem statements. An iterative solution of the boundary value problem is presented together with efficient coast arc computations, the right end conditions for various orbital missions, and some test results.

Essentially nonoscillatory postprocessing filtering methods

NASA Technical Reports Server (NTRS)

Lafon, F.; Osher, S.

1992-01-01

High order accurate centered flux approximations used in the computation of numerical solutions to nonlinear partial differential equations produce large oscillations in regions of sharp transitions. Here, we present a new class of filtering methods denoted by Essentially Nonoscillatory Least Squares (ENOLS), which constructs an upgraded filtered solution that is close to the physically correct weak solution of the original evolution equation. Our method relies on the evaluation of a least squares polynomial approximation to oscillatory data using a set of points which is determined via the ENO network. Numerical results are given in one and two space dimensions for both scalar and systems of hyperbolic conservation laws. Computational running time, efficiency, and robustness of method are illustrated in various examples such as Riemann initial data for both Burgers' and Euler's equations of gas dynamics. In all standard cases, the filtered solution appears to converge numerically to the correct solution of the original problem. Some interesting results based on nonstandard central difference schemes, which exactly preserve entropy, and have been recently shown generally not to be weakly convergent to a solution of the conservation law, are also obtained using our filters.

Efficiency Evaluation of Food Waste Materials for the Removal of Metals and Metalloids from Complex Multi-Element Solutions

PubMed Central

Giuliano, Antonella; Astolfi, Maria Luisa; Congedo, Rossana; Masotti, Andrea; Canepari, Silvia

2018-01-01

Recent studies have shown the potential of food waste materials as low cost adsorbents for the removal of heavy metals and toxic elements from wastewater. However, the adsorption experiments have been performed in heterogeneous conditions, consequently it is difficult to compare the efficiency of the individual adsorbents. In this study, the adsorption capacities of 12 food waste materials were evaluated by comparing the adsorbents’ efficiency for the removal of 23 elements from complex multi-element solutions, maintaining homogeneous experimental conditions. The examined materials resulted to be extremely efficient for the adsorption of many elements from synthetic multi-element solutions as well as from a heavy metal wastewater. The 12 adsorbent surfaces were analyzed by Fourier transform infrared spectroscopy and showed different types and amounts of functional groups, which demonstrated to act as adsorption active sites for various elements. By multivariate statistical computations of the obtained data, the 12 food waste materials were grouped in five clusters characterized by different elements’ removal efficiency which resulted to be in correlation with the specific adsorbents’ chemical structures. Banana peel, watermelon peel and grape waste resulted the least selective and the most efficient food waste materials for the removal of most of the elements. PMID:29495363

Efficiency Evaluation of Food Waste Materials for the Removal of Metals and Metalloids from Complex Multi-Element Solutions.

PubMed

Massimi, Lorenzo; Giuliano, Antonella; Astolfi, Maria Luisa; Congedo, Rossana; Masotti, Andrea; Canepari, Silvia

2018-02-26

Recent studies have shown the potential of food waste materials as low cost adsorbents for the removal of heavy metals and toxic elements from wastewater. However, the adsorption experiments have been performed in heterogeneous conditions, consequently it is difficult to compare the efficiency of the individual adsorbents. In this study, the adsorption capacities of 12 food waste materials were evaluated by comparing the adsorbents' efficiency for the removal of 23 elements from complex multi-element solutions, maintaining homogeneous experimental conditions. The examined materials resulted to be extremely efficient for the adsorption of many elements from synthetic multi-element solutions as well as from a heavy metal wastewater. The 12 adsorbent surfaces were analyzed by Fourier transform infrared spectroscopy and showed different types and amounts of functional groups, which demonstrated to act as adsorption active sites for various elements. By multivariate statistical computations of the obtained data, the 12 food waste materials were grouped in five clusters characterized by different elements' removal efficiency which resulted to be in correlation with the specific adsorbents' chemical structures. Banana peel, watermelon peel and grape waste resulted the least selective and the most efficient food waste materials for the removal of most of the elements.

Aeroacoustic Simulation of Nose Landing Gear on Adaptive Unstructured Grids With FUN3D

NASA Technical Reports Server (NTRS)

Vatsa, Veer N.; Khorrami, Mehdi R.; Park, Michael A.; Lockard, David P.

2013-01-01

Numerical simulations have been performed for a partially-dressed, cavity-closed nose landing gear configuration that was tested in NASA Langley s closed-wall Basic Aerodynamic Research Tunnel (BART) and in the University of Florida's open-jet acoustic facility known as the UFAFF. The unstructured-grid flow solver FUN3D, developed at NASA Langley Research center, is used to compute the unsteady flow field for this configuration. Starting with a coarse grid, a series of successively finer grids were generated using the adaptive gridding methodology available in the FUN3D code. A hybrid Reynolds-averaged Navier-Stokes/large eddy simulation (RANS/LES) turbulence model is used for these computations. Time-averaged and instantaneous solutions obtained on these grids are compared with the measured data. In general, the correlation with the experimental data improves with grid refinement. A similar trend is observed for sound pressure levels obtained by using these CFD solutions as input to a FfowcsWilliams-Hawkings noise propagation code to compute the farfield noise levels. In general, the numerical solutions obtained on adapted grids compare well with the hand-tuned enriched fine grid solutions and experimental data. In addition, the grid adaption strategy discussed here simplifies the grid generation process, and results in improved computational efficiency of CFD simulations.

[Clinical skills and outcomes of chair-side computer aided design and computer aided manufacture system].

PubMed

Yu, Q

2018-04-09

Computer aided design and computer aided manufacture (CAD/CAM) technology is a kind of oral digital system which is applied to clinical diagnosis and treatment. It overturns the traditional pattern, and provides a solution to restore defect tooth quickly and efficiently. In this paper we mainly discuss the clinical skills of chair-side CAD/CAM system, including tooth preparation, digital impression, the three-dimensional design of prosthesis, numerical control machining, clinical bonding and so on, and review the outcomes of several common kinds of materials at the same time.

Field-Programmable Gate Array Computer in Structural Analysis: An Initial Exploration

NASA Technical Reports Server (NTRS)

Singleterry, Robert C., Jr.; Sobieszczanski-Sobieski, Jaroslaw; Brown, Samuel

2002-01-01

This paper reports on an initial assessment of using a Field-Programmable Gate Array (FPGA) computational device as a new tool for solving structural mechanics problems. A FPGA is an assemblage of binary gates arranged in logical blocks that are interconnected via software in a manner dependent on the algorithm being implemented and can be reprogrammed thousands of times per second. In effect, this creates a computer specialized for the problem that automatically exploits all the potential for parallel computing intrinsic in an algorithm. This inherent parallelism is the most important feature of the FPGA computational environment. It is therefore important that if a problem offers a choice of different solution algorithms, an algorithm of a higher degree of inherent parallelism should be selected. It is found that in structural analysis, an 'analog computer' style of programming, which solves problems by direct simulation of the terms in the governing differential equations, yields a more favorable solution algorithm than current solution methods. This style of programming is facilitated by a 'drag-and-drop' graphic programming language that is supplied with the particular type of FPGA computer reported in this paper. Simple examples in structural dynamics and statics illustrate the solution approach used. The FPGA system also allows linear scalability in computing capability. As the problem grows, the number of FPGA chips can be increased with no loss of computing efficiency due to data flow or algorithmic latency that occurs when a single problem is distributed among many conventional processors that operate in parallel. This initial assessment finds the FPGA hardware and software to be in their infancy in regard to the user conveniences; however, they have enormous potential for shrinking the elapsed time of structural analysis solutions if programmed with algorithms that exhibit inherent parallelism and linear scalability. This potential warrants further development of FPGA-tailored algorithms for structural analysis.

Adaptive time stepping for fluid-structure interaction solvers

DOE PAGES

Mayr, M.; Wall, W. A.; Gee, M. W.

2017-12-22

In this work, a novel adaptive time stepping scheme for fluid-structure interaction (FSI) problems is proposed that allows for controlling the accuracy of the time-discrete solution. Furthermore, it eases practical computations by providing an efficient and very robust time step size selection. This has proven to be very useful, especially when addressing new physical problems, where no educated guess for an appropriate time step size is available. The fluid and the structure field, but also the fluid-structure interface are taken into account for the purpose of a posteriori error estimation, rendering it easy to implement and only adding negligible additionalmore » cost. The adaptive time stepping scheme is incorporated into a monolithic solution framework, but can straightforwardly be applied to partitioned solvers as well. The basic idea can be extended to the coupling of an arbitrary number of physical models. Accuracy and efficiency of the proposed method are studied in a variety of numerical examples ranging from academic benchmark tests to complex biomedical applications like the pulsatile blood flow through an abdominal aortic aneurysm. Finally, the demonstrated accuracy of the time-discrete solution in combination with reduced computational cost make this algorithm very appealing in all kinds of FSI applications.« less

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.

Adaptive time stepping for fluid-structure interaction solvers

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

Mayr, M.; Wall, W. A.; Gee, M. W.

In this work, a novel adaptive time stepping scheme for fluid-structure interaction (FSI) problems is proposed that allows for controlling the accuracy of the time-discrete solution. Furthermore, it eases practical computations by providing an efficient and very robust time step size selection. This has proven to be very useful, especially when addressing new physical problems, where no educated guess for an appropriate time step size is available. The fluid and the structure field, but also the fluid-structure interface are taken into account for the purpose of a posteriori error estimation, rendering it easy to implement and only adding negligible additionalmore » cost. The adaptive time stepping scheme is incorporated into a monolithic solution framework, but can straightforwardly be applied to partitioned solvers as well. The basic idea can be extended to the coupling of an arbitrary number of physical models. Accuracy and efficiency of the proposed method are studied in a variety of numerical examples ranging from academic benchmark tests to complex biomedical applications like the pulsatile blood flow through an abdominal aortic aneurysm. Finally, the demonstrated accuracy of the time-discrete solution in combination with reduced computational cost make this algorithm very appealing in all kinds of FSI applications.« less

Metalevel programming in robotics: Some issues

NASA Technical Reports Server (NTRS)

Kumarn, A.; Parameswaran, N.

1987-01-01

Computing in robotics has two important requirements: efficiency and flexibility. Algorithms for robot actions are implemented usually in procedural languages such as VAL and AL. But, since their excessive bindings create inflexible structures of computation, it is proposed that Logic Programming is a more suitable language for robot programming due to its non-determinism, declarative nature, and provision for metalevel programming. Logic Programming, however, results in inefficient computations. As a solution to this problem, researchers discuss a framework in which controls can be described to improve efficiency. They have divided controls into: (1) in-code and (2) metalevel and discussed them with reference to selection of rules and dataflow. Researchers illustrated the merit of Logic Programming by modelling the motion of a robot from one point to another avoiding obstacles.

A computational approach for hypersonic nonequilibrium radiation utilizing space partition algorithm and Gauss quadrature

NASA Astrophysics Data System (ADS)

Shang, J. S.; Andrienko, D. A.; Huang, P. G.; Surzhikov, S. T.

2014-06-01

An efficient computational capability for nonequilibrium radiation simulation via the ray tracing technique has been accomplished. The radiative rate equation is iteratively coupled with the aerodynamic conservation laws including nonequilibrium chemical and chemical-physical kinetic models. The spectral properties along tracing rays are determined by a space partition algorithm of the nearest neighbor search process, and the numerical accuracy is further enhanced by a local resolution refinement using the Gauss-Lobatto polynomial. The interdisciplinary governing equations are solved by an implicit delta formulation through the diminishing residual approach. The axisymmetric radiating flow fields over the reentry RAM-CII probe have been simulated and verified with flight data and previous solutions by traditional methods. A computational efficiency gain nearly forty times is realized over that of the existing simulation procedures.

Human motion planning based on recursive dynamics and optimal control techniques

NASA Technical Reports Server (NTRS)

Lo, Janzen; Huang, Gang; Metaxas, Dimitris

2002-01-01

This paper presents an efficient optimal control and recursive dynamics-based computer animation system for simulating and controlling the motion of articulated figures. A quasi-Newton nonlinear programming technique (super-linear convergence) is implemented to solve minimum torque-based human motion-planning problems. The explicit analytical gradients needed in the dynamics are derived using a matrix exponential formulation and Lie algebra. Cubic spline functions are used to make the search space for an optimal solution finite. Based on our formulations, our method is well conditioned and robust, in addition to being computationally efficient. To better illustrate the efficiency of our method, we present results of natural looking and physically correct human motions for a variety of human motion tasks involving open and closed loop kinematic chains.

Robust and efficient overset grid assembly for partitioned unstructured meshes

NASA Astrophysics Data System (ADS)

Roget, Beatrice; Sitaraman, Jayanarayanan

2014-03-01

This paper presents a method to perform efficient and automated Overset Grid Assembly (OGA) on a system of overlapping unstructured meshes in a parallel computing environment where all meshes are partitioned into multiple mesh-blocks and processed on multiple cores. The main task of the overset grid assembler is to identify, in parallel, among all points in the overlapping mesh system, at which points the flow solution should be computed (field points), interpolated (receptor points), or ignored (hole points). Point containment search or donor search, an algorithm to efficiently determine the cell that contains a given point, is the core procedure necessary for accomplishing this task. Donor search is particularly challenging for partitioned unstructured meshes because of the complex irregular boundaries that are often created during partitioning.

Accelerating Full Configuration Interaction Calculations for Nuclear Structure

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

Yang, Chao; Sternberg, Philip; Maris, Pieter

2008-04-14

One of the emerging computational approaches in nuclear physics is the full configuration interaction (FCI) method for solving the many-body nuclear Hamiltonian in a sufficiently large single-particle basis space to obtain exact answers - either directly or by extrapolation. The lowest eigenvalues and correspondingeigenvectors for very large, sparse and unstructured nuclear Hamiltonian matrices are obtained and used to evaluate additional experimental quantities. These matrices pose a significant challenge to the design and implementation of efficient and scalable algorithms for obtaining solutions on massively parallel computer systems. In this paper, we describe the computational strategies employed in a state-of-the-art FCI codemore » MFDn (Many Fermion Dynamics - nuclear) as well as techniques we recently developed to enhance the computational efficiency of MFDn. We will demonstrate the current capability of MFDn and report the latest performance improvement we have achieved. We will also outline our future research directions.« less

Computational Particle Dynamic Simulations on Multicore Processors (CPDMu) Final Report Phase I

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

Schmalz, Mark S

2011-07-24

Statement of Problem - Department of Energy has many legacy codes for simulation of computational particle dynamics and computational fluid dynamics applications that are designed to run on sequential processors and are not easily parallelized. Emerging high-performance computing architectures employ massively parallel multicore architectures (e.g., graphics processing units) to increase throughput. Parallelization of legacy simulation codes is a high priority, to achieve compatibility, efficiency, accuracy, and extensibility. General Statement of Solution - A legacy simulation application designed for implementation on mainly-sequential processors has been represented as a graph G. Mathematical transformations, applied to G, produce a graph representation {und G}more » for a high-performance architecture. Key computational and data movement kernels of the application were analyzed/optimized for parallel execution using the mapping G {yields} {und G}, which can be performed semi-automatically. This approach is widely applicable to many types of high-performance computing systems, such as graphics processing units or clusters comprised of nodes that contain one or more such units. Phase I Accomplishments - Phase I research decomposed/profiled computational particle dynamics simulation code for rocket fuel combustion into low and high computational cost regions (respectively, mainly sequential and mainly parallel kernels), with analysis of space and time complexity. Using the research team's expertise in algorithm-to-architecture mappings, the high-cost kernels were transformed, parallelized, and implemented on Nvidia Fermi GPUs. Measured speedups (GPU with respect to single-core CPU) were approximately 20-32X for realistic model parameters, without final optimization. Error analysis showed no loss of computational accuracy. Commercial Applications and Other Benefits - The proposed research will constitute a breakthrough in solution of problems related to efficient parallel computation of particle and fluid dynamics simulations. These problems occur throughout DOE, military and commercial sectors: the potential payoff is high. We plan to license or sell the solution to contractors for military and domestic applications such as disaster simulation (aerodynamic and hydrodynamic), Government agencies (hydrological and environmental simulations), and medical applications (e.g., in tomographic image reconstruction). Keywords - High-performance Computing, Graphic Processing Unit, Fluid/Particle Simulation. Summary for Members of Congress - Department of Energy has many simulation codes that must compute faster, to be effective. The Phase I research parallelized particle/fluid simulations for rocket combustion, for high-performance computing systems.« less

People efficiently explore the solution space of the computationally intractable traveling salesman problem to find near-optimal tours.

PubMed

Acuña, Daniel E; Parada, Víctor

2010-07-29

Humans need to solve computationally intractable problems such as visual search, categorization, and simultaneous learning and acting, yet an increasing body of evidence suggests that their solutions to instantiations of these problems are near optimal. Computational complexity advances an explanation to this apparent paradox: (1) only a small portion of instances of such problems are actually hard, and (2) successful heuristics exploit structural properties of the typical instance to selectively improve parts that are likely to be sub-optimal. We hypothesize that these two ideas largely account for the good performance of humans on computationally hard problems. We tested part of this hypothesis by studying the solutions of 28 participants to 28 instances of the Euclidean Traveling Salesman Problem (TSP). Participants were provided feedback on the cost of their solutions and were allowed unlimited solution attempts (trials). We found a significant improvement between the first and last trials and that solutions are significantly different from random tours that follow the convex hull and do not have self-crossings. More importantly, we found that participants modified their current better solutions in such a way that edges belonging to the optimal solution ("good" edges) were significantly more likely to stay than other edges ("bad" edges), a hallmark of structural exploitation. We found, however, that more trials harmed the participants' ability to tell good from bad edges, suggesting that after too many trials the participants "ran out of ideas." In sum, we provide the first demonstration of significant performance improvement on the TSP under repetition and feedback and evidence that human problem-solving may exploit the structure of hard problems paralleling behavior of state-of-the-art heuristics.

People Efficiently Explore the Solution Space of the Computationally Intractable Traveling Salesman Problem to Find Near-Optimal Tours

PubMed Central

Acuña, Daniel E.; Parada, Víctor

2010-01-01

Humans need to solve computationally intractable problems such as visual search, categorization, and simultaneous learning and acting, yet an increasing body of evidence suggests that their solutions to instantiations of these problems are near optimal. Computational complexity advances an explanation to this apparent paradox: (1) only a small portion of instances of such problems are actually hard, and (2) successful heuristics exploit structural properties of the typical instance to selectively improve parts that are likely to be sub-optimal. We hypothesize that these two ideas largely account for the good performance of humans on computationally hard problems. We tested part of this hypothesis by studying the solutions of 28 participants to 28 instances of the Euclidean Traveling Salesman Problem (TSP). Participants were provided feedback on the cost of their solutions and were allowed unlimited solution attempts (trials). We found a significant improvement between the first and last trials and that solutions are significantly different from random tours that follow the convex hull and do not have self-crossings. More importantly, we found that participants modified their current better solutions in such a way that edges belonging to the optimal solution (“good” edges) were significantly more likely to stay than other edges (“bad” edges), a hallmark of structural exploitation. We found, however, that more trials harmed the participants' ability to tell good from bad edges, suggesting that after too many trials the participants “ran out of ideas.” In sum, we provide the first demonstration of significant performance improvement on the TSP under repetition and feedback and evidence that human problem-solving may exploit the structure of hard problems paralleling behavior of state-of-the-art heuristics. PMID:20686597

Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads

PubMed Central

Stone, John E.; Hallock, Michael J.; Phillips, James C.; Peterson, Joseph R.; Luthey-Schulten, Zaida; Schulten, Klaus

2016-01-01

Many of the continuing scientific advances achieved through computational biology are predicated on the availability of ongoing increases in computational power required for detailed simulation and analysis of cellular processes on biologically-relevant timescales. A critical challenge facing the development of future exascale supercomputer systems is the development of new computing hardware and associated scientific applications that dramatically improve upon the energy efficiency of existing solutions, while providing increased simulation, analysis, and visualization performance. Mobile computing platforms have recently become powerful enough to support interactive molecular visualization tasks that were previously only possible on laptops and workstations, creating future opportunities for their convenient use for meetings, remote collaboration, and as head mounted displays for immersive stereoscopic viewing. We describe early experiences adapting several biomolecular simulation and analysis applications for emerging heterogeneous computing platforms that combine power-efficient system-on-chip multi-core CPUs with high-performance massively parallel GPUs. We present low-cost power monitoring instrumentation that provides sufficient temporal resolution to evaluate the power consumption of individual CPU algorithms and GPU kernels. We compare the performance and energy efficiency of scientific applications running on emerging platforms with results obtained on traditional platforms, identify hardware and algorithmic performance bottlenecks that affect the usability of these platforms, and describe avenues for improving both the hardware and applications in pursuit of the needs of molecular modeling tasks on mobile devices and future exascale computers. PMID:27516922

Improving the Efficiency of 3-D Hydrogeological Mixers: Dilution Enhancement Via Coupled Engineering-Induced Transient Flows and Spatial Heterogeneity

NASA Astrophysics Data System (ADS)

Di Dato, Mariaines; de Barros, Felipe P. J.; Fiori, Aldo; Bellin, Alberto

2018-03-01

Natural attenuation and in situ oxidation are commonly considered as low-cost alternatives to ex situ remediation. The efficiency of such remediation techniques is hindered by difficulties in obtaining good dilution and mixing of the contaminant, in particular if the plume deformation is physically constrained by an array of wells, which serves as a containment system. In that case, dilution may be enhanced by inducing an engineered sequence of injections and extractions from such pumping system, which also works as a hydraulic barrier. This way, the aquifer acts as a natural mixer, in a manner similar to the industrialized engineered mixers. Improving the efficiency of hydrogeological mixers is a challenging task, owing to the need to use a 3-D setup while relieving the computational burden. Analytical solutions, though approximated, are a suitable and efficient tool to seek the optimum solution among all possible flow configurations. Here we develop a novel physically based model to demonstrate how the combined spatiotemporal fluctuations of the water fluxes control solute trajectories and residence time distributions and therefore, the effectiveness of contaminant plume dilution and mixing. Our results show how external forcing configurations are capable of inducing distinct time-varying groundwater flow patterns which will yield different solute dilution rates.

KINEMATIC MODELING OF MULTIPHASE SOLUTE TRANSPORT IN THE VADOSE ZONE

EPA Science Inventory

The goal of this research was the development of a computationally efficient simulation model for multiphase flow of organic hazardous waste constituents in the shallow soil environment. Such a model is appropriate for investigation of fate and transport of organic chemicals intr...

The design and implementation of a parallel unstructured Euler solver using software primitives

NASA Technical Reports Server (NTRS)

Das, R.; Mavriplis, D. J.; Saltz, J.; Gupta, S.; Ponnusamy, R.

1992-01-01

This paper is concerned with the implementation of a three-dimensional unstructured grid Euler-solver on massively parallel distributed-memory computer architectures. The goal is to minimize solution time by achieving high computational rates with a numerically efficient algorithm. An unstructured multigrid algorithm with an edge-based data structure has been adopted, and a number of optimizations have been devised and implemented in order to accelerate the parallel communication rates. The implementation is carried out by creating a set of software tools, which provide an interface between the parallelization issues and the sequential code, while providing a basis for future automatic run-time compilation support. Large practical unstructured grid problems are solved on the Intel iPSC/860 hypercube and Intel Touchstone Delta machine. The quantitative effect of the various optimizations are demonstrated, and we show that the combined effect of these optimizations leads to roughly a factor of three performance improvement. The overall solution efficiency is compared with that obtained on the CRAY-YMP vector supercomputer.

Effective orthorhombic anisotropic models for wavefield extrapolation

NASA Astrophysics Data System (ADS)

Ibanez-Jacome, Wilson; Alkhalifah, Tariq; Waheed, Umair bin

2014-09-01

Wavefield extrapolation in orthorhombic anisotropic media incorporates complicated but realistic models to reproduce wave propagation phenomena in the Earth's subsurface. Compared with the representations used for simpler symmetries, such as transversely isotropic or isotropic, orthorhombic models require an extended and more elaborated formulation that also involves more expensive computational processes. The acoustic assumption yields more efficient description of the orthorhombic wave equation that also provides a simplified representation for the orthorhombic dispersion relation. However, such representation is hampered by the sixth-order nature of the acoustic wave equation, as it also encompasses the contribution of shear waves. To reduce the computational cost of wavefield extrapolation in such media, we generate effective isotropic inhomogeneous models that are capable of reproducing the first-arrival kinematic aspects of the orthorhombic wavefield. First, in order to compute traveltimes in vertical orthorhombic media, we develop a stable, efficient and accurate algorithm based on the fast marching method. The derived orthorhombic acoustic dispersion relation, unlike the isotropic or transversely isotropic ones, is represented by a sixth order polynomial equation with the fastest solution corresponding to outgoing P waves in acoustic media. The effective velocity models are then computed by evaluating the traveltime gradients of the orthorhombic traveltime solution, and using them to explicitly evaluate the corresponding inhomogeneous isotropic velocity field. The inverted effective velocity fields are source dependent and produce equivalent first-arrival kinematic descriptions of wave propagation in orthorhombic media. We extrapolate wavefields in these isotropic effective velocity models using the more efficient isotropic operator, and the results compare well, especially kinematically, with those obtained from the more expensive anisotropic extrapolator.

Accurate chemical master equation solution using multi-finite buffers

DOE PAGES

Cao, Youfang; Terebus, Anna; Liang, Jie

2016-06-29

Here, the discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multiscale nature of many networks where reaction rates have a large disparity, directly solving dCMEs is intractable due to the exploding size of the state space. It is important to truncate the state space effectively with quantified errors, so accurate solutions can be computed. It is also important to know if all major probabilistic peaks have been computed. Here we introduce the accurate CME (ACME) algorithm for obtaining direct solutions to dCMEs. With multifinite buffers for reducing the state spacemore » by $O(n!)$, exact steady-state and time-evolving network probability landscapes can be computed. We further describe a theoretical framework of aggregating microstates into a smaller number of macrostates by decomposing a network into independent aggregated birth and death processes and give an a priori method for rapidly determining steady-state truncation errors. The maximal sizes of the finite buffers for a given error tolerance can also be precomputed without costly trial solutions of dCMEs. We show exactly computed probability landscapes of three multiscale networks, namely, a 6-node toggle switch, 11-node phage-lambda epigenetic circuit, and 16-node MAPK cascade network, the latter two with no known solutions. We also show how probabilities of rare events can be computed from first-passage times, another class of unsolved problems challenging for simulation-based techniques due to large separations in time scales. Overall, the ACME method enables accurate and efficient solutions of the dCME for a large class of networks.« less

Accurate chemical master equation solution using multi-finite buffers

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

Cao, Youfang; Terebus, Anna; Liang, Jie

Here, the discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multiscale nature of many networks where reaction rates have a large disparity, directly solving dCMEs is intractable due to the exploding size of the state space. It is important to truncate the state space effectively with quantified errors, so accurate solutions can be computed. It is also important to know if all major probabilistic peaks have been computed. Here we introduce the accurate CME (ACME) algorithm for obtaining direct solutions to dCMEs. With multifinite buffers for reducing the state spacemore » by $O(n!)$, exact steady-state and time-evolving network probability landscapes can be computed. We further describe a theoretical framework of aggregating microstates into a smaller number of macrostates by decomposing a network into independent aggregated birth and death processes and give an a priori method for rapidly determining steady-state truncation errors. The maximal sizes of the finite buffers for a given error tolerance can also be precomputed without costly trial solutions of dCMEs. We show exactly computed probability landscapes of three multiscale networks, namely, a 6-node toggle switch, 11-node phage-lambda epigenetic circuit, and 16-node MAPK cascade network, the latter two with no known solutions. We also show how probabilities of rare events can be computed from first-passage times, another class of unsolved problems challenging for simulation-based techniques due to large separations in time scales. Overall, the ACME method enables accurate and efficient solutions of the dCME for a large class of networks.« less

Spectral Regularization Algorithms for Learning Large Incomplete Matrices.

PubMed

Mazumder, Rahul; Hastie, Trevor; Tibshirani, Robert

2010-03-01

We use convex relaxation techniques to provide a sequence of regularized low-rank solutions for large-scale matrix completion problems. Using the nuclear norm as a regularizer, we provide a simple and very efficient convex algorithm for minimizing the reconstruction error subject to a bound on the nuclear norm. Our algorithm Soft-Impute iteratively replaces the missing elements with those obtained from a soft-thresholded SVD. With warm starts this allows us to efficiently compute an entire regularization path of solutions on a grid of values of the regularization parameter. The computationally intensive part of our algorithm is in computing a low-rank SVD of a dense matrix. Exploiting the problem structure, we show that the task can be performed with a complexity linear in the matrix dimensions. Our semidefinite-programming algorithm is readily scalable to large matrices: for example it can obtain a rank-80 approximation of a 10(6) × 10(6) incomplete matrix with 10(5) observed entries in 2.5 hours, and can fit a rank 40 approximation to the full Netflix training set in 6.6 hours. Our methods show very good performance both in training and test error when compared to other competitive state-of-the art techniques.

Spectral Regularization Algorithms for Learning Large Incomplete Matrices

PubMed Central

Mazumder, Rahul; Hastie, Trevor; Tibshirani, Robert

2010-01-01

We use convex relaxation techniques to provide a sequence of regularized low-rank solutions for large-scale matrix completion problems. Using the nuclear norm as a regularizer, we provide a simple and very efficient convex algorithm for minimizing the reconstruction error subject to a bound on the nuclear norm. Our algorithm Soft-Impute iteratively replaces the missing elements with those obtained from a soft-thresholded SVD. With warm starts this allows us to efficiently compute an entire regularization path of solutions on a grid of values of the regularization parameter. The computationally intensive part of our algorithm is in computing a low-rank SVD of a dense matrix. Exploiting the problem structure, we show that the task can be performed with a complexity linear in the matrix dimensions. Our semidefinite-programming algorithm is readily scalable to large matrices: for example it can obtain a rank-80 approximation of a 106 × 106 incomplete matrix with 105 observed entries in 2.5 hours, and can fit a rank 40 approximation to the full Netflix training set in 6.6 hours. Our methods show very good performance both in training and test error when compared to other competitive state-of-the art techniques. PMID:21552465

Evaluation of Proteus as a Tool for the Rapid Development of Models of Hydrologic Systems

NASA Astrophysics Data System (ADS)

Weigand, T. M.; Farthing, M. W.; Kees, C. E.; Miller, C. T.

2013-12-01

Models of modern hydrologic systems can be complex and involve a variety of operators with varying character. The goal is to implement approximations of such models that are both efficient for the developer and computationally efficient, which is a set of naturally competing objectives. Proteus is a Python-based toolbox that supports prototyping of model formulations as well as a wide variety of modern numerical methods and parallel computing. We used Proteus to develop numerical approximations for three models: Richards' equation, a brine flow model derived using the Thermodynamically Constrained Averaging Theory (TCAT), and a multiphase TCAT-based tumor growth model. For Richards' equation, we investigated discontinuous Galerkin solutions with higher order time integration based on the backward difference formulas. The TCAT brine flow model was implemented using Proteus and a variety of numerical methods were compared to hand coded solutions. Finally, an existing tumor growth model was implemented in Proteus to introduce more advanced numerics and allow the code to be run in parallel. From these three example models, Proteus was found to be an attractive open-source option for rapidly developing high quality code for solving existing and evolving computational science models.

Computational Relativistic Astrophysics Using the Flowfield-Dependent Variation Theory

NASA Technical Reports Server (NTRS)

Richardson, G. A.; Chung, T. J.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Theoretical models, observations and measurements have preoccupied astrophysicists for many centuries. Only in recent years, has the theory of relativity as applied to astrophysical flows met the challenges of how the governing equations can be solved numerically with accuracy and efficiency. Even without the effects of relativity, the physics of magnetohydrodynamic flow instability, turbulence, radiation, and enhanced transport in accretion disks has not been completely resolved. Relativistic effects become pronounced in such cases as jet formation from black hole magnetized accretion disks and also in the study of Gamma-Ray bursts (GRB). Thus, our concern in this paper is to reexamine existing numerical simulation tools as to the accuracy and efficiency of computations and introduce a new approach known as the flowfield-dependent variation (FDV) method. The main feature of the FDV method consists of accommodating discontinuities of shock waves and high gradients of flow variables such as occur in turbulence and unstable motions. In this paper, the physics involved in the solution of relativistic hydrodynamics and solution strategies of the FDV theory are elaborated. The general relativistic astrophysical flow and shock solver (GRAFSS) is introduced, and some simple example problems for Computational Relativistic Astrophysics (CRA) are demonstrated.

Linear static structural and vibration analysis on high-performance computers

NASA Technical Reports Server (NTRS)

Baddourah, M. A.; Storaasli, O. O.; Bostic, S. W.

1993-01-01

Parallel computers offer the oppurtunity to significantly reduce the computation time necessary to analyze large-scale aerospace structures. This paper presents algorithms developed for and implemented on massively-parallel computers hereafter referred to as Scalable High-Performance Computers (SHPC), for the most computationally intensive tasks involved in structural analysis, namely, generation and assembly of system matrices, solution of systems of equations and calculation of the eigenvalues and eigenvectors. Results on SHPC are presented for large-scale structural problems (i.e. models for High-Speed Civil Transport). The goal of this research is to develop a new, efficient technique which extends structural analysis to SHPC and makes large-scale structural analyses tractable.

Supporting Regularized Logistic Regression Privately and Efficiently.

PubMed

Li, Wenfa; Liu, Hongzhe; Yang, Peng; Xie, Wei

2016-01-01

As one of the most popular statistical and machine learning models, logistic regression with regularization has found wide adoption in biomedicine, social sciences, information technology, and so on. These domains often involve data of human subjects that are contingent upon strict privacy regulations. Concerns over data privacy make it increasingly difficult to coordinate and conduct large-scale collaborative studies, which typically rely on cross-institution data sharing and joint analysis. Our work here focuses on safeguarding regularized logistic regression, a widely-used statistical model while at the same time has not been investigated from a data security and privacy perspective. We consider a common use scenario of multi-institution collaborative studies, such as in the form of research consortia or networks as widely seen in genetics, epidemiology, social sciences, etc. To make our privacy-enhancing solution practical, we demonstrate a non-conventional and computationally efficient method leveraging distributing computing and strong cryptography to provide comprehensive protection over individual-level and summary data. Extensive empirical evaluations on several studies validate the privacy guarantee, efficiency and scalability of our proposal. We also discuss the practical implications of our solution for large-scale studies and applications from various disciplines, including genetic and biomedical studies, smart grid, network analysis, etc.

Supporting Regularized Logistic Regression Privately and Efficiently

PubMed Central

Li, Wenfa; Liu, Hongzhe; Yang, Peng; Xie, Wei

2016-01-01

As one of the most popular statistical and machine learning models, logistic regression with regularization has found wide adoption in biomedicine, social sciences, information technology, and so on. These domains often involve data of human subjects that are contingent upon strict privacy regulations. Concerns over data privacy make it increasingly difficult to coordinate and conduct large-scale collaborative studies, which typically rely on cross-institution data sharing and joint analysis. Our work here focuses on safeguarding regularized logistic regression, a widely-used statistical model while at the same time has not been investigated from a data security and privacy perspective. We consider a common use scenario of multi-institution collaborative studies, such as in the form of research consortia or networks as widely seen in genetics, epidemiology, social sciences, etc. To make our privacy-enhancing solution practical, we demonstrate a non-conventional and computationally efficient method leveraging distributing computing and strong cryptography to provide comprehensive protection over individual-level and summary data. Extensive empirical evaluations on several studies validate the privacy guarantee, efficiency and scalability of our proposal. We also discuss the practical implications of our solution for large-scale studies and applications from various disciplines, including genetic and biomedical studies, smart grid, network analysis, etc. PMID:27271738

Finite volume solution of the compressible boundary-layer equations

NASA Technical Reports Server (NTRS)

Loyd, B.; Murman, E. M.

1986-01-01

A box-type finite volume discretization is applied to the integral form of the compressible boundary layer equations. Boundary layer scaling is introduced through the grid construction: streamwise grid lines follow eta = y/h = const., where y is the normal coordinate and h(x) is a scale factor proportional to the boundary layer thickness. With this grid, similarity can be applied explicity to calculate initial conditions. The finite volume method preserves the physical transparency of the integral equations in the discrete approximation. The resulting scheme is accurate, efficient, and conceptually simple. Computations for similar and non-similar flows show excellent agreement with tabulated results, solutions computed with Keller's Box scheme, and experimental data.

Accurate solutions for transonic viscous flow over finite wings

NASA Technical Reports Server (NTRS)

Vatsa, V. N.

1986-01-01

An explicit multistage Runge-Kutta type time-stepping scheme is used for solving the three-dimensional, compressible, thin-layer Navier-Stokes equations. A finite-volume formulation is employed to facilitate treatment of complex grid topologies encountered in three-dimensional calculations. Convergence to steady state is expedited through usage of acceleration techniques. Further numerical efficiency is achieved through vectorization of the computer code. The accuracy of the overall scheme is evaluated by comparing the computed solutions with the experimental data for a finite wing under different test conditions in the transonic regime. A grid refinement study ir conducted to estimate the grid requirements for adequate resolution of salient features of such flows.

Utilizing HDF4 File Content Maps for the Cloud

NASA Technical Reports Server (NTRS)

Lee, Hyokyung Joe

2016-01-01

We demonstrate a prototype study that HDF4 file content map can be used for efficiently organizing data in cloud object storage system to facilitate cloud computing. This approach can be extended to any binary data formats and to any existing big data analytics solution powered by cloud computing because HDF4 file content map project started as long term preservation of NASA data that doesn't require HDF4 APIs to access data.

Fault Tolerant Parallel Implementations of Iterative Algorithms for Optimal Control Problems

DTIC Science & Technology

1988-01-21

p/.V)] steps, but did not discuss any specific parallel implementation. Gajski [51 improved upon this result by performing the SIMD computation in...N = p2. our approach reduces to that of [51, except that Gajski presents the coefficient computation and partial solution phases as a single...8217>. the SIMD algo- rithm presented by Gajski [5] can be most efficiently mapped to a unidirec- tional ring network with broadcasting capability. Based

Finite element analysis and computer graphics visualization of flow around pitching and plunging airfoils

NASA Technical Reports Server (NTRS)

Bratanow, T.; Ecer, A.

1973-01-01

A general computational method for analyzing unsteady flow around pitching and plunging airfoils was developed. The finite element method was applied in developing an efficient numerical procedure for the solution of equations describing the flow around airfoils. The numerical results were employed in conjunction with computer graphics techniques to produce visualization of the flow. The investigation involved mathematical model studies of flow in two phases: (1) analysis of a potential flow formulation and (2) analysis of an incompressible, unsteady, viscous flow from Navier-Stokes equations.

Inverse kinematics of a dual linear actuator pitch/roll heliostat

NASA Astrophysics Data System (ADS)

Freeman, Joshua; Shankar, Balakrishnan; Sundaram, Ganesh

2017-06-01

This work presents a simple, computationally efficient inverse kinematics solution for a pitch/roll heliostat using two linear actuators. The heliostat design and kinematics have been developed, modeled and tested using computer simulation software. A physical heliostat prototype was fabricated to validate the theoretical computations and data. Pitch/roll heliostats have numerous advantages including reduced cost potential and reduced space requirements, with a primary disadvantage being the significantly more complicated kinematics, which are solved here. Novel methods are applied to simplify the inverse kinematics problem which could be applied to other similar problems.

Computer-aided programming for message-passing system; Problems and a solution

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

Wu, M.Y.; Gajski, D.D.

1989-12-01

As the number of processors and the complexity of problems to be solved increase, programming multiprocessing systems becomes more difficult and error-prone. Program development tools are necessary since programmers are not able to develop complex parallel programs efficiently. Parallel models of computation, parallelization problems, and tools for computer-aided programming (CAP) are discussed. As an example, a CAP tool that performs scheduling and inserts communication primitives automatically is described. It also generates the performance estimates and other program quality measures to help programmers in improving their algorithms and programs.

When Does Changing Representation Improve Problem-Solving Performance?

NASA Technical Reports Server (NTRS)

Holte, Robert; Zimmer, Robert; MacDonald, Alan

1992-01-01

The aim of changing representation is the improvement of problem-solving efficiency. For the most widely studied family of methods of change of representation it is shown that the value of a single parameter, called the expulsion factor, is critical in determining (1) whether the change of representation will improve or degrade problem-solving efficiency and (2) whether the solutions produced using the change of representation will or will not be exponentially longer than the shortest solution. A method of computing the expansion factor for a given change of representation is sketched in general and described in detail for homomorphic changes of representation. The results are illustrated with homomorphic decompositions of the Towers of Hanoi problem.

Further investigation on "A multiplicative regularization for force reconstruction"

NASA Astrophysics Data System (ADS)

Aucejo, M.; De Smet, O.

2018-05-01

We have recently proposed a multiplicative regularization to reconstruct mechanical forces acting on a structure from vibration measurements. This method does not require any selection procedure for choosing the regularization parameter, since the amount of regularization is automatically adjusted throughout an iterative resolution process. The proposed iterative algorithm has been developed with performance and efficiency in mind, but it is actually a simplified version of a full iterative procedure not described in the original paper. The present paper aims at introducing the full resolution algorithm and comparing it with its simplified version in terms of computational efficiency and solution accuracy. In particular, it is shown that both algorithms lead to very similar identified solutions.

Fast globally optimal segmentation of cells in fluorescence microscopy images.

PubMed

Bergeest, Jan-Philip; Rohr, Karl

2011-01-01

Accurate and efficient segmentation of cells in fluorescence microscopy images is of central importance for the quantification of protein expression in high-throughput screening applications. We propose a new approach for segmenting cell nuclei which is based on active contours and convex energy functionals. Compared to previous work, our approach determines the global solution. Thus, the approach does not suffer from local minima and the segmentation result does not depend on the initialization. We also suggest a numeric approach for efficiently computing the solution. The performance of our approach has been evaluated using fluorescence microscopy images of different cell types. We have also performed a quantitative comparison with previous segmentation approaches.

Computation of Transonic Nozzle Sound Transmission and Rotor Problems by the Dispersion-Relation-Preserving Scheme

NASA Technical Reports Server (NTRS)

Tam, Christopher K. W.; Aganin, Alexei

2000-01-01

The transonic nozzle transmission problem and the open rotor noise radiation problem are solved computationally. Both are multiple length scales problems. For efficient and accurate numerical simulation, the multiple-size-mesh multiple-time-step Dispersion-Relation-Preserving scheme is used to calculate the time periodic solution. To ensure an accurate solution, high quality numerical boundary conditions are also needed. For the nozzle problem, a set of nonhomogeneous, outflow boundary conditions are required. The nonhomogeneous boundary conditions not only generate the incoming sound waves but also, at the same time, allow the reflected acoustic waves and entropy waves, if present, to exit the computation domain without reflection. For the open rotor problem, there is an apparent singularity at the axis of rotation. An analytic extension approach is developed to provide a high quality axis boundary treatment.

Effect of virtual memory on efficient solution of two model problems

NASA Technical Reports Server (NTRS)

Lambiotte, J. J., Jr.

1977-01-01

Computers with virtual memory architecture allow programs to be written as if they were small enough to be contained in memory. Two types of problems are investigated to show that this luxury can lead to quite an inefficient performance if the programmer does not interact strongly with the characteristics of the operating system when developing the program. The two problems considered are the simultaneous solutions of a large linear system of equations by Gaussian elimination and a model three-dimensional finite-difference problem. The Control Data STAR-100 computer runs are made to demonstrate the inefficiencies of programming the problems in the manner one would naturally do if the problems were indeed, small enough to be contained in memory. Program redesigns are presented which achieve large improvements in performance through changes in the computational procedure and the data base arrangement.

A massively parallel computational approach to coupled thermoelastic/porous gas flow problems

NASA Technical Reports Server (NTRS)

Shia, David; Mcmanus, Hugh L.

1995-01-01

A new computational scheme for coupled thermoelastic/porous gas flow problems is presented. Heat transfer, gas flow, and dynamic thermoelastic governing equations are expressed in fully explicit form, and solved on a massively parallel computer. The transpiration cooling problem is used as an example problem. The numerical solutions have been verified by comparison to available analytical solutions. Transient temperature, pressure, and stress distributions have been obtained. Small spatial oscillations in pressure and stress have been observed, which would be impractical to predict with previously available schemes. Comparisons between serial and massively parallel versions of the scheme have also been made. The results indicate that for small scale problems the serial and parallel versions use practically the same amount of CPU time. However, as the problem size increases the parallel version becomes more efficient than the serial version.

Efficient multiscale magnetic-domain analysis of iron-core material under mechanical stress

NASA Astrophysics Data System (ADS)

Nishikubo, Atsushi; Ito, Shumpei; Mifune, Takeshi; Matsuo, Tetsuji; Kaido, Chikara; Takahashi, Yasuhito; Fujiwara, Koji

2018-05-01

For an efficient analysis of magnetization, a partial-implicit solution method is improved using an assembled domain structure model with six-domain mesoscopic particles exhibiting pinning-type hysteresis. The quantitative analysis of non-oriented silicon steel succeeds in predicting the stress dependence of hysteresis loss with computation times greatly reduced by using the improved partial-implicit method. The effect of cell division along the thickness direction is also evaluated.

Rapid Optimization of External Quantum Efficiency of Thin Film Solar Cells Using Surrogate Modeling of Absorptivity.

PubMed

Kaya, Mine; Hajimirza, Shima

2018-05-25

This paper uses surrogate modeling for very fast design of thin film solar cells with improved solar-to-electricity conversion efficiency. We demonstrate that the wavelength-specific optical absorptivity of a thin film multi-layered amorphous-silicon-based solar cell can be modeled accurately with Neural Networks and can be efficiently approximated as a function of cell geometry and wavelength. Consequently, the external quantum efficiency can be computed by averaging surrogate absorption and carrier recombination contributions over the entire irradiance spectrum in an efficient way. Using this framework, we optimize a multi-layer structure consisting of ITO front coating, metallic back-reflector and oxide layers for achieving maximum efficiency. Our required computation time for an entire model fitting and optimization is 5 to 20 times less than the best previous optimization results based on direct Finite Difference Time Domain (FDTD) simulations, therefore proving the value of surrogate modeling. The resulting optimization solution suggests at least 50% improvement in the external quantum efficiency compared to bare silicon, and 25% improvement compared to a random design.

Space shuttle main engine numerical modeling code modifications and analysis

NASA Technical Reports Server (NTRS)

Ziebarth, John P.

1988-01-01

The user of computational fluid dynamics (CFD) codes must be concerned with the accuracy and efficiency of the codes if they are to be used for timely design and analysis of complicated three-dimensional fluid flow configurations. A brief discussion of how accuracy and efficiency effect the CFD solution process is given. A more detailed discussion of how efficiency can be enhanced by using a few Cray Research Inc. utilities to address vectorization is presented and these utilities are applied to a three-dimensional Navier-Stokes CFD code (INS3D).

A brief overview of computational structures technology related activities at NASA Lewis Research Center

NASA Technical Reports Server (NTRS)

Hopkins, Dale A.

1992-01-01

The presentation gives a partial overview of research and development underway in the Structures Division of LeRC, which collectively is referred to as the Computational Structures Technology Program. The activities in the program are diverse and encompass four major categories: (1) composite materials and structures; (2) probabilistic analysis and reliability; (3) design optimization and expert systems; and (4) computational methods and simulation. The approach of the program is comprehensive and entails exploration of fundamental theories of structural mechanics to accurately represent the complex physics governing engine structural performance, formulation, and implementation of computational techniques and integrated simulation strategies to provide accurate and efficient solutions of the governing theoretical models by exploiting the emerging advances in computer technology, and validation and verification through numerical and experimental tests to establish confidence and define the qualities and limitations of the resulting theoretical models and computational solutions. The program comprises both in-house and sponsored research activities. The remainder of the presentation provides a sample of activities to illustrate the breadth and depth of the program and to demonstrate the accomplishments and benefits that have resulted.

Upwind schemes and bifurcating solutions in real gas computations

NASA Technical Reports Server (NTRS)

Suresh, Ambady; Liou, Meng-Sing

1992-01-01

The area of high speed flow is seeing a renewed interest due to advanced propulsion concepts such as the National Aerospace Plane (NASP), Space Shuttle, and future civil transport concepts. Upwind schemes to solve such flows have become increasingly popular in the last decade due to their excellent shock capturing properties. In the first part of this paper the authors present the extension of the Osher scheme to equilibrium and non-equilibrium gases. For simplicity, the source terms are treated explicitly. Computations based on the above scheme are presented to demonstrate the feasibility, accuracy and efficiency of the proposed scheme. One of the test problems is a Chapman-Jouguet detonation problem for which numerical solutions have been known to bifurcate into spurious weak detonation solutions on coarse grids. Results indicate that the numerical solution obtained depends both on the upwinding scheme used and the limiter employed to obtain second order accuracy. For example, the Osher scheme gives the correct CJ solution when the super-bee limiter is used, but gives the spurious solution when the Van Leer limiter is used. With the Roe scheme the spurious solution is obtained for all limiters.

AN INTEGRAL EQUATION REPRESENTATION OF WIDE-BAND ELECTROMAGNETIC SCATTERING BY THIN SHEETS

EPA Science Inventory

An efficient, accurate numerical modeling scheme has been developed, based on the integral equation solution to compute electromagnetic (EM) responses of thin sheets over a wide frequency band. The thin-sheet approach is useful for simulating the EM response of a fracture system ...

Massively Parallel Solution of Poisson Equation on Coarse Grain MIMD Architectures

NASA Technical Reports Server (NTRS)

Fijany, A.; Weinberger, D.; Roosta, R.; Gulati, S.

1998-01-01

In this paper a new algorithm, designated as Fast Invariant Imbedding algorithm, for solution of Poisson equation on vector and massively parallel MIMD architectures is presented. This algorithm achieves the same optimal computational efficiency as other Fast Poisson solvers while offering a much better structure for vector and parallel implementation. Our implementation on the Intel Delta and Paragon shows that a speedup of over two orders of magnitude can be achieved even for moderate size problems.

Multiple Objective Evolution Strategies (MOES): A User’s Guide to Running the Software

DTIC Science & Technology

2014-11-01

L2-norm distance is computed in parameter space between each pair of solutions in the elite population and tested against the tolerance Dclone, which...the most efficient solutions to the test problems in the Input_Files directory. The developers recommend using mu,kappa,lambda. The mu,kappa,lambda...be used as a sanity test for complicated multimodal problems. Whenever the optimum cannot be reached by a local search, the evolutionary results

Effects of forcefield and sampling method in all-atom simulations of inherently disordered proteins: Application to conformational preferences of human amylin

PubMed Central

Peng, Enxi; Todorova, Nevena

2017-01-01

Although several computational modelling studies have investigated the conformational behaviour of inherently disordered protein (IDP) amylin, discrepancies in identifying its preferred solution conformations still exist between various forcefields and sampling methods used. Human islet amyloid polypeptide has long been a subject of research, both experimentally and theoretically, as the aggregation of this protein is believed to be the lead cause of type-II diabetes. In this work, we present a systematic forcefield assessment using one of the most advanced non-biased sampling techniques, Replica Exchange with Solute Tempering (REST2), by comparing the secondary structure preferences of monomeric amylin in solution. This study also aims to determine the ability of common forcefields to sample a transition of the protein from a helical membrane bound conformation into the disordered solution state of amylin. Our results demonstrated that the CHARMM22* forcefield showed the best ability to sample multiple conformational states inherent for amylin. It is revealed that REST2 yielded results qualitatively consistent with experiments and in quantitative agreement with other sampling methods, however far more computationally efficiently and without any bias. Therefore, combining an unbiased sampling technique such as REST2 with a vigorous forcefield testing could be suggested as an important step in developing an efficient and robust strategy for simulating IDPs. PMID:29023509

Effects of forcefield and sampling method in all-atom simulations of inherently disordered proteins: Application to conformational preferences of human amylin.

PubMed

Peng, Enxi; Todorova, Nevena; Yarovsky, Irene

2017-01-01

Although several computational modelling studies have investigated the conformational behaviour of inherently disordered protein (IDP) amylin, discrepancies in identifying its preferred solution conformations still exist between various forcefields and sampling methods used. Human islet amyloid polypeptide has long been a subject of research, both experimentally and theoretically, as the aggregation of this protein is believed to be the lead cause of type-II diabetes. In this work, we present a systematic forcefield assessment using one of the most advanced non-biased sampling techniques, Replica Exchange with Solute Tempering (REST2), by comparing the secondary structure preferences of monomeric amylin in solution. This study also aims to determine the ability of common forcefields to sample a transition of the protein from a helical membrane bound conformation into the disordered solution state of amylin. Our results demonstrated that the CHARMM22* forcefield showed the best ability to sample multiple conformational states inherent for amylin. It is revealed that REST2 yielded results qualitatively consistent with experiments and in quantitative agreement with other sampling methods, however far more computationally efficiently and without any bias. Therefore, combining an unbiased sampling technique such as REST2 with a vigorous forcefield testing could be suggested as an important step in developing an efficient and robust strategy for simulating IDPs.

Heterogeneous Distributed Computing for Computational Aerosciences

NASA Technical Reports Server (NTRS)

Sunderam, Vaidy S.

1998-01-01

The research supported under this award focuses on heterogeneous distributed computing for high-performance applications, with particular emphasis on computational aerosciences. The overall goal of this project was to and investigate issues in, and develop solutions to, efficient execution of computational aeroscience codes in heterogeneous concurrent computing environments. In particular, we worked in the context of the PVM[1] system and, subsequent to detailed conversion efforts and performance benchmarking, devising novel techniques to increase the efficacy of heterogeneous networked environments for computational aerosciences. Our work has been based upon the NAS Parallel Benchmark suite, but has also recently expanded in scope to include the NAS I/O benchmarks as specified in the NHT-1 document. In this report we summarize our research accomplishments under the auspices of the grant.

Investigation of advanced counterrotation blade configuration concepts for high speed turboprop systems. Task 4: Advanced fan section aerodynamic analysis computer program user's manual

NASA Technical Reports Server (NTRS)

Crook, Andrew J.; Delaney, Robert A.

1992-01-01

The computer program user's manual for the ADPACAPES (Advanced Ducted Propfan Analysis Code-Average Passage Engine Simulation) program is included. The objective of the computer program is development of a three-dimensional Euler/Navier-Stokes flow analysis for fan section/engine geometries containing multiple blade rows and multiple spanwise flow splitters. An existing procedure developed by Dr. J. J. Adamczyk and associates at the NASA Lewis Research Center was modified to accept multiple spanwise splitter geometries and simulate engine core conditions. The numerical solution is based upon a finite volume technique with a four stage Runge-Kutta time marching procedure. Multiple blade row solutions are based upon the average-passage system of equations. The numerical solutions are performed on an H-type grid system, with meshes meeting the requirement of maintaining a common axisymmetric mesh for each blade row grid. The analysis was run on several geometry configurations ranging from one to five blade rows and from one to four radial flow splitters. The efficiency of the solution procedure was shown to be the same as the original analysis.

A comparison of three-dimensional nonequilibrium solution algorithms applied to hypersonic flows with stiff chemical source terms

NASA Technical Reports Server (NTRS)

Palmer, Grant; Venkatapathy, Ethiraj

1993-01-01

Three solution algorithms, explicit underrelaxation, point implicit, and lower upper symmetric Gauss-Seidel (LUSGS), are used to compute nonequilibrium flow around the Apollo 4 return capsule at 62 km altitude. By varying the Mach number, the efficiency and robustness of the solution algorithms were tested for different levels of chemical stiffness. The performance of the solution algorithms degraded as the Mach number and stiffness of the flow increased. At Mach 15, 23, and 30, the LUSGS method produces an eight order of magnitude drop in the L2 norm of the energy residual in 1/3 to 1/2 the Cray C-90 computer time as compared to the point implicit and explicit under-relaxation methods. The explicit under-relaxation algorithm experienced convergence difficulties at Mach 23 and above. At Mach 40 the performance of the LUSGS algorithm deteriorates to the point it is out-performed by the point implicit method. The effects of the viscous terms are investigated. Grid dependency questions are explored.

Swimming in a two-dimensional Brinkman fluid: Computational modeling and regularized solutions

NASA Astrophysics Data System (ADS)

Leiderman, Karin; Olson, Sarah D.

2016-02-01

The incompressible Brinkman equation represents the homogenized fluid flow past obstacles that comprise a small volume fraction. In nondimensional form, the Brinkman equation can be characterized by a single parameter that represents the friction or resistance due to the obstacles. In this work, we derive an exact fundamental solution for 2D Brinkman flow driven by a regularized point force and describe the numerical method to use it in practice. To test our solution and method, we compare numerical results with an analytic solution of a stationary cylinder in a uniform Brinkman flow. Our method is also compared to asymptotic theory; for an infinite-length, undulating sheet of small amplitude, we recover an increasing swimming speed as the resistance is increased. With this computational framework, we study a model swimmer of finite length and observe an enhancement in propulsion and efficiency for small to moderate resistance. Finally, we study the interaction of two swimmers where attraction does not occur when the initial separation distance is larger than the screening length.

Dimension reduction method for SPH equations

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

Tartakovsky, Alexandre M.; Scheibe, Timothy D.

2011-08-26

Smoothed Particle Hydrodynamics model of a complex multiscale processe often results in a system of ODEs with an enormous number of unknowns. Furthermore, a time integration of the SPH equations usually requires time steps that are smaller than the observation time by many orders of magnitude. A direct solution of these ODEs can be extremely expensive. Here we propose a novel dimension reduction method that gives an approximate solution of the SPH ODEs and provides an accurate prediction of the average behavior of the modeled system. The method consists of two main elements. First, effective equationss for evolution of averagemore » variables (e.g. average velocity, concentration and mass of a mineral precipitate) are obtained by averaging the SPH ODEs over the entire computational domain. These effective ODEs contain non-local terms in the form of volume integrals of functions of the SPH variables. Second, a computational closure is used to close the system of the effective equations. The computational closure is achieved via short bursts of the SPH model. The dimension reduction model is used to simulate flow and transport with mixing controlled reactions and mineral precipitation. An SPH model is used model transport at the porescale. Good agreement between direct solutions of the SPH equations and solutions obtained with the dimension reduction method for different boundary conditions confirms the accuracy and computational efficiency of the dimension reduction model. The method significantly accelerates SPH simulations, while providing accurate approximation of the solution and accurate prediction of the average behavior of the system.« less

Progress on a Taylor weak statement finite element algorithm for high-speed aerodynamic flows

NASA Technical Reports Server (NTRS)

Baker, A. J.; Freels, J. D.

1989-01-01

A new finite element numerical Computational Fluid Dynamics (CFD) algorithm has matured to the point of efficiently solving two-dimensional high speed real-gas compressible flow problems in generalized coordinates on modern vector computer systems. The algorithm employs a Taylor Weak Statement classical Galerkin formulation, a variably implicit Newton iteration, and a tensor matrix product factorization of the linear algebra Jacobian under a generalized coordinate transformation. Allowing for a general two-dimensional conservation law system, the algorithm has been exercised on the Euler and laminar forms of the Navier-Stokes equations. Real-gas fluid properties are admitted, and numerical results verify solution accuracy, efficiency, and stability over a range of test problem parameters.

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

PubMed Central

Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.

2012-01-01

It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924

Development of Efficient Real-Fluid Model in Simulating Liquid Rocket Injector Flows

NASA Technical Reports Server (NTRS)

Cheng, Gary; Farmer, Richard

2003-01-01

The characteristics of propellant mixing near the injector have a profound effect on the liquid rocket engine performance. However, the flow features near the injector of liquid rocket engines are extremely complicated, for example supercritical-pressure spray, turbulent mixing, and chemical reactions are present. Previously, a homogeneous spray approach with a real-fluid property model was developed to account for the compressibility and evaporation effects such that thermodynamics properties of a mixture at a wide range of pressures and temperatures can be properly calculated, including liquid-phase, gas- phase, two-phase, and dense fluid regions. The developed homogeneous spray model demonstrated a good success in simulating uni- element shear coaxial injector spray combustion flows. However, the real-fluid model suffered a computational deficiency when applied to a pressure-based computational fluid dynamics (CFD) code. The deficiency is caused by the pressure and enthalpy being the independent variables in the solution procedure of a pressure-based code, whereas the real-fluid model utilizes density and temperature as independent variables. The objective of the present research work is to improve the computational efficiency of the real-fluid property model in computing thermal properties. The proposed approach is called an efficient real-fluid model, and the improvement of computational efficiency is achieved by using a combination of a liquid species and a gaseous species to represent a real-fluid species.

A FAST ITERATIVE METHOD FOR SOLVING THE EIKONAL EQUATION ON TETRAHEDRAL DOMAINS

PubMed Central

Fu, Zhisong; Kirby, Robert M.; Whitaker, Ross T.

2014-01-01

Generating numerical solutions to the eikonal equation and its many variations has a broad range of applications in both the natural and computational sciences. Efficient solvers on cutting-edge, parallel architectures require new algorithms that may not be theoretically optimal, but that are designed to allow asynchronous solution updates and have limited memory access patterns. This paper presents a parallel algorithm for solving the eikonal equation on fully unstructured tetrahedral meshes. The method is appropriate for the type of fine-grained parallelism found on modern massively-SIMD architectures such as graphics processors and takes into account the particular constraints and capabilities of these computing platforms. This work builds on previous work for solving these equations on triangle meshes; in this paper we adapt and extend previous two-dimensional strategies to accommodate three-dimensional, unstructured, tetrahedralized domains. These new developments include a local update strategy with data compaction for tetrahedral meshes that provides solutions on both serial and parallel architectures, with a generalization to inhomogeneous, anisotropic speed functions. We also propose two new update schemes, specialized to mitigate the natural data increase observed when moving to three dimensions, and the data structures necessary for efficiently mapping data to parallel SIMD processors in a way that maintains computational density. Finally, we present descriptions of the implementations for a single CPU, as well as multicore CPUs with shared memory and SIMD architectures, with comparative results against state-of-the-art eikonal solvers. PMID:25221418

Self-adaptive multi-objective harmony search for optimal design of water distribution networks

NASA Astrophysics Data System (ADS)

Choi, Young Hwan; Lee, Ho Min; Yoo, Do Guen; Kim, Joong Hoon

2017-11-01

In multi-objective optimization computing, it is important to assign suitable parameters to each optimization problem to obtain better solutions. In this study, a self-adaptive multi-objective harmony search (SaMOHS) algorithm is developed to apply the parameter-setting-free technique, which is an example of a self-adaptive methodology. The SaMOHS algorithm attempts to remove some of the inconvenience from parameter setting and selects the most adaptive parameters during the iterative solution search process. To verify the proposed algorithm, an optimal least cost water distribution network design problem is applied to three different target networks. The results are compared with other well-known algorithms such as multi-objective harmony search and the non-dominated sorting genetic algorithm-II. The efficiency of the proposed algorithm is quantified by suitable performance indices. The results indicate that SaMOHS can be efficiently applied to the search for Pareto-optimal solutions in a multi-objective solution space.

A novel hybrid genetic algorithm to solve the make-to-order sequence-dependent flow-shop scheduling problem

NASA Astrophysics Data System (ADS)

Mirabi, Mohammad; Fatemi Ghomi, S. M. T.; Jolai, F.

2014-04-01

Flow-shop scheduling problem (FSP) deals with the scheduling of a set of n jobs that visit a set of m machines in the same order. As the FSP is NP-hard, there is no efficient algorithm to reach the optimal solution of the problem. To minimize the holding, delay and setup costs of large permutation flow-shop scheduling problems with sequence-dependent setup times on each machine, this paper develops a novel hybrid genetic algorithm (HGA) with three genetic operators. Proposed HGA applies a modified approach to generate a pool of initial solutions, and also uses an improved heuristic called the iterated swap procedure to improve the initial solutions. We consider the make-to-order production approach that some sequences between jobs are assumed as tabu based on maximum allowable setup cost. In addition, the results are compared to some recently developed heuristics and computational experimental results show that the proposed HGA performs very competitively with respect to accuracy and efficiency of solution.

3D Tensorial Elastodynamics for Isotropic Media on Vertically Deformed Meshes

NASA Astrophysics Data System (ADS)

Shragge, J. C.

2017-12-01

Solutions of the 3D elastodynamic wave equation are sometimes required in industrial and academic applications of elastic reverse-time migration (E-RTM) and full waveform inversion (E-FWI) that involve vertically deformed meshes. Examples include incorporating irregular free-surface topography and handling internal boundaries (e.g., water bottom) directly into the computational meshes. In 3D E-RTM and E-FWI applications, the number of forward modeling simulations can number in the tens of thousands (per iteration), which necessitates the development of stable, accurate and efficient 3D elastodynamics solvers. For topographic scenarios, most finite-difference solution approaches use a change-of-variable strategy that has a number of associated computational challenges, including difficulties in handling of the free-surface boundary condition. In this study, I follow a tensorial approach and use a generalized family of analytic transforms to develop a set of analytic equations for 3D elastodynamics that directly incorporates vertical grid deformations. Importantly, this analytic approach allows for the specification of an analytic free-surface boundary condition appropriate for vertically deformed meshes. These equations are both straightforward and efficient to solve using a velocity-stress formulation with finite-difference (MFD) operators implemented on a fully staggered grid. Moreover, I demonstrate that the use of mimetic finite difference (MFD) methods allows stable, accurate, and efficient numerical solutions to be simulated for typical topographic scenarios. Examples demonstrate that high-quality elastic wavefields can be generated for topographic surfaces exhibiting significant topographic relief.

Adaptive surrogate model based multiobjective optimization for coastal aquifer management

NASA Astrophysics Data System (ADS)

Song, Jian; Yang, Yun; Wu, Jianfeng; Wu, Jichun; Sun, Xiaomin; Lin, Jin

2018-06-01

In this study, a novel surrogate model assisted multiobjective memetic algorithm (SMOMA) is developed for optimal pumping strategies of large-scale coastal groundwater problems. The proposed SMOMA integrates an efficient data-driven surrogate model with an improved non-dominated sorted genetic algorithm-II (NSGAII) that employs a local search operator to accelerate its convergence in optimization. The surrogate model based on Kernel Extreme Learning Machine (KELM) is developed and evaluated as an approximate simulator to generate the patterns of regional groundwater flow and salinity levels in coastal aquifers for reducing huge computational burden. The KELM model is adaptively trained during evolutionary search to satisfy desired fidelity level of surrogate so that it inhibits error accumulation of forecasting and results in correctly converging to true Pareto-optimal front. The proposed methodology is then applied to a large-scale coastal aquifer management in Baldwin County, Alabama. Objectives of minimizing the saltwater mass increase and maximizing the total pumping rate in the coastal aquifers are considered. The optimal solutions achieved by the proposed adaptive surrogate model are compared against those solutions obtained from one-shot surrogate model and original simulation model. The adaptive surrogate model does not only improve the prediction accuracy of Pareto-optimal solutions compared with those by the one-shot surrogate model, but also maintains the equivalent quality of Pareto-optimal solutions compared with those by NSGAII coupled with original simulation model, while retaining the advantage of surrogate models in reducing computational burden up to 94% of time-saving. This study shows that the proposed methodology is a computationally efficient and promising tool for multiobjective optimizations of coastal aquifer managements.

Differential geometry based solvation model I: Eulerian formulation

NASA Astrophysics Data System (ADS)

Chen, Zhan; Baker, Nathan A.; Wei, G. W.

2010-11-01

This paper presents a differential geometry based model for the analysis and computation of the equilibrium property of solvation. Differential geometry theory of surfaces is utilized to define and construct smooth interfaces with good stability and differentiability for use in characterizing the solvent-solute boundaries and in generating continuous dielectric functions across the computational domain. A total free energy functional is constructed to couple polar and nonpolar contributions to the solvation process. Geometric measure theory is employed to rigorously convert a Lagrangian formulation of the surface energy into an Eulerian formulation so as to bring all energy terms into an equal footing. By optimizing the total free energy functional, we derive coupled generalized Poisson-Boltzmann equation (GPBE) and generalized geometric flow equation (GGFE) for the electrostatic potential and the construction of realistic solvent-solute boundaries, respectively. By solving the coupled GPBE and GGFE, we obtain the electrostatic potential, the solvent-solute boundary profile, and the smooth dielectric function, and thereby improve the accuracy and stability of implicit solvation calculations. We also design efficient second-order numerical schemes for the solution of the GPBE and GGFE. Matrix resulted from the discretization of the GPBE is accelerated with appropriate preconditioners. An alternative direct implicit (ADI) scheme is designed to improve the stability of solving the GGFE. Two iterative approaches are designed to solve the coupled system of nonlinear partial differential equations. Extensive numerical experiments are designed to validate the present theoretical model, test computational methods, and optimize numerical algorithms. Example solvation analysis of both small compounds and proteins are carried out to further demonstrate the accuracy, stability, efficiency and robustness of the present new model and numerical approaches. Comparison is given to both experimental and theoretical results in the literature.

Differential geometry based solvation model I: Eulerian formulation

PubMed Central

Chen, Zhan; Baker, Nathan A.; Wei, G. W.

2010-01-01

This paper presents a differential geometry based model for the analysis and computation of the equilibrium property of solvation. Differential geometry theory of surfaces is utilized to define and construct smooth interfaces with good stability and differentiability for use in characterizing the solvent-solute boundaries and in generating continuous dielectric functions across the computational domain. A total free energy functional is constructed to couple polar and nonpolar contributions to the salvation process. Geometric measure theory is employed to rigorously convert a Lagrangian formulation of the surface energy into an Eulerian formulation so as to bring all energy terms into an equal footing. By minimizing the total free energy functional, we derive coupled generalized Poisson-Boltzmann equation (GPBE) and generalized geometric flow equation (GGFE) for the electrostatic potential and the construction of realistic solvent-solute boundaries, respectively. By solving the coupled GPBE and GGFE, we obtain the electrostatic potential, the solvent-solute boundary profile, and the smooth dielectric function, and thereby improve the accuracy and stability of implicit solvation calculations. We also design efficient second order numerical schemes for the solution of the GPBE and GGFE. Matrix resulted from the discretization of the GPBE is accelerated with appropriate preconditioners. An alternative direct implicit (ADI) scheme is designed to improve the stability of solving the GGFE. Two iterative approaches are designed to solve the coupled system of nonlinear partial differential equations. Extensive numerical experiments are designed to validate the present theoretical model, test computational methods, and optimize numerical algorithms. Example solvation analysis of both small compounds and proteins are carried out to further demonstrate the accuracy, stability, efficiency and robustness of the present new model and numerical approaches. Comparison is given to both experimental and theoretical results in the literature. PMID:20938489

Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension.

PubMed

Yang, Mingjun; Huang, Jing; MacKerell, Alexander D

2015-06-09

Replica exchange (REX) is a powerful computational tool for overcoming the quasi-ergodic sampling problem of complex molecular systems. Recently, several multidimensional extensions of this method have been developed to realize exchanges in both temperature and biasing potential space or the use of multiple biasing potentials to improve sampling efficiency. However, increased computational cost due to the multidimensionality of exchanges becomes challenging for use on complex systems under explicit solvent conditions. In this study, we develop a one-dimensional (1D) REX algorithm to concurrently combine the advantages of overall enhanced sampling from Hamiltonian solute scaling and the specific enhancement of collective variables using Hamiltonian biasing potentials. In the present Hamiltonian replica exchange method, termed HREST-BP, Hamiltonian solute scaling is applied to the solute subsystem, and its interactions with the environment to enhance overall conformational transitions and biasing potentials are added along selected collective variables associated with specific conformational transitions, thereby balancing the sampling of different hierarchical degrees of freedom. The two enhanced sampling approaches are implemented concurrently allowing for the use of a small number of replicas (e.g., 6 to 8) in 1D, thus greatly reducing the computational cost in complex system simulations. The present method is applied to conformational sampling of two nitrogen-linked glycans (N-glycans) found on the HIV gp120 envelope protein. Considering the general importance of the conformational sampling problem, HREST-BP represents an efficient procedure for the study of complex saccharides, and, more generally, the method is anticipated to be of general utility for the conformational sampling in a wide range of macromolecular systems.

Simultaneous multigrid techniques for nonlinear eigenvalue problems: Solutions of the nonlinear Schrödinger-Poisson eigenvalue problem in two and three dimensions

NASA Astrophysics Data System (ADS)

Costiner, Sorin; Ta'asan, Shlomo

1995-07-01

Algorithms for nonlinear eigenvalue problems (EP's) often require solving self-consistently a large number of EP's. Convergence difficulties may occur if the solution is not sought in an appropriate region, if global constraints have to be satisfied, or if close or equal eigenvalues are present. Multigrid (MG) algorithms for nonlinear problems and for EP's obtained from discretizations of partial differential EP have often been shown to be more efficient than single level algorithms. This paper presents MG techniques and a MG algorithm for nonlinear Schrödinger Poisson EP's. The algorithm overcomes the above mentioned difficulties combining the following techniques: a MG simultaneous treatment of the eigenvectors and nonlinearity, and with the global constrains; MG stable subspace continuation techniques for the treatment of nonlinearity; and a MG projection coupled with backrotations for separation of solutions. These techniques keep the solutions in an appropriate region, where the algorithm converges fast, and reduce the large number of self-consistent iterations to only a few or one MG simultaneous iteration. The MG projection makes it possible to efficiently overcome difficulties related to clusters of close and equal eigenvalues. Computational examples for the nonlinear Schrödinger-Poisson EP in two and three dimensions, presenting special computational difficulties that are due to the nonlinearity and to the equal and closely clustered eigenvalues are demonstrated. For these cases, the algorithm requires O(qN) operations for the calculation of q eigenvectors of size N and for the corresponding eigenvalues. One MG simultaneous cycle per fine level was performed. The total computational cost is equivalent to only a few Gauss-Seidel relaxations per eigenvector. An asymptotic convergence rate of 0.15 per MG cycle is attained.

Cross Validation Through Two-Dimensional Solution Surface for Cost-Sensitive SVM.

PubMed

Gu, Bin; Sheng, Victor S; Tay, Keng Yeow; Romano, Walter; Li, Shuo

2017-06-01

Model selection plays an important role in cost-sensitive SVM (CS-SVM). It has been proven that the global minimum cross validation (CV) error can be efficiently computed based on the solution path for one parameter learning problems. However, it is a challenge to obtain the global minimum CV error for CS-SVM based on one-dimensional solution path and traditional grid search, because CS-SVM is with two regularization parameters. In this paper, we propose a solution and error surfaces based CV approach (CV-SES). More specifically, we first compute a two-dimensional solution surface for CS-SVM based on a bi-parameter space partition algorithm, which can fit solutions of CS-SVM for all values of both regularization parameters. Then, we compute a two-dimensional validation error surface for each CV fold, which can fit validation errors of CS-SVM for all values of both regularization parameters. Finally, we obtain the CV error surface by superposing K validation error surfaces, which can find the global minimum CV error of CS-SVM. Experiments are conducted on seven datasets for cost sensitive learning and on four datasets for imbalanced learning. Experimental results not only show that our proposed CV-SES has a better generalization ability than CS-SVM with various hybrids between grid search and solution path methods, and than recent proposed cost-sensitive hinge loss SVM with three-dimensional grid search, but also show that CV-SES uses less running time.

TRIM—3D: a three-dimensional model for accurate simulation of shallow water flow

USGS Publications Warehouse

Casulli, Vincenzo; Bertolazzi, Enrico; Cheng, Ralph T.

1993-01-01

A semi-implicit finite difference formulation for the numerical solution of three-dimensional tidal circulation is discussed. The governing equations are the three-dimensional Reynolds equations in which the pressure is assumed to be hydrostatic. A minimal degree of implicitness has been introduced in the finite difference formula so that the resulting algorithm permits the use of large time steps at a minimal computational cost. This formulation includes the simulation of flooding and drying of tidal flats, and is fully vectorizable for an efficient implementation on modern vector computers. The high computational efficiency of this method has made it possible to provide the fine details of circulation structure in complex regions that previous studies were unable to obtain. For proper interpretation of the model results suitable interactive graphics is also an essential tool.

Biological production models as elements of coupled, atmosphere-ocean models for climate research

NASA Technical Reports Server (NTRS)

Platt, Trevor; Sathyendranath, Shubha

1991-01-01

Process models of phytoplankton production are discussed with respect to their suitability for incorporation into global-scale numerical ocean circulation models. Exact solutions are given for integrals over the mixed layer and the day of analytic, wavelength-independent models of primary production. Within this class of model, the bias incurred by using a triangular approximation (rather than a sinusoidal one) to the variation of surface irradiance through the day is computed. Efficient computation algorithms are given for the nonspectral models. More exact calculations require a spectrally sensitive treatment. Such models exist but must be integrated numerically over depth and time. For these integrations, resolution in wavelength, depth, and time are considered and recommendations made for efficient computation. The extrapolation of the one-(spatial)-dimension treatment to large horizontal scale is discussed.

Algebraic model checking for Boolean gene regulatory networks.

PubMed

Tran, Quoc-Nam

2011-01-01

We present a computational method in which modular and Groebner bases (GB) computation in Boolean rings are used for solving problems in Boolean gene regulatory networks (BN). In contrast to other known algebraic approaches, the degree of intermediate polynomials during the calculation of Groebner bases using our method will never grow resulting in a significant improvement in running time and memory space consumption. We also show how calculation in temporal logic for model checking can be done by means of our direct and efficient Groebner basis computation in Boolean rings. We present our experimental results in finding attractors and control strategies of Boolean networks to illustrate our theoretical arguments. The results are promising. Our algebraic approach is more efficient than the state-of-the-art model checker NuSMV on BNs. More importantly, our approach finds all solutions for the BN problems.

Coupling HYDRUS-1D Code with PA-DDS Algorithms for Inverse Calibration

NASA Astrophysics Data System (ADS)

Wang, Xiang; Asadzadeh, Masoud; Holländer, Hartmut

2017-04-01

Numerical modelling requires calibration to predict future stages. A standard method for calibration is inverse calibration where generally multi-objective optimization algorithms are used to find a solution, e.g. to find an optimal solution of the van Genuchten Mualem (VGM) parameters to predict water fluxes in the vadose zone. We coupled HYDRUS-1D with PA-DDS to add a new, robust function for inverse calibration to the model. The PA-DDS method is a recently developed multi-objective optimization algorithm, which combines Dynamically Dimensioned Search (DDS) and Pareto Archived Evolution Strategy (PAES). The results were compared to a standard method (Marquardt-Levenberg method) implemented in HYDRUS-1D. Calibration performance is evaluated using observed and simulated soil moisture at two soil layers in the Southern Abbotsford, British Columbia, Canada in the terms of the root mean squared error (RMSE) and the Nash-Sutcliffe Efficiency (NSE). Results showed low RMSE values of 0.014 and 0.017 and strong NSE values of 0.961 and 0.939. Compared to the results by the Marquardt-Levenberg method, we received better calibration results for deeper located soil sensors. However, VGM parameters were similar comparing with previous studies. Both methods are equally computational efficient. We claim that a direct implementation of PA-DDS into HYDRUS-1D should reduce the computation effort further. This, the PA-DDS method is efficient for calibrating recharge for complex vadose zone modelling with multiple soil layer and can be a potential tool for calibration of heat and solute transport. Future work should focus on the effectiveness of PA-DDS for calibrating more complex versions of the model with complex vadose zone settings, with more soil layers, and against measured heat and solute transport. Keywords: Recharge, Calibration, HYDRUS-1D, Multi-objective Optimization

Towards a flexible middleware for context-aware pervasive and wearable systems.

PubMed

Muro, Marco; Amoretti, Michele; Zanichelli, Francesco; Conte, Gianni

2012-11-01

Ambient intelligence and wearable computing call for innovative hardware and software technologies, including a highly capable, flexible and efficient middleware, allowing for the reuse of existing pervasive applications when developing new ones. In the considered application domain, middleware should also support self-management, interoperability among different platforms, efficient communications, and context awareness. In the on-going "everything is networked" scenario scalability appears as a very important issue, for which the peer-to-peer (P2P) paradigm emerges as an appealing solution for connecting software components in an overlay network, allowing for efficient and balanced data distribution mechanisms. In this paper, we illustrate how all these concepts can be placed into a theoretical tool, called networked autonomic machine (NAM), implemented into a NAM-based middleware, and evaluated against practical problems of pervasive computing.

Nonperturbative methods in HZE ion transport

NASA Technical Reports Server (NTRS)

Wilson, John W.; Badavi, Francis F.; Costen, Robert C.; Shinn, Judy L.

1993-01-01

A nonperturbative analytic solution of the high charge and energy (HZE) Green's function is used to implement a computer code for laboratory ion beam transport. The code is established to operate on the Langley Research Center nuclear fragmentation model used in engineering applications. Computational procedures are established to generate linear energy transfer (LET) distributions for a specified ion beam and target for comparison with experimental measurements. The code is highly efficient and compares well with the perturbation approximations.

A singularity free analytical solution of artificial satellite motion with drag

NASA Technical Reports Server (NTRS)

Mueller, A.

1978-01-01

An analytical satellite theory based on the regular, canonical Poincare-Similar (PS phi) elements is described along with an accurate density model which can be implemented into the drag theory. A computationally efficient manner in which to expand the equations of motion into a fourier series is discussed.

Geometric Models for Collaborative Search and Filtering

ERIC Educational Resources Information Center

Bitton, Ephrat

2011-01-01

This dissertation explores the use of geometric and graphical models for a variety of information search and filtering applications. These models serve to provide an intuitive understanding of the problem domains and as well as computational efficiencies to our solution approaches. We begin by considering a search and rescue scenario where both…

Remote access to very large image repositories, a high performance computing perspective

NASA Technical Reports Server (NTRS)

Plesea, Lucian

2005-01-01

The main challenges of using the increasingly large repositories of remote imagery data can be summarized in one word: efficiency. In this paper, a number of concrete problems and the chosen solutions are described, based on the construction of a 5TB global Landsat 7 mosaic.

Use of parallel computing in mass processing of laser data

NASA Astrophysics Data System (ADS)

Będkowski, J.; Bratuś, R.; Prochaska, M.; Rzonca, A.

2015-12-01

The first part of the paper includes a description of the rules used to generate the algorithm needed for the purpose of parallel computing and also discusses the origins of the idea of research on the use of graphics processors in large scale processing of laser scanning data. The next part of the paper includes the results of an efficiency assessment performed for an array of different processing options, all of which were substantially accelerated with parallel computing. The processing options were divided into the generation of orthophotos using point clouds, coloring of point clouds, transformations, and the generation of a regular grid, as well as advanced processes such as the detection of planes and edges, point cloud classification, and the analysis of data for the purpose of quality control. Most algorithms had to be formulated from scratch in the context of the requirements of parallel computing. A few of the algorithms were based on existing technology developed by the Dephos Software Company and then adapted to parallel computing in the course of this research study. Processing time was determined for each process employed for a typical quantity of data processed, which helped confirm the high efficiency of the solutions proposed and the applicability of parallel computing to the processing of laser scanning data. The high efficiency of parallel computing yields new opportunities in the creation and organization of processing methods for laser scanning data.

Fermilab computing at the Intensity Frontier

DOE PAGES

Group, Craig; Fuess, S.; Gutsche, O.; ...

2015-12-23

The Intensity Frontier refers to a diverse set of particle physics experiments using high- intensity beams. In this paper I will focus the discussion on the computing requirements and solutions of a set of neutrino and muon experiments in progress or planned to take place at the Fermi National Accelerator Laboratory located near Chicago, Illinois. In addition, the experiments face unique challenges, but also have overlapping computational needs. In principle, by exploiting the commonality and utilizing centralized computing tools and resources, requirements can be satisfied efficiently and scientists of individual experiments can focus more on the science and less onmore » the development of tools and infrastructure.« less

Leveraging the Cloud for Robust and Efficient Lunar Image Processing

NASA Technical Reports Server (NTRS)

Chang, George; Malhotra, Shan; Wolgast, Paul

2011-01-01

The Lunar Mapping and Modeling Project (LMMP) is tasked to aggregate lunar data, from the Apollo era to the latest instruments on the LRO spacecraft, into a central repository accessible by scientists and the general public. A critical function of this task is to provide users with the best solution for browsing the vast amounts of imagery available. The image files LMMP manages range from a few gigabytes to hundreds of gigabytes in size with new data arriving every day. Despite this ever-increasing amount of data, LMMP must make the data readily available in a timely manner for users to view and analyze. This is accomplished by tiling large images into smaller images using Hadoop, a distributed computing software platform implementation of the MapReduce framework, running on a small cluster of machines locally. Additionally, the software is implemented to use Amazon's Elastic Compute Cloud (EC2) facility. We also developed a hybrid solution to serve images to users by leveraging cloud storage using Amazon's Simple Storage Service (S3) for public data while keeping private information on our own data servers. By using Cloud Computing, we improve upon our local solution by reducing the need to manage our own hardware and computing infrastructure, thereby reducing costs. Further, by using a hybrid of local and cloud storage, we are able to provide data to our users more efficiently and securely. 12 This paper examines the use of a distributed approach with Hadoop to tile images, an approach that provides significant improvements in image processing time, from hours to minutes. This paper describes the constraints imposed on the solution and the resulting techniques developed for the hybrid solution of a customized Hadoop infrastructure over local and cloud resources in managing this ever-growing data set. It examines the performance trade-offs of using the more plentiful resources of the cloud, such as those provided by S3, against the bandwidth limitations such use encounters with remote resources. As part of this discussion this paper will outline some of the technologies employed, the reasons for their selection, the resulting performance metrics and the direction the project is headed based upon the demonstrated capabilities thus far.

Cox process representation and inference for stochastic reaction-diffusion processes

NASA Astrophysics Data System (ADS)

Schnoerr, David; Grima, Ramon; Sanguinetti, Guido

2016-05-01

Complex behaviour in many systems arises from the stochastic interactions of spatially distributed particles or agents. Stochastic reaction-diffusion processes are widely used to model such behaviour in disciplines ranging from biology to the social sciences, yet they are notoriously difficult to simulate and calibrate to observational data. Here we use ideas from statistical physics and machine learning to provide a solution to the inverse problem of learning a stochastic reaction-diffusion process from data. Our solution relies on a non-trivial connection between stochastic reaction-diffusion processes and spatio-temporal Cox processes, a well-studied class of models from computational statistics. This connection leads to an efficient and flexible algorithm for parameter inference and model selection. Our approach shows excellent accuracy on numeric and real data examples from systems biology and epidemiology. Our work provides both insights into spatio-temporal stochastic systems, and a practical solution to a long-standing problem in computational modelling.

Developing and utilizing an Euler computational method for predicting the airframe/propulsion effects for an aft-mounted turboprop transport. Volume 1: Theory document

NASA Technical Reports Server (NTRS)

Chen, H. C.; Yu, N. Y.

1991-01-01

An Euler flow solver was developed for predicting the airframe/propulsion integration effects for an aft-mounted turboprop transport. This solver employs a highly efficient multigrid scheme, with a successive mesh-refinement procedure to accelerate the convergence of the solution. A new dissipation model was also implemented to render solutions that are grid insensitive. The propeller power effects are simulated by the actuator disk concept. An embedded flow solution method was developed for predicting the detailed flow characteristics in the local vicinity of an aft-mounted propfan engine in the presence of a flow field induced by a complete aircraft. Results from test case analysis are presented. A user's guide for execution of computer programs, including format of various input files, sample job decks, and sample input files, is provided in an accompanying volume.

The Coverage Problem in Video-Based Wireless Sensor Networks: A Survey

PubMed Central

Costa, Daniel G.; Guedes, Luiz Affonso

2010-01-01

Wireless sensor networks typically consist of a great number of tiny low-cost electronic devices with limited sensing and computing capabilities which cooperatively communicate to collect some kind of information from an area of interest. When wireless nodes of such networks are equipped with a low-power camera, visual data can be retrieved, facilitating a new set of novel applications. The nature of video-based wireless sensor networks demands new algorithms and solutions, since traditional wireless sensor networks approaches are not feasible or even efficient for that specialized communication scenario. The coverage problem is a crucial issue of wireless sensor networks, requiring specific solutions when video-based sensors are employed. In this paper, it is surveyed the state of the art of this particular issue, regarding strategies, algorithms and general computational solutions. Open research areas are also discussed, envisaging promising investigation considering coverage in video-based wireless sensor networks. PMID:22163651

The Ordered Clustered Travelling Salesman Problem: A Hybrid Genetic Algorithm

PubMed Central

Ahmed, Zakir Hussain

2014-01-01

The ordered clustered travelling salesman problem is a variation of the usual travelling salesman problem in which a set of vertices (except the starting vertex) of the network is divided into some prespecified clusters. The objective is to find the least cost Hamiltonian tour in which vertices of any cluster are visited contiguously and the clusters are visited in the prespecified order. The problem is NP-hard, and it arises in practical transportation and sequencing problems. This paper develops a hybrid genetic algorithm using sequential constructive crossover, 2-opt search, and a local search for obtaining heuristic solution to the problem. The efficiency of the algorithm has been examined against two existing algorithms for some asymmetric and symmetric TSPLIB instances of various sizes. The computational results show that the proposed algorithm is very effective in terms of solution quality and computational time. Finally, we present solution to some more symmetric TSPLIB instances. PMID:24701148

Efficient Privacy-Aware Record Integration.

PubMed

Kuzu, Mehmet; Kantarcioglu, Murat; Inan, Ali; Bertino, Elisa; Durham, Elizabeth; Malin, Bradley

2013-01-01

The integration of information dispersed among multiple repositories is a crucial step for accurate data analysis in various domains. In support of this goal, it is critical to devise procedures for identifying similar records across distinct data sources. At the same time, to adhere to privacy regulations and policies, such procedures should protect the confidentiality of the individuals to whom the information corresponds. Various private record linkage (PRL) protocols have been proposed to achieve this goal, involving secure multi-party computation (SMC) and similarity preserving data transformation techniques. SMC methods provide secure and accurate solutions to the PRL problem, but are prohibitively expensive in practice, mainly due to excessive computational requirements. Data transformation techniques offer more practical solutions, but incur the cost of information leakage and false matches. In this paper, we introduce a novel model for practical PRL, which 1) affords controlled and limited information leakage, 2) avoids false matches resulting from data transformation. Initially, we partition the data sources into blocks to eliminate comparisons for records that are unlikely to match. Then, to identify matches, we apply an efficient SMC technique between the candidate record pairs. To enable efficiency and privacy, our model leaks a controlled amount of obfuscated data prior to the secure computations. Applied obfuscation relies on differential privacy which provides strong privacy guarantees against adversaries with arbitrary background knowledge. In addition, we illustrate the practical nature of our approach through an empirical analysis with data derived from public voter records.

Multitrace/singletrace formulations and Domain Decomposition Methods for the solution of Helmholtz transmission problems for bounded composite scatterers

NASA Astrophysics Data System (ADS)

Jerez-Hanckes, Carlos; Pérez-Arancibia, Carlos; Turc, Catalin

2017-12-01

We present Nyström discretizations of multitrace/singletrace formulations and non-overlapping Domain Decomposition Methods (DDM) for the solution of Helmholtz transmission problems for bounded composite scatterers with piecewise constant material properties. We investigate the performance of DDM with both classical Robin and optimized transmission boundary conditions. The optimized transmission boundary conditions incorporate square root Fourier multiplier approximations of Dirichlet to Neumann operators. While the multitrace/singletrace formulations as well as the DDM that use classical Robin transmission conditions are not particularly well suited for Krylov subspace iterative solutions of high-contrast high-frequency Helmholtz transmission problems, we provide ample numerical evidence that DDM with optimized transmission conditions constitute efficient computational alternatives for these type of applications. In the case of large numbers of subdomains with different material properties, we show that the associated DDM linear system can be efficiently solved via hierarchical Schur complements elimination.

Spatial adaptation procedures on tetrahedral meshes for unsteady aerodynamic flow calculations

NASA Technical Reports Server (NTRS)

Rausch, Russ D.; Batina, John T.; Yang, Henry T. Y.

1993-01-01

Spatial adaptation procedures for the accurate and efficient solution of steady and unsteady inviscid flow problems are described. The adaptation procedures were developed and implemented within a three-dimensional, unstructured-grid, upwind-type Euler code. These procedures involve mesh enrichment and mesh coarsening to either add points in high gradient regions of the flow or remove points where they are not needed, respectively, to produce solutions of high spatial accuracy at minimal computational cost. A detailed description of the enrichment and coarsening procedures are presented and comparisons with experimental data for an ONERA M6 wing and an exact solution for a shock-tube problem are presented to provide an assessment of the accuracy and efficiency of the capability. Steady and unsteady results, obtained using spatial adaptation procedures, are shown to be of high spatial accuracy, primarily in that discontinuities such as shock waves are captured very sharply.

Spatial adaptation procedures on tetrahedral meshes for unsteady aerodynamic flow calculations

NASA Technical Reports Server (NTRS)

Rausch, Russ D.; Batina, John T.; Yang, Henry T. Y.

1993-01-01

Spatial adaptation procedures for the accurate and efficient solution of steady and unsteady inviscid flow problems are described. The adaptation procedures were developed and implemented within a three-dimensional, unstructured-grid, upwind-type Euler code. These procedures involve mesh enrichment and mesh coarsening to either add points in high gradient regions of the flow or remove points where they are not needed, respectively, to produce solutions of high spatial accuracy at minimal computational cost. The paper gives a detailed description of the enrichment and coarsening procedures and presents comparisons with experimental data for an ONERA M6 wing and an exact solution for a shock-tube problem to provide an assessment of the accuracy and efficiency of the capability. Steady and unsteady results, obtained using spatial adaptation procedures, are shown to be of high spatial accuracy, primarily in that discontinuities such as shock waves are captured very sharply.

Simulated annealing with probabilistic analysis for solving traveling salesman problems

NASA Astrophysics Data System (ADS)

Hong, Pei-Yee; Lim, Yai-Fung; Ramli, Razamin; Khalid, Ruzelan

2013-09-01

Simulated Annealing (SA) is a widely used meta-heuristic that was inspired from the annealing process of recrystallization of metals. Therefore, the efficiency of SA is highly affected by the annealing schedule. As a result, in this paper, we presented an empirical work to provide a comparable annealing schedule to solve symmetric traveling salesman problems (TSP). Randomized complete block design is also used in this study. The results show that different parameters do affect the efficiency of SA and thus, we propose the best found annealing schedule based on the Post Hoc test. SA was tested on seven selected benchmarked problems of symmetric TSP with the proposed annealing schedule. The performance of SA was evaluated empirically alongside with benchmark solutions and simple analysis to validate the quality of solutions. Computational results show that the proposed annealing schedule provides a good quality of solution.

The Osher scheme for non-equilibrium reacting flows

NASA Technical Reports Server (NTRS)

Suresh, Ambady; Liou, Meng-Sing

1992-01-01

An extension of the Osher upwind scheme to nonequilibrium reacting flows is presented. Owing to the presence of source terms, the Riemann problem is no longer self-similar and therefore its approximate solution becomes tedious. With simplicity in mind, a linearized approach which avoids an iterative solution is used to define the intermediate states and sonic points. The source terms are treated explicitly. Numerical computations are presented to demonstrate the feasibility, efficiency and accuracy of the proposed method. The test problems include a ZND (Zeldovich-Neumann-Doring) detonation problem for which spurious numerical solutions which propagate at mesh speed have been observed on coarse grids. With the present method, a change of limiter causes the solution to change from the physically correct CJ detonation solution to the spurious weak detonation solution.

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.

SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules.

PubMed

Bardhan, Jaydeep; Park, Sanghyun; Makowski, Lee

2009-10-01

This paper describes a computational approach to estimating wide-angle X-ray solution scattering (WAXS) from proteins, which has been implemented in a computer program called SoftWAXS. The accuracy and efficiency of SoftWAXS are analyzed for analytically solvable model problems as well as for proteins. Key features of the approach include a numerical procedure for performing the required spherical averaging and explicit representation of the solute-solvent boundary and the surface of the hydration layer. These features allow the Fourier transform of the excluded volume and hydration layer to be computed directly and with high accuracy. This approach will allow future investigation of different treatments of the electron density in the hydration shell. Numerical results illustrate the differences between this approach to modeling the excluded volume and a widely used model that treats the excluded-volume function as a sum of Gaussians representing the individual atomic excluded volumes. Comparison of the results obtained here with those from explicit-solvent molecular dynamics clarifies shortcomings inherent to the representation of solvent as a time-averaged electron-density profile. In addition, an assessment is made of how the calculated scattering patterns depend on input parameters such as the solute-atom radii, the width of the hydration shell and the hydration-layer contrast. These results suggest that obtaining predictive calculations of high-resolution WAXS patterns may require sophisticated treatments of solvent.

Portfolios of quantum algorithms.

PubMed

Maurer, S M; Hogg, T; Huberman, B A

2001-12-17

Quantum computation holds promise for the solution of many intractable problems. However, since many quantum algorithms are stochastic in nature they can find the solution of hard problems only probabilistically. Thus the efficiency of the algorithms has to be characterized by both the expected time to completion and the associated variance. In order to minimize both the running time and its uncertainty, we show that portfolios of quantum algorithms analogous to those of finance can outperform single algorithms when applied to the NP-complete problems such as 3-satisfiability.

Unstructured mesh algorithms for aerodynamic calculations

NASA Technical Reports Server (NTRS)

Mavriplis, D. J.

1992-01-01

The use of unstructured mesh techniques for solving complex aerodynamic flows is discussed. The principle advantages of unstructured mesh strategies, as they relate to complex geometries, adaptive meshing capabilities, and parallel processing are emphasized. The various aspects required for the efficient and accurate solution of aerodynamic flows are addressed. These include mesh generation, mesh adaptivity, solution algorithms, convergence acceleration, and turbulence modeling. Computations of viscous turbulent two-dimensional flows and inviscid three-dimensional flows about complex configurations are demonstrated. Remaining obstacles and directions for future research are also outlined.

Innovation Incubator: LiquidCool Solutions Technical Evaluation. Laboratory Study and Demonstration Results of a Directed-Flow, Liquid Submerged Server for High-Efficiency Data Centers

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

Kozubal, Eric J

LiquidCool Solutions (LCS) has developed liquid submerged server (LSS) technology that changes the way computer electronics are cooled. The technology provides an option to cool electronics by the direct contact flow of dielectric fluid (coolant) into a sealed enclosure housing all the electronics of a single server. The intimate dielectric fluid contact with electronics improves the effectiveness of heat removal from the electronics.

Assessment of Preconditioner for a USM3D Hierarchical Adaptive Nonlinear Method (HANIM) (Invited)

NASA Technical Reports Server (NTRS)

Pandya, Mohagna J.; Diskin, Boris; Thomas, James L.; Frink, Neal T.

2016-01-01

Enhancements to the previously reported mixed-element USM3D Hierarchical Adaptive Nonlinear Iteration Method (HANIM) framework have been made to further improve robustness, efficiency, and accuracy of computational fluid dynamic simulations. The key enhancements include a multi-color line-implicit preconditioner, a discretely consistent symmetry boundary condition, and a line-mapping method for the turbulence source term discretization. The USM3D iterative convergence for the turbulent flows is assessed on four configurations. The configurations include a two-dimensional (2D) bump-in-channel, the 2D NACA 0012 airfoil, a three-dimensional (3D) bump-in-channel, and a 3D hemisphere cylinder. The Reynolds Averaged Navier Stokes (RANS) solutions have been obtained using a Spalart-Allmaras turbulence model and families of uniformly refined nested grids. Two types of HANIM solutions using line- and point-implicit preconditioners have been computed. Additional solutions using the point-implicit preconditioner alone (PA) method that broadly represents the baseline solver technology have also been computed. The line-implicit HANIM shows superior iterative convergence in most cases with progressively increasing benefits on finer grids.

Krylov-Subspace Recycling via the POD-Augmented Conjugate-Gradient Method

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

Carlberg, Kevin; Forstall, Virginia; Tuminaro, Ray

This paper presents a new Krylov-subspace-recycling method for efficiently solving sequences of linear systems of equations characterized by varying right-hand sides and symmetric-positive-definite matrices. As opposed to typical truncation strategies used in recycling such as deflation, we propose a truncation method inspired by goal-oriented proper orthogonal decomposition (POD) from model reduction. This idea is based on the observation that model reduction aims to compute a low-dimensional subspace that contains an accurate solution; as such, we expect the proposed method to generate a low-dimensional subspace that is well suited for computing solutions that can satisfy inexact tolerances. In particular, we proposemore » specific goal-oriented POD `ingredients' that align the optimality properties of POD with the objective of Krylov-subspace recycling. To compute solutions in the resulting 'augmented' POD subspace, we propose a hybrid direct/iterative three-stage method that leverages 1) the optimal ordering of POD basis vectors, and 2) well-conditioned reduced matrices. Numerical experiments performed on solid-mechanics problems highlight the benefits of the proposed method over existing approaches for Krylov-subspace recycling.« less

Krylov-Subspace Recycling via the POD-Augmented Conjugate-Gradient Method

DOE PAGES

Carlberg, Kevin; Forstall, Virginia; Tuminaro, Ray

2016-01-01

This paper presents a new Krylov-subspace-recycling method for efficiently solving sequences of linear systems of equations characterized by varying right-hand sides and symmetric-positive-definite matrices. As opposed to typical truncation strategies used in recycling such as deflation, we propose a truncation method inspired by goal-oriented proper orthogonal decomposition (POD) from model reduction. This idea is based on the observation that model reduction aims to compute a low-dimensional subspace that contains an accurate solution; as such, we expect the proposed method to generate a low-dimensional subspace that is well suited for computing solutions that can satisfy inexact tolerances. In particular, we proposemore » specific goal-oriented POD `ingredients' that align the optimality properties of POD with the objective of Krylov-subspace recycling. To compute solutions in the resulting 'augmented' POD subspace, we propose a hybrid direct/iterative three-stage method that leverages 1) the optimal ordering of POD basis vectors, and 2) well-conditioned reduced matrices. Numerical experiments performed on solid-mechanics problems highlight the benefits of the proposed method over existing approaches for Krylov-subspace recycling.« less

Global Load Balancing with Parallel Mesh Adaption on Distributed-Memory Systems

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Oliker, Leonid; Sohn, Andrew

1996-01-01

Dynamic mesh adaption on unstructured grids is a powerful tool for efficiently computing unsteady problems to resolve solution features of interest. Unfortunately, this causes load imbalance among processors on a parallel machine. This paper describes the parallel implementation of a tetrahedral mesh adaption scheme and a new global load balancing method. A heuristic remapping algorithm is presented that assigns partitions to processors such that the redistribution cost is minimized. Results indicate that the parallel performance of the mesh adaption code depends on the nature of the adaption region and show a 35.5X speedup on 64 processors of an SP2 when 35% of the mesh is randomly adapted. For large-scale scientific computations, our load balancing strategy gives almost a sixfold reduction in solver execution times over non-balanced loads. Furthermore, our heuristic remapper yields processor assignments that are less than 3% off the optimal solutions but requires only 1% of the computational time.

A self-adaptive-grid method with application to airfoil flow

NASA Technical Reports Server (NTRS)

Nakahashi, K.; Deiwert, G. S.

1985-01-01

A self-adaptive-grid method is described that is suitable for multidimensional steady and unsteady computations. Based on variational principles, a spring analogy is used to redistribute grid points in an optimal sense to reduce the overall solution error. User-specified parameters, denoting both maximum and minimum permissible grid spacings, are used to define the all-important constants, thereby minimizing the empiricism and making the method self-adaptive. Operator splitting and one-sided controls for orthogonality and smoothness are used to make the method practical, robust, and efficient. Examples are included for both steady and unsteady viscous flow computations about airfoils in two dimensions, as well as for a steady inviscid flow computation and a one-dimensional case. These examples illustrate the precise control the user has with the self-adaptive method and demonstrate a significant improvement in accuracy and quality of the solutions.

Numerical Algorithms for Acoustic Integrals - The Devil is in the Details

NASA Technical Reports Server (NTRS)

Brentner, Kenneth S.

1996-01-01

The accurate prediction of the aeroacoustic field generated by aerospace vehicles or nonaerospace machinery is necessary for designers to control and reduce source noise. Powerful computational aeroacoustic methods, based on various acoustic analogies (primarily the Lighthill acoustic analogy) and Kirchhoff methods, have been developed for prediction of noise from complicated sources, such as rotating blades. Both methods ultimately predict the noise through a numerical evaluation of an integral formulation. In this paper, we consider three generic acoustic formulations and several numerical algorithms that have been used to compute the solutions to these formulations. Algorithms for retarded-time formulations are the most efficient and robust, but they are difficult to implement for supersonic-source motion. Collapsing-sphere and emission-surface formulations are good alternatives when supersonic-source motion is present, but the numerical implementations of these formulations are more computationally demanding. New algorithms - which utilize solution adaptation to provide a specified error level - are needed.

Simple model of hydrophobic hydration.

PubMed

Lukšič, Miha; Urbic, Tomaz; Hribar-Lee, Barbara; Dill, Ken A

2012-05-31

Water is an unusual liquid in its solvation properties. Here, we model the process of transferring a nonpolar solute into water. Our goal was to capture the physical balance between water's hydrogen bonding and van der Waals interactions in a model that is simple enough to be nearly analytical and not heavily computational. We develop a 2-dimensional Mercedes-Benz-like model of water with which we compute the free energy, enthalpy, entropy, and the heat capacity of transfer as a function of temperature, pressure, and solute size. As validation, we find that this model gives the same trends as Monte Carlo simulations of the underlying 2D model and gives qualitative agreement with experiments. The advantages of this model are that it gives simple insights and that computational time is negligible. It may provide a useful starting point for developing more efficient and more realistic 3D models of aqueous solvation.

Decision and function problems based on boson sampling

NASA Astrophysics Data System (ADS)

Nikolopoulos, Georgios M.; Brougham, Thomas

2016-07-01

Boson sampling is a mathematical problem that is strongly believed to be intractable for classical computers, whereas passive linear interferometers can produce samples efficiently. So far, the problem remains a computational curiosity, and the possible usefulness of boson-sampling devices is mainly limited to the proof of quantum supremacy. The purpose of this work is to investigate whether boson sampling can be used as a resource of decision and function problems that are computationally hard, and may thus have cryptographic applications. After the definition of a rather general theoretical framework for the design of such problems, we discuss their solution by means of a brute-force numerical approach, as well as by means of nonboson samplers. Moreover, we estimate the sample sizes required for their solution by passive linear interferometers, and it is shown that they are independent of the size of the Hilbert space.

Computational Relativistic Astrophysics Using the Flow Field-Dependent Variation Theory

NASA Technical Reports Server (NTRS)

Richardson, G. A.; Chung, T. J.

2002-01-01

We present our method for solving general relativistic nonideal hydrodynamics. Relativistic effects become pronounced in such cases as jet formation from black hole magnetized accretion disks which may lead to the study of gamma-ray bursts. Nonideal flows are present where radiation, magnetic forces, viscosities, and turbulence play an important role. Our concern in this paper is to reexamine existing numerical simulation tools as to the accuracy and efficiency of computations and introduce a new approach known as the flow field-dependent variation (FDV) method. The main feature of the FDV method consists of accommodating discontinuities of shock waves and high gradients of flow variables such as occur in turbulence and unstable motions. In this paper, the physics involved in the solution of relativistic hydrodynamics and solution strategies of the FDV theory are elaborated. The general relativistic astrophysical flow and shock solver (GRAFSS) is introduced, and some simple example problems for computational relativistic astrophysics (CRA) are demonstrated.

An algorithmic approach to solving polynomial equations associated with quantum circuits

NASA Astrophysics Data System (ADS)

Gerdt, V. P.; Zinin, M. V.

2009-12-01

In this paper we present two algorithms for reducing systems of multivariate polynomial equations over the finite field F 2 to the canonical triangular form called lexicographical Gröbner basis. This triangular form is the most appropriate for finding solutions of the system. On the other hand, the system of polynomials over F 2 whose variables also take values in F 2 (Boolean polynomials) completely describes the unitary matrix generated by a quantum circuit. In particular, the matrix itself can be computed by counting the number of solutions (roots) of the associated polynomial system. Thereby, efficient construction of the lexicographical Gröbner bases over F 2 associated with quantum circuits gives a method for computing their circuit matrices that is alternative to the direct numerical method based on linear algebra. We compare our implementation of both algorithms with some other software packages available for computing Gröbner bases over F 2.

A note on improved F-expansion method combined with Riccati equation applied to nonlinear evolution equations.

PubMed

Islam, Md Shafiqul; Khan, Kamruzzaman; Akbar, M Ali; Mastroberardino, Antonio

2014-10-01

The purpose of this article is to present an analytical method, namely the improved F-expansion method combined with the Riccati equation, for finding exact solutions of nonlinear evolution equations. The present method is capable of calculating all branches of solutions simultaneously, even if multiple solutions are very close and thus difficult to distinguish with numerical techniques. To verify the computational efficiency, we consider the modified Benjamin-Bona-Mahony equation and the modified Korteweg-de Vries equation. Our results reveal that the method is a very effective and straightforward way of formulating the exact travelling wave solutions of nonlinear wave equations arising in mathematical physics and engineering.

A note on improved F-expansion method combined with Riccati equation applied to nonlinear evolution equations

PubMed Central

Islam, Md. Shafiqul; Khan, Kamruzzaman; Akbar, M. Ali; Mastroberardino, Antonio

2014-01-01

The purpose of this article is to present an analytical method, namely the improved F-expansion method combined with the Riccati equation, for finding exact solutions of nonlinear evolution equations. The present method is capable of calculating all branches of solutions simultaneously, even if multiple solutions are very close and thus difficult to distinguish with numerical techniques. To verify the computational efficiency, we consider the modified Benjamin–Bona–Mahony equation and the modified Korteweg-de Vries equation. Our results reveal that the method is a very effective and straightforward way of formulating the exact travelling wave solutions of nonlinear wave equations arising in mathematical physics and engineering. PMID:26064530

Finite-difference solution of the compressible stability eigenvalue problem

NASA Technical Reports Server (NTRS)

Malik, M. R.

1982-01-01

A compressible stability analysis computer code is developed. The code uses a matrix finite difference method for local eigenvalue solution when a good guess for the eigenvalue is available and is significantly more computationally efficient than the commonly used initial value approach. The local eigenvalue search procedure also results in eigenfunctions and, at little extra work, group velocities. A globally convergent eigenvalue procedure is also developed which may be used when no guess for the eigenvalue is available. The global problem is formulated in such a way that no unstable spurious modes appear so that the method is suitable for use in a black box stability code. Sample stability calculations are presented for the boundary layer profiles of a Laminar Flow Control (LFC) swept wing.

Newton's method applied to finite-difference approximations for the steady-state compressible Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Bailey, Harry E.; Beam, Richard M.

1991-01-01

Finite-difference approximations for steady-state compressible Navier-Stokes equations, whose two spatial dimensions are written in generalized curvilinear coordinates and strong conservation-law form, are presently solved by means of Newton's method in order to obtain a lifting-airfoil flow field under subsonic and transonnic conditions. In addition to ascertaining the computational requirements of an initial guess ensuring convergence and the degree of computational efficiency obtainable via the approximate Newton method's freezing of the Jacobian matrices, attention is given to the need for auxiliary methods assessing the temporal stability of steady-state solutions. It is demonstrated that nonunique solutions of the finite-difference equations are obtainable by Newton's method in conjunction with a continuation method.

Solvers for the Cardiac Bidomain Equations

PubMed Central

Vigmond, E.J.; Weber dos Santos, R.; Prassl, A.J.; Deo, M.; Plank, G.

2010-01-01

The bidomain equations are widely used for the simulation of electrical activity in cardiac tissue. They are especially important for accurately modelling extracellular stimulation, as evidenced by their prediction of virtual electrode polarization before experimental verification. However, solution of the equations is computationally expensive due to the fine spatial and temporal discretization needed. This limits the size and duration of the problem which can be modeled. Regardless of the specific form into which they are cast, the computational bottleneck becomes the repeated solution of a large, linear system. The purpose of this review is to give an overview of the equations, and the methods by which they have been solved. Of particular note are recent developments in multigrid methods, which have proven to be the most efficient. PMID:17900668

Application of multigrid methods to the solution of liquid crystal equations on a SIMD computer

NASA Technical Reports Server (NTRS)

Farrell, Paul A.; Ruttan, Arden; Zeller, Reinhardt R.

1993-01-01

We will describe a finite difference code for computing the equilibrium configurations of the order-parameter tensor field for nematic liquid crystals in rectangular regions by minimization of the Landau-de Gennes Free Energy functional. The implementation of the free energy functional described here includes magnetic fields, quadratic gradient terms, and scalar bulk terms through the fourth order. Boundary conditions include the effects of strong surface anchoring. The target architectures for our implementation are SIMD machines, with interconnection networks which can be configured as 2 or 3 dimensional grids, such as the Wavetracer DTC. We also discuss the relative efficiency of a number of iterative methods for the solution of the linear systems arising from this discretization on such architectures.

A QR accelerated volume-to-surface boundary condition for finite element solution of eddy current problems

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

White, D; Fasenfest, B; Rieben, R

2006-09-08

We are concerned with the solution of time-dependent electromagnetic eddy current problems using a finite element formulation on three-dimensional unstructured meshes. We allow for multiple conducting regions, and our goal is to develop an efficient computational method that does not require a computational mesh of the air/vacuum regions. This requires a sophisticated global boundary condition specifying the total fields on the conductor boundaries. We propose a Biot-Savart law based volume-to-surface boundary condition to meet this requirement. This Biot-Savart approach is demonstrated to be very accurate. In addition, this approach can be accelerated via a low-rank QR approximation of the discretizedmore » Biot-Savart law.« less

Convection equation modeling: A non-iterative direct matrix solution algorithm for use with SINDA

NASA Technical Reports Server (NTRS)

Schrage, Dean S.

1993-01-01

The determination of the boundary conditions for a component-level analysis, applying discrete finite element and finite difference modeling techniques often requires an analysis of complex coupled phenomenon that cannot be described algebraically. For example, an analysis of the temperature field of a coldplate surface with an integral fluid loop requires a solution to the parabolic heat equation and also requires the boundary conditions that describe the local fluid temperature. However, the local fluid temperature is described by a convection equation that can only be solved with the knowledge of the locally-coupled coldplate temperatures. Generally speaking, it is not computationally efficient, and sometimes, not even possible to perform a direct, coupled phenomenon analysis of the component-level and boundary condition models within a single analysis code. An alternative is to perform a disjoint analysis, but transmit the necessary information between models during the simulation to provide an indirect coupling. For this approach to be effective, the component-level model retains full detail while the boundary condition model is simplified to provide a fast, first-order prediction of the phenomenon in question. Specifically for the present study, the coldplate structure is analyzed with a discrete, numerical model (SINDA) while the fluid loop convection equation is analyzed with a discrete, analytical model (direct matrix solution). This indirect coupling allows a satisfactory prediction of the boundary condition, while not subjugating the overall computational efficiency of the component-level analysis. In the present study a discussion of the complete analysis of the derivation and direct matrix solution algorithm of the convection equation is presented. Discretization is analyzed and discussed to extend of solution accuracy, stability and computation speed. Case studies considering a pulsed and harmonic inlet disturbance to the fluid loop are analyzed to assist in the discussion of numerical dissipation and accuracy. In addition, the issues of code melding or integration with standard class solvers such as SINDA are discussed to advise the user of the potential problems to be encountered.

Efficient simulation and model reformulation of two-dimensional electrochemical thermal behavior of lithium-ion batteries

DOE PAGES

Northrop, Paul W. C.; Pathak, Manan; Rife, Derek; ...

2015-03-09

Lithium-ion batteries are an important technology to facilitate efficient energy storage and enable a shift from petroleum based energy to more environmentally benign sources. Such systems can be utilized most efficiently if good understanding of performance can be achieved for a range of operating conditions. Mathematical models can be useful to predict battery behavior to allow for optimization of design and control. An analytical solution is ideally preferred to solve the equations of a mathematical model, as it eliminates the error that arises when using numerical techniques and is usually computationally cheap. An analytical solution provides insight into the behaviormore » of the system and also explicitly shows the effects of different parameters on the behavior. However, most engineering models, including the majority of battery models, cannot be solved analytically due to non-linearities in the equations and state dependent transport and kinetic parameters. The numerical method used to solve the system of equations describing a battery operation can have a significant impact on the computational cost of the simulation. In this paper, a model reformulation of the porous electrode pseudo three dimensional (P3D) which significantly reduces the computational cost of lithium ion battery simulation, while maintaining high accuracy, is discussed. This reformulation enables the use of the P3D model into applications that would otherwise be too computationally expensive to justify its use, such as online control, optimization, and parameter estimation. Furthermore, the P3D model has proven to be robust enough to allow for the inclusion of additional physical phenomena as understanding improves. In this study, the reformulated model is used to allow for more complicated physical phenomena to be considered for study, including thermal effects.« less

Low rank approximation method for efficient Green's function calculation of dissipative quantum transport

NASA Astrophysics Data System (ADS)

Zeng, Lang; He, Yu; Povolotskyi, Michael; Liu, XiaoYan; Klimeck, Gerhard; Kubis, Tillmann

2013-06-01

In this work, the low rank approximation concept is extended to the non-equilibrium Green's function (NEGF) method to achieve a very efficient approximated algorithm for coherent and incoherent electron transport. This new method is applied to inelastic transport in various semiconductor nanodevices. Detailed benchmarks with exact NEGF solutions show (1) a very good agreement between approximated and exact NEGF results, (2) a significant reduction of the required memory, and (3) a large reduction of the computational time (a factor of speed up as high as 150 times is observed). A non-recursive solution of the inelastic NEGF transport equations of a 1000 nm long resistor on standard hardware illustrates nicely the capability of this new method.

Nonuniform depth grids in parabolic equation solutions.

PubMed

Sanders, William M; Collins, Michael D

2013-04-01

The parabolic wave equation is solved using a finite-difference solution in depth that involves a nonuniform grid. The depth operator is discretized using Galerkin's method with asymmetric hat functions. Examples are presented to illustrate that this approach can be used to improve efficiency for problems in ocean acoustics and seismo-acoustics. For shallow water problems, accuracy is sensitive to the precise placement of the ocean bottom interface. This issue is often addressed with the inefficient approach of using a fine grid spacing over all depth. Efficiency may be improved by using a relatively coarse grid with nonuniform sampling to precisely position the interface. Efficiency may also be improved by reducing the sampling in the sediment and in an absorbing layer that is used to truncate the computational domain. Nonuniform sampling may also be used to improve the implementation of a single-scattering approximation for sloping fluid-solid interfaces.

Efficient globally optimal segmentation of cells in fluorescence microscopy images using level sets and convex energy functionals.

PubMed

Bergeest, Jan-Philip; Rohr, Karl

2012-10-01

In high-throughput applications, accurate and efficient segmentation of cells in fluorescence microscopy images is of central importance for the quantification of protein expression and the understanding of cell function. We propose an approach for segmenting cell nuclei which is based on active contours using level sets and convex energy functionals. Compared to previous work, our approach determines the global solution. Thus, the approach does not suffer from local minima and the segmentation result does not depend on the initialization. We consider three different well-known energy functionals for active contour-based segmentation and introduce convex formulations of these functionals. We also suggest a numeric approach for efficiently computing the solution. The performance of our approach has been evaluated using fluorescence microscopy images from different experiments comprising different cell types. We have also performed a quantitative comparison with previous segmentation approaches. Copyright © 2012 Elsevier B.V. All rights reserved.

Efficient field-theoretic simulation of polymer solutions

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

Villet, Michael C.; Fredrickson, Glenn H., E-mail: ghf@mrl.ucsb.edu; Department of Materials, University of California, Santa Barbara, California 93106

2014-12-14

We present several developments that facilitate the efficient field-theoretic simulation of polymers by complex Langevin sampling. A regularization scheme using finite Gaussian excluded volume interactions is used to derive a polymer solution model that appears free of ultraviolet divergences and hence is well-suited for lattice-discretized field theoretic simulation. We show that such models can exhibit ultraviolet sensitivity, a numerical pathology that dramatically increases sampling error in the continuum lattice limit, and further show that this pathology can be eliminated by appropriate model reformulation by variable transformation. We present an exponential time differencing algorithm for integrating complex Langevin equations for fieldmore » theoretic simulation, and show that the algorithm exhibits excellent accuracy and stability properties for our regularized polymer model. These developments collectively enable substantially more efficient field-theoretic simulation of polymers, and illustrate the importance of simultaneously addressing analytical and numerical pathologies when implementing such computations.« less

Stochastic Evolutionary Algorithms for Planning Robot Paths

NASA Technical Reports Server (NTRS)

Fink, Wolfgang; Aghazarian, Hrand; Huntsberger, Terrance; Terrile, Richard

2006-01-01

A computer program implements stochastic evolutionary algorithms for planning and optimizing collision-free paths for robots and their jointed limbs. Stochastic evolutionary algorithms can be made to produce acceptably close approximations to exact, optimal solutions for path-planning problems while often demanding much less computation than do exhaustive-search and deterministic inverse-kinematics algorithms that have been used previously for this purpose. Hence, the present software is better suited for application aboard robots having limited computing capabilities (see figure). The stochastic aspect lies in the use of simulated annealing to (1) prevent trapping of an optimization algorithm in local minima of an energy-like error measure by which the fitness of a trial solution is evaluated while (2) ensuring that the entire multidimensional configuration and parameter space of the path-planning problem is sampled efficiently with respect to both robot joint angles and computation time. Simulated annealing is an established technique for avoiding local minima in multidimensional optimization problems, but has not, until now, been applied to planning collision-free robot paths by use of low-power computers.

Interoperating Cloud-based Virtual Farms

NASA Astrophysics Data System (ADS)

Bagnasco, S.; Colamaria, F.; Colella, D.; Casula, E.; Elia, D.; Franco, A.; Lusso, S.; Luparello, G.; Masera, M.; Miniello, G.; Mura, D.; Piano, S.; Vallero, S.; Venaruzzo, M.; Vino, G.

2015-12-01

The present work aims at optimizing the use of computing resources available at the grid Italian Tier-2 sites of the ALICE experiment at CERN LHC by making them accessible to interactive distributed analysis, thanks to modern solutions based on cloud computing. The scalability and elasticity of the computing resources via dynamic (“on-demand”) provisioning is essentially limited by the size of the computing site, reaching the theoretical optimum only in the asymptotic case of infinite resources. The main challenge of the project is to overcome this limitation by federating different sites through a distributed cloud facility. Storage capacities of the participating sites are seen as a single federated storage area, preventing the need of mirroring data across them: high data access efficiency is guaranteed by location-aware analysis software and storage interfaces, in a transparent way from an end-user perspective. Moreover, the interactive analysis on the federated cloud reduces the execution time with respect to grid batch jobs. The tests of the investigated solutions for both cloud computing and distributed storage on wide area network will be presented.

Improved dynamic analysis method using load-dependent Ritz vectors

NASA Technical Reports Server (NTRS)

Escobedo-Torres, J.; Ricles, J. M.

1993-01-01

The dynamic analysis of large space structures is important in order to predict their behavior under operating conditions. Computer models of large space structures are characterized by having a large number of degrees of freedom, and the computational effort required to carry out the analysis is very large. Conventional methods of solution utilize a subset of the eigenvectors of the system, but for systems with many degrees of freedom, the solution of the eigenproblem is in many cases the most costly phase of the analysis. For this reason, alternate solution methods need to be considered. It is important that the method chosen for the analysis be efficient and that accurate results be obtainable. It is important that the method chosen for the analysis be efficient and that accurate results be obtainable. The load dependent Ritz vector method is presented as an alternative to the classical normal mode methods for obtaining dynamic responses of large space structures. A simplified model of a space station is used to compare results. Results show that the load dependent Ritz vector method predicts the dynamic response better than the classical normal mode method. Even though this alternate method is very promising, further studies are necessary to fully understand its attributes and limitations.

Model reduction method using variable-separation for stochastic saddle point problems

NASA Astrophysics Data System (ADS)

Jiang, Lijian; Li, Qiuqi

2018-02-01

In this paper, we consider a variable-separation (VS) method to solve the stochastic saddle point (SSP) problems. The VS method is applied to obtain the solution in tensor product structure for stochastic partial differential equations (SPDEs) in a mixed formulation. The aim of such a technique is to construct a reduced basis approximation of the solution of the SSP problems. The VS method attempts to get a low rank separated representation of the solution for SSP in a systematic enrichment manner. No iteration is performed at each enrichment step. In order to satisfy the inf-sup condition in the mixed formulation, we enrich the separated terms for the primal system variable at each enrichment step. For the SSP problems by regularization or penalty, we propose a more efficient variable-separation (VS) method, i.e., the variable-separation by penalty method. This can avoid further enrichment of the separated terms in the original mixed formulation. The computation of the variable-separation method decomposes into offline phase and online phase. Sparse low rank tensor approximation method is used to significantly improve the online computation efficiency when the number of separated terms is large. For the applications of SSP problems, we present three numerical examples to illustrate the performance of the proposed methods.

A Reconstructed Discontinuous Galerkin Method for the Compressible Euler Equations on Arbitrary Grids

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

Hong Luo; Luquing Luo; Robert Nourgaliev

2009-06-01

A reconstruction-based discontinuous Galerkin (DG) method is presented for the solution of the compressible Euler equations on arbitrary grids. By taking advantage of handily available and yet invaluable information, namely the derivatives, in the context of the discontinuous Galerkin methods, a solution polynomial of one degree higher is reconstructed using a least-squares method. The stencils used in the reconstruction involve only the van Neumann neighborhood (face-neighboring cells) and are compact and consistent with the underlying DG method. The resulting DG method can be regarded as an improvement of a recovery-based DG method in the sense that it shares the samemore » nice features as the recovery-based DG method, such as high accuracy and efficiency, and yet overcomes some of its shortcomings such as a lack of flexibility, compactness, and robustness. The developed DG method is used to compute a variety of flow problems on arbitrary meshes to demonstrate the accuracy and efficiency of the method. The numerical results indicate that this reconstructed DG method is able to obtain a third-order accurate solution at a slightly higher cost than its second-order DG method and provide an increase in performance over the third order DG method in terms of computing time and storage requirement.« less

Light extraction efficiency analysis of GaN-based light-emitting diodes with nanopatterned sapphire substrates.

PubMed

Pan, Jui-Wen; Tsai, Pei-Jung; Chang, Kao-Der; Chang, Yung-Yuan

2013-03-01

In this paper, we propose a method to analyze the light extraction efficiency (LEE) enhancement of a nanopatterned sapphire substrates (NPSS) light-emitting diode (LED) by comparing wave optics software with ray optics software. Finite-difference time-domain (FDTD) simulations represent the wave optics software and Light Tools (LTs) simulations represent the ray optics software. First, we find the trends of and an optimal solution for the LEE enhancement when the 2D-FDTD simulations are used to save on simulation time and computational memory. The rigorous coupled-wave analysis method is utilized to explain the trend we get from the 2D-FDTD algorithm. The optimal solution is then applied in 3D-FDTD and LTs simulations. The results are similar and the difference in LEE enhancement between the two simulations does not exceed 8.5% in the small LED chip area. More than 10(4) times computational memory is saved during the LTs simulation in comparison to the 3D-FDTD simulation. Moreover, LEE enhancement from the side of the LED can be obtained in the LTs simulation. An actual-size NPSS LED is simulated using the LTs. The results show a more than 307% improvement in the total LEE enhancement of the NPSS LED with the optimal solution compared to the conventional LED.

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

NASA Astrophysics Data System (ADS)

Valiev, M.; Bylaska, E. J.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Van Dam, H. J. J.; Wang, D.; Nieplocha, J.; Apra, E.; Windus, T. L.; de Jong, W. A.

2010-09-01

The latest release of NWChem delivers an open-source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance. Program summaryProgram title: NWChem Catalogue identifier: AEGI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Open Source Educational Community License No. of lines in distributed program, including test data, etc.: 11 709 543 No. of bytes in distributed program, including test data, etc.: 680 696 106 Distribution format: tar.gz Programming language: Fortran 77, C Computer: all Linux based workstations and parallel supercomputers, Windows and Apple machines Operating system: Linux, OS X, Windows Has the code been vectorised or parallelized?: Code is parallelized Classification: 2.1, 2.2, 3, 7.3, 7.7, 16.1, 16.2, 16.3, 16.10, 16.13 Nature of problem: Large-scale atomistic simulations of chemical and biological systems require efficient and reliable methods for ground and excited solutions of many-electron Hamiltonian, analysis of the potential energy surface, and dynamics. Solution method: Ground and excited solutions of many-electron Hamiltonian are obtained utilizing density-functional theory, many-body perturbation approach, and coupled cluster expansion. These solutions or a combination thereof with classical descriptions are then used to analyze potential energy surface and perform dynamical simulations. Additional comments: Full documentation is provided in the distribution file. This includes an INSTALL file giving details of how to build the package. A set of test runs is provided in the examples directory. The distribution file for this program is over 90 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Running time depends on the size of the chemical system, complexity of the method, number of cpu's and the computational task. It ranges from several seconds for serial DFT energy calculations on a few atoms to several hours for parallel coupled cluster energy calculations on tens of atoms or ab-initio molecular dynamics simulation on hundreds of atoms.

A pressure flux-split technique for computation of inlet flow behavior

NASA Technical Reports Server (NTRS)

Pordal, H. S.; Khosla, P. K.; Rubin, S. G.

1991-01-01

A method for calculating the flow field in aircraft engine inlets is presented. The phenomena of inlet unstart and restart are investigated. Solutions of the reduced Navier-Stokes (RNS) equations are obtained with a time consistent direct sparse matrix solver that computes the transient flow field both internal and external to the inlet. Time varying shocks and time varying recirculation regions can be efficiently analyzed. The code is quite general and is suitable for the computation of flow for a wide variety of geometries and over a wide range of Mach and Reynolds numbers.

Bistatic passive radar simulator with spatial filtering subsystem

NASA Astrophysics Data System (ADS)

Hossa, Robert; Szlachetko, Boguslaw; Lewandowski, Andrzej; Górski, Maksymilian

2009-06-01

The purpose of this paper is to briefly introduce the structure and features of the developed virtual passive FM radar implemented in Matlab system of numerical computations and to present many alternative ways of its performance. An idea of the proposed solution is based on analytic representation of transmitted direct signals and reflected echo signals. As a spatial filtering subsystem a beamforming network of ULA and UCA dipole configuration dedicated to bistatic radar concept is considered and computationally efficient procedures are presented in details. Finally, exemplary results of the computer simulations of the elaborated virtual simulator are provided and discussed.

Feedback quantum control of molecular electronic population transfer

NASA Astrophysics Data System (ADS)

Bardeen, Christopher J.; Yakovlev, Vladislav V.; Wilson, Kent R.; Carpenter, Scott D.; Weber, Peter M.; Warren, Warren S.

1997-11-01

Feedback quantum control, where the sample `teaches' a computer-controlled arbitrary lightform generator to find the optimal light field, is experimentally demonstrated for a molecular system. Femtosecond pulses tailored by a computer-controlled acousto-optic pulse shaper excite fluorescence from laser dye molecules in solution. Fluorescence and laser power are monitored, and the computer uses the experimental data and a genetic algorithm to optimize population transfer from ground to first excited state. Both efficiency (the ratio of excited state population to laser energy) and effectiveness (total excited state population) are optimized. Potential use as an `automated theory tester' is discussed.

Stability and error estimation for Component Adaptive Grid methods

NASA Technical Reports Server (NTRS)

Oliger, Joseph; Zhu, Xiaolei

1994-01-01

Component adaptive grid (CAG) methods for solving hyperbolic partial differential equations (PDE's) are discussed in this paper. Applying recent stability results for a class of numerical methods on uniform grids. The convergence of these methods for linear problems on component adaptive grids is established here. Furthermore, the computational error can be estimated on CAG's using the stability results. Using these estimates, the error can be controlled on CAG's. Thus, the solution can be computed efficiently on CAG's within a given error tolerance. Computational results for time dependent linear problems in one and two space dimensions are presented.

Development of efficient time-evolution method based on three-term recurrence relation

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

Akama, Tomoko, E-mail: a.tomo---s-b-l-r@suou.waseda.jp; Kobayashi, Osamu; Nanbu, Shinkoh, E-mail: shinkoh.nanbu@sophia.ac.jp

The advantage of the real-time (RT) propagation method is a direct solution of the time-dependent Schrödinger equation which describes frequency properties as well as all dynamics of a molecular system composed of electrons and nuclei in quantum physics and chemistry. Its applications have been limited by computational feasibility, as the evaluation of the time-evolution operator is computationally demanding. In this article, a new efficient time-evolution method based on the three-term recurrence relation (3TRR) was proposed to reduce the time-consuming numerical procedure. The basic formula of this approach was derived by introducing a transformation of the operator using the arcsine function.more » Since this operator transformation causes transformation of time, we derived the relation between original and transformed time. The formula was adapted to assess the performance of the RT time-dependent Hartree-Fock (RT-TDHF) method and the time-dependent density functional theory. Compared to the commonly used fourth-order Runge-Kutta method, our new approach decreased computational time of the RT-TDHF calculation by about factor of four, showing the 3TRR formula to be an efficient time-evolution method for reducing computational cost.« less

A Mathematica program for the approximate analytical solution to a nonlinear undamped Duffing equation by a new approximate approach

NASA Astrophysics Data System (ADS)

Wu, Dongmei; Wang, Zhongcheng

2006-03-01

According to Mickens [R.E. Mickens, Comments on a Generalized Galerkin's method for non-linear oscillators, J. Sound Vib. 118 (1987) 563], the general HB (harmonic balance) method is an approximation to the convergent Fourier series representation of the periodic solution of a nonlinear oscillator and not an approximation to an expansion in terms of a small parameter. Consequently, for a nonlinear undamped Duffing equation with a driving force Bcos(ωx), to find a periodic solution when the fundamental frequency is identical to ω, the corresponding Fourier series can be written as y˜(x)=∑n=1m acos[(2n-1)ωx]. How to calculate the coefficients of the Fourier series efficiently with a computer program is still an open problem. For HB method, by substituting approximation y˜(x) into force equation, expanding the resulting expression into a trigonometric series, then letting the coefficients of the resulting lowest-order harmonic be zero, one can obtain approximate coefficients of approximation y˜(x) [R.E. Mickens, Comments on a Generalized Galerkin's method for non-linear oscillators, J. Sound Vib. 118 (1987) 563]. But for nonlinear differential equations such as Duffing equation, it is very difficult to construct higher-order analytical approximations, because the HB method requires solving a set of algebraic equations for a large number of unknowns with very complex nonlinearities. To overcome the difficulty, forty years ago, Urabe derived a computational method for Duffing equation based on Galerkin procedure [M. Urabe, A. Reiter, Numerical computation of nonlinear forced oscillations by Galerkin's procedure, J. Math. Anal. Appl. 14 (1966) 107-140]. Dooren obtained an approximate solution of the Duffing oscillator with a special set of parameters by using Urabe's method [R. van Dooren, Stabilization of Cowell's classic finite difference method for numerical integration, J. Comput. Phys. 16 (1974) 186-192]. In this paper, in the frame of the general HB method, we present a new iteration algorithm to calculate the coefficients of the Fourier series. By using this new method, the iteration procedure starts with a(x)cos(ωx)+b(x)sin(ωx), and the accuracy may be improved gradually by determining new coefficients a,a,… will be produced automatically in an one-by-one manner. In all the stage of calculation, we need only to solve a cubic equation. Using this new algorithm, we develop a Mathematica program, which demonstrates following main advantages over the previous HB method: (1) it avoids solving a set of associate nonlinear equations; (2) it is easier to be implemented into a computer program, and produces a highly accurate solution with analytical expression efficiently. It is interesting to find that, generally, for a given set of parameters, a nonlinear Duffing equation can have three independent oscillation modes. For some sets of the parameters, it can have two modes with complex displacement and one with real displacement. But in some cases, it can have three modes, all of them having real displacement. Therefore, we can divide the parameters into two classes, according to the solution property: there is only one mode with real displacement and there are three modes with real displacement. This program should be useful to study the dynamically periodic behavior of a Duffing oscillator and can provide an approximate analytical solution with high-accuracy for testing the error behavior of newly developed numerical methods with a wide range of parameters. Program summaryTitle of program:AnalyDuffing.nb Catalogue identifier:ADWR_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWR_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions:none Computer for which the program is designed and others on which it has been tested:the program has been designed for a microcomputer and been tested on the microcomputer. Computers:IBM PC Installations:the address(es) of your computer(s) Operating systems under which the program has been tested:Windows XP Programming language used:Software Mathematica 4.2, 5.0 and 5.1 No. of lines in distributed program, including test data, etc.:23 663 No. of bytes in distributed program, including test data, etc.:152 321 Distribution format:tar.gz Memory required to execute with typical data:51 712 Bytes No. of bits in a word: No. of processors used:1 Has the code been vectorized?:no Peripherals used:no Program Library subprograms used:no Nature of physical problem:To find an approximate solution with analytical expressions for the undamped nonlinear Duffing equation with periodic driving force when the fundamental frequency is identical to the driving force. Method of solution:In the frame of the general HB method, by using a new iteration algorithm to calculate the coefficients of the Fourier series, we can obtain an approximate analytical solution with high-accuracy efficiently. Restrictions on the complexity of the problem:For problems, which have a large driving frequency, the convergence may be a little slow, because more iterative times are needed. Typical running time:several seconds Unusual features of the program:For an undamped Duffing equation, it can provide all the solutions or the oscillation modes with real displacement for any interesting parameters, for the required accuracy, efficiently. The program can be used to study the dynamically periodic behavior of a nonlinear oscillator, and can provide a high-accurate approximate analytical solution for developing high-accurate numerical method.

Spatial operator factorization and inversion of the manipulator mass matrix

NASA Technical Reports Server (NTRS)

Rodriguez, Guillermo; Kreutz-Delgado, Kenneth

1992-01-01

This paper advances two linear operator factorizations of the manipulator mass matrix. Embedded in the factorizations are many of the techniques that are regarded as very efficient computational solutions to inverse and forward dynamics problems. The operator factorizations provide a high-level architectural understanding of the mass matrix and its inverse, which is not visible in the detailed algorithms. They also lead to a new approach to the development of computer programs or organize complexity in robot dynamics.

Black hole state counting in loop quantum gravity: a number-theoretical approach.

PubMed

Agulló, Iván; Barbero G, J Fernando; Díaz-Polo, Jacobo; Fernández-Borja, Enrique; Villaseñor, Eduardo J S

2008-05-30

We give an efficient method, combining number-theoretic and combinatorial ideas, to exactly compute black hole entropy in the framework of loop quantum gravity. Along the way we provide a complete characterization of the relevant sector of the spectrum of the area operator, including degeneracies, and explicitly determine the number of solutions to the projection constraint. We use a computer implementation of the proposed algorithm to confirm and extend previous results on the detailed structure of the black hole degeneracy spectrum.

Approximate Green's function methods for HZE transport in multilayered materials

NASA Technical Reports Server (NTRS)

Wilson, John W.; Badavi, Francis F.; Shinn, Judy L.; Costen, Robert C.

1993-01-01

A nonperturbative analytic solution of the high charge and energy (HZE) Green's function is used to implement a computer code for laboratory ion beam transport in multilayered materials. The code is established to operate on the Langley nuclear fragmentation model used in engineering applications. Computational procedures are established to generate linear energy transfer (LET) distributions for a specified ion beam and target for comparison with experimental measurements. The code was found to be highly efficient and compared well with the perturbation approximation.

Numerical calculations of two dimensional, unsteady transonic flows with circulation

NASA Technical Reports Server (NTRS)

Beam, R. M.; Warming, R. F.

1974-01-01

The feasibility of obtaining two-dimensional, unsteady transonic aerodynamic data by numerically integrating the Euler equations is investigated. An explicit, third-order-accurate, noncentered, finite-difference scheme is used to compute unsteady flows about airfoils. Solutions for lifting and nonlifting airfoils are presented and compared with subsonic linear theory. The applicability and efficiency of the numerical indicial function method are outlined. Numerically computed subsonic and transonic oscillatory aerodynamic coefficients are presented and compared with those obtained from subsonic linear theory and transonic wind-tunnel data.

Cubic spline numerical solution of an ablation problem with convective backface cooling

NASA Astrophysics Data System (ADS)

Lin, S.; Wang, P.; Kahawita, R.

1984-08-01

An implicit numerical technique using cubic splines is presented for solving an ablation problem on a thin wall with convective cooling. A non-uniform computational mesh with 6 grid points has been used for the numerical integration. The method has been found to be computationally efficient, providing for the care under consideration of an overall error of about 1 percent. The results obtained indicate that the convective cooling is an important factor in reducing the ablation thickness.

Modeling of fatigue crack induced nonlinear ultrasonics using a highly parallelized explicit local interaction simulation approach

NASA Astrophysics Data System (ADS)

Shen, Yanfeng; Cesnik, Carlos E. S.

2016-04-01

This paper presents a parallelized modeling technique for the efficient simulation of nonlinear ultrasonics introduced by the wave interaction with fatigue cracks. The elastodynamic wave equations with contact effects are formulated using an explicit Local Interaction Simulation Approach (LISA). The LISA formulation is extended to capture the contact-impact phenomena during the wave damage interaction based on the penalty method. A Coulomb friction model is integrated into the computation procedure to capture the stick-slip contact shear motion. The LISA procedure is coded using the Compute Unified Device Architecture (CUDA), which enables the highly parallelized supercomputing on powerful graphic cards. Both the explicit contact formulation and the parallel feature facilitates LISA's superb computational efficiency over the conventional finite element method (FEM). The theoretical formulations based on the penalty method is introduced and a guideline for the proper choice of the contact stiffness is given. The convergence behavior of the solution under various contact stiffness values is examined. A numerical benchmark problem is used to investigate the new LISA formulation and results are compared with a conventional contact finite element solution. Various nonlinear ultrasonic phenomena are successfully captured using this contact LISA formulation, including the generation of nonlinear higher harmonic responses. Nonlinear mode conversion of guided waves at fatigue cracks is also studied.

Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions

PubMed Central

Deng, Shaozhong; Xue, Changfeng; Baumketner, Andriy; Jacobs, Donald; Cai, Wei

2013-01-01

This paper extends the image charge solvation model (ICSM) [J. Chem. Phys. 131, 154103 (2009)], a hybrid explicit/implicit method to treat electrostatic interactions in computer simulations of biomolecules formulated for spherical cavities, to prolate spheroidal and triaxial ellipsoidal cavities, designed to better accommodate non-spherical solutes in molecular dynamics (MD) simulations. In addition to the utilization of a general truncated octahedron as the MD simulation box, central to the proposed extension is an image approximation method to compute the reaction field for a point charge placed inside such a non-spherical cavity by using a single image charge located outside the cavity. The resulting generalized image charge solvation model (GICSM) is tested in simulations of liquid water, and the results are analyzed in comparison with those obtained from the ICSM simulations as a reference. We find that, for improved computational efficiency due to smaller simulation cells and consequently a less number of explicit solvent molecules, the generalized model can still faithfully reproduce known static and dynamic properties of liquid water at least for systems considered in the present paper, indicating its great potential to become an accurate but more efficient alternative to the ICSM when bio-macromolecules of irregular shapes are to be simulated. PMID:23913979

VOFTools - A software package of calculation tools for volume of fluid methods using general convex grids

NASA Astrophysics Data System (ADS)

López, J.; Hernández, J.; Gómez, P.; Faura, F.

2018-02-01

The VOFTools library includes efficient analytical and geometrical routines for (1) area/volume computation, (2) truncation operations that typically arise in VOF (volume of fluid) methods, (3) area/volume conservation enforcement (VCE) in PLIC (piecewise linear interface calculation) reconstruction and(4) computation of the distance from a given point to the reconstructed interface. The computation of a polyhedron volume uses an efficient formula based on a quadrilateral decomposition and a 2D projection of each polyhedron face. The analytical VCE method is based on coupling an interpolation procedure to bracket the solution with an improved final calculation step based on the above volume computation formula. Although the library was originally created to help develop highly accurate advection and reconstruction schemes in the context of VOF methods, it may have more general applications. To assess the performance of the supplied routines, different tests, which are provided in FORTRAN and C, were implemented for several 2D and 3D geometries.

An adaptive discontinuous Galerkin solver for aerodynamic flows

NASA Astrophysics Data System (ADS)

Burgess, Nicholas K.

This work considers the accuracy, efficiency, and robustness of an unstructured high-order accurate discontinuous Galerkin (DG) solver for computational fluid dynamics (CFD). Recently, there has been a drive to reduce the discretization error of CFD simulations using high-order methods on unstructured grids. However, high-order methods are often criticized for lacking robustness and having high computational cost. The goal of this work is to investigate methods that enhance the robustness of high-order discontinuous Galerkin (DG) methods on unstructured meshes, while maintaining low computational cost and high accuracy of the numerical solutions. This work investigates robustness enhancement of high-order methods by examining effective non-linear solvers, shock capturing methods, turbulence model discretizations and adaptive refinement techniques. The goal is to develop an all encompassing solver that can simulate a large range of physical phenomena, where all aspects of the solver work together to achieve a robust, efficient and accurate solution strategy. The components and framework for a robust high-order accurate solver that is capable of solving viscous, Reynolds Averaged Navier-Stokes (RANS) and shocked flows is presented. In particular, this work discusses robust discretizations of the turbulence model equation used to close the RANS equations, as well as stable shock capturing strategies that are applicable across a wide range of discretization orders and applicable to very strong shock waves. Furthermore, refinement techniques are considered as both efficiency and robustness enhancement strategies. Additionally, efficient non-linear solvers based on multigrid and Krylov subspace methods are presented. The accuracy, efficiency, and robustness of the solver is demonstrated using a variety of challenging aerodynamic test problems, which include turbulent high-lift and viscous hypersonic flows. Adaptive mesh refinement was found to play a critical role in obtaining a robust and efficient high-order accurate flow solver. A goal-oriented error estimation technique has been developed to estimate the discretization error of simulation outputs. For high-order discretizations, it is shown that functional output error super-convergence can be obtained, provided the discretization satisfies a property known as dual consistency. The dual consistency of the DG methods developed in this work is shown via mathematical analysis and numerical experimentation. Goal-oriented error estimation is also used to drive an hp-adaptive mesh refinement strategy, where a combination of mesh or h-refinement, and order or p-enrichment, is employed based on the smoothness of the solution. The results demonstrate that the combination of goal-oriented error estimation and hp-adaptation yield superior accuracy, as well as enhanced robustness and efficiency for a variety of aerodynamic flows including flows with strong shock waves. This work demonstrates that DG discretizations can be the basis of an accurate, efficient, and robust CFD solver. Furthermore, enhancing the robustness of DG methods does not adversely impact the accuracy or efficiency of the solver for challenging and complex flow problems. In particular, when considering the computation of shocked flows, this work demonstrates that the available shock capturing techniques are sufficiently accurate and robust, particularly when used in conjunction with adaptive mesh refinement . This work also demonstrates that robust solutions of the Reynolds Averaged Navier-Stokes (RANS) and turbulence model equations can be obtained for complex and challenging aerodynamic flows. In this context, the most robust strategy was determined to be a low-order turbulence model discretization coupled to a high-order discretization of the RANS equations. Although RANS solutions using high-order accurate discretizations of the turbulence model were obtained, the behavior of current-day RANS turbulence models discretized to high-order was found to be problematic, leading to solver robustness issues. This suggests that future work is warranted in the area of turbulence model formulation for use with high-order discretizations. Alternately, the use of Large-Eddy Simulation (LES) subgrid scale models with high-order DG methods offers the potential to leverage the high accuracy of these methods for very high fidelity turbulent simulations. This thesis has developed the algorithmic improvements that will lay the foundation for the development of a three-dimensional high-order flow solution strategy that can be used as the basis for future LES simulations.

Adaptive Implicit Non-Equilibrium Radiation Diffusion

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

Philip, Bobby; Wang, Zhen; Berrill, Mark A

2013-01-01

We describe methods for accurate and efficient long term time integra- tion of non-equilibrium radiation diffusion systems: implicit time integration for effi- cient long term time integration of stiff multiphysics systems, local control theory based step size control to minimize the required global number of time steps while control- ling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton-Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

Perspectives in astrophysical databases

NASA Astrophysics Data System (ADS)

Frailis, Marco; de Angelis, Alessandro; Roberto, Vito

2004-07-01

Astrophysics has become a domain extremely rich of scientific data. Data mining tools are needed for information extraction from such large data sets. This asks for an approach to data management emphasizing the efficiency and simplicity of data access; efficiency is obtained using multidimensional access methods and simplicity is achieved by properly handling metadata. Moreover, clustering and classification techniques on large data sets pose additional requirements in terms of computation and memory scalability and interpretability of results. In this study we review some possible solutions.

Spectrally formulated user-defined element in conventional finite element environment for wave motion analysis in 2-D composite structures

NASA Astrophysics Data System (ADS)

Khalili, Ashkan; Jha, Ratneshwar; Samaratunga, Dulip

2016-11-01

Wave propagation analysis in 2-D composite structures is performed efficiently and accurately through the formulation of a User-Defined Element (UEL) based on the wavelet spectral finite element (WSFE) method. The WSFE method is based on the first-order shear deformation theory which yields accurate results for wave motion at high frequencies. The 2-D WSFE model is highly efficient computationally and provides a direct relationship between system input and output in the frequency domain. The UEL is formulated and implemented in Abaqus (commercial finite element software) for wave propagation analysis in 2-D composite structures with complexities. Frequency domain formulation of WSFE leads to complex valued parameters, which are decoupled into real and imaginary parts and presented to Abaqus as real values. The final solution is obtained by forming a complex value using the real number solutions given by Abaqus. Five numerical examples are presented in this article, namely undamaged plate, impacted plate, plate with ply drop, folded plate and plate with stiffener. Wave motions predicted by the developed UEL correlate very well with Abaqus simulations. The results also show that the UEL largely retains computational efficiency of the WSFE method and extends its ability to model complex features.

An efficient non-dominated sorting method for evolutionary algorithms.

PubMed

Fang, Hongbing; Wang, Qian; Tu, Yi-Cheng; Horstemeyer, Mark F

2008-01-01

We present a new non-dominated sorting algorithm to generate the non-dominated fronts in multi-objective optimization with evolutionary algorithms, particularly the NSGA-II. The non-dominated sorting algorithm used by NSGA-II has a time complexity of O(MN(2)) in generating non-dominated fronts in one generation (iteration) for a population size N and M objective functions. Since generating non-dominated fronts takes the majority of total computational time (excluding the cost of fitness evaluations) of NSGA-II, making this algorithm faster will significantly improve the overall efficiency of NSGA-II and other genetic algorithms using non-dominated sorting. The new non-dominated sorting algorithm proposed in this study reduces the number of redundant comparisons existing in the algorithm of NSGA-II by recording the dominance information among solutions from their first comparisons. By utilizing a new data structure called the dominance tree and the divide-and-conquer mechanism, the new algorithm is faster than NSGA-II for different numbers of objective functions. Although the number of solution comparisons by the proposed algorithm is close to that of NSGA-II when the number of objectives becomes large, the total computational time shows that the proposed algorithm still has better efficiency because of the adoption of the dominance tree structure and the divide-and-conquer mechanism.

Understanding security failures of two authentication and key agreement schemes for telecare medicine information systems.

PubMed

Mishra, Dheerendra

2015-03-01

Smart card based authentication and key agreement schemes for telecare medicine information systems (TMIS) enable doctors, nurses, patients and health visitors to use smart cards for secure login to medical information systems. In recent years, several authentication and key agreement schemes have been proposed to present secure and efficient solution for TMIS. Most of the existing authentication schemes for TMIS have either higher computation overhead or are vulnerable to attacks. To reduce the computational overhead and enhance the security, Lee recently proposed an authentication and key agreement scheme using chaotic maps for TMIS. Xu et al. also proposed a password based authentication and key agreement scheme for TMIS using elliptic curve cryptography. Both the schemes provide better efficiency from the conventional public key cryptography based schemes. These schemes are important as they present an efficient solution for TMIS. We analyze the security of both Lee's scheme and Xu et al.'s schemes. Unfortunately, we identify that both the schemes are vulnerable to denial of service attack. To understand the security failures of these cryptographic schemes which are the key of patching existing schemes and designing future schemes, we demonstrate the security loopholes of Lee's scheme and Xu et al.'s scheme in this paper.

DL_MG: A Parallel Multigrid Poisson and Poisson-Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution.

PubMed

Womack, James C; Anton, Lucian; Dziedzic, Jacek; Hasnip, Phil J; Probert, Matt I J; Skylaris, Chris-Kriton

2018-03-13

The solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential-a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the Poisson equation, featuring nonhomogeneous dielectric permittivities, ionic concentrations with nonlinear dependencies, and diverse boundary conditions. The analytic solutions generally used to solve the Poisson equation in vacuum (or with homogeneous permittivity) are not applicable in these circumstances, and numerical methods must be used. In this work, we present DL_MG, a flexible, scalable, and accurate solver library, developed specifically to tackle the challenges of solving the Poisson equation in modern large-scale electronic structure calculations on parallel computers. Our solver is based on the multigrid approach and uses an iterative high-order defect correction method to improve the accuracy of solutions. Using two chemically relevant model systems, we tested the accuracy and computational performance of DL_MG when solving the generalized Poisson and Poisson-Boltzmann equations, demonstrating excellent agreement with analytic solutions and efficient scaling to ∼10 9 unknowns and 100s of CPU cores. We also applied DL_MG in actual large-scale electronic structure calculations, using the ONETEP linear-scaling electronic structure package to study a 2615 atom protein-ligand complex with routinely available computational resources. In these calculations, the overall execution time with DL_MG was not significantly greater than the time required for calculations using a conventional FFT-based solver.

Technique Developed for Optimizing Traveling-Wave Tubes

NASA Technical Reports Server (NTRS)

Wilson, Jeffrey D.

1999-01-01

A traveling-wave tube (TWT) is an electron beam device that is used to amplify electromagnetic communication waves at radio and microwave frequencies. TWT s are critical components in deep-space probes, geosynchronous communication satellites, and high-power radar systems. Power efficiency is of paramount importance for TWT s employed in deep-space probes and communications satellites. Consequently, increasing the power efficiency of TWT s has been the primary goal of the TWT group at the NASA Lewis Research Center over the last 25 years. An in-house effort produced a technique (ref. 1) to design TWT's for optimized power efficiency. This technique is based on simulated annealing, which has an advantage over conventional optimization techniques in that it enables the best possible solution to be obtained (ref. 2). A simulated annealing algorithm was created and integrated into the NASA TWT computer model (ref. 3). The new technique almost doubled the computed conversion power efficiency of a TWT from 7.1 to 13.5 percent (ref. 1).

Mechanical Computing Redux: Limitations at the Nanoscale

NASA Astrophysics Data System (ADS)

Liu, Tsu-Jae King

2014-03-01

Technology solutions for overcoming the energy efficiency limits of nanoscale complementary metal oxide semiconductor (CMOS) technology ultimately will be needed in order to address the growing issue of integrated-circuit chip power density. Off-state leakage current sets a fundamental lower limit in energy per operation for any voltage-level-based digital logic implemented with transistors (CMOS and beyond), which leads to practical limits for device density (i.e. cost) and operating frequency (i.e. system performance). Mechanical switches have zero off-state leakag and hence can overcome this fundamental limit. Contact adhesive force sets a lower limit for the switching energy of a mechanical switch, however, and also directly impacts its performance. This paper will review recent progress toward the development of nano-electro-mechanical relay technology and discuss remaining challenges for realizing the promise of mechanical computing for ultra-low-power computing. Supported by the Center for Energy Efficient Electronics Science (NSF Award 0939514).

PRESAGE: PRivacy-preserving gEnetic testing via SoftwAre Guard Extension.

PubMed

Chen, Feng; Wang, Chenghong; Dai, Wenrui; Jiang, Xiaoqian; Mohammed, Noman; Al Aziz, Md Momin; Sadat, Md Nazmus; Sahinalp, Cenk; Lauter, Kristin; Wang, Shuang

2017-07-26

Advances in DNA sequencing technologies have prompted a wide range of genomic applications to improve healthcare and facilitate biomedical research. However, privacy and security concerns have emerged as a challenge for utilizing cloud computing to handle sensitive genomic data. We present one of the first implementations of Software Guard Extension (SGX) based securely outsourced genetic testing framework, which leverages multiple cryptographic protocols and minimal perfect hash scheme to enable efficient and secure data storage and computation outsourcing. We compared the performance of the proposed PRESAGE framework with the state-of-the-art homomorphic encryption scheme, as well as the plaintext implementation. The experimental results demonstrated significant performance over the homomorphic encryption methods and a small computational overhead in comparison to plaintext implementation. The proposed PRESAGE provides an alternative solution for secure and efficient genomic data outsourcing in an untrusted cloud by using a hybrid framework that combines secure hardware and multiple crypto protocols.

Fast and Efficient Discrimination of Traveling Salesperson Problem Stimulus Difficulty

ERIC Educational Resources Information Center

Dry, Matthew J.; Fontaine, Elizabeth L.

2014-01-01

The Traveling Salesperson Problem (TSP) is a computationally difficult combinatorial optimization problem. In spite of its relative difficulty, human solvers are able to generate close-to-optimal solutions in a close-to-linear time frame, and it has been suggested that this is due to the visual system's inherent sensitivity to certain geometric…

Supporting Blended-Learning: Tool Requirements and Solutions with OWLish

ERIC Educational Resources Information Center

Álvarez, Ainhoa; Martín, Maite; Fernández-Castro, Isabel; Urretavizcaya, Maite

2016-01-01

Currently, most of the educational approaches applied to higher education combine face-to-face (F2F) and computer-mediated instruction in a Blended-Learning (B-Learning) approach. One of the main challenges of these approaches is fully integrating the traditional brick-and-mortar classes with online learning environments in an efficient and…

SCAMP: Automatic Astrometric and Photometric Calibration

NASA Astrophysics Data System (ADS)

Bertin, Emmanuel

2010-10-01

Astrometric and photometric calibrations have remained the most tiresome step in the reduction of large imaging surveys. SCAMP has been written to address this problem. The program efficiently computes accurate astrometric and photometric solutions for any arbitrary sequence of FITS images in a completely automatic way. SCAMP is released under the GNU General Public License.

A Hands-On Approach for Teaching Denial of Service Attacks: A Case Study

ERIC Educational Resources Information Center

Trabelsi, Zouheir; Ibrahim, Walid

2013-01-01

Nowadays, many academic institutions are including ethical hacking in their information security and Computer Science programs. Information security students need to experiment common ethical hacking techniques in order to be able to implement the appropriate security solutions. This will allow them to more efficiently protect the confidentiality,…

Framework to trade optimality for local processing in large-scale wavefront reconstruction problems.

PubMed

Haber, Aleksandar; Verhaegen, Michel

2016-11-15

We show that the minimum variance wavefront estimation problems permit localized approximate solutions, in the sense that the wavefront value at a point (excluding unobservable modes, such as the piston mode) can be approximated by a linear combination of the wavefront slope measurements in the point's neighborhood. This enables us to efficiently compute a wavefront estimate by performing a single sparse matrix-vector multiplication. Moreover, our results open the possibility for the development of wavefront estimators that can be easily implemented in a decentralized/distributed manner, and in which the estimate optimality can be easily traded for computational efficiency. We numerically validate our approach on Hudgin wavefront sensor geometries, and the results can be easily generalized to Fried geometries.

Machine learning action parameters in lattice quantum chromodynamics

NASA Astrophysics Data System (ADS)

Shanahan, Phiala E.; Trewartha, Daniel; Detmold, William

2018-05-01

Numerical lattice quantum chromodynamics studies of the strong interaction are important in many aspects of particle and nuclear physics. Such studies require significant computing resources to undertake. A number of proposed methods promise improved efficiency of lattice calculations, and access to regions of parameter space that are currently computationally intractable, via multi-scale action-matching approaches that necessitate parametric regression of generated lattice datasets. The applicability of machine learning to this regression task is investigated, with deep neural networks found to provide an efficient solution even in cases where approaches such as principal component analysis fail. The high information content and complex symmetries inherent in lattice QCD datasets require custom neural network layers to be introduced and present opportunities for further development.

Towards developing robust algorithms for solving partial differential equations on MIMD machines

NASA Technical Reports Server (NTRS)

Saltz, Joel H.; Naik, Vijay K.

1988-01-01

Methods for efficient computation of numerical algorithms on a wide variety of MIMD machines are proposed. These techniques reorganize the data dependency patterns to improve the processor utilization. The model problem finds the time-accurate solution to a parabolic partial differential equation discretized in space and implicitly marched forward in time. The algorithms are extensions of Jacobi and SOR. The extensions consist of iterating over a window of several timesteps, allowing efficient overlap of computation with communication. The methods increase the degree to which work can be performed while data are communicated between processors. The effect of the window size and of domain partitioning on the system performance is examined both by implementing the algorithm on a simulated multiprocessor system.

Towards developing robust algorithms for solving partial differential equations on MIMD machines

NASA Technical Reports Server (NTRS)

Saltz, J. H.; Naik, V. K.

1985-01-01

Methods for efficient computation of numerical algorithms on a wide variety of MIMD machines are proposed. These techniques reorganize the data dependency patterns to improve the processor utilization. The model problem finds the time-accurate solution to a parabolic partial differential equation discretized in space and implicitly marched forward in time. The algorithms are extensions of Jacobi and SOR. The extensions consist of iterating over a window of several timesteps, allowing efficient overlap of computation with communication. The methods increase the degree to which work can be performed while data are communicated between processors. The effect of the window size and of domain partitioning on the system performance is examined both by implementing the algorithm on a simulated multiprocessor system.

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.

Gradient-based Optimization for Poroelastic and Viscoelastic MR Elastography

PubMed Central

Tan, Likun; McGarry, Matthew D.J.; Van Houten, Elijah E.W.; Ji, Ming; Solamen, Ligin; Weaver, John B.

2017-01-01

We describe an efficient gradient computation for solving inverse problems arising in magnetic resonance elastography (MRE). The algorithm can be considered as a generalized ‘adjoint method’ based on a Lagrangian formulation. One requirement for the classic adjoint method is assurance of the self-adjoint property of the stiffness matrix in the elasticity problem. In this paper, we show this property is no longer a necessary condition in our algorithm, but the computational performance can be as efficient as the classic method, which involves only two forward solutions and is independent of the number of parameters to be estimated. The algorithm is developed and implemented in material property reconstructions using poroelastic and viscoelastic modeling. Various gradient- and Hessian-based optimization techniques have been tested on simulation, phantom and in vivo brain data. The numerical results show the feasibility and the efficiency of the proposed scheme for gradient calculation. PMID:27608454

A Computationally Efficient Parallel Levenberg-Marquardt Algorithm for Large-Scale Big-Data Inversion

NASA Astrophysics Data System (ADS)

Lin, Y.; O'Malley, D.; Vesselinov, V. V.

2015-12-01

Inverse modeling seeks model parameters given a set of observed state variables. However, for many practical problems due to the facts that the observed data sets are often large and model parameters are often numerous, conventional methods for solving the inverse modeling can be computationally expensive. We have developed a new, computationally-efficient Levenberg-Marquardt method for solving large-scale inverse modeling. Levenberg-Marquardt methods require the solution of a dense linear system of equations which can be prohibitively expensive to compute for large-scale inverse problems. Our novel method projects the original large-scale linear problem down to a Krylov subspace, such that the dimensionality of the measurements can be significantly reduced. Furthermore, instead of solving the linear system for every Levenberg-Marquardt damping parameter, we store the Krylov subspace computed when solving the first damping parameter and recycle it for all the following damping parameters. The efficiency of our new inverse modeling algorithm is significantly improved by using these computational techniques. We apply this new inverse modeling method to invert for a random transitivity field. Our algorithm is fast enough to solve for the distributed model parameters (transitivity) at each computational node in the model domain. The inversion is also aided by the use regularization techniques. The algorithm is coded in Julia and implemented in the MADS computational framework (http://mads.lanl.gov). Julia is an advanced high-level scientific programing language that allows for efficient memory management and utilization of high-performance computational resources. By comparing with a Levenberg-Marquardt method using standard linear inversion techniques, our Levenberg-Marquardt method yields speed-up ratio of 15 in a multi-core computational environment and a speed-up ratio of 45 in a single-core computational environment. Therefore, our new inverse modeling method is a powerful tool for large-scale applications.

Application of Four-Point Newton-EGSOR iteration for the numerical solution of 2D Porous Medium Equations

NASA Astrophysics Data System (ADS)

Chew, J. V. L.; Sulaiman, J.

2017-09-01

Partial differential equations that are used in describing the nonlinear heat and mass transfer phenomena are difficult to be solved. For the case where the exact solution is difficult to be obtained, it is necessary to use a numerical procedure such as the finite difference method to solve a particular partial differential equation. In term of numerical procedure, a particular method can be considered as an efficient method if the method can give an approximate solution within the specified error with the least computational complexity. Throughout this paper, the two-dimensional Porous Medium Equation (2D PME) is discretized by using the implicit finite difference scheme to construct the corresponding approximation equation. Then this approximation equation yields a large-sized and sparse nonlinear system. By using the Newton method to linearize the nonlinear system, this paper deals with the application of the Four-Point Newton-EGSOR (4NEGSOR) iterative method for solving the 2D PMEs. In addition to that, the efficiency of the 4NEGSOR iterative method is studied by solving three examples of the problems. Based on the comparative analysis, the Newton-Gauss-Seidel (NGS) and the Newton-SOR (NSOR) iterative methods are also considered. The numerical findings show that the 4NEGSOR method is superior to the NGS and the NSOR methods in terms of the number of iterations to get the converged solutions, the time of computation and the maximum absolute errors produced by the methods.

CSM solutions of rotating blade dynamics using integrating matrices

NASA Technical Reports Server (NTRS)

Lakin, William D.

1992-01-01

The dynamic behavior of flexible rotating beams continues to receive considerable research attention as it constitutes a fundamental problem in applied mechanics. Further, beams comprise parts of many rotating structures of engineering significance. A topic of particular interest at the present time involves the development of techniques for obtaining the behavior in both space and time of a rotor acted upon by a simple airload loading. Most current work on problems of this type use solution techniques based on normal modes. It is certainly true that normal modes cannot be disregarded, as knowledge of natural blade frequencies is always important. However, the present work has considered a computational structural mechanics (CSM) approach to rotor blade dynamics problems in which the physical properties of the rotor blade provide input for a direct numerical solution of the relevant boundary-and-initial-value problem. Analysis of the dynamics of a given rotor system may require solution of the governing equations over a long time interval corresponding to many revolutions of the loaded flexible blade. For this reason, most of the common techniques in computational mechanics, which treat the space-time behavior concurrently, cannot be applied to the rotor dynamics problem without a large expenditure of computational resources. By contrast, the integrating matrix technique of computational mechanics has the ability to consistently incorporate boundary conditions and 'remove' dependence on a space variable. For problems involving both space and time, this feature of the integrating matrix approach thus can generate a 'splitting' which forms the basis of an efficient CSM method for numerical solution of rotor dynamics problems.

Extending compile-time reverse mode and exploiting partial separability in ADIFOR

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

Bischof, C.H.; El-Khadiri, M.

1992-10-01

The numerical methods employed in the solution of many scientific computing problems require the computation of the gradient of a function f: R[sup n] [yields] R. ADIFOR is a source translator that, given a collection of subroutines to compute f, generates Fortran 77 code for computing the derivative of this function. Using the so-called torsion problem from the MINPACK-2 test collection as an example, this paper explores two issues in automatic differentiation: the efficient computation of derivatives for partial separable functions and the use of the compile-time reverse mode for the generation of derivatives. We show that orders of magnitudesmore » of improvement are possible when exploiting partial separability and maximizing use of the reverse mode.« less

ADM For Solving Linear Second-Order Fredholm Integro-Differential Equations

NASA Astrophysics Data System (ADS)

Karim, Mohd F.; Mohamad, Mahathir; Saifullah Rusiman, Mohd; Che-Him, Norziha; Roslan, Rozaini; Khalid, Kamil

2018-04-01

In this paper, we apply Adomian Decomposition Method (ADM) as numerically analyse linear second-order Fredholm Integro-differential Equations. The approximate solutions of the problems are calculated by Maple package. Some numerical examples have been considered to illustrate the ADM for solving this equation. The results are compared with the existing exact solution. Thus, the Adomian decomposition method can be the best alternative method for solving linear second-order Fredholm Integro-Differential equation. It converges to the exact solution quickly and in the same time reduces computational work for solving the equation. The result obtained by ADM shows the ability and efficiency for solving these equations.

A DAG Scheduling Scheme on Heterogeneous Computing Systems Using Tuple-Based Chemical Reaction Optimization

PubMed Central

Jiang, Yuyi; Shao, Zhiqing; Guo, Yi

2014-01-01

A complex computing problem can be solved efficiently on a system with multiple computing nodes by dividing its implementation code into several parallel processing modules or tasks that can be formulated as directed acyclic graph (DAG) problems. The DAG jobs may be mapped to and scheduled on the computing nodes to minimize the total execution time. Searching an optimal DAG scheduling solution is considered to be NP-complete. This paper proposed a tuple molecular structure-based chemical reaction optimization (TMSCRO) method for DAG scheduling on heterogeneous computing systems, based on a very recently proposed metaheuristic method, chemical reaction optimization (CRO). Comparing with other CRO-based algorithms for DAG scheduling, the design of tuple reaction molecular structure and four elementary reaction operators of TMSCRO is more reasonable. TMSCRO also applies the concept of constrained critical paths (CCPs), constrained-critical-path directed acyclic graph (CCPDAG) and super molecule for accelerating convergence. In this paper, we have also conducted simulation experiments to verify the effectiveness and efficiency of TMSCRO upon a large set of randomly generated graphs and the graphs for real world problems. PMID:25143977

A DAG scheduling scheme on heterogeneous computing systems using tuple-based chemical reaction optimization.

PubMed

Jiang, Yuyi; Shao, Zhiqing; Guo, Yi

2014-01-01

A complex computing problem can be solved efficiently on a system with multiple computing nodes by dividing its implementation code into several parallel processing modules or tasks that can be formulated as directed acyclic graph (DAG) problems. The DAG jobs may be mapped to and scheduled on the computing nodes to minimize the total execution time. Searching an optimal DAG scheduling solution is considered to be NP-complete. This paper proposed a tuple molecular structure-based chemical reaction optimization (TMSCRO) method for DAG scheduling on heterogeneous computing systems, based on a very recently proposed metaheuristic method, chemical reaction optimization (CRO). Comparing with other CRO-based algorithms for DAG scheduling, the design of tuple reaction molecular structure and four elementary reaction operators of TMSCRO is more reasonable. TMSCRO also applies the concept of constrained critical paths (CCPs), constrained-critical-path directed acyclic graph (CCPDAG) and super molecule for accelerating convergence. In this paper, we have also conducted simulation experiments to verify the effectiveness and efficiency of TMSCRO upon a large set of randomly generated graphs and the graphs for real world problems.

Model Reduction of Computational Aerothermodynamics for Multi-Discipline Analysis in High Speed Flows

NASA Astrophysics Data System (ADS)

Crowell, Andrew Rippetoe

This dissertation describes model reduction techniques for the computation of aerodynamic heat flux and pressure loads for multi-disciplinary analysis of hypersonic vehicles. NASA and the Department of Defense have expressed renewed interest in the development of responsive, reusable hypersonic cruise vehicles capable of sustained high-speed flight and access to space. However, an extensive set of technical challenges have obstructed the development of such vehicles. These technical challenges are partially due to both the inability to accurately test scaled vehicles in wind tunnels and to the time intensive nature of high-fidelity computational modeling, particularly for the fluid using Computational Fluid Dynamics (CFD). The aim of this dissertation is to develop efficient and accurate models for the aerodynamic heat flux and pressure loads to replace the need for computationally expensive, high-fidelity CFD during coupled analysis. Furthermore, aerodynamic heating and pressure loads are systematically evaluated for a number of different operating conditions, including: simple two-dimensional flow over flat surfaces up to three-dimensional flows over deformed surfaces with shock-shock interaction and shock-boundary layer interaction. An additional focus of this dissertation is on the implementation and computation of results using the developed aerodynamic heating and pressure models in complex fluid-thermal-structural simulations. Model reduction is achieved using a two-pronged approach. One prong focuses on developing analytical corrections to isothermal, steady-state CFD flow solutions in order to capture flow effects associated with transient spatially-varying surface temperatures and surface pressures (e.g., surface deformation, surface vibration, shock impingements, etc.). The second prong is focused on minimizing the computational expense of computing the steady-state CFD solutions by developing an efficient surrogate CFD model. The developed two-pronged approach is found to exhibit balanced performance in terms of accuracy and computational expense, relative to several existing approaches. This approach enables CFD-based loads to be implemented into long duration fluid-thermal-structural simulations.

Computational complexity of ecological and evolutionary spatial dynamics

PubMed Central

Ibsen-Jensen, Rasmus; Chatterjee, Krishnendu; Nowak, Martin A.

2015-01-01

There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant) will take over a resident population? We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP). PMID:26644569

An efficient hybrid pseudospectral/finite-difference scheme for solving the TTI pure P-wave equation

NASA Astrophysics Data System (ADS)

Zhan, Ge; Pestana, Reynam C.; Stoffa, Paul L.

2013-04-01

The pure P-wave equation for modelling and migration in tilted transversely isotropic (TTI) media has attracted more and more attention in imaging seismic data with anisotropy. The desirable feature is that it is absolutely free of shear-wave artefacts and the consequent alleviation of numerical instabilities generally suffered by some systems of coupled equations. However, due to several forward-backward Fourier transforms in wavefield updating at each time step, the computational cost is significant, and thereby hampers its prevalence. We propose to use a hybrid pseudospectral (PS) and finite-difference (FD) scheme to solve the pure P-wave equation. In the hybrid solution, most of the cost-consuming wavenumber terms in the equation are replaced by inexpensive FD operators, which in turn accelerates the computation and reduces the computational cost. To demonstrate the benefit in cost saving of the new scheme, 2D and 3D reverse-time migration (RTM) examples using the hybrid solution to the pure P-wave equation are carried out, and respective runtimes are listed and compared. Numerical results show that the hybrid strategy demands less computation time and is faster than using the PS method alone. Furthermore, this new TTI RTM algorithm with the hybrid method is computationally less expensive than that with the FD solution to conventional TTI coupled equations.

Enabling Predictive Simulation and UQ of Complex Multiphysics PDE Systems by the Development of Goal-Oriented Variational Sensitivity Analysis and a-Posteriori Error Estimation Methods

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

Estep, Donald

2015-11-30

This project addressed the challenge of predictive computational analysis of strongly coupled, highly nonlinear multiphysics systems characterized by multiple physical phenomena that span a large range of length- and time-scales. Specifically, the project was focused on computational estimation of numerical error and sensitivity analysis of computational solutions with respect to variations in parameters and data. In addition, the project investigated the use of accurate computational estimates to guide efficient adaptive discretization. The project developed, analyzed and evaluated new variational adjoint-based techniques for integration, model, and data error estimation/control and sensitivity analysis, in evolutionary multiphysics multiscale simulations.

Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems

PubMed Central

Cilfone, Nicholas A.; Kirschner, Denise E.; Linderman, Jennifer J.

2015-01-01

Biologically related processes operate across multiple spatiotemporal scales. For computational modeling methodologies to mimic this biological complexity, individual scale models must be linked in ways that allow for dynamic exchange of information across scales. A powerful methodology is to combine a discrete modeling approach, agent-based models (ABMs), with continuum models to form hybrid models. Hybrid multi-scale ABMs have been used to simulate emergent responses of biological systems. Here, we review two aspects of hybrid multi-scale ABMs: linking individual scale models and efficiently solving the resulting model. We discuss the computational choices associated with aspects of linking individual scale models while simultaneously maintaining model tractability. We demonstrate implementations of existing numerical methods in the context of hybrid multi-scale ABMs. Using an example model describing Mycobacterium tuberculosis infection, we show relative computational speeds of various combinations of numerical methods. Efficient linking and solution of hybrid multi-scale ABMs is key to model portability, modularity, and their use in understanding biological phenomena at a systems level. PMID:26366228

Toward the design of alkynylimidazole fluorophores: computational and experimental characterization of spectroscopic features in solution and in poly(methyl methacrylate).

PubMed

Barone, Vincenzo; Bellina, Fabio; Biczysko, Malgorzata; Bloino, Julien; Fornaro, Teresa; Latouche, Camille; Lessi, Marco; Marianetti, Giulia; Minei, Pierpaolo; Panattoni, Alessandro; Pucci, Andrea

2015-10-28

The possibilities offered by organic fluorophores in the preparation of advanced plastic materials have been increased by designing novel alkynylimidazole dyes, featuring different push and pull groups. This new family of fluorescent dyes was synthesized by means of a one-pot sequential bromination-alkynylation of the heteroaromatic core, and their optical properties were investigated in tetrahydrofuran and in poly(methyl methacrylate). An efficient in silico pre-screening scheme was devised as consisting of a step-by-step procedure employing computational methodologies by simulation of electronic spectra within simple vertical energy and more sophisticated vibronic approaches. Such an approach was also extended to efficiently simulate one-photon absorption and emission spectra of the dyes in the polymer environment for their potential application in luminescent solar concentrators. Besides the specific applications of this novel material, the integration of computational and experimental techniques reported here provides an efficient protocol that can be applied to make a selection among similar dye candidates, which constitute the essential responsive part of those fluorescent plastic materials.

Nonnegative least-squares image deblurring: improved gradient projection approaches

NASA Astrophysics Data System (ADS)

Benvenuto, F.; Zanella, R.; Zanni, L.; Bertero, M.

2010-02-01

The least-squares approach to image deblurring leads to an ill-posed problem. The addition of the nonnegativity constraint, when appropriate, does not provide regularization, even if, as far as we know, a thorough investigation of the ill-posedness of the resulting constrained least-squares problem has still to be done. Iterative methods, converging to nonnegative least-squares solutions, have been proposed. Some of them have the 'semi-convergence' property, i.e. early stopping of the iteration provides 'regularized' solutions. In this paper we consider two of these methods: the projected Landweber (PL) method and the iterative image space reconstruction algorithm (ISRA). Even if they work well in many instances, they are not frequently used in practice because, in general, they require a large number of iterations before providing a sensible solution. Therefore, the main purpose of this paper is to refresh these methods by increasing their efficiency. Starting from the remark that PL and ISRA require only the computation of the gradient of the functional, we propose the application to these algorithms of special acceleration techniques that have been recently developed in the area of the gradient methods. In particular, we propose the application of efficient step-length selection rules and line-search strategies. Moreover, remarking that ISRA is a scaled gradient algorithm, we evaluate its behaviour in comparison with a recent scaled gradient projection (SGP) method for image deblurring. Numerical experiments demonstrate that the accelerated methods still exhibit the semi-convergence property, with a considerable gain both in the number of iterations and in the computational time; in particular, SGP appears definitely the most efficient one.

Realistic and efficient 2D crack simulation

NASA Astrophysics Data System (ADS)

Yadegar, Jacob; Liu, Xiaoqing; Singh, Abhishek

2010-04-01

Although numerical algorithms for 2D crack simulation have been studied in Modeling and Simulation (M&S) and computer graphics for decades, realism and computational efficiency are still major challenges. In this paper, we introduce a high-fidelity, scalable, adaptive and efficient/runtime 2D crack/fracture simulation system by applying the mathematically elegant Peano-Cesaro triangular meshing/remeshing technique to model the generation of shards/fragments. The recursive fractal sweep associated with the Peano-Cesaro triangulation provides efficient local multi-resolution refinement to any level-of-detail. The generated binary decomposition tree also provides efficient neighbor retrieval mechanism used for mesh element splitting and merging with minimal memory requirements essential for realistic 2D fragment formation. Upon load impact/contact/penetration, a number of factors including impact angle, impact energy, and material properties are all taken into account to produce the criteria of crack initialization, propagation, and termination leading to realistic fractal-like rubble/fragments formation. The aforementioned parameters are used as variables of probabilistic models of cracks/shards formation, making the proposed solution highly adaptive by allowing machine learning mechanisms learn the optimal values for the variables/parameters based on prior benchmark data generated by off-line physics based simulation solutions that produce accurate fractures/shards though at highly non-real time paste. Crack/fracture simulation has been conducted on various load impacts with different initial locations at various impulse scales. The simulation results demonstrate that the proposed system has the capability to realistically and efficiently simulate 2D crack phenomena (such as window shattering and shards generation) with diverse potentials in military and civil M&S applications such as training and mission planning.

Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy.

PubMed

Ogorzalek, Tadeusz L; Hura, Greg L; Belsom, Adam; Burnett, Kathryn H; Kryshtafovych, Andriy; Tainer, John A; Rappsilber, Juri; Tsutakawa, Susan E; Fidelis, Krzysztof

2018-03-01

Experimental data offers empowering constraints for structure prediction. These constraints can be used to filter equivalently scored models or more powerfully within optimization functions toward prediction. In CASP12, Small Angle X-ray Scattering (SAXS) and Cross-Linking Mass Spectrometry (CLMS) data, measured on an exemplary set of novel fold targets, were provided to the CASP community of protein structure predictors. As solution-based techniques, SAXS and CLMS can efficiently measure states of the full-length sequence in its native solution conformation and assembly. However, this experimental data did not substantially improve prediction accuracy judged by fits to crystallographic models. One issue, beyond intrinsic limitations of the algorithms, was a disconnect between crystal structures and solution-based measurements. Our analyses show that many targets had substantial percentages of disordered regions (up to 40%) or were multimeric or both. Thus, solution measurements of flexibility and assembly support variations that may confound prediction algorithms trained on crystallographic data and expecting globular fully-folded monomeric proteins. Here, we consider the CLMS and SAXS data collected, the information in these solution measurements, and the challenges in incorporating them into computational prediction. As improvement opportunities were only partly realized in CASP12, we provide guidance on how data from the full-length biological unit and the solution state can better aid prediction of the folded monomer or subunit. We furthermore describe strategic integrations of solution measurements with computational prediction programs with the aim of substantially improving foundational knowledge and the accuracy of computational algorithms for biologically-relevant structure predictions for proteins in solution. © 2018 Wiley Periodicals, Inc.

Local ventilation solution for large, warm emission sources.

PubMed

Kulmala, Ilpo; Hynynen, Pasi; Welling, Irma; Säämänen, Arto

2007-01-01

In a foundry casting line, contaminants are released from a large area. Casting fumes include both volatile and particulate compounds. The volatile fraction contains hydrocarbons, whereas the particulate fraction mostly comprises a mixture of vaporized metal fumes. Casting fumes lower the air quality in foundries. The design of local ventilation for the casting area is a challenging task, because of the large casting area and convection plumes from warm moulds. A local ventilation solution for the mould casting area was designed and dimensioned with the aid of computational fluid dynamic (CFD) calculations. According to the calculations, the most efficient solution was a push-pull ventilation system. The prototype of the push-pull system was built and tested in actual operation at the foundry. The push flow was generated by a free plane jet that blew across the 10 m wide casting area towards an exhaust hood on the opposite side of the casting lines. The capture efficiency of the prototype was determined by the tracer gas method. The measured capture efficiencies with push jet varied between 40 and 80%, depending on the distance between the source and the exhaust. With the aid of the push flow, the average capture efficiency was increased from 40 (without jet) to 60%.

MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

NASA Astrophysics Data System (ADS)

Vergara-Perez, Sandra; Marucho, Marcelo

2016-01-01

One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson-Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post-analysis of structural and electrical properties of biomolecules.

MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

PubMed Central

Vergara-Perez, Sandra; Marucho, Marcelo

2015-01-01

One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post- analysis of structural and electrical properties of biomolecules. PMID:26924848

MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations.

PubMed

Vergara-Perez, Sandra; Marucho, Marcelo

2016-01-01

One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post- analysis of structural and electrical properties of biomolecules.

The study on the extraction and recovery of Au from scrap of the used computer using chloride solvent

NASA Astrophysics Data System (ADS)

Oh, Su-ji; Choi, Eunju; Choi, Nagchoul; Park, Cheonyoung

2013-04-01

Recently, due to the realization of environmental problems of cyanide, it is a worldwide quest to find viable alternatives. One of the alternatives is a chloride solvent(chlorine-hypochlorite acid) with an appropriate oxidizing agent. The rate of dissolution of Au by chloride solvent is much faster than that by cyanide. Also, due to presence of chloride ions, there is no passivation of gold surfaces during chlorination. The objective of this work was to investigate the effect of Au extraction efficiency under various experimental conditions(pulp density, chlorine-hypochlorite ratio and concentration of NaCl) from scrap of the used computer by chloride solvent. In addition, the recovery experiment was conducted to examine of the precipitation efficiency of Au under various metabisulfite concentration from extracted solution. In an EDS analysis, valuable metals such as Cu, Sn, Sb, Al, Ni, Pb and Au were observed in scrap of the used computer. The result of extraction experiment showed that the highest extraction rate was obtained under 1% of pulp density with a chlorine-hypochlorite ratio of 2:1, and a concentration of NaCl at 2M. The highest Au recovery(precipitation) rate was observed the addition of sodium metabisulfite at 2M concentration. Under these conditions, chlorine-hypochlorite could effectively Au extraction from scrap of the used computer sections and the additive reagent using sodium metabisulfite could easily precipitate the Au from the chlorine-hypochlorite solution.

Quasi-3D Modeling and Efficient Simulation of Laminar Flows in Microfluidic Devices.

PubMed

Islam, Md Zahurul; Tsui, Ying Yin

2016-10-03

A quasi-3D model has been developed to simulate the flow in planar microfluidic systems with low Reynolds numbers. The model was developed by decomposing the flow profile along the height of a microfluidic system into a Fourier series. It was validated against the analytical solution for flow in a straight rectangular channel and the full 3D numerical COMSOL Navier-Stokes solver for flow in a T-channel. Comparable accuracy to the full 3D numerical solution was achieved by using only three Fourier terms with a significant decrease in computation time. The quasi-3D model was used to model flows in a micro-flow cytometer chip on a desktop computer and good agreement between the simulation and the experimental results was found.

Quasi-3D Modeling and Efficient Simulation of Laminar Flows in Microfluidic Devices

PubMed Central

Islam, Md. Zahurul; Tsui, Ying Yin

2016-01-01

A quasi-3D model has been developed to simulate the flow in planar microfluidic systems with low Reynolds numbers. The model was developed by decomposing the flow profile along the height of a microfluidic system into a Fourier series. It was validated against the analytical solution for flow in a straight rectangular channel and the full 3D numerical COMSOL Navier-Stokes solver for flow in a T-channel. Comparable accuracy to the full 3D numerical solution was achieved by using only three Fourier terms with a significant decrease in computation time. The quasi-3D model was used to model flows in a micro-flow cytometer chip on a desktop computer and good agreement between the simulation and the experimental results was found. PMID:27706104

Protein Hydration Thermodynamics: The Influence of Flexibility and Salt on Hydrophobin II Hydration.

PubMed

Remsing, Richard C; Xi, Erte; Patel, Amish J

2018-04-05

The solubility of proteins and other macromolecular solutes plays an important role in numerous biological, chemical, and medicinal processes. An important determinant of protein solubility is the solvation free energy of the protein, which quantifies the overall strength of the interactions between the protein and the aqueous solution that surrounds it. Here we present an all-atom explicit-solvent computational framework for the rapid estimation of protein solvation free energies. Using this framework, we estimate the hydration free energy of hydrophobin II, an amphiphilic fungal protein, in a computationally efficient manner. We further explore how the protein hydration free energy is influenced by enhancing flexibility and by the addition of sodium chloride, and find that it increases in both cases, making protein hydration less favorable.

Fluid-structure finite-element vibrational analysis

NASA Technical Reports Server (NTRS)

Feng, G. C.; Kiefling, L.

1974-01-01

A fluid finite element has been developed for a quasi-compressible fluid. Both kinetic and potential energy are expressed as functions of nodal displacements. Thus, the formulation is similar to that used for structural elements, with the only differences being that the fluid can possess gravitational potential, and the constitutive equations for fluid contain no shear coefficients. Using this approach, structural and fluid elements can be used interchangeably in existing efficient sparse-matrix structural computer programs such as SPAR. The theoretical development of the element formulations and the relationships of the local and global coordinates are shown. Solutions of fluid slosh, liquid compressibility, and coupled fluid-shell oscillation problems which were completed using a temporary digital computer program are shown. The frequency correlation of the solutions with classical theory is excellent.