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Sample records for conjugate gradient methods

  1. Variable metric conjugate gradient methods

    SciTech Connect

    Barth, T.; Manteuffel, T.

    1994-07-01

    1.1 Motivation. In this paper we present a framework that includes many well known iterative methods for the solution of nonsymmetric linear systems of equations, Ax = b. Section 2 begins with a brief review of the conjugate gradient method. Next, we describe a broader class of methods, known as projection methods, to which the conjugate gradient (CG) method and most conjugate gradient-like methods belong. The concept of a method having either a fixed or a variable metric is introduced. Methods that have a metric are referred to as either fixed or variable metric methods. Some relationships between projection methods and fixed (variable) metric methods are discussed. The main emphasis of the remainder of this paper is on variable metric methods. In Section 3 we show how the biconjugate gradient (BCG), and the quasi-minimal residual (QMR) methods fit into this framework as variable metric methods. By modifying the underlying Lanczos biorthogonalization process used in the implementation of BCG and QMR, we obtain other variable metric methods. These, we refer to as generalizations of BCG and QMR.

  2. Approximate error conjugation gradient minimization methods

    DOEpatents

    Kallman, Jeffrey S

    2013-05-21

    In one embodiment, a method includes selecting a subset of rays from a set of all rays to use in an error calculation for a constrained conjugate gradient minimization problem, calculating an approximate error using the subset of rays, and calculating a minimum in a conjugate gradient direction based on the approximate error. In another embodiment, a system includes a processor for executing logic, logic for selecting a subset of rays from a set of all rays to use in an error calculation for a constrained conjugate gradient minimization problem, logic for calculating an approximate error using the subset of rays, and logic for calculating a minimum in a conjugate gradient direction based on the approximate error. In other embodiments, computer program products, methods, and systems are described capable of using approximate error in constrained conjugate gradient minimization problems.

  3. A new nonlinear conjugate gradient method

    NASA Astrophysics Data System (ADS)

    Abdelrahman, Awad; Mamat, Mustafa; Mohd, Ismail bin; Rivaie, Mohd; Omer, Osman

    2015-02-01

    Conjugate gradient (CG) methods are essential for solving large-scale unconstrained optimization problems. Many of studies and modifications have been practiced to improve this method. In this paper, a new class of conjugate gradient coefficients (βk) with a new parameter m = ‖g/k‖ ‖dk-1‖ that possess global convergence properties is presented. The global convergence and sufficient decent property result is established using inexact line searches to determine the step size of CG, denoted as ∝k. Numerical result shows that the new formula is superior and more efficient when compared to other CG coefficients.

  4. M-step preconditioned conjugate gradient methods

    NASA Technical Reports Server (NTRS)

    Adams, L.

    1983-01-01

    Preconditioned conjugate gradient methods for solving sparse symmetric and positive finite systems of linear equations are described. Necessary and sufficient conditions are given for when these preconditioners can be used and an analysis of their effectiveness is given. Efficient computer implementations of these methods are discussed and results on the CYBER 203 and the Finite Element Machine under construction at NASA Langley Research Center are included.

  5. The multigrid preconditioned conjugate gradient method

    NASA Technical Reports Server (NTRS)

    Tatebe, Osamu

    1993-01-01

    A multigrid preconditioned conjugate gradient method (MGCG method), which uses the multigrid method as a preconditioner of the PCG method, is proposed. The multigrid method has inherent high parallelism and improves convergence of long wavelength components, which is important in iterative methods. By using this method as a preconditioner of the PCG method, an efficient method with high parallelism and fast convergence is obtained. First, it is considered a necessary condition of the multigrid preconditioner in order to satisfy requirements of a preconditioner of the PCG method. Next numerical experiments show a behavior of the MGCG method and that the MGCG method is superior to both the ICCG method and the multigrid method in point of fast convergence and high parallelism. This fast convergence is understood in terms of the eigenvalue analysis of the preconditioned matrix. From this observation of the multigrid preconditioner, it is realized that the MGCG method converges in very few iterations and the multigrid preconditioner is a desirable preconditioner of the conjugate gradient method.

  6. Polynomial preconditioning for conjugate gradient methods

    SciTech Connect

    Ashby, S.F.

    1987-12-01

    The solution of a linear system of equations, Ax = b, arises in many scientific applications. If A is large and sparse, an iterative method is required. When A is hermitian positive definite (hpd), the conjugate gradient method of Hestenes and Stiefel is popular. When A is hermitian indefinite (hid), the conjugate residual method may be used. If A is ill-conditioned, these methods may converge slowly, in which case a preconditioner is needed. In this thesis we examine the use of polynomial preconditioning in CG methods for both hermitian positive definite and indefinite matrices. Such preconditioners are easy to employ and well-suited to vector and/or parallel architectures. We first show that any CG method is characterized by three matrices: an hpd inner product matrix B, a preconditioning matrix C, and the hermitian matrix A. The resulting method, CG(B,C,A), minimizes the B-norm of the error over a Krylov subspace. We next exploit the versatility of polynomial preconditioners to design several new CG methods. To obtain an optimum preconditioner, we solve a constrained minimax approximation problem. The preconditioning polynomial, C(lambda), is optimum in that it minimizes a bound on the condition number of the preconditioned matrix, p/sub m/(A). An adaptive procedure for dynamically determining the optimum preconditioner is also discussed. Finally, in a variety of numerical experiments, conducted on a Cray X-MP/48, we demonstrate the effectiveness of polynomial preconditioning. 66 ref., 19 figs., 39 tabs.

  7. A taxonomy for conjugate gradient methods

    SciTech Connect

    Ashby, S.F.; Manteuffel, T.A.; Saylor, P.E.

    1988-03-01

    The conjugate method of Hestenes and Stiefel is an effective method to solve large, sparse hermitian positive definite (hpd) systems of linear equations, Ax = b. Generalizations to non-hpd matrices have long been sought. The recent theory of Faber and Manteuffle gives necessary and sufficient conditions for the existence of CG method. This paper uses these conditions to develop and organize such methods. We show that any CG method for Ax = b is characterized by and hpd inner product matrix B and a left preconditioning matrix C. At each step the method minimizes the B-norm of the error over a Krylov space. This characterization is then used to classify known and new methods. Finally, it is shown how eigenvalue estimates may be obtained from the iteration parameters, generalizing the well known connection between CG and Lanczos. Such estimates allow implementation of a stopping criterion based more nearly on the true error. 29 refs., 4 tabs.

  8. Comparison of genetic algorithms with conjugate gradient methods

    NASA Technical Reports Server (NTRS)

    Bosworth, J. L.; Foo, N. Y.; Zeigler, B. P.

    1972-01-01

    Genetic algorithms for mathematical function optimization are modeled on search strategies employed in natural adaptation. Comparisons of genetic algorithms with conjugate gradient methods, which were made on an IBM 1800 digital computer, show that genetic algorithms display superior performance over gradient methods for functions which are poorly behaved mathematically, for multimodal functions, and for functions obscured by additive random noise. Genetic methods offer performance comparable to gradient methods for many of the standard functions.

  9. Application of Conjugate Gradient methods to tidal simulation

    USGS Publications Warehouse

    Barragy, E.; Carey, G.F.; Walters, R.A.

    1993-01-01

    A harmonic decomposition technique is applied to the shallow water equations to yield a complex, nonsymmetric, nonlinear, Helmholtz type problem for the sea surface and an accompanying complex, nonlinear diagonal problem for the velocities. The equation for the sea surface is linearized using successive approximation and then discretized with linear, triangular finite elements. The study focuses on applying iterative methods to solve the resulting complex linear systems. The comparative evaluation includes both standard iterative methods for the real subsystems and complex versions of the well known Bi-Conjugate Gradient and Bi-Conjugate Gradient Squared methods. Several Incomplete LU type preconditioners are discussed, and the effects of node ordering, rejection strategy, domain geometry and Coriolis parameter (affecting asymmetry) are investigated. Implementation details for the complex case are discussed. Performance studies are presented and comparisons made with a frontal solver. ?? 1993.

  10. Two modified Dai-Yuan nonlinear conjugate gradient methods

    NASA Astrophysics Data System (ADS)

    Zhang, Li

    2009-01-01

    In this paper, we propose two modified versions of the Dai-Yuan (DY) nonlinear conjugate gradient method. One is based on the MBFGS method (Li and Fukushima, J Comput Appl Math 129:15-35, 2001) and inherits all nice properties of the DY method. Moreover, this method converges globally for nonconvex functions even if the standard Armijo line search is used. The other is based on the ideas of Wei et al. (Appl Math Comput 183:1341-1350, 2006), Zhang et al. (Numer Math 104:561-572, 2006) and possesses good performance of the Hestenes-Stiefel method. Numerical results are also reported.

  11. A Penalized Linear and Nonlinear Combined Conjugate Gradient Method for the Reconstruction of Fluorescence Molecular Tomography

    PubMed Central

    Shang, Shang; Bai, Jing; Song, Xiaolei; Wang, Hongkai; Lau, Jaclyn

    2007-01-01

    Conjugate gradient method is verified to be efficient for nonlinear optimization problems of large-dimension data. In this paper, a penalized linear and nonlinear combined conjugate gradient method for the reconstruction of fluorescence molecular tomography (FMT) is presented. The algorithm combines the linear conjugate gradient method and the nonlinear conjugate gradient method together based on a restart strategy, in order to take advantage of the two kinds of conjugate gradient methods and compensate for the disadvantages. A quadratic penalty method is adopted to gain a nonnegative constraint and reduce the illposedness of the problem. Simulation studies show that the presented algorithm is accurate, stable, and fast. It has a better performance than the conventional conjugate gradient-based reconstruction algorithms. It offers an effective approach to reconstruct fluorochrome information for FMT. PMID:18354740

  12. New iterative gridding algorithm using conjugate gradient method

    NASA Astrophysics Data System (ADS)

    Jiang, Xuguang; Thedens, Daniel

    2004-05-01

    Non-uniformly sampled data in MRI applications must be interpolated onto a regular Cartesian grid to perform fast image reconstruction using FFT. The conventional method for this is gridding, which requires a density compensation function (DCF). The calculation of DCF may be time-consuming, ambiguously defined, and may not be always reusable due to changes in k-space trajectories. A recently proposed reconstruction method that eliminates the requirement of DCF is block uniform resampling (BURS) which uses singular value decomposition (SVD). However, the SVD is still computationally intensive. In this work, we present a modified BURS algorithm using conjugate gradient method (CGM) in place of direct SVD calculation. Calculation of a block of grid point values in each iteration further reduces the computational load. The new method reduces the calculation complexity while maintaining a high-quality reconstruction result. For an n-by-n matrix, the time complexity per iteration is reduced from O(n*n*n) in SVD to O(n*n) in CGM. The time can be further reduced when we stop the iteration in CGM earlier according to the norm of the residual vector. Using this method, the quality of the reconstructed image improves compared to regularized BURS. The reduced time complexity and improved reconstruction result make the new algorithm promising in dealing with large-sized images and 3D images.

  13. Weighted graph based ordering techniques for preconditioned conjugate gradient methods

    NASA Technical Reports Server (NTRS)

    Clift, Simon S.; Tang, Wei-Pai

    1994-01-01

    We describe the basis of a matrix ordering heuristic for improving the incomplete factorization used in preconditioned conjugate gradient techniques applied to anisotropic PDE's. Several new matrix ordering techniques, derived from well-known algorithms in combinatorial graph theory, which attempt to implement this heuristic, are described. These ordering techniques are tested against a number of matrices arising from linear anisotropic PDE's, and compared with other matrix ordering techniques. A variation of RCM is shown to generally improve the quality of incomplete factorization preconditioners.

  14. Preconditioned Conjugate Gradient methods for low speed flow calculations

    NASA Technical Reports Server (NTRS)

    Ajmani, Kumud; Ng, Wing-Fai; Liou, Meng-Sing

    1993-01-01

    An investigation is conducted into the viability of using a generalized Conjugate Gradient-like method as an iterative solver to obtain steady-state solutions of very low-speed fluid flow problems. Low-speed flow at Mach 0.1 over a backward-facing step is chosen as a representative test problem. The unsteady form of the two dimensional, compressible Navier-Stokes equations are integrated in time using discrete time-steps. The Navier-Stokes equations are cast in an implicit, upwind finite-volume, flux split formulation. The new iterative solver is used to solve a linear system of equations at each step of the time-integration. Preconditioning techniques are used with the new solver to enhance the stability and the convergence rate of the solver and are found to be critical to the overall success of the solver. A study of various preconditioners reveals that a preconditioner based on the lower-upper (L-U)-successive symmetric over-relaxation iterative scheme is more efficient than a preconditioner based on incomplete L-U factorizations of the iteration matrix. The performance of the new preconditioned solver is compared with a conventional line Gauss-Seidel relaxation (LGSR) solver. Overall speed-up factors of 28 (in terms of global time-steps required to converge to a steady-state solution) and 20 (in terms of total CPU time on one processor of a CRAY-YMP) are found in favor of the new preconditioned solver, when compared with the LGSR solver.

  15. On Meinardus' examples for the conjugate gradient method

    NASA Astrophysics Data System (ADS)

    Li, Ren-Cang

    2008-03-01

    The conjugate gradient (CG) method is widely used to solve a positive definite linear system AxDb of order N . It is well known that the relative residual of the k th approximate solution by CG (with the initial approximation x_0D0 ) is bounded above by 2left[Delta_{kappa}^k+Delta_{kappa}^{-k}right]^{-1} with quad Delta_{kappa}Dfrac {sqrt{kappa}+1}{sqrt{kappa}-1}, where kappaequivkappa(A)DVert AVert _2Vert A^{-1}Vert _2 is A 's spectral condition number. In 1963, Meinardus (Numer. Math., 5 (1963), pp. 14-23) gave an example to achieve this bound for kDN-1 but without saying anything about all other 1le k

  16. A finite element conjugate gradient FFT method for scattering

    NASA Technical Reports Server (NTRS)

    Collins, Jeffery D.; Ross, Dan; Jin, J.-M.; Chatterjee, A.; Volakis, John L.

    1991-01-01

    Validated results are presented for the new 3D body of revolution finite element boundary integral code. A Fourier series expansion of the vector electric and mangnetic fields is employed to reduce the dimensionality of the system, and the exact boundary condition is employed to terminate the finite element mesh. The mesh termination boundary is chosen such that is leads to convolutional boundary operatores of low O(n) memory demand. Improvements of this code are discussed along with the proposed formulation for a full 3D implementation of the finite element boundary integral method in conjunction with a conjugate gradiant fast Fourier transformation (CGFFT) solution.

  17. Blockwise conjugate gradient methods for image reconstruction in volumetric CT.

    PubMed

    Qiu, W; Titley-Peloquin, D; Soleimani, M

    2012-11-01

    Cone beam computed tomography (CBCT) enables volumetric image reconstruction from 2D projection data and plays an important role in image guided radiation therapy (IGRT). Filtered back projection is still the most frequently used algorithm in applications. The algorithm discretizes the scanning process (forward projection) into a system of linear equations, which must then be solved to recover images from measured projection data. The conjugate gradients (CG) algorithm and its variants can be used to solve (possibly regularized) linear systems of equations Ax=b and linear least squares problems minx∥b-Ax∥2, especially when the matrix A is very large and sparse. Their applications can be found in a general CT context, but in tomography problems (e.g. CBCT reconstruction) they have not widely been used. Hence, CBCT reconstruction using the CG-type algorithm LSQR was implemented and studied in this paper. In CBCT reconstruction, the main computational challenge is that the matrix A usually is very large, and storing it in full requires an amount of memory well beyond the reach of commodity computers. Because of these memory capacity constraints, only a small fraction of the weighting matrix A is typically used, leading to a poor reconstruction. In this paper, to overcome this difficulty, the matrix A is partitioned and stored blockwise, and blockwise matrix-vector multiplications are implemented within LSQR. This implementation allows us to use the full weighting matrix A for CBCT reconstruction without further enhancing computer standards. Tikhonov regularization can also be implemented in this fashion, and can produce significant improvement in the reconstructed images. PMID:22325240

  18. A modified form of conjugate gradient method for unconstrained optimization problems

    NASA Astrophysics Data System (ADS)

    Ghani, Nur Hamizah Abdul; Rivaie, Mohd.; Mamat, Mustafa

    2016-06-01

    Conjugate gradient (CG) methods have been recognized as an interesting technique to solve optimization problems, due to the numerical efficiency, simplicity and low memory requirements. In this paper, we propose a new CG method based on the study of Rivaie et al. [7] (Comparative study of conjugate gradient coefficient for unconstrained Optimization, Aus. J. Bas. Appl. Sci. 5(2011) 947-951). Then, we show that our method satisfies sufficient descent condition and converges globally with exact line search. Numerical results show that our proposed method is efficient for given standard test problems, compare to other existing CG methods.

  19. Generalized conjugate gradient squared

    SciTech Connect

    Fokkema, D.R.; Sleijpen, G.L.G.

    1994-12-31

    In order to solve non-symmetric linear systems of equations, the Conjugate Gradient Squared (CGS) is a well-known and widely used iterative method. In practice the method converges fast, often twice as fast as the Bi-Conjugate Gradient method. This is what you may expect, since CGS uses the square of the BiCG polynomial. However, CGS may suffer from its erratic convergence behavior. The method may diverge or the approximate solution may be inaccurate. BiCGSTAB uses the BiCG polynomial and a product of linear factors in an attempt to smoothen the convergence. In many cases, this has proven to be very effective. Unfortunately, the convergence of BiCGSTAB may stall when a linear factor (nearly) degenerates. BiCGstab({ell}) is designed to overcome this degeneration of linear factors. It generalizes BiCGSTAB and uses both the BiCG polynomial and a product of higher order factors. Still, CGS may converge faster than BiCGSTAB or BiCGstab({ell}). So instead of using a product of linear or higher order factors, it may be worthwhile to look for other polynomials. Since the BiCG polynomial is based on a three term recursion, a natural choice would be a polynomial based on another three term recursion. Possibly, a suitable choice of recursion coefficients would result in method that converges faster or as fast as CGS, but less erratic. It turns out that an algorithm for such a method can easily be formulated. One particular choice for the recursion coefficients leads to CGS. Therefore one could call this algorithm generalized CGS. Another choice for the recursion coefficients leads to BiCGSTAB. It is therefore possible to mix linear factors and some polynomial based on a three term recursion. This way one may get the best of both worlds. The authors will report on their findings.

  20. An M-step preconditioned conjugate gradient method for parallel computation

    NASA Technical Reports Server (NTRS)

    Adams, L.

    1983-01-01

    This paper describes a preconditioned conjugate gradient method that can be effectively implemented on both vector machines and parallel arrays to solve sparse symmetric and positive definite systems of linear equations. The implementation on the CYBER 203/205 and on the Finite Element Machine is discussed and results obtained using the method on these machines are given.

  1. A new type of descent conjugate gradient method with exact line search

    NASA Astrophysics Data System (ADS)

    Hajar, Nurul; Mamat, Mustafa; Rivaie, Mohd.; Jusoh, Ibrahim

    2016-06-01

    Nowadays, conjugate gradient (CG) methods are impressive for solving nonlinear unconstrained optimization problems. In this paper, a new CG method is proposed and analyzed. This new CG method satisfies descent condition and its global convergence is established using exact line search. Numerical results show that this new CG method substantially outperforms the previous CG methods. This new CG method is considered robust, efficient and provided faster and stable convergence.

  2. A promising nonlinear conjugate-gradient method proposed to design nonlinear domains with a disordered distribution

    NASA Astrophysics Data System (ADS)

    Zhao, Li-Ming; Yue, Gui-Kuan; Zhou, Yun-Song; Wang, Fu-He

    2015-04-01

    A new method, namely the nonlinear conjugate-gradient (NCG) method, is proposed to design nonlinear domains with a disordered distribution, in which an efficient broadband second harmonic generation can be achieved simultaneously with high conversion efficiency. It is demonstrated by numerical simulation that the NCG method has obvious advantages in realizing the optimal quasi-phase-matching, in comparison with the traditional simulated annealing method.

  3. Conjugate gradient type methods for linear systems with complex symmetric coefficient matrices

    NASA Technical Reports Server (NTRS)

    Freund, Roland

    1989-01-01

    We consider conjugate gradient type methods for the solution of large sparse linear system Ax equals b with complex symmetric coefficient matrices A equals A(T). Such linear systems arise in important applications, such as the numerical solution of the complex Helmholtz equation. Furthermore, most complex non-Hermitian linear systems which occur in practice are actually complex symmetric. We investigate conjugate gradient type iterations which are based on a variant of the nonsymmetric Lanczos algorithm for complex symmetric matrices. We propose a new approach with iterates defined by a quasi-minimal residual property. The resulting algorithm presents several advantages over the standard biconjugate gradient method. We also include some remarks on the obvious approach to general complex linear systems by solving equivalent real linear systems for the real and imaginary parts of x. Finally, numerical experiments for linear systems arising from the complex Helmholtz equation are reported.

  4. SAGRAD: A Program for Neural Network Training with Simulated Annealing and the Conjugate Gradient Method

    PubMed Central

    Bernal, Javier; Torres-Jimenez, Jose

    2015-01-01

    SAGRAD (Simulated Annealing GRADient), a Fortran 77 program for computing neural networks for classification using batch learning, is discussed. Neural network training in SAGRAD is based on a combination of simulated annealing and Møller’s scaled conjugate gradient algorithm, the latter a variation of the traditional conjugate gradient method, better suited for the nonquadratic nature of neural networks. Different aspects of the implementation of the training process in SAGRAD are discussed, such as the efficient computation of gradients and multiplication of vectors by Hessian matrices that are required by Møller’s algorithm; the (re)initialization of weights with simulated annealing required to (re)start Møller’s algorithm the first time and each time thereafter that it shows insufficient progress in reaching a possibly local minimum; and the use of simulated annealing when Møller’s algorithm, after possibly making considerable progress, becomes stuck at a local minimum or flat area of weight space. Outlines of the scaled conjugate gradient algorithm, the simulated annealing procedure and the training process used in SAGRAD are presented together with results from running SAGRAD on two examples of training data. PMID:26958442

  5. SAGRAD: A Program for Neural Network Training with Simulated Annealing and the Conjugate Gradient Method.

    PubMed

    Bernal, Javier; Torres-Jimenez, Jose

    2015-01-01

    SAGRAD (Simulated Annealing GRADient), a Fortran 77 program for computing neural networks for classification using batch learning, is discussed. Neural network training in SAGRAD is based on a combination of simulated annealing and Møller's scaled conjugate gradient algorithm, the latter a variation of the traditional conjugate gradient method, better suited for the nonquadratic nature of neural networks. Different aspects of the implementation of the training process in SAGRAD are discussed, such as the efficient computation of gradients and multiplication of vectors by Hessian matrices that are required by Møller's algorithm; the (re)initialization of weights with simulated annealing required to (re)start Møller's algorithm the first time and each time thereafter that it shows insufficient progress in reaching a possibly local minimum; and the use of simulated annealing when Møller's algorithm, after possibly making considerable progress, becomes stuck at a local minimum or flat area of weight space. Outlines of the scaled conjugate gradient algorithm, the simulated annealing procedure and the training process used in SAGRAD are presented together with results from running SAGRAD on two examples of training data. PMID:26958442

  6. A finite element conjugate gradient FFT method for scattering

    NASA Technical Reports Server (NTRS)

    Collins, Jeffery D.; Zapp, John; Hsa, Chang-Yu; Volakis, John L.

    1990-01-01

    An extension of a two dimensional formulation is presented for a three dimensional body of revolution. With the introduction of a Fourier expansion of the vector electric and magnetic fields, a coupled two dimensional system is generated and solved via the finite element method. An exact boundary condition is employed to terminate the mesh and the fast fourier transformation (FFT) is used to evaluate the boundary integrals for low O(n) memory demand when an iterative solution algorithm is used. By virtue of the finite element method, the algorithm is applicable to structures of arbitrary material composition. Several improvements to the two dimensional algorithm are also described. These include: (1) modifications for terminating the mesh at circular boundaries without distorting the convolutionality of the boundary integrals; (2) the development of nonproprietary mesh generation routines for two dimensional applications; (3) the development of preprocessors for interfacing SDRC IDEAS with the main algorithm; and (4) the development of post-processing algorithms based on the public domain package GRAFIC to generate two and three dimensional gray level and color field maps.

  7. Preconditioned conjugate gradient methods for the Navier-Stokes equations

    NASA Technical Reports Server (NTRS)

    Ajmani, Kumud; Ng, Wing-Fai; Liou, Meng-Sing

    1994-01-01

    A preconditioned Krylov subspace method (GMRES) is used to solve the linear systems of equations formed at each time-integration step of the unsteady, two-dimensional, compressible Navier-Stokes equations of fluid flow. The Navier-Stokes equations are cast in an implicit, upwind finite-volume, flux-split formulation. Several preconditioning techniques are investigated to enhance the efficiency and convergence rate of the implicit solver based on the GMRES algorithm. The superiority of the new solver is established by comparisons with a conventional implicit solver, namely line Gauss-Seidel relaxation (LGSR). Computational test results for low-speed (incompressible flow over a backward-facing step at Mach 0.1), transonic flow (trailing edge flow in a transonic turbine cascade), and hypersonic flow (shock-on-shock interactions on a cylindrical leading edge at Mach 6.0) are presented. For the Mach 0.1 case, overall speedup factors of up to 17 (in terms of time-steps) and 15 (in terms of CPU time on a CRAY-YMP/8) are found in favor of the preconditioned GMRES solver, when compared with the LGSR solver. The corresponding speedup factors for the transonic flow case are 17 and 23, respectively. The hypersonic flow case shows slightly lower speedup factors of 9 and 13, respectively. The study of preconditioners conducted in this research reveals that a new LUSGS-type preconditioner is much more efficient than a conventional incomplete LU-type preconditioner.

  8. Preconditioned conjugate gradient methods for the Navier-Stokes equations

    SciTech Connect

    Ajmani, K.; Ng, Wing Fai ); Liou, Meng Sing )

    1994-01-01

    A preconditioned Krylov subspace method (GMRES) is used to solve the linear systems of equations formed at each time-integration step of the unsteady, two-dimensional, compressible Navier-Stokes equations of fluid flow. The Navier-Stokes equations are cast in an implicit, upwind finite-volume, flux-split formulations. Several preconditioning techniques are investigated to enhance the efficiency and convergence rate of the implicit solver based on the GMRES algorithm. The superiority of the new solver is established by comparisons with a (LGSR). Computational test results for low-speed (incompressible flow over a backward-facing step at Mach 0.1), transonic flow (trailing edge flow in a transonic turbine cascade), and hypersonic flow (shock-on-shock interactions on a cylindrical leading edge at Mach 6.0) are presented. For the Mach 0.1 case, overall speedup factors of up to 17 (in terms of time-steps) and 15 (in terms of CPU times on a CRAY-YMP/8) are found in favor of the preconditioned GMRES solver, when compared with the LGSR solver. The corresponding speedup factors for the transonic flow cases are 17 and 23, respectively. The hypersonic flow case shows slightly lower speedup factors of 9 and 13, respectively. The study of preconditioners conducted in this research reveals that a new LUSGS-type preconditioner is much more efficient than a conventional incomplete LU-type preconditioner. 34 refs., 15 figs.

  9. Orderings for conjugate gradient preconditionings

    NASA Technical Reports Server (NTRS)

    Ortega, James M.

    1991-01-01

    The effect of orderings on the rate of convergence of the conjugate gradient method with SSOR or incomplete Cholesky preconditioning is examined. Some results also are presented that help to explain why red/black ordering gives an inferior rate of convergence.

  10. A spectral KRMI conjugate gradient method under the strong-Wolfe line search

    NASA Astrophysics Data System (ADS)

    Khadijah, Wan; Rivaie, Mohd.; Mamat, Mustafa; Jusoh, Ibrahim

    2016-06-01

    In this paper, a modification of spectral conjugate gradient (CG) method is proposed which combines the advantages of the spectral CG method and the RMIL method namely as spectral Khadijah-Rivaie-Mustafa-Ibrahim (SKRMI) to solve unconstrained optimization problems. Based on inexact line searches, the objective function generates a sufficient descent direction and the global convergence property for the proposed method has been proved. Moreover, the method reduces to the standard RMIL method if exact line search is applied. Numerical results are also presented to examine the efficiency of the proposed method.

  11. A new Liu-Storey type nonlinear conjugate gradient method for unconstrained optimization problems

    NASA Astrophysics Data System (ADS)

    Zhang, Li

    2009-03-01

    Although the Liu-Storey (LS) nonlinear conjugate gradient method has a similar structure as the well-known Polak-Ribière-Polyak (PRP) and Hestenes-Stiefel (HS) methods, research about this method is very rare. In this paper, based on the memoryless BFGS quasi-Newton method, we propose a new LS type method, which converges globally for general functions with the Grippo-Lucidi line search. Moreover, we modify this new LS method such that the modified scheme is globally convergent for nonconvex minimization if the strong Wolfe line search is used. Numerical results are also reported.

  12. A modification of classical conjugate gradient method using strong Wolfe line search

    NASA Astrophysics Data System (ADS)

    Shoid, Syazni; Rivaie, Mohd.; Mamat, Mustafa

    2016-06-01

    Recently many researches try to develop and improve the Conjugate Gradient (CG) methods because of its convergence properties and low computation costing. In this paper, another CG coefficient (βk) will be proposed which is categorized as modification in such a way to improve the performance of the classical CG methods. This paper is focused on generating βk with several desirable properties: (1) generate descent search direction at each iterations; and (2) converge globally by using strong Wolfe line search. Numerical comparisons of three CG methods show the robustness and the efficiency of the new method in solving all given problems.

  13. The conjugate gradient method for linear ill-posed problems with operator perturbations

    NASA Astrophysics Data System (ADS)

    Plato, Robert

    1999-03-01

    We consider an ill-posed problem Ta = f* in Hilbert spaces and suppose that the linear bounded operator T is approximately available, with a known estimate for the operator perturbation at the solution. As a numerical scheme the CGNR-method is considered, that is, the classical method of conjugate gradients by Hestenes and Stiefel applied to the associated normal equations. Two a posteriori stopping rules are introduced, and convergence results are provided for the corresponding approximations, respectively. As a specific application, a parameter estimation problem is considered.

  14. Multi-color incomplete Cholesky conjugate gradient methods for vector computers. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Poole, E. L.

    1986-01-01

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

  15. Non Linear Conjugate Gradient

    Energy Science and Technology Software Center (ESTSC)

    2006-11-17

    Software that simulates and inverts electromagnetic field data for subsurface electrical properties (electrical conductivity) of geological media. The software treats data produced by a time harmonic source field excitation arising from the following antenna geometery: loops and grounded bipoles, as well as point electric and magnetic dioples. The inversion process is carried out using a non-linear conjugate gradient optimization scheme, which minimizes the misfit between field data and model data using a least squares criteria.more » The software is an upgrade from the code NLCGCS_MP ver 1.0. The upgrade includes the following components: Incorporation of new 1 D field sourcing routines to more accurately simulate the 3D electromagnetic field for arbitrary geologic& media, treatment for generalized finite length transmitting antenna geometry (antennas with vertical and horizontal component directions). In addition, the software has been upgraded to treat transverse anisotropy in electrical conductivity.« less

  16. Identification techniques for phenomenological models of hysteresis based on the conjugate gradient method

    NASA Astrophysics Data System (ADS)

    Andrei, Petru; Oniciuc, Liviu; Stancu, Alexandru; Stoleriu, Laurentiu

    2007-09-01

    An identification technique for the parameters of phenomenological models of hysteresis is presented. The basic idea of our technique is to set up a system of equations for the parameters of the model as a function of known quantities on the major or minor hysteresis loops (e.g. coercive force, susceptibilities at various points, remanence), or other magnetization curves. This system of equations can be either over or underspecified and is solved by using the conjugate gradient method. Numerical results related to the identification of parameters in the Energetic, Jiles-Atherton, and Preisach models are presented.

  17. Comparison of the deflated preconditioned conjugate gradient method and algebraic multigrid for composite materials

    NASA Astrophysics Data System (ADS)

    Jönsthövel, T. B.; van Gijzen, M. B.; MacLachlan, S.; Vuik, C.; Scarpas, A.

    2012-09-01

    Many applications in computational science and engineering concern composite materials, which are characterized by large discontinuities in the material properties. Such applications require fine-scale finite-element meshes, which lead to large linear systems that are challenging to solve with current direct and iterative solutions algorithms. In this paper, we consider the simulation of asphalt concrete, which is a mixture of components with large differences in material stiffness. The discontinuities in material stiffness give rise to many small eigenvalues that negatively affect the convergence of iterative solution algorithms such as the preconditioned conjugate gradient (PCG) method. This paper considers the deflated preconditioned conjugate gradient (DPCG) method in which the rigid body modes of sets of elements with homogeneous material properties are used as deflation vectors. As preconditioner we consider several variants of the algebraic multigrid smoothed aggregation method. We evaluate the performance of the DPCG method on a parallel computer using up to 64 processors. Our test problems are derived from real asphalt core samples, obtained using CT scans. We show that the DPCG method is an efficient and robust technique for solving these challenging linear systems.

  18. Real Space DFT by Locally Optimal Block Preconditioned Conjugate Gradient Method

    NASA Astrophysics Data System (ADS)

    Michaud, Vincent; Guo, Hong

    2012-02-01

    Real space approaches solve the Kohn-Sham (KS) DFT problem as a system of partial differential equations (PDE) in real space numerical grids. In such techniques, the Hamiltonian matrix is typically much larger but sparser than the matrix arising in state-of-the-art DFT codes which are often based on directly minimizing the total energy functional. Evidence of good performance of real space methods - by Chebyshev filtered subspace iteration (CFSI) - was reported by Zhou, Saad, Tiago and Chelikowsky [1]. We found that the performance of the locally optimal block preconditioned conjugate gradient method (LOGPCG) introduced by Knyazev [2], when used in conjunction with CFSI, generally exceeds that of CFSI for solving the KS equations. We will present our implementation of the LOGPCG based real space electronic structure calculator. [4pt] [1] Y. Zhou, Y. Saad, M. L. Tiago, and J. R. Chelikowsky, ``Self-consistent-field calculations using Chebyshev-filtered subspace iteration,'' J. Comput. Phys., vol. 219,pp. 172-184, November 2006. [0pt] [2] A. V. Knyazev, ``Toward the optimal preconditioned eigensolver: Locally optimal block preconditioned conjugate gradient method,'' SIAM J. Sci. Comput, vol. 23, pp. 517-541, 2001.

  19. A conjugate gradient method for solving the non-LTE line radiation transfer problem

    NASA Astrophysics Data System (ADS)

    Paletou, F.; Anterrieu, E.

    2009-12-01

    This study concerns the fast and accurate solution of the line radiation transfer problem, under non-LTE conditions. We propose and evaluate an alternative iterative scheme to the classical ALI-Jacobi method, and to the more recently proposed Gauss-Seidel and successive over-relaxation (GS/SOR) schemes. Our study is indeed based on applying a preconditioned bi-conjugate gradient method (BiCG-P). Standard tests, in 1D plane parallel geometry and in the frame of the two-level atom model with monochromatic scattering are discussed. Rates of convergence between the previously mentioned iterative schemes are compared, as are their respective timing properties. The smoothing capability of the BiCG-P method is also demonstrated.

  20. A 3-D Poisson Solver Based on Conjugate Gradients Compared to Standard Iterative Methods and Its Performance on Vector Computers

    NASA Astrophysics Data System (ADS)

    Kapitza, H.; Eppel, D.

    1987-02-01

    A conjugate gradient method for solving a 3-D Poisson equation in Cartesian unequally spaced coordinates is tested in concurrence to standard iterative methods. It is found that the tested algorithm is far superior to Red-Black-SOR with optimal parameter. In the conjugate gradient method no relaxation parameter is needed, and there are no restrictions on the number of gridpoints in the three directions. The iteration routine is vectorizable to a large extent by the compiler of a CYBER 205 without any special preparations. Utilizing some special features of vector computers it is completely vectorizable with only minor changes in the code.

  1. A modified conjugate gradient method based on the Tikhonov system for computerized tomography (CT).

    PubMed

    Wang, Qi; Wang, Huaxiang

    2011-04-01

    During the past few decades, computerized tomography (CT) was widely used for non-destructive testing (NDT) and non-destructive examination (NDE) in the industrial area because of its characteristics of non-invasiveness and visibility. Recently, CT technology has been applied to multi-phase flow measurement. Using the principle of radiation attenuation measurements along different directions through the investigated object with a special reconstruction algorithm, cross-sectional information of the scanned object can be worked out. It is a typical inverse problem and has always been a challenge for its nonlinearity and ill-conditions. The Tikhonov regulation method is widely used for similar ill-posed problems. However, the conventional Tikhonov method does not provide reconstructions with qualities good enough, the relative errors between the reconstructed images and the real distribution should be further reduced. In this paper, a modified conjugate gradient (CG) method is applied to a Tikhonov system (MCGT method) for reconstructing CT images. The computational load is dominated by the number of independent measurements m, and a preconditioner is imported to lower the condition number of the Tikhonov system. Both simulation and experiment results indicate that the proposed method can reduce the computational time and improve the quality of image reconstruction. PMID:21129739

  2. Program generator for the Incomplete Cholesky Conjugate Gradient (ICCG) method with a symmetrizing preprocessor. [GENIC code package

    SciTech Connect

    Kuo-Petravic, G.; Petravic, M.

    1980-03-01

    This paper is an extension of the previous paper, A Program Generator for the Incomplete LU-Decomposition-Conjugate Gradient (ILUCG) Method which appeared in Computer Physics Communications. In that paper a generator program was presented which produced a code package to solve the system of equations Ax/sub approx./ = b/sub approx./, where A is an arbitrary nonsingular matrix, by the ILUCG method. In the present paper an alternative generator program is offered which produces a code package applicable to the case where A is symmetric and positive definite. The numerical algorithm used is the Incomplete Cholesky Conjugate Gradient (ICCG) method of Meijerink and Van der Vorst, which executes approximately twice as fast per iteration as the ILUCG method. In addition, an optional preprocessor is provided to treat the case of a not diagonally dominant nonsymmetric and nonsingular matrix A by solving the equation A/sup T/Ax/sub approx./ = A/sup T/b/sub approx./.

  3. Conjugate gradient algorithms using multiple recursions

    SciTech Connect

    Barth, T.; Manteuffel, T.

    1996-12-31

    Much is already known about when a conjugate gradient method can be implemented with short recursions for the direction vectors. The work done in 1984 by Faber and Manteuffel gave necessary and sufficient conditions on the iteration matrix A, in order for a conjugate gradient method to be implemented with a single recursion of a certain form. However, this form does not take into account all possible recursions. This became evident when Jagels and Reichel used an algorithm of Gragg for unitary matrices to demonstrate that the class of matrices for which a practical conjugate gradient algorithm exists can be extended to include unitary and shifted unitary matrices. The implementation uses short double recursions for the direction vectors. This motivates the study of multiple recursion algorithms.

  4. Preconditioned conjugate-gradient methods for low-speed flow calculations

    NASA Technical Reports Server (NTRS)

    Ajmani, Kumud; Ng, Wing-Fai; Liou, Meng-Sing

    1993-01-01

    An investigation is conducted into the viability of using a generalized Conjugate Gradient-like method as an iterative solver to obtain steady-state solutions of very low-speed fluid flow problems. Low-speed flow at Mach 0.1 over a backward-facing step is chosen as a representative test problem. The unsteady form of the two dimensional, compressible Navier-Stokes equations is integrated in time using discrete time-steps. The Navier-Stokes equations are cast in an implicit, upwind finite-volume, flux split formulation. The new iterative solver is used to solve a linear system of equations at each step of the time-integration. Preconditioning techniques are used with the new solver to enhance the stability and convergence rate of the solver and are found to be critical to the overall success of the solver. A study of various preconditioners reveals that a preconditioner based on the Lower-Upper Successive Symmetric Over-Relaxation iterative scheme is more efficient than a preconditioner based on Incomplete L-U factorizations of the iteration matrix. The performance of the new preconditioned solver is compared with a conventional Line Gauss-Seidel Relaxation (LGSR) solver. Overall speed-up factors of 28 (in terms of global time-steps required to converge to a steady-state solution) and 20 (in terms of total CPU time on one processor of a CRAY-YMP) are found in favor of the new preconditioned solver, when compared with the LGSR solver.

  5. On conjugate gradient type methods and polynomial preconditioners for a class of complex non-Hermitian matrices

    NASA Technical Reports Server (NTRS)

    Freund, Roland

    1988-01-01

    Conjugate gradient type methods are considered for the solution of large linear systems Ax = b with complex coefficient matrices of the type A = T + i(sigma)I where T is Hermitian and sigma, a real scalar. Three different conjugate gradient type approaches with iterates defined by a minimal residual property, a Galerkin type condition, and an Euclidian error minimization, respectively, are investigated. In particular, numerically stable implementations based on the ideas behind Paige and Saunder's SYMMLQ and MINRES for real symmetric matrices are proposed. Error bounds for all three methods are derived. It is shown how the special shift structure of A can be preserved by using polynomial preconditioning. Results on the optimal choice of the polynomial preconditioner are given. Also, some numerical experiments for matrices arising from finite difference approximations to the complex Helmholtz equation are reported.

  6. Linear regression models, least-squares problems, normal equations, and stopping criteria for the conjugate gradient method

    NASA Astrophysics Data System (ADS)

    Arioli, M.; Gratton, S.

    2012-11-01

    Minimum-variance unbiased estimates for linear regression models can be obtained by solving least-squares problems. The conjugate gradient method can be successfully used in solving the symmetric and positive definite normal equations obtained from these least-squares problems. Taking into account the results of Golub and Meurant (1997, 2009) [10,11], Hestenes and Stiefel (1952) [17], and Strakoš and Tichý (2002) [16], which make it possible to approximate the energy norm of the error during the conjugate gradient iterative process, we adapt the stopping criterion introduced by Arioli (2005) [18] to the normal equations taking into account the statistical properties of the underpinning linear regression problem. Moreover, we show how the energy norm of the error is linked to the χ2-distribution and to the Fisher-Snedecor distribution. Finally, we present the results of several numerical tests that experimentally validate the effectiveness of our stopping criteria.

  7. Applications of the conjugate gradient FFT method in scattering and radiation including simulations with impedance boundary conditions

    NASA Technical Reports Server (NTRS)

    Barkeshli, Kasra; Volakis, John L.

    1991-01-01

    The theoretical and computational aspects related to the application of the Conjugate Gradient FFT (CGFFT) method in computational electromagnetics are examined. The advantages of applying the CGFFT method to a class of large scale scattering and radiation problems are outlined. The main advantages of the method stem from its iterative nature which eliminates a need to form the system matrix (thus reducing the computer memory allocation requirements) and guarantees convergence to the true solution in a finite number of steps. Results are presented for various radiators and scatterers including thin cylindrical dipole antennas, thin conductive and resistive strips and plates, as well as dielectric cylinders. Solutions of integral equations derived on the basis of generalized impedance boundary conditions (GIBC) are also examined. The boundary conditions can be used to replace the profile of a material coating by an impedance sheet or insert, thus, eliminating the need to introduce unknown polarization currents within the volume of the layer. A general full wave analysis of 2-D and 3-D rectangular grooves and cavities is presented which will also serve as a reference for future work.

  8. Three-dimension Cole-Cole model inversion of induced polarization data based on regularized conjugate gradient method

    NASA Astrophysics Data System (ADS)

    Xu, Zhengwei

    Modeling of induced polarization (IP) phenomena is important for developing effective methods for remote sensing of subsurface geology and is widely used in mineral exploration. However, the quantitative interpretation of IP data in a complex 3D environment is still a challenging problem of applied geophysics. In this dissertation I use the regularized conjugate gradient method to determine the 3D distribution of the four parameters of the Cole-Cole model based on surface induced polarization (IP) data. This method takes into account the nonlinear nature of both electromagnetic induction (EMI) and IP phenomena. The solution of the 3D IP inverse problem is based on the regularized smooth inversion only. The method was tested on synthetic models with DC conductivity, intrinsic chargeability, time constant, and relaxation parameters, and it was also applied to the practical 3D IP survey data. I demonstrate that the four parameters of the Cole-Cole model, DC electrical resistivity, rho 0 , chargeability, eta time constant, tau and the relaxation parameter, C, can be recovered from the observed IP data simultaneously. There are four Cole-Cole parameters involved in the inversion, in other words, within each cell, there are DC conductivity (sigma0 ), chargeability (eta), time parameters (tau), and relaxation parameters (C) compared to conductivity only, used in EM only inversion. In addition to more inversion parameters used in IP survey, dipole-dipole configuration which requires more sources and receivers. One the other hand, calculating Green tensor and Frechet matrix time consuming and storing them requires a lot of memory. So, I develop parallel computation using MATLAB parallel tool to speed up the calculation.

  9. A fast, preconditioned conjugate gradient Toeplitz solver

    NASA Technical Reports Server (NTRS)

    Pan, Victor; Schrieber, Robert

    1989-01-01

    A simple factorization is given of an arbitrary hermitian, positive definite matrix in which the factors are well-conditioned, hermitian, and positive definite. In fact, given knowledge of the extreme eigenvalues of the original matrix A, an optimal improvement can be achieved, making the condition numbers of each of the two factors equal to the square root of the condition number of A. This technique is to applied to the solution of hermitian, positive definite Toeplitz systems. Large linear systems with hermitian, positive definite Toeplitz matrices arise in some signal processing applications. A stable fast algorithm is given for solving these systems that is based on the preconditioned conjugate gradient method. The algorithm exploits Toeplitz structure to reduce the cost of an iteration to O(n log n) by applying the fast Fourier Transform to compute matrix-vector products. Matrix factorization is used as a preconditioner.

  10. A modified conjugate gradient solver for very large systems

    NASA Astrophysics Data System (ADS)

    Barkai, D.; Moriarty, K. J. M.; Rebbi, C.

    1985-03-01

    A modified conjugate gradient method is derived which requires only one pass through the coefficients and the temporary vectors. The method is applicable to problems which may be complex and non-symmetric. The method is implemented on a vector processor (the CDC CYBER 205) and applied to a high-energy physics lattice gauge theory problem, though the implementation methodology is quite general.

  11. A new classical conjugate gradient coefficient with exact line search

    NASA Astrophysics Data System (ADS)

    Shapiee, Norrlaili; Rivaie, Mohd.; Mamat, Mustafa

    2016-06-01

    In this paper, we proposed a new classical conjugate gradient method. The global convergence is established using exact line search. Numerical results are presented based on number of iterations and CPU time. This numerical result shows that our method is performs better than classical CG method for a given standard test problems.

  12. Experiments with conjugate gradient algorithms for homotopy curve tracking

    NASA Technical Reports Server (NTRS)

    Irani, Kashmira M.; Ribbens, Calvin J.; Watson, Layne T.; Kamat, Manohar P.; Walker, Homer F.

    1991-01-01

    There are algorithms for finding zeros or fixed points of nonlinear systems of equations that are globally convergent for almost all starting points, i.e., with probability one. The essence of all such algorithms is the construction of an appropriate homotopy map and then tracking some smooth curve in the zero set of this homotopy map. HOMPACK is a mathematical software package implementing globally convergent homotopy algorithms with three different techniques for tracking a homotopy zero curve, and has separate routines for dense and sparse Jacobian matrices. The HOMPACK algorithms for sparse Jacobian matrices use a preconditioned conjugate gradient algorithm for the computation of the kernel of the homotopy Jacobian matrix, a required linear algebra step for homotopy curve tracking. Here, variants of the conjugate gradient algorithm are implemented in the context of homotopy curve tracking and compared with Craig's preconditioned conjugate gradient method used in HOMPACK. The test problems used include actual large scale, sparse structural mechanics problems.

  13. Conjugate-Gradient Algorithms For Dynamics Of Manipulators

    NASA Technical Reports Server (NTRS)

    Fijany, Amir; Scheid, Robert E.

    1993-01-01

    Algorithms for serial and parallel computation of forward dynamics of multiple-link robotic manipulators by conjugate-gradient method developed. Parallel algorithms have potential for speedup of computations on multiple linked, specialized processors implemented in very-large-scale integrated circuits. Such processors used to stimulate dynamics, possibly faster than in real time, for purposes of planning and control.

  14. Comparison of Conjugate Gradient Density Matrix Search and Chebyshev Expansion Methods for Avoiding Diagonalization in Large-Scale Electronic Structure Calculations

    NASA Technical Reports Server (NTRS)

    Bates, Kevin R.; Daniels, Andrew D.; Scuseria, Gustavo E.

    1998-01-01

    We report a comparison of two linear-scaling methods which avoid the diagonalization bottleneck of traditional electronic structure algorithms. The Chebyshev expansion method (CEM) is implemented for carbon tight-binding calculations of large systems and its memory and timing requirements compared to those of our previously implemented conjugate gradient density matrix search (CG-DMS). Benchmark calculations are carried out on icosahedral fullerenes from C60 to C8640 and the linear scaling memory and CPU requirements of the CEM demonstrated. We show that the CPU requisites of the CEM and CG-DMS are similar for calculations with comparable accuracy.

  15. Two New PRP Conjugate Gradient Algorithms for Minimization Optimization Models

    PubMed Central

    Yuan, Gonglin; Duan, Xiabin; Liu, Wenjie; Wang, Xiaoliang; Cui, Zengru; Sheng, Zhou

    2015-01-01

    Two new PRP conjugate Algorithms are proposed in this paper based on two modified PRP conjugate gradient methods: the first algorithm is proposed for solving unconstrained optimization problems, and the second algorithm is proposed for solving nonlinear equations. The first method contains two aspects of information: function value and gradient value. The two methods both possess some good properties, as follows: 1)βk ≥ 0 2) the search direction has the trust region property without the use of any line search method 3) the search direction has sufficient descent property without the use of any line search method. Under some suitable conditions, we establish the global convergence of the two algorithms. We conduct numerical experiments to evaluate our algorithms. The numerical results indicate that the first algorithm is effective and competitive for solving unconstrained optimization problems and that the second algorithm is effective for solving large-scale nonlinear equations. PMID:26502409

  16. Minimizing inner product data dependencies in conjugate gradient iteration

    NASA Technical Reports Server (NTRS)

    Vanrosendale, J.

    1983-01-01

    The amount of concurrency available in conjugate gradient iteration is limited by the summations required in the inner product computations. The inner product of two vectors of length N requires time c log(N), if N or more processors are available. This paper describes an algebraic restructuring of the conjugate gradient algorithm which minimizes data dependencies due to inner product calculations. After an initial start up, the new algorithm can perform a conjugate gradient iteration in time c*log(log(N)).

  17. A matrix analysis of conjugate gradient algorithms

    SciTech Connect

    Ashby, S.F.; Gutknecht, M.H.

    1993-04-01

    This paper explores the relationships between the conjugate gradient algorithms Orthodir, Orthomin, and Orthores. To facilitate this exploration, a matrix formulation for each algorithm is given. It is shown that Orthodir directly computes a Hessenberg matrix H{sub k} at step k. Orthores also computes a Hessenberg matrix, G{sub k}, which is similar to a Hessenberg matrix obtained from H{sub k} by perturbing its last column. (This perturbation vanishes at convergence.) Orthomin, on the other hand, computes a UL and LU factorization of the perturbed H{sub k} and G{sub k}, respectively. The breakdown of Orthomin and Orthores are interpreted in terms of these underlying matrix factorizations. A connection with Lanczos algorithms is also examined, as is the special case of B-normal(1) matrices (for which efficient three-term CG algorithms exist).

  18. The Grassman-metal Conjugate Gradient Method (DFT) and its application to composite thin metal films of Co, Cu and Ni.

    NASA Astrophysics Data System (ADS)

    Canning, Andrew; Raczkowski, David; Leung, Mary Ann; Wang, Lin-Wang; An, Joonhee; van Hove, Michel A.

    2003-03-01

    We will present the Grassman-metal conjugate gradient (GMCG) method for iterative diagonalization for the solution of the Kohn-Sham equations with a plane wave basis set. This is an all-bands method with variable occupancy for iterative diagonalization at fixed charge density. We will then present some results for sandwiches of Co, Cu and Ni systems which exhibit quantum well states. In particular we will show the effect of a single Ni layer at different positions on Quantum well states in a Co/Cu system. We have found that these systems are extremely difficult to converge without the use of the Grassman-metal approach. (This work was supported by the Director, Office of Advanced Scientific Computing Research, Division of Mathematical, Information and Computational Sciences of the U.S. Department of Energy and the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under contract number DE-AC03-76SF00098)

  19. Conjugate gradient coupled with multigrid for an indefinite problem

    NASA Technical Reports Server (NTRS)

    Gozani, J.; Nachshon, A.; Turkel, E.

    1984-01-01

    An iterative algorithm for the Helmholtz equation is presented. This scheme was based on the preconditioned conjugate gradient method for the normal equations. The preconditioning is one cycle of a multigrid method for the discrete Laplacian. The smoothing algorithm is red-black Gauss-Seidel and is constructed so it is a symmetric operator. The total number of iterations needed by the algorithm is independent of h. By varying the number of grids, the number of iterations depends only weakly on k when k(3)h(2) is constant. Comparisons with a SSOR preconditioner are presented.

  20. 3D Electromagnetic inversion using conjugate gradients

    SciTech Connect

    Newman, G.A.; Alumbaugh, D.L.

    1997-06-01

    In large scale 3D EM inverse problems it may not be possible to directly invert a full least-squares system matrix involving model sensitivity elements. Thus iterative methods must be employed. For the inverse problem, we favor either a linear or non-linear (NL) CG scheme, depending on the application. In a NL CG scheme, the gradient of the objective function is required at each relaxation step along with a univariate line search needed to determine the optimum model update. Solution examples based on both approaches will be presented.

  1. TV-based conjugate gradient method and discrete L-curve for few-view CT reconstruction of X-ray in vivo data

    SciTech Connect

    Yang, Xiaoli; Hofmann, Ralf; Dapp, Robin; van de Kamp, Thomas; Rolo, Tomy dos Santos; Xiao, Xianghui; Moosmann, Julian; Kashef, Jubin; Stotzka, Rainer

    2015-01-01

    High-resolution, three-dimensional (3D) imaging of soft tissues requires the solution of two inverse problems: phase retrieval and the reconstruction of the 3D image from a tomographic stack of two-dimensional (2D) projections. The number of projections per stack should be small to accommodate fast tomography of rapid processes and to constrain X-ray radiation dose to optimal levels to either increase the duration of in vivo time-lapse series at a given goal for spatial resolution and/or the conservation of structure under X-ray irradiation. In pursuing the 3D reconstruction problem in the sense of compressive sampling theory, we propose to reduce the number of projections by applying an advanced algebraic technique subject to the minimisation of the total variation (TV) in the reconstructed slice. This problem is formulated in a Lagrangian multiplier fashion with the parameter value determined by appealing to a discrete L-curve in conjunction with a conjugate gradient method. The usefulness of this reconstruction modality is demonstrated for simulated and in vivo data, the latter acquired in parallel-beam imaging experiments using synchrotron radiation. (C) 2015 Optical Society of America

  2. An overview of NSPCG: A nonsymmetric preconditioned conjugate gradient package

    NASA Astrophysics Data System (ADS)

    Oppe, Thomas C.; Joubert, Wayne D.; Kincaid, David R.

    1989-05-01

    The most recent research-oriented software package developed as part of the ITPACK Project is called "NSPCG" since it contains many nonsymmetric preconditioned conjugate gradient procedures. It is designed to solve large sparse systems of linear algebraic equations by a variety of different iterative methods. One of the main purposes for the development of the package is to provide a common modular structure for research on iterative methods for nonsymmetric matrices. Another purpose for the development of the package is to investigate the suitability of several iterative methods for vector computers. Since the vectorizability of an iterative method depends greatly on the matrix structure, NSPCG allows great flexibility in the operator representation. The coefficient matrix can be passed in one of several different matrix data storage schemes. These sparse data formats allow matrices with a wide range of structures from highly structured ones such as those with all nonzeros along a relatively small number of diagonals to completely unstructured sparse matrices. Alternatively, the package allows the user to call the accelerators directly with user-supplied routines for performing certain matrix operations. In this case, one can use the data format from an application program and not be required to copy the matrix into one of the package formats. This is particularly advantageous when memory space is limited. Some of the basic preconditioners that are available are point methods such as Jacobi, Incomplete LU Decomposition and Symmetric Successive Overrelaxation as well as block and multicolor preconditioners. The user can select from a large collection of accelerators such as Conjugate Gradient (CG), Chebyshev (SI, for semi-iterative), Generalized Minimal Residual (GMRES), Biconjugate Gradient Squared (BCGS) and many others. The package is modular so that almost any accelerator can be used with almost any preconditioner.

  3. Another hybrid conjugate gradient algorithm for unconstrained optimization

    NASA Astrophysics Data System (ADS)

    Andrei, Neculai

    2008-02-01

    Another hybrid conjugate gradient algorithm is subject to analysis. The parameter ? k is computed as a convex combination of beta ^{{HS}}_{k} (Hestenes-Stiefel) and beta ^{{DY}}_{k} (Dai-Yuan) algorithms, i.eE beta ^{C}_{k} = {left( {1 - theta _{k} } right)}beta ^{{HS}}_{k} + theta _{k} beta ^{{DY}}_{k} . The parameter ? k in the convex combination is computed in such a way so that the direction corresponding to the conjugate gradient algorithm to be the Newton direction and the pair (s k , y k ) to satisfy the quasi-Newton equation nabla ^{2} f{left( {x_{{k + 1}} } right)}s_{k} = y_{k} , where s_{k} = x_{{k + 1}} - x_{k} and y_{k} = g_{{k + 1}} - g_{k} . The algorithm uses the standard Wolfe line search conditions. Numerical comparisons with conjugate gradient algorithms show that this hybrid computational scheme outperforms the Hestenes-Stiefel and the Dai-Yuan conjugate gradient algorithms as well as the hybrid conjugate gradient algorithms of Dai and Yuan. A set of 750 unconstrained optimization problems are used, some of them from the CUTE library.

  4. Integrated gravity and gravity gradient 3D inversion using the non-linear conjugate gradient

    NASA Astrophysics Data System (ADS)

    Qin, Pengbo; Huang, Danian; Yuan, Yuan; Geng, Meixia; Liu, Jie

    2016-03-01

    Gravity data, which are critical in mineral, oil, and gas exploration, are obtained from the vertical component of the gravity field, while gravity gradient data are measured from changes in the gravity field in three directions. However, few studies have sought to improve exploration techniques by integrating gravity and gravity gradient data using inversion methods. In this study, we developed a new method to integrate gravity and gravity gradient data in a 3D density inversion using the non-linear conjugate gradient (NLCG) method and the minimum gradient support (MGS) functional to regularize the 3D inverse problem and to obtain a clear and accurate image of the anomalous body. The NLCG algorithm, which is suitable for solving large-scale nonlinear optimization problems and requires no memory storage, was compared to the Broyden-Fletcher-Goldfarb-Shanno (BFGS) quasi-Newton algorithm and the results indicated that the convergence rate of NLCG is slower, but that the storage requirement and computation time is lower. To counteract the decay in kernel function, we introduced a depth weighting function for anomalous bodies at the same depth, with information about anomalous body depth obtained from well log and seismic exploration data. For anomalous bodies at different depths, we introduced a spatial gradient weighting function to incorporate additional information obtained in the inversion. We concluded that the spatial gradient weighting function enhanced the spatial resolution of the recovered model. Furthermore, our results showed that including multiple components for inversion increased the resolution of the recovered model. We validated our model by applying our inversion method to survey data from Vinton salt dome, Louisiana, USA. The results showed good agreement with known geologic information; thus confirming the accuracy of this approach.

  5. Preconditioned conjugate gradient algorithms and software for solving large sparse linear systems

    SciTech Connect

    Young, D.M.; Jea, K.C.; Mai, Tsun-Zee

    1987-03-01

    The classical form of the conjugate gradient method (CG method), developed by Hestenes and Stiefel, for solving the linear system Au = b is applicable when the coefficient matrix A is symmetric and positive definite (SPD). In this paper we consider various alternative forms of the CG method as well as generalizations to cases where A is not necessarily SPD. This analysis includes the ''preconditioned conjugate gradient method'' which is equivalent to conjugate gradient acceleration of a basic iterative method corresponding to a preconditioned system. Both the symmetrizable case and the nonsymmetrizable case are considered. For the nonsymmetrizable case there are very few useful theoretical results available. A package of programs, known as ITPACK, has been developed as a tool for carrying out experimental studies on various algorithms. Preliminary conclusions based on experimental results are given. 42 refs.

  6. Parallel conjugate gradient algorithms for manipulator dynamic simulation

    NASA Technical Reports Server (NTRS)

    Fijany, Amir; Scheld, Robert E.

    1989-01-01

    Parallel conjugate gradient algorithms for the computation of multibody dynamics are developed for the specialized case of a robot manipulator. For an n-dimensional positive-definite linear system, the Classical Conjugate Gradient (CCG) algorithms are guaranteed to converge in n iterations, each with a computation cost of O(n); this leads to a total computational cost of O(n sq) on a serial processor. A conjugate gradient algorithms is presented that provide greater efficiency using a preconditioner, which reduces the number of iterations required, and by exploiting parallelism, which reduces the cost of each iteration. Two Preconditioned Conjugate Gradient (PCG) algorithms are proposed which respectively use a diagonal and a tridiagonal matrix, composed of the diagonal and tridiagonal elements of the mass matrix, as preconditioners. Parallel algorithms are developed to compute the preconditioners and their inversions in O(log sub 2 n) steps using n processors. A parallel algorithm is also presented which, on the same architecture, achieves the computational time of O(log sub 2 n) for each iteration. Simulation results for a seven degree-of-freedom manipulator are presented. Variants of the proposed algorithms are also developed which can be efficiently implemented on the Robot Mathematics Processor (RMP).

  7. Ship wake-detection procedure using conjugate gradient trained artificial neural networks

    SciTech Connect

    Fitch, J.P.; Lehman, S.K.; Dowla, F.U.; Lu, S.Y.; Johansson, E.M.; Goodman, D.M. )

    1991-09-01

    This paper reports that a method has been developed to reduce large two-dimensional images to significantly smaller feature lists. These feature lists overcome the problem of storing and manipulating large amounts of data. A new artificial neural network using conjugate gradient training methods, operating on sets of feature lists, was successfully trained to determine the presence or absence of wakes in synthetic aperture radar images. A comparison has been made between the different conjugate gradient and steepest-descent training methods and has demonstrated the superiority of the former over the latter.

  8. Partial least squares, conjugate gradient and the fisher discriminant

    SciTech Connect

    Faber, V.

    1996-12-31

    The theory of multivariate regression has been extensively studied and is commonly used in many diverse scientific areas. A wide variety of techniques are currently available for solving the problem of multivariate calibration. The volume of literature on this subject is so extensive that understanding which technique to apply can often be very confusing. A common class of techniques for solving linear systems, and consequently applications of linear systems to multivariate analysis, are iterative methods. While common linear system solvers typically involve the factorization of the coefficient matrix A in solving the system Ax = b, this method can be impractical if A is large and sparse. Iterative methods such as Gauss-Seidel, SOR, Chebyshev semi-iterative, and related methods also often depend upon parameters that require calibration and which are sometimes hard to choose properly. An iterative method which surmounts many of these difficulties is the method of conjugate gradient. Algorithms of this type find solutions iteratively, by optimally calculating the next approximation from the residuals.

  9. Syntheses of Gradient pi-Conjugated Copolymers of Thiophene

    SciTech Connect

    Locke, Jonas R.; McNeil, Anne J.

    2010-11-09

    we prepared the first gradient π-conjugated copolymers via Ni-catalyzed chain-growth copolymerization of 3-hexylthiophene and 3-((hexyloxy)methyl)thiophene. Because rate studies indicated little difference in monomer reactivities, one monomer was gradually added to the polymerization over time to form gradient copolymers. Now that controlled sequence π-conjugated copolymers can be synthesized, the next goal is to identify their unique properties, including phase-compatibilizing abilities in homopolymer blends. Preliminary data reported herein suggest that the solid-state optical and physical properties are influenced by the copolymer sequence. Finally, although the Ni-catalyzed copolymerizations are chain growth under the conditions reported herein, our preliminary attempts to expand the substrate scope by examining the copolymerization of monomers with varying steric and electronic properties has highlighted a need for developing improved catalysts.

  10. A constrained conjugate gradient algorithm for computed tomography

    SciTech Connect

    Azevedo, S.G.; Goodman, D.M.

    1994-11-15

    Image reconstruction from projections of x-ray, gamma-ray, protons and other penetrating radiation is a well-known problem in a variety of fields, and is commonly referred to as computed tomography (CT). Various analytical and series expansion methods of reconstruction and been used in the past to provide three-dimensional (3D) views of some interior quantity. The difficulties of these approaches lie in the cases where (a) the number of views attainable is limited, (b) the Poisson (or other) uncertainties are significant, (c) quantifiable knowledge of the object is available, but not implementable, or (d) other limitations of the data exist. We have adapted a novel nonlinear optimization procedure developed at LLNL to address limited-data image reconstruction problems. The technique, known as nonlinear least squares with general constraints or constrained conjugate gradients (CCG), has been successfully applied to a number of signal and image processing problems, and is now of great interest to the image reconstruction community. Previous applications of this algorithm to deconvolution problems and x-ray diffraction images for crystallography have shown the great promise.

  11. A complete implementation of the conjugate gradient algorithm on a reconfigurable supercomputer

    SciTech Connect

    Dubois, David H; Dubois, Andrew J; Connor, Carolyn M; Boorman, Thomas M; Poole, Stephen W

    2008-01-01

    The conjugate gradient is a prominent iterative method for solving systems of sparse linear equations. Large-scale scientific applications often utilize a conjugate gradient solver at their computational core. In this paper we present a field programmable gate array (FPGA) based implementation of a double precision, non-preconditioned, conjugate gradient solver for fmite-element or finite-difference methods. OUf work utilizes the SRC Computers, Inc. MAPStation hardware platform along with the 'Carte' software programming environment to ease the programming workload when working with the hybrid (CPUIFPGA) environment. The implementation is designed to handle large sparse matrices of up to order N x N where N <= 116,394, with up to 7 non-zero, 64-bit elements per sparse row. This implementation utilizes an optimized sparse matrix-vector multiply operation which is critical for obtaining high performance. Direct parallel implementations of loop unrolling and loop fusion are utilized to extract performance from the various vector/matrix operations. Rather than utilize the FPGA devices as function off-load accelerators, our implementation uses the FPGAs to implement the core conjugate gradient algorithm. Measured run-time performance data is presented comparing the FPGA implementation to a software-only version showing that the FPGA can outperform processors running up to 30x the clock rate. In conclusion we take a look at the new SRC-7 system and estimate the performance of this algorithm on that architecture.

  12. JAC2D: A two-dimensional finite element computer program for the nonlinear quasi-static response of solids with the conjugate gradient method; Yucca Mountain Site Characterization Project

    SciTech Connect

    Biffle, J.H.; Blanford, M.L.

    1994-05-01

    JAC2D is a two-dimensional finite element program designed to solve quasi-static nonlinear mechanics problems. A set of continuum equations describes the nonlinear mechanics involving large rotation and strain. A nonlinear conjugate gradient method is used to solve the equations. The method is implemented in a two-dimensional setting with various methods for accelerating convergence. Sliding interface logic is also implemented. A four-node Lagrangian uniform strain element is used with hourglass stiffness to control the zero-energy modes. This report documents the elastic and isothermal elastic/plastic material model. Other material models, documented elsewhere, are also available. The program is vectorized for efficient performance on Cray computers. Sample problems described are the bending of a thin beam, the rotation of a unit cube, and the pressurization and thermal loading of a hollow sphere.

  13. JAC3D -- A three-dimensional finite element computer program for the nonlinear quasi-static response of solids with the conjugate gradient method; Yucca Mountain Site Characterization Project

    SciTech Connect

    Biffle, J.H.

    1993-02-01

    JAC3D is a three-dimensional finite element program designed to solve quasi-static nonlinear mechanics problems. A set of continuum equations describes the nonlinear mechanics involving large rotation and strain. A nonlinear conjugate gradient method is used to solve the equation. The method is implemented in a three-dimensional setting with various methods for accelerating convergence. Sliding interface logic is also implemented. An eight-node Lagrangian uniform strain element is used with hourglass stiffness to control the zero-energy modes. This report documents the elastic and isothermal elastic-plastic material model. Other material models, documented elsewhere, are also available. The program is vectorized for efficient performance on Cray computers. Sample problems described are the bending of a thin beam, the rotation of a unit cube, and the pressurization and thermal loading of a hollow sphere.

  14. Two grid iteration with a conjugate gradient fine grid smoother applied to a groundwater flow model

    SciTech Connect

    Hagger, M.J.; Spence, A.; Cliffe, K.A.

    1994-12-31

    This talk is concerned with the efficient solution of Ax=b, where A is a large, sparse, symmetric positive definite matrix arising from a standard finite element discretisation of the groundwater flow problem {triangledown}{sm_bullet}(k{triangledown}p)=0. Here k is the coefficient of rock permeability in applications and is highly discontinuous. The discretisation is carried out using the Harwell NAMMU finite element package, using, for 2D, 9 node biquadratic rectangular elements, and 27 node biquadratics for 3D. The aim is to develop a robust technique for iterative solutions of 3D problems based on a regional groundwater flow model of a geological area with sharply varying hydrogeological properties. Numerical experiments with polynomial preconditioned conjugate gradient methods on a 2D groundwater flow model were found to yield very poor results, converging very slowly. In order to utilise the fact that A comes from the discretisation of a PDE the authors try the two grid method as is well analysed from studies of multigrid methods, see for example {open_quotes}Multi-Grid Methods and Applications{close_quotes} by W. Hackbusch. Specifically they consider two discretisations resulting in stiffness matrices A{sub N} and A{sub n}, of size N and n respectively, where N > n, for both a model problem and the geological model. They perform a number of conjugate gradient steps on the fine grid, ie using A{sub N}, followed by an exact coarse grid solve, using A{sub n}, and then update the fine grid solution, the exact coarse grid solve being done using a frontal method factorisation of A{sub n}. Note that in the context of the standard two grid method this is equivalent to using conjugate gradients as a fine grid smoothing step. Experimental results are presented to show the superiority of the two grid iteration method over the polynomial preconditioned conjugate gradient method.

  15. Efficient conjugate gradient algorithms for computation of the manipulator forward dynamics

    NASA Technical Reports Server (NTRS)

    Fijany, Amir; Scheid, Robert E.

    1989-01-01

    The applicability of conjugate gradient algorithms for computation of the manipulator forward dynamics is investigated. The redundancies in the previously proposed conjugate gradient algorithm are analyzed. A new version is developed which, by avoiding these redundancies, achieves a significantly greater efficiency. A preconditioned conjugate gradient algorithm is also presented. A diagonal matrix whose elements are the diagonal elements of the inertia matrix is proposed as the preconditioner. In order to increase the computational efficiency, an algorithm is developed which exploits the synergism between the computation of the diagonal elements of the inertia matrix and that required by the conjugate gradient algorithm.

  16. Conjugate and method for forming aminomethyl phosphorus conjugates

    DOEpatents

    Katti, Kattesh V.; Berning, Douglas E.; Volkert, Wynn A.; Ketring, Alan R.; Churchill, Robert

    1999-01-01

    A method of forming phosphine-amine conjugates includes reacting a hydroxymethyl phosphine group of an amine-free first molecule with at least one free amine group of a second molecule to covalently bond the first molecule with the second molecule through an aminomethyl phosphorus linkage and the conjugates formed thereby.

  17. Solving large test-day models by iteration on data and preconditioned conjugate gradient.

    PubMed

    Lidauer, M; Strandén, I; Mäntysaari, E A; Pösö, J; Kettunen, A

    1999-12-01

    A preconditioned conjugate gradient method was implemented into an iteration on a program for data estimation of breeding values, and its convergence characteristics were studied. An algorithm was used as a reference in which one fixed effect was solved by Gauss-Seidel method, and other effects were solved by a second-order Jacobi method. Implementation of the preconditioned conjugate gradient required storing four vectors (size equal to number of unknowns in the mixed model equations) in random access memory and reading the data at each round of iteration. The preconditioner comprised diagonal blocks of the coefficient matrix. Comparison of algorithms was based on solutions of mixed model equations obtained by a single-trait animal model and a single-trait, random regression test-day model. Data sets for both models used milk yield records of primiparous Finnish dairy cows. Animal model data comprised 665,629 lactation milk yields and random regression test-day model data of 6,732,765 test-day milk yields. Both models included pedigree information of 1,099,622 animals. The animal model ¿random regression test-day model¿ required 122 ¿305¿ rounds of iteration to converge with the reference algorithm, but only 88 ¿149¿ were required with the preconditioned conjugate gradient. To solve the random regression test-day model with the preconditioned conjugate gradient required 237 megabytes of random access memory and took 14% of the computation time needed by the reference algorithm. PMID:10629827

  18. T2CG1, a package of preconditioned conjugate gradient solvers for TOUGH2

    SciTech Connect

    Moridis, G.; Pruess, K.; Antunez, E.

    1994-03-01

    Most of the computational work in the numerical simulation of fluid and heat flows in permeable media arises in the solution of large systems of linear equations. The simplest technique for solving such equations is by direct methods. However, because of large storage requirements and accumulation of roundoff errors, the application of direct solution techniques is limited, depending on matrix bandwidth, to systems of a few hundred to at most a few thousand simultaneous equations. T2CG1, a package of preconditioned conjugate gradient solvers, has been added to TOUGH2 to complement its direct solver and significantly increase the size of problems tractable on PCs. T2CG1 includes three different solvers: a Bi-Conjugate Gradient (BCG) solver, a Bi-Conjugate Gradient Squared (BCGS) solver, and a Generalized Minimum Residual (GMRES) solver. Results from six test problems with up to 30,000 equations show that T2CG1 (1) is significantly (and invariably) faster and requires far less memory than the MA28 direct solver, (2) it makes possible the solution of very large three-dimensional problems on PCs, and (3) that the BCGS solver is the fastest of the three in the tested problems. Sample problems are presented related to heat and fluid flow at Yucca Mountain and WIPP, environmental remediation by the Thermal Enhanced Vapor Extraction System, and geothermal resources.

  19. Conjugate-Gradient Neural Networks in Classification of Multisource and Very-High-Dimensional Remote Sensing Data

    NASA Technical Reports Server (NTRS)

    Benediktsson, J. A.; Swain, P. H.; Ersoy, O. K.

    1993-01-01

    Application of neural networks to classification of remote sensing data is discussed. Conventional two-layer backpropagation is found to give good results in classification of remote sensing data but is not efficient in training. A more efficient variant, based on conjugate-gradient optimization, is used for classification of multisource remote sensing and geographic data and very-high-dimensional data. The conjugate-gradient neural networks give excellent performance in classification of multisource data, but do not compare as well with statistical methods in classification of very-high-dimentional data.

  20. A preliminary investigation of 3D preconditioned conjugate gradient reconstruction for cone-beam CT

    NASA Astrophysics Data System (ADS)

    Fu, Lin; De Man, Bruno; Zeng, Kai; Benson, Thomas M.; Yu, Zhou; Cao, Guangzhi; Thibault, Jean-Baptiste

    2012-03-01

    Model-based iterative reconstruction (MBIR) methods based on maximum a posteriori (MAP) estimation have been recently introduced to multi-slice CT scanners. The model-based approach has shown promising image quality improvement with reduced radiation dose compared to conventional FBP methods, but the associated high computation cost limits its widespread use in clinical environments. Among the various choices of numerical algorithms to optimize the MAP cost function, simultaneous update methods such as the conjugate gradient (CG) method have a relatively high level of parallelism to take full advantage of a new generation of many-core computing hardware. With proper preconditioning techniques, fast convergence speeds of CG algorithms have been demonstrated in 3D emission and 2D transmission reconstruction. However, 3D transmission reconstruction using preconditioned conjugate gradient (PCG) has not been reported. Additional challenges in applying PCG in 3D CT reconstruction include the large size of clinical CT data, shift-variant and incomplete sampling, and complex regularization schemes to meet the diagnostic standard of image quality. In this paper, we present a ramp-filter based PCG algorithm for 3D CT MBIR. Convergence speeds of algorithms with and without using the preconditioner are compared.

  1. Non-preconditioned conjugate gradient on cell and FPCA-based hybrid supercomputer nodes

    SciTech Connect

    Dubois, David H; Dubois, Andrew J; Boorman, Thomas M; Connor, Carolyn M

    2009-03-10

    This work presents a detailed implementation of a double precision, Non-Preconditioned, Conjugate Gradient algorithm on a Roadrunner heterogeneous supercomputer node. These nodes utilize the Cell Broadband Engine Architecture{trademark} in conjunction with x86 Opteron{trademark} processors from AMD. We implement a common Conjugate Gradient algorithm, on a variety of systems, to compare and contrast performance. Implementation results are presented for the Roadrunner hybrid supercomputer, SRC Computers, Inc. MAPStation SRC-6 FPGA enhanced hybrid supercomputer, and AMD Opteron only. In all hybrid implementations wall clock time is measured, including all transfer overhead and compute timings.

  2. Non-preconditioned conjugate gradient on cell and FPGA based hybrid supercomputer nodes

    SciTech Connect

    Dubois, David H; Dubois, Andrew J; Boorman, Thomas M; Connor, Carolyn M

    2009-01-01

    This work presents a detailed implementation of a double precision, non-preconditioned, Conjugate Gradient algorithm on a Roadrunner heterogeneous supercomputer node. These nodes utilize the Cell Broadband Engine Architecture{sup TM} in conjunction with x86 Opteron{sup TM} processors from AMD. We implement a common Conjugate Gradient algorithm, on a variety of systems, to compare and contrast performance. Implementation results are presented for the Roadrunner hybrid supercomputer, SRC Computers, Inc. MAPStation SRC-6 FPGA enhanced hybrid supercomputer, and AMD Opteron only. In all hybrid implementations wall clock time is measured, including all transfer overhead and compute timings.

  3. Reducing communication costs in the conjugate gradient algorithm on distributed memory multiprocessors

    SciTech Connect

    D'Azevedo, E.F.; Romine, C.H.

    1992-09-01

    The standard formulation of the conjugate gradient algorithm involves two inner product computations. The results of these two inner products are needed to update the search direction and the computed solution. In a distributed memory parallel environment, the computation and subsequent distribution of these two values requires two separate communication and synchronization phases. In this paper, we present a mathematically equivalent rearrangement of the standard algorithm that reduces the number of communication phases. We give a second derivation of the modified conjugate gradient algorithm in terms of the natural relationship with the underlying Lanczos process. We also present empirical evidence of the stability of this modified algorithm.

  4. PRECONDITIONED CONJUGATE-GRADIENT 2 (PCG2), a computer program for solving ground-water flow equations

    USGS Publications Warehouse

    Hill, Mary C.

    1990-01-01

    This report documents PCG2 : a numerical code to be used with the U.S. Geological Survey modular three-dimensional, finite-difference, ground-water flow model . PCG2 uses the preconditioned conjugate-gradient method to solve the equations produced by the model for hydraulic head. Linear or nonlinear flow conditions may be simulated. PCG2 includes two reconditioning options : modified incomplete Cholesky preconditioning, which is efficient on scalar computers; and polynomial preconditioning, which requires less computer storage and, with modifications that depend on the computer used, is most efficient on vector computers . Convergence of the solver is determined using both head-change and residual criteria. Nonlinear problems are solved using Picard iterations. This documentation provides a description of the preconditioned conjugate gradient method and the two preconditioners, detailed instructions for linking PCG2 to the modular model, sample data inputs, a brief description of PCG2, and a FORTRAN listing.

  5. The conjugate gradient NAS parallel benchmark on the IBM SP1

    SciTech Connect

    Trefethen, A.E.; Zhang, T.

    1994-12-31

    The NAS Parallel Benchmarks are a suite of eight benchmark problems developed at the NASA Ames Research Center. They are specified in such a way that the benchmarkers are free to choose the language and method of implementation to suit the system in which they are interested. In this presentation the authors will discuss the Conjugate Gradient benchmark and its implementation on the IBM SP1. The SP1 is a parallel system which is comprised of RS/6000 nodes connected by a high performance switch. They will compare the results of the SP1 implementation with those reported for other machines. At this time, such a comparison shows the SP1 to be very competitive.

  6. Method of Conjugate Radii for Solving Linear and Nonlinear Systems

    NASA Technical Reports Server (NTRS)

    Nachtsheim, Philip R.

    1999-01-01

    This paper describes a method to solve a system of N linear equations in N steps. A quadratic form is developed involving the sum of the squares of the residuals of the equations. Equating the quadratic form to a constant yields a surface which is an ellipsoid. For different constants, a family of similar ellipsoids can be generated. Starting at an arbitrary point an orthogonal basis is constructed and the center of the family of similar ellipsoids is found in this basis by a sequence of projections. The coordinates of the center in this basis are the solution of linear system of equations. A quadratic form in N variables requires N projections. That is, the current method is an exact method. It is shown that the sequence of projections is equivalent to a special case of the Gram-Schmidt orthogonalization process. The current method enjoys an advantage not shared by the classic Method of Conjugate Gradients. The current method can be extended to nonlinear systems without modification. For nonlinear equations the Method of Conjugate Gradients has to be augmented with a line-search procedure. Results for linear and nonlinear problems are presented.

  7. A Conjugate Gradient Algorithm with Function Value Information and N-Step Quadratic Convergence for Unconstrained Optimization

    PubMed Central

    Li, Xiangrong; Zhao, Xupei; Duan, Xiabin; Wang, Xiaoliang

    2015-01-01

    It is generally acknowledged that the conjugate gradient (CG) method achieves global convergence—with at most a linear convergence rate—because CG formulas are generated by linear approximations of the objective functions. The quadratically convergent results are very limited. We introduce a new PRP method in which the restart strategy is also used. Moreover, the method we developed includes not only n-step quadratic convergence but also both the function value information and gradient value information. In this paper, we will show that the new PRP method (with either the Armijo line search or the Wolfe line search) is both linearly and quadratically convergent. The numerical experiments demonstrate that the new PRP algorithm is competitive with the normal CG method. PMID:26381742

  8. Use of the preconditioned conjugate gradient algorithm as a generic solver for mixed-model equations in animal breeding applications.

    PubMed

    Tsuruta, S; Misztal, I; Strandén, I

    2001-05-01

    Utility of the preconditioned conjugate gradient algorithm with a diagonal preconditioner for solving mixed-model equations in animal breeding applications was evaluated with 16 test problems. The problems included single- and multiple-trait analyses, with data on beef, dairy, and swine ranging from small examples to national data sets. Multiple-trait models considered low and high genetic correlations. Convergence was based on relative differences between left- and right-hand sides. The ordering of equations was fixed effects followed by random effects, with no special ordering within random effects. The preconditioned conjugate gradient program implemented with double precision converged for all models. However, when implemented in single precision, the preconditioned conjugate gradient algorithm did not converge for seven large models. The preconditioned conjugate gradient and successive overrelaxation algorithms were subsequently compared for 13 of the test problems. The preconditioned conjugate gradient algorithm was easy to implement with the iteration on data for general models. However, successive overrelaxation requires specific programming for each set of models. On average, the preconditioned conjugate gradient algorithm converged in three times fewer rounds of iteration than successive overrelaxation. With straightforward implementations, programs using the preconditioned conjugate gradient algorithm may be two or more times faster than those using successive overrelaxation. However, programs using the preconditioned conjugate gradient algorithm would use more memory than would comparable implementations using successive overrelaxation. Extensive optimization of either algorithm can influence rankings. The preconditioned conjugate gradient implemented with iteration on data, a diagonal preconditioner, and in double precision may be the algorithm of choice for solving mixed-model equations when sufficient memory is available and ease of implementation is

  9. Realization of preconditioned Lanczos and conjugate gradient algorithms on optical linear algebra processors.

    PubMed

    Ghosh, A

    1988-08-01

    Lanczos and conjugate gradient algorithms are important in computational linear algebra. In this paper, a parallel pipelined realization of these algorithms on a ring of optical linear algebra processors is described. The flow of data is designed to minimize the idle times of the optical multiprocessor and the redundancy of computations. The effects of optical round-off errors on the solutions obtained by the optical Lanczos and conjugate gradient algorithms are analyzed, and it is shown that optical preconditioning can improve the accuracy of these algorithms substantially. Algorithms for optical preconditioning and results of numerical experiments on solving linear systems of equations arising from partial differential equations are discussed. Since the Lanczos algorithm is used mostly with sparse matrices, a folded storage scheme to represent sparse matrices on spatial light modulators is also described. PMID:20531907

  10. 2D resistivity inversion using conjugate gradients for a finite element discretization

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    In this work we present a DC 2D inversion algorithm using conjugate gradients relaxation to solve the maximum likelihood inverse equations. We apply, according to Zhang (1995), the maximum likelihood inverse theory developed by Tarantola and Valette (1982) to our 2D resistivity inversion. This algorithm was chosen to this research because it doesn't need to calculate the field's derivatives. Since conjugate gradient techniques only need the results of the sensitivity matrix à or its transpose ÃT multiplying a vector, the actual computation of the sensitivity matrix are not performed, according to the methodology described in Zhang (1995). In Zhang (1995), the terms Ãx and ÃTy, are dependent of the stiffness matrix K and its partial derivative ∂K⁄∂ρ. The inversion methodology described in Zhang (1995) is for the case of 3D electrical resistivity by finite differences discretization. So it was necessary to make a series of adjustments to obtain a satisfactory result for 2D electrical inversion using finite element method. The difference between the modeling of 3D resistivity with finite difference and the 2D finite element method are in the integration variable, used in the 2D case. In the 2D case the electrical potential are initially calculated in the transformed domain, including the stiffness matrix, and only in the end is transformed in Cartesian domain. In the case of 3D, described by Zhang (1995) this is done differently, the calculation is done directly in the Cartesian domain. In the literature was not found any work describing how to deal with this problem. Because the calculations of Ãx and ÃTy must be done without having the real stiffness matrix, the adaptation consist in calculate the stiffness matrix and its partial derivative using a set of integration variables. We transform those matrix in the same form has in the potential case, but with different sets of variables. The results will be presented and are very promising.

  11. A nonrecursive order N preconditioned conjugate gradient: Range space formulation of MDOF dynamics

    NASA Technical Reports Server (NTRS)

    Kurdila, Andrew J.

    1990-01-01

    While excellent progress has been made in deriving algorithms that are efficient for certain combinations of system topologies and concurrent multiprocessing hardware, several issues must be resolved to incorporate transient simulation in the control design process for large space structures. Specifically, strategies must be developed that are applicable to systems with numerous degrees of freedom. In addition, the algorithms must have a growth potential in that they must also be amenable to implementation on forthcoming parallel system architectures. For mechanical system simulation, this fact implies that algorithms are required that induce parallelism on a fine scale, suitable for the emerging class of highly parallel processors; and transient simulation methods must be automatically load balancing for a wider collection of system topologies and hardware configurations. These problems are addressed by employing a combination range space/preconditioned conjugate gradient formulation of multi-degree-of-freedom dynamics. The method described has several advantages. In a sequential computing environment, the method has the features that: by employing regular ordering of the system connectivity graph, an extremely efficient preconditioner can be derived from the 'range space metric', as opposed to the system coefficient matrix; because of the effectiveness of the preconditioner, preliminary studies indicate that the method can achieve performance rates that depend linearly upon the number of substructures, hence the title 'Order N'; and the method is non-assembling. Furthermore, the approach is promising as a potential parallel processing algorithm in that the method exhibits a fine parallel granularity suitable for a wide collection of combinations of physical system topologies/computer architectures; and the method is easily load balanced among processors, and does not rely upon system topology to induce parallelism.

  12. Implementation of a conjugate gradient algorithm for thermal diffusivity identification in a moving boundaries system

    NASA Astrophysics Data System (ADS)

    Perez, L.; Autrique, L.; Gillet, M.

    2008-11-01

    The aim of this paper is to investigate the thermal diffusivity identification of a multilayered material dedicated to fire protection. In a military framework, fire protection needs to meet specific requirements, and operational protective systems must be constantly improved in order to keep up with the development of new weapons. In the specific domain of passive fire protections, intumescent coatings can be an effective solution on the battlefield. Intumescent materials have the ability to swell up when they are heated, building a thick multi-layered coating which provides efficient thermal insulation to the underlying material. Due to the heat aggressions (fire or explosion) leading to the intumescent phenomena, high temperatures are considered and prevent from linearization of the mathematical model describing the system state evolution. Previous sensitivity analysis has shown that the thermal diffusivity of the multilayered intumescent coating is a key parameter in order to validate the predictive numerical tool and therefore for thermal protection optimisation. A conjugate gradient method is implemented in order to minimise the quadratic cost function related to the error between predicted temperature and measured temperature. This regularisation algorithm is well adapted for a large number of unknown parameters.

  13. Embedding SAS approach into conjugate gradient algorithms for asymmetric 3D elasticity problems

    SciTech Connect

    Chen, Hsin-Chu; Warsi, N.A.; Sameh, A.

    1996-12-31

    In this paper, we present two strategies to embed the SAS (symmetric-and-antisymmetric) scheme into conjugate gradient (CG) algorithms to make solving 3D elasticity problems, with or without global reflexive symmetry, more efficient. The SAS approach is physically a domain decomposition scheme that takes advantage of reflexive symmetry of discretized physical problems, and algebraically a matrix transformation method that exploits special reflexivity properties of the matrix resulting from discretization. In addition to offering large-grain parallelism, which is valuable in a multiprocessing environment, the SAS scheme also has the potential for reducing arithmetic operations in the numerical solution of a reasonably wide class of scientific and engineering problems. This approach can be applied directly to problems that have global reflexive symmetry, yielding smaller and independent subproblems to solve, or indirectly to problems with partial symmetry, resulting in loosely coupled subproblems. The decomposition is achieved by separating the reflexive subspace from the antireflexive one, possessed by a special class of matrices A, A {element_of} C{sup n x n} that satisfy the relation A = PAP where P is a reflection matrix (symmetric signed permutation matrix).

  14. Appraisal of current density in Very Low Frequency electromagnetic measurements using preconditioned conjugate gradient approach

    NASA Astrophysics Data System (ADS)

    Singh, A.; Sharma, S. P.

    2015-12-01

    We describe the implementation of a new fast imaging technique to invert very low frequency (VLF) data measured on profiles into corresponding apparent current density systems over the 2D earth. First, a formulation has been derived to compute the vertical component of the magnetic field for a given 2D current density distribution in the Earth's subsurface. Since the vertical component of the magnetic field is proportional to the real anomaly of VLF electromagnetic measurement, the derived formulation has been used for imaging subsurface structures. The 2D inversion code incorporating the preconditioned conjugate gradient approach was developed for imaging of the subsurface conductors using the real VLF anomaly in terms of apparent current density distribution in the subsurface. The preconditioner determined by the distances between the cells and the observation points greatly improved the quality of the very low frequency imaging. Finally, we tested our method using synthetic and real data and all tests returned favorable results. The presented formulation were also compared with other imaging techniques in terms of apparent current density and resistivity distribution using a standard numerical forward modeling and inversion technique. The presented imaging technique shows improvement with respect to the filtering approaches in depicting subsurface conductors. Further, results obtained using the presented approach is closer to the results of rigorous resistivity inversion.

  15. Direct reconstruction of cardiac PET kinetic parametric images using a preconditioned conjugate gradient approach

    PubMed Central

    Rakvongthai, Yothin; Ouyang, Jinsong; Guerin, Bastien; Li, Quanzheng; Alpert, Nathaniel M.; El Fakhri, Georges

    2013-01-01

    Purpose: Our research goal is to develop an algorithm to reconstruct cardiac positron emission tomography (PET) kinetic parametric images directly from sinograms and compare its performance with the conventional indirect approach. Methods: Time activity curves of a NCAT phantom were computed according to a one-tissue compartmental kinetic model with realistic kinetic parameters. The sinograms at each time frame were simulated using the activity distribution for the time frame. The authors reconstructed the parametric images directly from the sinograms by optimizing a cost function, which included the Poisson log-likelihood and a spatial regularization terms, using the preconditioned conjugate gradient (PCG) algorithm with the proposed preconditioner. The proposed preconditioner is a diagonal matrix whose diagonal entries are the ratio of the parameter and the sensitivity of the radioactivity associated with parameter. The authors compared the reconstructed parametric images using the direct approach with those reconstructed using the conventional indirect approach. Results: At the same bias, the direct approach yielded significant relative reduction in standard deviation by 12%–29% and 32%–70% for 50 × 106 and 10 × 106 detected coincidences counts, respectively. Also, the PCG method effectively reached a constant value after only 10 iterations (with numerical convergence achieved after 40–50 iterations), while more than 500 iterations were needed for CG. Conclusions: The authors have developed a novel approach based on the PCG algorithm to directly reconstruct cardiac PET parametric images from sinograms, and yield better estimation of kinetic parameters than the conventional indirect approach, i.e., curve fitting of reconstructed images. The PCG method increases the convergence rate of reconstruction significantly as compared to the conventional CG method. PMID:24089922

  16. Preconditioned conjugate gradient wave-front reconstructors for multiconjugate adaptive optics.

    PubMed

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

    2003-09-10

    Multiconjugate adaptive optics (MCAO) systems with 10(4)-10(5) degrees of freedom have been proposed for future giant telescopes. Using standard matrix methods to compute, optimize, and implement wavefront control algorithms for these systems is impractical, since the number of calculations required to compute and apply the reconstruction matrix scales respectively with the cube and the square of the number of adaptive optics degrees of freedom. We develop scalable open-loop iterative sparse matrix implementations of minimum variance wave-front reconstruction for telescope diameters up to 32 m with more than 10(4) actuators. The basic approach is the preconditioned conjugate gradient method with an efficient preconditioner, whose block structure is defined by the atmospheric turbulent layers very much like the layer-oriented MCAO algorithms of current interest. Two cost-effective preconditioners are investigated: a multigrid solver and a simpler block symmetric Gauss-Seidel (BSGS) sweep. Both options require off-line sparse Cholesky factorizations of the diagonal blocks of the matrix system. The cost to precompute these factors scales approximately as the three-halves power of the number of estimated phase grid points per atmospheric layer, and their average update rate is typically of the order of 10(-2) Hz, i.e., 4-5 orders of magnitude lower than the typical 10(3) Hz temporal sampling rate. All other computations scale almost linearly with the total number of estimated phase grid points. We present numerical simulation results to illustrate algorithm convergence. Convergence rates of both preconditioners are similar, regardless of measurement noise level, indicating that the layer-oriented BSGS sweep is as effective as the more elaborated multiresolution preconditioner. PMID:14503692

  17. Preconditioned conjugate gradient wave-front reconstructors for multiconjugate adaptive optics

    NASA Astrophysics Data System (ADS)

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

    2003-09-01

    Multiconjugate adaptive optics (MCAO) systems with 104-105 degrees of freedom have been proposed for future giant telescopes. Using standard matrix methods to compute, optimize, and implement wave-front control algorithms for these systems is impractical, since the number of calculations required to compute and apply the reconstruction matrix scales respectively with the cube and the square of the number of adaptive optics degrees of freedom. We develop scalable open-loop iterative sparse matrix implementations of minimum variance wave-front reconstruction for telescope diameters up to 32 m with more than 104 actuators. The basic approach is the preconditioned conjugate gradient method with an efficient preconditioner, whose block structure is defined by the atmospheric turbulent layers very much like the layer-oriented MCAO algorithms of current interest. Two cost-effective preconditioners are investigated: a multigrid solver and a simpler block symmetric Gauss-Seidel (BSGS) sweep. Both options require off-line sparse Cholesky factorizations of the diagonal blocks of the matrix system. The cost to precompute these factors scales approximately as the three-halves power of the number of estimated phase grid points per atmospheric layer, and their average update rate is typically of the order of 10-2 Hz, i.e., 4-5 orders of magnitude lower than the typical 103 Hz temporal sampling rate. All other computations scale almost linearly with the total number of estimated phase grid points. We present numerical simulation results to illustrate algorithm convergence. Convergence rates of both preconditioners are similar, regardless of measurement noise level, indicating that the layer-oriented BSGS sweep is as effective as the more elaborated multiresolution preconditioner.

  18. Non-linear Conjugate Gradient Time-Domain Controlled Inversion Source

    SciTech Connect

    Newman, Gregory A.; Commer, Michael

    2006-11-16

    Software that simulates and inverts time-domain electromagnetic field data for subsurface electrical properties (electrical conductivity) of geological media. The software treats data produced by a step-wise source signal from either galvanic (grounded wires) or inductive (magnetic loops) sources. The inversion process is carried inductive (magnetic loops) sources. The inversion process is carried out using a non-linear conjugate gradient optimization scheme, which minimizes the misfit between field data and model data using a least squares criteria. The software is an upgrade from the code TEM3D ver. 2.0. The upgrade includes the following components: (1) Improved (faster)memory access during gradient computation. (2) Data parellelization scheme: Multiple transmitters (sources) can be distributed accross several banks of processors (daa-planes). Similarly, the receivers of each source are also distributed accross the corresponding data-plane. (3) Improved data-IO.

  19. Non-linear Conjugate Gradient Time-Domain Controlled Inversion Source

    Energy Science and Technology Software Center (ESTSC)

    2006-11-16

    Software that simulates and inverts time-domain electromagnetic field data for subsurface electrical properties (electrical conductivity) of geological media. The software treats data produced by a step-wise source signal from either galvanic (grounded wires) or inductive (magnetic loops) sources. The inversion process is carried inductive (magnetic loops) sources. The inversion process is carried out using a non-linear conjugate gradient optimization scheme, which minimizes the misfit between field data and model data using a least squares criteria.more » The software is an upgrade from the code TEM3D ver. 2.0. The upgrade includes the following components: (1) Improved (faster)memory access during gradient computation. (2) Data parellelization scheme: Multiple transmitters (sources) can be distributed accross several banks of processors (daa-planes). Similarly, the receivers of each source are also distributed accross the corresponding data-plane. (3) Improved data-IO.« less

  20. Method for synthesizing peptides with saccharide linked enzyme polymer conjugates

    DOEpatents

    Callstrom, M.R.; Bednarski, M.D.; Gruber, P.R.

    1997-06-17

    A method is disclosed for synthesizing peptides using water soluble enzyme polymer conjugates. The method comprises catalyzing the peptide synthesis with enzyme which has been covalently bonded to a polymer through at least three linkers which linkers have three or more hydroxyl groups. The enzyme is conjugated at lysines or arginines. 19 figs.

  1. Method for synthesizing peptides with saccharide linked enzyme polymer conjugates

    DOEpatents

    Callstrom, Matthew R.; Bednarski, Mark D.; Gruber, Patrick R.

    1997-01-01

    A method is disclosed for synthesizing peptides using water soluble enzyme polymer conjugates. The method comprises catalyzing the peptide synthesis with enzyme which has been covalently bonded to a polymer through at least three linkers which linkers have three or more hydroxyl groups. The enzyme is conjugated at lysines or arginines.

  2. Preconditioned conjugate gradient technique for the analysis of symmetric anisotropic structures

    NASA Technical Reports Server (NTRS)

    Noor, Ahmed K.; Peters, Jeanne M.

    1987-01-01

    An efficient preconditioned conjugate gradient (PCG) technique and a computational procedure are presented for the analysis of symmetric anisotropic structures. The technique is based on selecting the preconditioning matrix as the orthotropic part of the global stiffness matrix of the structure, with all the nonorthotropic terms set equal to zero. This particular choice of the preconditioning matrix results in reducing the size of the analysis model of the anisotropic structure to that of the corresponding orthotropic structure. The similarities between the proposed PCG technique and a reduction technique previously presented by the authors are identified and exploited to generate from the PCG technique direct measures for the sensitivity of the different response quantities to the nonorthotropic (anisotropic) material coefficients of the structure. The effectiveness of the PCG technique is demonstrated by means of a numerical example of an anisotropic cylindrical panel.

  3. A projected preconditioned conjugate gradient algorithm for computing many extreme eigenpairs of a Hermitian matrix

    SciTech Connect

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

    2015-06-01

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

  4. Parallel conjugate gradient: effects of ordering strategies, programming paradigms, and architectural platforms

    SciTech Connect

    Oliker, L.; Li, X.; Heber, G.; Biswas, R.

    2000-05-01

    The Conjugate Gradient (CG) algorithm is perhaps the best-known iterative technique to solve sparse linear systems that are symmetric and positive definite. A sparse matrix-vector multiply (SPMV) usually accounts for most of the floating-point operations with a CG iteration. In this paper, we investigate the effects of various ordering and partitioning strategies on the performance of parallel CG and SPMV using different programming and architectures. Results show that for this class of applications, ordering significantly improves overall performance, that cache reuse may be more important than reducing communication, and that it is possible to achieve message passing performance using shared memory constructs through careful data ordering and distribution. However, a multithreaded implementation of CG on the Tera MTA does not require special ordering or partitioning to obtain high efficiency and scalability.

  5. Parallel Conjugate Gradient: Effects of Ordering Strategies, Programming Paradigms, and Architectural Platforms

    NASA Technical Reports Server (NTRS)

    Oliker, Leonid; Heber, Gerd; Biswas, Rupak

    2000-01-01

    The Conjugate Gradient (CG) algorithm is perhaps the best-known iterative technique to solve sparse linear systems that are symmetric and positive definite. A sparse matrix-vector multiply (SPMV) usually accounts for most of the floating-point operations within a CG iteration. In this paper, we investigate the effects of various ordering and partitioning strategies on the performance of parallel CG and SPMV using different programming paradigms and architectures. Results show that for this class of applications, ordering significantly improves overall performance, that cache reuse may be more important than reducing communication, and that it is possible to achieve message passing performance using shared memory constructs through careful data ordering and distribution. However, a multi-threaded implementation of CG on the Tera MTA does not require special ordering or partitioning to obtain high efficiency and scalability.

  6. A conjugate gradient algorithm for the astrometric core solution of Gaia

    NASA Astrophysics Data System (ADS)

    Bombrun, A.; Lindegren, L.; Hobbs, D.; Holl, B.; Lammers, U.; Bastian, U.

    2012-02-01

    Context. The ESA space astrometry mission Gaia, planned to be launched in 2013, has been designed to make angular measurements on a global scale with micro-arcsecond accuracy. A key component of the data processing for Gaia is the astrometric core solution, which must implement an efficient and accurate numerical algorithm to solve the resulting, extremely large least-squares problem. The Astrometric Global Iterative Solution (AGIS) is a framework that allows to implement a range of different iterative solution schemes suitable for a scanning astrometric satellite. Aims: Our aim is to find a computationally efficient and numerically accurate iteration scheme for the astrometric solution, compatible with the AGIS framework, and a convergence criterion for deciding when to stop the iterations. Methods: We study an adaptation of the classical conjugate gradient (CG) algorithm, and compare it to the so-called simple iteration (SI) scheme that was previously known to converge for this problem, although very slowly. The different schemes are implemented within a software test bed for AGIS known as AGISLab. This allows to define, simulate and study scaled astrometric core solutions with a much smaller number of unknowns than in AGIS, and therefore to perform a large number of numerical experiments in a reasonable time. After successful testing in AGISLab, the CG scheme has been implemented also in AGIS. Results: The two algorithms CG and SI eventually converge to identical solutions, to within the numerical noise (of the order of 0.00001 micro-arcsec). These solutions are moreover independent of the starting values (initial star catalogue), and we conclude that they are equivalent to a rigorous least-squares estimation of the astrometric parameters. The CG scheme converges up to a factor four faster than SI in the tested cases, and in particular spatially correlated truncation errors are much more efficiently damped out with the CG scheme. While it appears to be difficult

  7. A conjugate gradients/trust regions algorithms for training multilayer perceptrons for nonlinear mapping

    NASA Technical Reports Server (NTRS)

    Madyastha, Raghavendra K.; Aazhang, Behnaam; Henson, Troy F.; Huxhold, Wendy L.

    1992-01-01

    This paper addresses the issue of applying a globally convergent optimization algorithm to the training of multilayer perceptrons, a class of Artificial Neural Networks. The multilayer perceptrons are trained towards the solution of two highly nonlinear problems: (1) signal detection in a multi-user communication network, and (2) solving the inverse kinematics for a robotic manipulator. The research is motivated by the fact that a multilayer perceptron is theoretically capable of approximating any nonlinear function to within a specified accuracy. The algorithm that has been employed in this study combines the merits of two well known optimization algorithms, the Conjugate Gradients and the Trust Regions Algorithms. The performance is compared to a widely used algorithm, the Backpropagation Algorithm, that is basically a gradient-based algorithm, and hence, slow in converging. The performances of the two algorithms are compared with the convergence rate. Furthermore, in the case of the signal detection problem, performances are also benchmarked by the decision boundaries drawn as well as the probability of error obtained in either case.

  8. The U.S. Geological Survey Modular Ground-Water Model - PCGN: A Preconditioned Conjugate Gradient Solver with Improved Nonlinear Control

    USGS Publications Warehouse

    Naff, Richard L.; Banta, Edward R.

    2008-01-01

    The preconditioned conjugate gradient with improved nonlinear control (PCGN) package provides addi-tional means by which the solution of nonlinear ground-water flow problems can be controlled as compared to existing solver packages for MODFLOW. Picard iteration is used to solve nonlinear ground-water flow equations by iteratively solving a linear approximation of the nonlinear equations. The linear solution is provided by means of the preconditioned conjugate gradient algorithm where preconditioning is provided by the modi-fied incomplete Cholesky algorithm. The incomplete Cholesky scheme incorporates two levels of fill, 0 and 1, in which the pivots can be modified so that the row sums of the preconditioning matrix and the original matrix are approximately equal. A relaxation factor is used to implement the modified pivots, which determines the degree of modification allowed. The effects of fill level and degree of pivot modification are briefly explored by means of a synthetic, heterogeneous finite-difference matrix; results are reported in the final section of this report. The preconditioned conjugate gradient method is coupled with Picard iteration so as to efficiently solve the nonlinear equations associated with many ground-water flow problems. The description of this coupling of the linear solver with Picard iteration is a primary concern of this document.

  9. A direct MP2 gradient method

    NASA Astrophysics Data System (ADS)

    Frisch, Michael J.; Head-Gordon, Martin; Pople, John A.

    1990-02-01

    We present a direct method for evaluating the gradient of the second-order Møller-Plesset (MP2) energy without storing any quartic quantities, such as two-electron repulsion integrals (ERIs), double substitution amplitudes or the two-particle density matrix. For an N-basis-function calculation, N3 memory is required, and the ERIs and their first derivatives are computed up to O (number of occupied orbitals) times, plus additional ERI evaluations to obtain the Hartree-Fock (HF) orbitals and solve the coupled perturbed HF equation. Larger amounts of memory are used to reduce the O evaluations in the MP2 step. The floating point operation count is still proportional to ON4, as in conventional MP2 gradient codes since ERI evaluation is just an N4 step. Illustrative calculations are reported to assess the performance of the algorithm.

  10. Methods to Design and Synthesize Antibody-Drug Conjugates (ADCs)

    PubMed Central

    Yao, Houzong; Jiang, Feng; Lu, Aiping; Zhang, Ge

    2016-01-01

    Antibody-drug conjugates (ADCs) have become a promising targeted therapy strategy that combines the specificity, favorable pharmacokinetics and biodistributions of antibodies with the destructive potential of highly potent drugs. One of the biggest challenges in the development of ADCs is the application of suitable linkers for conjugating drugs to antibodies. Recently, the design and synthesis of linkers are making great progress. In this review, we present the methods that are currently used to synthesize antibody-drug conjugates by using thiols, amines, alcohols, aldehydes and azides. PMID:26848651

  11. The application of projected conjugate gradient solvers on graphical processing units

    SciTech Connect

    Lin, Youzuo; Renaut, Rosemary

    2011-01-26

    Graphical processing units introduce the capability for large scale computation at the desktop. Presented numerical results verify that efficiencies and accuracies of basic linear algebra subroutines of all levels when implemented in CUDA and Jacket are comparable. But experimental results demonstrate that the basic linear algebra subroutines of level three offer the greatest potential for improving efficiency of basic numerical algorithms. We consider the solution of the multiple right hand side set of linear equations using Krylov subspace-based solvers. Thus, for the multiple right hand side case, it is more efficient to make use of a block implementation of the conjugate gradient algorithm, rather than to solve each system independently. Jacket is used for the implementation. Furthermore, including projection from one system to another improves efficiency. A relevant example, for which simulated results are provided, is the reconstruction of a three dimensional medical image volume acquired from a positron emission tomography scanner. Efficiency of the reconstruction is improved by using projection across nearby slices.

  12. Conjugate heat transfer with the entropic lattice Boltzmann method.

    PubMed

    Pareschi, G; Frapolli, N; Chikatamarla, S S; Karlin, I V

    2016-07-01

    A conjugate heat-transfer model is presented based on the two-population entropic lattice Boltzmann method. The present approach relies on the extension of Grad's boundary conditions to the two-population model for thermal flows, as well as on the appropriate exact conjugate heat-transfer condition imposed at the fluid-solid interface. The simplicity and efficiency of the lattice Boltzmann method (LBM), and in particular of the entropic multirelaxation LBM, are retained in the present approach, thus enabling simulations of turbulent high Reynolds number flows and complex wall boundaries. The model is validated by means of two-dimensional parametric studies of various setups, including pure solid conduction, conjugate heat transfer with a backward-facing step flow, and conjugate heat transfer with the flow past a circular heated cylinder. Further validations are performed in three dimensions for the case of a turbulent flow around a heated mounted cube. PMID:27575234

  13. Conjugate heat transfer with the entropic lattice Boltzmann method

    NASA Astrophysics Data System (ADS)

    Pareschi, G.; Frapolli, N.; Chikatamarla, S. S.; Karlin, I. V.

    2016-07-01

    A conjugate heat-transfer model is presented based on the two-population entropic lattice Boltzmann method. The present approach relies on the extension of Grad's boundary conditions to the two-population model for thermal flows, as well as on the appropriate exact conjugate heat-transfer condition imposed at the fluid-solid interface. The simplicity and efficiency of the lattice Boltzmann method (LBM), and in particular of the entropic multirelaxation LBM, are retained in the present approach, thus enabling simulations of turbulent high Reynolds number flows and complex wall boundaries. The model is validated by means of two-dimensional parametric studies of various setups, including pure solid conduction, conjugate heat transfer with a backward-facing step flow, and conjugate heat transfer with the flow past a circular heated cylinder. Further validations are performed in three dimensions for the case of a turbulent flow around a heated mounted cube.

  14. On the applicability of fragmentation methods to conjugated π systems within density functional framework

    NASA Astrophysics Data System (ADS)

    Yeole, Sachin D.; Gadre, Shridhar R.

    2010-03-01

    For the accurate ab initio treatment of large molecular systems, linear scaling methods (LSMs) have been devised and successfully applied to covalently bonded systems as well as to those involving weak intra/intermolecular bonds. Very few attempts to apply LSM to highly conjugated molecules, especially to two-dimensional systems, have so far been reported in the literature. The present article examines the applicability of a LSM, viz., molecular tailoring approach (MTA), to π-conjugated systems within density functional theory. A few test cases within second order Møller-Plesset framework are also reported. MTA is applied to some one-dimensional π-conjugated molecules, for which the difference between MTA energy and actual energy is found out to be less than 1 mhartree and also reduced computation time as well as hardware requirements. The method is also extended to some small/medium-sized two-dimensional π-conjugated molecules by developing a systematic algorithm for tailoring such systems. However, for such systems, although the energies are in error by a few millihartrees, gradients are found to match reasonably well their actual counterparts. Hence, geometry optimization of these systems within MTA framework is attempted. The geometries thus generated are found to be in good agreement with their actual counterparts, with the actual single point energies matching within 1 mhartree, along with reduced computational effort. These results point toward the potential applicability of MTA to large two- and three-dimensional π-conjugated systems.

  15. Multigrid preconditioned conjugate gradients for the numerical simulation of groundwater flow on the Cray T3D

    SciTech Connect

    Ashby, S.F.; Falgout, R.D.; Smith, S.G.; Fogwell, T.W.

    1994-09-01

    This paper discusses the numerical simulation of groundwater flow through heterogeneous porous media. The focus is on the performance of a parallel multigrid preconditioner for accelerating convergence of conjugate gradients, which is used to compute the hydraulic pressure head. The numerical investigation considers the effects of enlarging the domain, increasing the grid resolution, and varying the geostatistical parameters used to define the subsurface realization. The results were obtained using the PARFLOW groundwater flow simulator on the Cray T3D massively parallel computer.

  16. A new solver for the elastic normal contact problem using conjugate gradients, deflation, and an FFT-based preconditioner

    NASA Astrophysics Data System (ADS)

    Vollebregt, E. A. H.

    2014-01-01

    This paper presents our new solver BCCG+FAI for solving elastic normal contact problems. This is a comprehensible approach that is based on the Conjugate Gradients (CG) algorithm and that uses FFTs. A first novel aspect is the definition of the “FFT-based Approximate Inverse” preconditioner. The underlying idea is that the inverse matrix can be approximated well using a Toeplitz or block-Toeplitz form, which can be computed using the FFT of the original matrix elements. This preconditioner makes the total number of CG iterations effectively constant in 2D and very slowly increasing in 3D problems. A second novelty is how we deal with a prescribed total force. This uses a deflation technique in such a way that CGs convergence and finite termination properties are maintained. Numerical results show that this solver is more effective than existing CG-based strategies, such that it can compete with Multi-Grid strategies over a much larger problem range. In our opinion it could be the new method of choice because of its simple structure and elegant theory, and because robust performance is achieved independently of any problem specific parameters.

  17. A method for easily customizable gradient gel electrophoresis.

    PubMed

    Miller, Andrew J; Roman, Brandon; Norstrom, Eric

    2016-09-15

    Gradient polyacrylamide gel electrophoresis is a powerful tool for the resolution of polypeptides by relative mobility. Here, we present a simplified method for generating polyacrylamide gradient gels for routine analysis without the need for specialized mixing equipment. The method allows for easily customizable gradients which can be optimized for specific polypeptide resolution requirements. Moreover, the method eliminates the possibility of buffer cross contamination in mixing equipment, and the time and resources saved with this method in place of traditional gradient mixing, or the purchase of pre-cast gels, are noteworthy given the frequency with which many labs use gradient gel SDS-PAGE. PMID:27393767

  18. A nonrecursive 'Order N' preconditioned conjugate gradient/range space formulation of MDOF dynamics

    NASA Technical Reports Server (NTRS)

    Kurdila, A. J.; Menon, R.; Sunkel, John

    1991-01-01

    This paper addresses the requirements of present-day mechanical system simulations of algorithms that induce parallelism on a fine scale and of transient simulation methods which must be automatically load balancing for a wide collection of system topologies and hardware configurations. To this end, a combination range space/preconditioned conjugage gradient formulation of multidegree-of-freedon dynamics is developed, which, by employing regular ordering of the system connectivity graph, makes it possible to derive an extremely efficient preconditioner from the range space metric (as opposed to the system coefficient matrix). Because of the effectiveness of the preconditioner, the method can achieve performance rates that depend linearly on the number of substructures. The method, termed 'Order N' does not require the assembly of system mass or stiffness matrices, and is therefore amenable to implementation on work stations. Using this method, a 13-substructure model of the Space Station was constructed.

  19. CPDES2: A preconditioned conjugate gradient solver for linear asymmetric matrix equations arising from coupled partial differential equations in two dimensions

    NASA Astrophysics Data System (ADS)

    Anderson, D. V.; Koniges, A. E.; Shumaker, D. E.

    1988-11-01

    Many physical problems require the solution of coupled partial differential equations on two-dimensional domains. When the time scales of interest dictate an implicit discretization of the equations a rather complicated global matrix system needs solution. The exact form of the matrix depends on the choice of spatial grids and on the finite element or finite difference approximations employed. CPDES2 allows each spatial operator to have 5 or 9 point stencils and allows for general couplings between all of the component PDE's and it automatically generates the matrix structures needed to perform the algorithm. The resulting sparse matrix equation is solved by either the preconditioned conjugate gradient (CG) method or by the preconditioned biconjugate gradient (BCG) algorithm. An arbitrary number of component equations are permitted only limited by available memory. In the sub-band representation used, we generate an algorithm that is written compactly in terms of indirect indices which is vectorizable on some of the newer scientific computers.

  20. Conjugate gradient determination of optimal plane changes for a class of three-impulse transfers between noncoplanar circular orbits

    NASA Technical Reports Server (NTRS)

    Burrows, R. R.

    1972-01-01

    A particular type of three-impulse transfer between two circular orbits is analyzed. The possibility of three plane changes is recognized, and the problem is to optimally distribute these plane changes to minimize the sum of the individual impulses. Numerical difficulties and their solution are discussed. Numerical results obtained from a conjugate gradient technique are presented for both the case where the individual plane changes are unconstrained and for the case where they are constrained. Possibly not unexpectedly, multiple minima are found. The techniques presented could be extended to the finite burn case, but primarily the contents are addressed to preliminary mission design and vehicle sizing.

  1. One-Step Conjugation Method for Site-Specific Antibody-Drug Conjugates through Reactive Cysteine-Engineered Antibodies.

    PubMed

    Shinmi, Daisuke; Taguchi, Eri; Iwano, Junko; Yamaguchi, Tsuyoshi; Masuda, Kazuhiro; Enokizono, Junichi; Shiraishi, Yasuhisa

    2016-05-18

    Engineered cysteine residues are particularly convenient for site-specific conjugation of antibody-drug conjugates (ADC), because no cell engineering and additives are required. Usually, unpaired cysteine residues form mixed disulfides during fermentation in Chinese hamster ovarian (CHO) cells; therefore, additional reduction and oxidization steps are required prior to conjugation. In this study, we prepared light chain (Lc)-Q124C variants in IgG and examined the conjugation efficiency. Intriguingly, Lc-Q124C exhibited high thiol reactivity and directly generated site-specific ADC without any pretreatment (named active thiol antibody: Actibody). Most of the cysteine-maleimide conjugates including Lc-Q124C showed retro-Michael reaction with cysteine 34 in albumin and were decomposed over time. In order to acquire resistance to a maleimide exchange reaction, the facile procedure for succinimide hydrolysis on anion exchange resin was employed. Hydrolyzed Lc-Q124C conjugate prepared with anion exchange procedure retained high stability in plasma. Recently, various stable linkage schemes for cysteine conjugation have been reported. The combination with direct conjugation by the use of Actibody and stable linker technology could enable the generation of stable site-specific ADC through a simple method. Actibody technology with Lc-Q124C at a less exposed position opens a new path for cysteine-based conjugation, and contributes to reducing entry barriers to the preparation and evaluation of ADC. PMID:27074832

  2. Multi-gradient drilling method and system

    DOEpatents

    Maurer, William C.; Medley, Jr., George H.; McDonald, William J.

    2003-01-01

    A multi-gradient system for drilling a well bore from a surface location into a seabed includes an injector for injecting buoyant substantially incompressible articles into a column of drilling fluid associated with the well bore. Preferably, the substantially incompressible articles comprises hollow substantially spherical bodies.

  3. WARP3D-Release 10.8: Dynamic Nonlinear Analysis of Solids using a Preconditioned Conjugate Gradient Software Architecture

    NASA Technical Reports Server (NTRS)

    Koppenhoefer, Kyle C.; Gullerud, Arne S.; Ruggieri, Claudio; Dodds, Robert H., Jr.; Healy, Brian E.

    1998-01-01

    This report describes theoretical background material and commands necessary to use the WARP3D finite element code. WARP3D is under continuing development as a research code for the solution of very large-scale, 3-D solid models subjected to static and dynamic loads. Specific features in the code oriented toward the investigation of ductile fracture in metals include a robust finite strain formulation, a general J-integral computation facility (with inertia, face loading), an element extinction facility to model crack growth, nonlinear material models including viscoplastic effects, and the Gurson-Tver-gaard dilatant plasticity model for void growth. The nonlinear, dynamic equilibrium equations are solved using an incremental-iterative, implicit formulation with full Newton iterations to eliminate residual nodal forces. The history integration of the nonlinear equations of motion is accomplished with Newmarks Beta method. A central feature of WARP3D involves the use of a linear-preconditioned conjugate gradient (LPCG) solver implemented in an element-by-element format to replace a conventional direct linear equation solver. This software architecture dramatically reduces both the memory requirements and CPU time for very large, nonlinear solid models since formation of the assembled (dynamic) stiffness matrix is avoided. Analyses thus exhibit the numerical stability for large time (load) steps provided by the implicit formulation coupled with the low memory requirements characteristic of an explicit code. In addition to the much lower memory requirements of the LPCG solver, the CPU time required for solution of the linear equations during each Newton iteration is generally one-half or less of the CPU time required for a traditional direct solver. All other computational aspects of the code (element stiffnesses, element strains, stress updating, element internal forces) are implemented in the element-by- element, blocked architecture. This greatly improves

  4. Gradient porous hydroxyapatite ceramics fabricated by freeze casting method

    NASA Astrophysics Data System (ADS)

    Zuo, Kai-hui; zhang, Yuan; Jiang, Dongliang; Zeng, Yu-Ping

    2011-04-01

    By controlling the cooling rates and the composition of slurries, the gradient porous hydroxyapatite ceramics are fabricated by the freeze casting method. According to the different cooling rate, the pores of HAP ceramics fabricated by gradient freeze casting are divided into three parts: one is lamellar pores, another is column pore and the last one is fine round pores. The laminated freeze casting is in favour of obtaining the gradient porous ceramics composed of different materials and the ceramics have unclear interfaces.

  5. Methods for calculating conjugate problems of heat transfer

    NASA Astrophysics Data System (ADS)

    Kalinin, E. K.; Dreitser, G. A.; Kostiuk, V. V.; Berlin, I. I.

    Methods are examined for calculating various conjugate problems of heat transfer in channels and closed vessels in cases of single-phase and two-phase flow in steady and unsteady conditions. The single-phase-flow studies involve the investigation of gaseous and liquid heat-carriers in pipes, annular and plane channels, and pipe bundles in cases of cooling and heating. General relationships are presented for heat transfer in cases of film, transition, and nucleate boiling, as well as for boiling crises. Attention is given to methods for analyzing the filling and cooling of conduits and tanks by cryogenic liquids; and ways to intensify heat transfer in these conditions are examined.

  6. Rationally Engineering Phototherapy Modules of Eosin-Conjugated Responsive Polymeric Nanocarriers via Intracellular Endocytic pH Gradients.

    PubMed

    Liu, Guhuan; Hu, Jinming; Zhang, Guoying; Liu, Shiyong

    2015-07-15

    Spatiotemporal switching of respective phototherapy modes at the cellular level with minimum side effects and high therapeutic efficacy is a major challenge for cancer phototherapy. Herein we demonstrate how to address this issue by employing photosensitizer-conjugated pH-responsive block copolymers in combination with intracellular endocytic pH gradients. At neutral pH corresponding to extracellular and cytosol milieu, the copolymers self-assemble into micelles with prominently quenched fluorescence emission and low (1)O2 generation capability, favoring a highly efficient photothermal module. Under mildly acidic pH associated with endolysosomes, protonation-triggered micelle-to-unimer transition results in recovered emission and enhanced photodynamic (1)O2 efficiency, which synergistically actuates release of encapsulated drugs, endosomal escape, and photochemical internalization processes. PMID:25514473

  7. Efficient algorithms for the recognition of topologically conjugate gradient-like diffeomorhisms

    NASA Astrophysics Data System (ADS)

    Grines, Vyacheslav Z.; Malyshev, Dmitry S.; Pochinka, Olga V.; Zinina, Svetlana Kh.

    2016-03-01

    It is well known that the topological classification of structurally stable flows on surfaces as well as the topological classification of some multidimensional gradient-like systems can be reduced to a combinatorial problem of distinguishing graphs up to isomorphism. The isomorphism problem of general graphs obviously can be solved by a standard enumeration algorithm. However, an efficient algorithm (i. e., polynomial in the number of vertices) has not yet been developed for it, and the problem has not been proved to be intractable (i. e., NPcomplete). We give polynomial-time algorithms for recognition of the corresponding graphs for two gradient-like systems. Moreover, we present efficient algorithms for determining the orientability and the genus of the ambient surface. This result, in particular, sheds light on the classification of configurations that arise from simple, point-source potential-field models in efforts to determine the nature of the quiet-Sun magnetic field.

  8. Adaptive method of realizing natural gradient learning for multilayer perceptrons.

    PubMed

    Amari, S; Park, H; Fukumizu, K

    2000-06-01

    The natural gradient learning method is known to have ideal performances for on-line training of multilayer perceptrons. It avoids plateaus, which give rise to slow convergence of the backpropagation method. It is Fisher efficient, whereas the conventional method is not. However, for implementing the method, it is necessary to calculate the Fisher information matrix and its inverse, which is practically very difficult. This article proposes an adaptive method of directly obtaining the inverse of the Fisher information matrix. It generalizes the adaptive Gauss-Newton algorithms and provides a solid theoretical justification of them. Simulations show that the proposed adaptive method works very well for realizing natural gradient learning. PMID:10935719

  9. Preconditioned conjugate residual methods for the solution of spectral equations

    NASA Technical Reports Server (NTRS)

    Wong, Y. S.; Zang, T. A.; Hussaini, M. Y.

    1986-01-01

    Conjugate residual methods for the solution of spectral equations are described. An inexact finite-difference operator is introduced as a preconditioner in the iterative procedures. Application of these techniques is limited to problems for which the symmetric part of the coefficient matrix is positive definite. Although the spectral equation is a very ill-conditioned and full matrix problem, the computational effort of the present iterative methods for solving such a system is comparable to that for the sparse matrix equations obtained from the application of either finite-difference or finite-element methods to the same problems. Numerical experiments are shown for a self-adjoint elliptic partial differential equation with Dirichlet boundary conditions, and comparison with other solution procedures for spectral equations is presented.

  10. Counter-extrapolation method for conjugate interfaces in computational heat and mass transfer.

    PubMed

    Le, Guigao; Oulaid, Othmane; Zhang, Junfeng

    2015-03-01

    In this paper a conjugate interface method is developed by performing extrapolations along the normal direction. Compared to other existing conjugate models, our method has several technical advantages, including the simple and straightforward algorithm, accurate representation of the interface geometry, applicability to any interface-lattice relative orientation, and availability of the normal gradient. The model is validated by simulating the steady and unsteady convection-diffusion system with a flat interface and the steady diffusion system with a circular interface, and good agreement is observed when comparing the lattice Boltzmann results with respective analytical solutions. A more general system with unsteady convection-diffusion process and a curved interface, i.e., the cooling process of a hot cylinder in a cold flow, is also simulated as an example to illustrate the practical usefulness of our model, and the effects of the cylinder heat capacity and thermal diffusivity on the cooling process are examined. Results show that the cylinder with a larger heat capacity can release more heat energy into the fluid and the cylinder temperature cools down slower, while the enhanced heat conduction inside the cylinder can facilitate the cooling process of the system. Although these findings appear obvious from physical principles, the confirming results demonstrates the application potential of our method in more complex systems. In addition, the basic idea and algorithm of the counter-extrapolation procedure presented here can be readily extended to other lattice Boltzmann models and even other computational technologies for heat and mass transfer systems. PMID:25871245

  11. DFT methods for conjugated materials: From benchmarks to functionals

    NASA Astrophysics Data System (ADS)

    Sears, John; Bredas, Jean-Luc

    2012-02-01

    From a theoretical standpoint, many of the problems of interest in the study of pi-conjugated materials for organic electronics applications pose a particular challenge for many modern density functional theory methods. Systematic errors have been observed, for instance, in the description of charge-transfer excitations at donor/acceptor interfaces, in linear and non-linear polarizabilites, as well as in the geometric and electronic properties of conjugated polymers [1,2]. We will discuss recent results in our lab aimed at: (i) understanding the sources of error for some of these problems; (ii) addressing these errors using tuned long-range corrected functionals; and (iii) using these results to guide the development of state-of-the-art methodologies in a new open-source DFT code. [4pt] [1] J. S. Sears, T. Korzdorfer, C. R. Zhang, and J. L. Bredas, J. Chem. Phys. 135 151103 (2011)[0pt] [2] T. Korzdorfer, J. S. Sears, C. Sutton, and J. L. Bredas, J. Chem. Phys., accepted.

  12. Multivalent display of DNA conjugates on semiconductor quantum dots utilizing a novel conjugation method

    NASA Astrophysics Data System (ADS)

    Prasuhn, Duane E.; Blanco-Canosa, Juan B.; Vora, Gary J.; Mattoussi, Hedi M.; Dawson, Philip E.; Medintz, Igor L.

    2009-02-01

    One of the most prominent research areas in nanotechnology is the development of nanoparticle systems for biomedical applications. This is founded upon the expectation that such species could ultimately be imbued with multiple simultaneous functions, such as the presentation of a therapeutic payload or diagnostic sensor for in vivo trafficking to desired cell types. In recent years, semiconductor quantum dots (QDs) have been actively explored as novel display systems, because of their unique photophysical properties. Using an aniline-mediated hydrazone coupling, a polyhisitidine-appended peptide was derivatized with a DNA strand and successfully self-assembled to QDs, yielding nanoparticles displaying up to approximately 15 peptide/DNA conjugates. This ligation method is a viable chemistry for displaying biomolecules, because of the orthogonality of the ketone and hydrazine moieties to most biological functionality and the reaction can be performed under mild conditions in aqueous media. The modified QDs were further characterized by gel electrophoresis, and microarray studies; showing the self-assembly was successful and the DNA strands were still available for hybridization with a complement sequence.

  13. CPDES3: A preconditioned conjugate gradient solver for linear asymmetric matrix equations arising from coupled partial differential equations in three dimensions

    NASA Astrophysics Data System (ADS)

    Anderson, D. V.; Koniges, A. E.; Shumaker, D. E.

    1988-11-01

    Many physical problems require the solution of coupled partial differential equations on three-dimensional domains. When the time scales of interest dictate an implicit discretization of the equations a rather complicated global matrix system needs solution. The exact form of the matrix depends on the choice of spatial grids and on the finite element or finite difference approximations employed. CPDES3 allows each spatial operator to have 7, 15, 19, or 27 point stencils and allows for general couplings between all of the component PDE's and it automatically generates the matrix structures needed to perform the algorithm. The resulting sparse matrix equation is solved by either the preconditioned conjugate gradient (CG) method or by the preconditioned biconjugate gradient (BCG) algorithm. An arbitrary number of component equations are permitted only limited by available memory. In the sub-band representation used, we generate an algorithm that is written compactly in terms of indirect induces which is vectorizable on some of the newer scientific computers.

  14. Water-soluble luminescent quantum dots and biomolecular conjugates thereof and related compositions and method of use

    DOEpatents

    Nie, Shuming; Chan, Warren C. W.; Emory, Steven R.

    2002-01-01

    The present invention provides a water-soluble luminescent quantum dot, a biomolecular conjugate thereof and a composition comprising such a quantum dot or conjugate. Additionally, the present invention provides a method of obtaining a luminescent quantum dot, a method of making a biomolecular conjugate thereof, and methods of using a biomolecular conjugate for ultrasensitive nonisotopic detection in vitro and in vivo.

  15. Water-soluble luminescent quantum dots and biomolecular conjugates thereof and related compositions and methods of use

    DOEpatents

    Nie, Shuming; Chan, Warren C. W.; Emory, Stephen

    2007-03-20

    The present invention provides a water-soluble luminescent quantum dot, a biomolecular conjugate thereof and a composition comprising such a quantum dot or conjugate. Additionally, the present invention provides a method of obtaining a luminescent quantum dot, a method of making a biomolecular conjugate thereof, and methods of using a biomolecular conjugate for ultrasensitive nonisotopic detection in vitro and in vivo.

  16. A composite step conjugate gradients squared algorithm for solving nonsymmetric linear systems

    NASA Astrophysics Data System (ADS)

    Chan, Tony; Szeto, Tedd

    1994-03-01

    We propose a new and more stable variant of the CGS method [27] for solving nonsymmetric linear systems. The method is based on squaring the Composite Step BCG method, introduced recently by Bank and Chan [1,2], which itself is a stabilized variant of BCG in that it skips over steps for which the BCG iterate is not defined and causes one kind of breakdown in BCG. By doing this, we obtain a method (Composite Step CGS or CSCGS) which not only handles the breakdowns described above, but does so with the advantages of CGS, namely, no multiplications by the transpose matrix and a faster convergence rate than BCG. Our strategy for deciding whether to skip a step does not involve any machine dependent parameters and is designed to skip near breakdowns as well as produce smoother iterates. Numerical experiments show that the new method does produce improved performance over CGS on practical problems.

  17. Variable methods to estimate the ionospheric horizontal gradient

    NASA Astrophysics Data System (ADS)

    Nagarajoo, Karthigesu

    2016-06-01

    DGPS or differential Global Positioning System is a system where the range error at a reference station (after eliminating the error due to its’ clock, hardware delay and multipath) will be eliminated from the range measurement at the user, which view the same satellite, presuming that the satellites path to both the reference station and the user experience common errors due to the ionosphere, clock errors etc. In this assumption, the error due to the ionospheric refraction is assumed to be the same for the two closely spaced paths (such as a baseline length between reference station and the user of 10km as used in simulations throughout this paper, unless otherwise stated) and thus the presence of ionospheric horizontal gradient is ignored. If a user's path is exposed to a drastically large ionosphere gradient, the large difference of ionosphere delays between the reference station and the user can result in significant position error for the user. Several examples of extremely large ionosphere gradients that could cause the significant user errors have been observed. The ionospheric horizontal gradient could be obtained instead from the gradient of the Total Electron Content, TEC observed from a number of received GPS satellites at one or more reference stations or based on empirical models updated with real time data. To investigate the former, in this work, the dual frequency method has been used to obtain both South-North and East-West gradients by using four different receiving stations separated in those directions. In addition, observation data from Navy Ionospheric Monitoring System (NIMS) receivers and the TEC contour map from Rutherford Appleton Laboratory (RAL) UK have also been used in order to define the magnitude and direction of the gradient.

  18. A new simple method to estimate fracture pressure gradient

    SciTech Connect

    Rocha, L.A.; Bourgoyne, A.T.

    1994-12-31

    Projecting safer and more economic wells calls for estimating correctly the fracture pressure gradient. On the other hand, a poor prediction of the fracture pressure gradient may lead to serious accidents such as lost circulation followed by a kick. Although these kinds of accidents can occur in any phase of the well, drilling shallow formations can offer additional dangerous due to shallow gas kicks, because they have the potential of becoming a shallow gas blowout leading sometimes to the formation of craters. Often, one of the main problems when estimating the fracture pressure gradient is the lack of data. In fact, drilling engineers generally face situations where only leak off test data (frequently having questionable results) are available. This problem is normally the case when drilling shallow formations where very few information is collected. This paper presents a new method to estimate fracture pressure gradient. The proposed method has the advantage of (a) using only the knowledge of leak off test data and (b) being independent of the pore pressure. The method is based on a new concept called pseudo-overburden pressure, defined as the overburden pressure a formation would exhibit if it were plastic. The method was applied in several areas of the world such as US Gulf Coast (Mississippi Canyon and Green Canyon) with very good results.

  19. Discontinuous Galerkin finite element methods for gradient plasticity.

    SciTech Connect

    Garikipati, Krishna.; Ostien, Jakob T.

    2010-10-01

    In this report we apply discontinuous Galerkin finite element methods to the equations of an incompatibility based formulation of gradient plasticity. The presentation is motivated with a brief overview of the description of dislocations within a crystal lattice. A tensor representing a measure of the incompatibility with the lattice is used in the formulation of a gradient plasticity model. This model is cast in a variational formulation, and discontinuous Galerkin machinery is employed to implement the formulation into a finite element code. Finally numerical examples of the model are shown.

  20. Bundle block adjustment of large-scale remote sensing data with Block-based Sparse Matrix Compression combined with Preconditioned Conjugate Gradient

    NASA Astrophysics Data System (ADS)

    Zheng, Maoteng; Zhang, Yongjun; Zhou, Shunping; Zhu, Junfeng; Xiong, Xiaodong

    2016-07-01

    In recent years, new platforms and sensors in photogrammetry, remote sensing and computer vision areas have become available, such as Unmanned Aircraft Vehicles (UAV), oblique camera systems, common digital cameras and even mobile phone cameras. Images collected by all these kinds of sensors could be used as remote sensing data sources. These sensors can obtain large-scale remote sensing data which consist of a great number of images. Bundle block adjustment of large-scale data with conventional algorithm is very time and space (memory) consuming due to the super large normal matrix arising from large-scale data. In this paper, an efficient Block-based Sparse Matrix Compression (BSMC) method combined with the Preconditioned Conjugate Gradient (PCG) algorithm is chosen to develop a stable and efficient bundle block adjustment system in order to deal with the large-scale remote sensing data. The main contribution of this work is the BSMC-based PCG algorithm which is more efficient in time and memory than the traditional algorithm without compromising the accuracy. Totally 8 datasets of real data are used to test our proposed method. Preliminary results have shown that the BSMC method can efficiently decrease the time and memory requirement of large-scale data.

  1. Material point method enhanced by modified gradient of shape function

    NASA Astrophysics Data System (ADS)

    Zhang, Duan Z.; Ma, Xia; Giguere, Paul T.

    2011-07-01

    A numerical scheme of computing quantities involving gradients of shape functions is introduced for the material point method (MPM), so that the quantities are continuous as material points move across cell boundaries. The noise and instability caused by cell crossing of the material points are then eliminated. In this scheme, the formulas used to compute these quantities can be expressed in the same forms as in the original material point method, but with the gradient of the shape function modified. For one-dimensional cases, the gradient of the shape function used in the generalized interpolation material point (GIMP) method is a special case of the modified gradient if the characteristic function of a material point is introduced. The characteristic function of a material point is not otherwise needed in this scheme, therefore difficulties in tracking its evolution are avoided. Although the support of the modified gradient of a shape function is enlarged from the cell containing the material point to also include the immediate neighbor cells, all the non-local effects of a material point can be accounted for by two consecutive local operations. Therefore this scheme can be used in calculations with unstructured grids. This scheme is proved to satisfy mass and momentum conservations exactly. The error in energy conservation is shown to be second order on both spatial and temporal discretizations. Although the error in energy conservation is the same order as that in the original material point method, numerical examples show that this scheme has significantly better energy conservation properties than those of the original material point method.

  2. Iterative methods for elliptic finite element equations on general meshes

    NASA Technical Reports Server (NTRS)

    Nicolaides, R. A.; Choudhury, Shenaz

    1986-01-01

    Iterative methods for arbitrary mesh discretizations of elliptic partial differential equations are surveyed. The methods discussed are preconditioned conjugate gradients, algebraic multigrid, deflated conjugate gradients, an element-by-element techniques, and domain decomposition. Computational results are included.

  3. Development of Levenberg-Marquardt, Resilient Back-Propagation, and Conjugate Gradient Powell-Beale Artificial Neural Networks for Peak Urban Water Demand Forecasting in Nicosia, Cyprus

    NASA Astrophysics Data System (ADS)

    Adamowski, J. F.

    2008-12-01

    Cyprus is in the middle of an unprecedented water crisis that has lasted several years. Four ideas that have been considered to aid in resolving the problem include imposing effective water use restrictions, implementing water demand reduction programs, optimizing water supply systems, and developing alternative water source strategies. A critical component of each of these initiatives is the accurate forecasting of short- term peak water demands. This study compared multiple linear regression and three types of artificial neural networks (ANNs) as methods for peak weekly water demand forecast modeling. Analysis was performed on six years of peak weekly water demand data and meteorological variables (maximum weekly temperature and total weekly rainfall) for two different regions (Athalassa and Public Garden) in the city of Nicosia, Cyprus. Twenty multiple linear regression models, twenty Levenberg-Marquardt ANN models, twenty Resilient Back- Propagation ANN models, and twenty Conjugate Gradient Powell-Beale ANN models were developed and their relative performance was compared. For both the Athalassa and Public Garden regions in Nicosia, the Levenberg-Marquardt ANN method was found to provide a more accurate forecast of peak weekly water demand than the other two types of ANNs and multiple linear regression. It was also found that the peak weekly water demand in Nicosia is better correlated with the rainfall occurrence rather than the amount of rainfall itself.

  4. Tomographic fluorescence reconstruction by a spectral projected gradient pursuit method

    NASA Astrophysics Data System (ADS)

    Ye, Jinzuo; An, Yu; Mao, Yamin; Jiang, Shixin; Yang, Xin; Chi, Chongwei; Tian, Jie

    2015-03-01

    In vivo fluorescence molecular imaging (FMI) has played an increasingly important role in biomedical research of preclinical area. Fluorescence molecular tomography (FMT) further upgrades the two-dimensional FMI optical information to three-dimensional fluorescent source distribution, which can greatly facilitate applications in related studies. However, FMT presents a challenging inverse problem which is quite ill-posed and ill-conditioned. Continuous efforts to develop more practical and efficient methods for FMT reconstruction are still needed. In this paper, a method based on spectral projected gradient pursuit (SPGP) has been proposed for FMT reconstruction. The proposed method was based on the directional pursuit framework. A mathematical strategy named the nonmonotone line search was associated with the SPGP method, which guaranteed the global convergence. In addition, the Barzilai-Borwein step length was utilized to build the new step length of the SPGP method, which was able to speed up the convergence of this gradient method. To evaluate the performance of the proposed method, several heterogeneous simulation experiments including multisource cases as well as comparative analyses have been conducted. The results demonstrated that, the proposed method was able to achieve satisfactory source localizations with a bias less than 1 mm; the computational efficiency of the method was one order of magnitude faster than the contrast method; and the fluorescence reconstructed by the proposed method had a higher contrast to the background than the contrast method. All the results demonstrated the potential for practical FMT applications with the proposed method.

  5. Gradient-Based Aerodynamic Shape Optimization Using ADI Method for Large-Scale Problems

    NASA Technical Reports Server (NTRS)

    Pandya, Mohagna J.; Baysal, Oktay

    1997-01-01

    A gradient-based shape optimization methodology, that is intended for practical three-dimensional aerodynamic applications, has been developed. It is based on the quasi-analytical sensitivities. The flow analysis is rendered by a fully implicit, finite volume formulation of the Euler equations.The aerodynamic sensitivity equation is solved using the alternating-direction-implicit (ADI) algorithm for memory efficiency. A flexible wing geometry model, that is based on surface parameterization and platform schedules, is utilized. The present methodology and its components have been tested via several comparisons. Initially, the flow analysis for for a wing is compared with those obtained using an unfactored, preconditioned conjugate gradient approach (PCG), and an extensively validated CFD code. Then, the sensitivities computed with the present method have been compared with those obtained using the finite-difference and the PCG approaches. Effects of grid refinement and convergence tolerance on the analysis and shape optimization have been explored. Finally the new procedure has been demonstrated in the design of a cranked arrow wing at Mach 2.4. Despite the expected increase in the computational time, the results indicate that shape optimization, which require large numbers of grid points can be resolved with a gradient-based approach.

  6. Distributed Kalman filtering compared to Fourier domain preconditioned conjugate gradient for laser guide star tomography on extremely large telescopes.

    PubMed

    Gilles, Luc; Massioni, Paolo; Kulcsár, Caroline; Raynaud, Henri-François; Ellerbroek, Brent

    2013-05-01

    This paper discusses the performance and cost of two computationally efficient Fourier-based tomographic wavefront reconstruction algorithms for wide-field laser guide star (LGS) adaptive optics (AO). The first algorithm is the iterative Fourier domain preconditioned conjugate gradient (FDPCG) algorithm developed by Yang et al. [Appl. Opt.45, 5281 (2006)], combined with pseudo-open-loop control (POLC). FDPCG's computational cost is proportional to N log(N), where N denotes the dimensionality of the tomography problem. The second algorithm is the distributed Kalman filter (DKF) developed by Massioni et al. [J. Opt. Soc. Am. A28, 2298 (2011)], which is a noniterative spatially invariant controller. When implemented in the Fourier domain, DKF's cost is also proportional to N log(N). Both algorithms are capable of estimating spatial frequency components of the residual phase beyond the wavefront sensor (WFS) cutoff frequency thanks to regularization, thereby reducing WFS spatial aliasing at the expense of more computations. We present performance and cost analyses for the LGS multiconjugate AO system under design for the Thirty Meter Telescope, as well as DKF's sensitivity to uncertainties in wind profile prior information. We found that, provided the wind profile is known to better than 10% wind speed accuracy and 20 deg wind direction accuracy, DKF, despite its spatial invariance assumptions, delivers a significantly reduced wavefront error compared to the static FDPCG minimum variance estimator combined with POLC. Due to its nonsequential nature and high degree of parallelism, DKF is particularly well suited for real-time implementation on inexpensive off-the-shelf graphics processing units. PMID:23695321

  7. Iterative reconstruction methods in atmospheric tomography: FEWHA, Kaczmarz and Gradient-based algorithm

    NASA Astrophysics Data System (ADS)

    Ramlau, R.; Saxenhuber, D.; Yudytskiy, M.

    2014-07-01

    The problem of atmospheric tomography arises in ground-based telescope imaging with adaptive optics (AO), where one aims to compensate in real-time for the rapidly changing optical distortions in the atmosphere. Many of these systems depend on a sufficient reconstruction of the turbulence profiles in order to obtain a good correction. Due to steadily growing telescope sizes, there is a strong increase in the computational load for atmospheric reconstruction with current methods, first and foremost the MVM. In this paper we present and compare three novel iterative reconstruction methods. The first iterative approach is the Finite Element- Wavelet Hybrid Algorithm (FEWHA), which combines wavelet-based techniques and conjugate gradient schemes to efficiently and accurately tackle the problem of atmospheric reconstruction. The method is extremely fast, highly flexible and yields superior quality. Another novel iterative reconstruction algorithm is the three step approach which decouples the problem in the reconstruction of the incoming wavefronts, the reconstruction of the turbulent layers (atmospheric tomography) and the computation of the best mirror correction (fitting step). For the atmospheric tomography problem within the three step approach, the Kaczmarz algorithm and the Gradient-based method have been developed. We present a detailed comparison of our reconstructors both in terms of quality and speed performance in the context of a Multi-Object Adaptive Optics (MOAO) system for the E-ELT setting on OCTOPUS, the ESO end-to-end simulation tool.

  8. Gradient-based image recovery methods from incomplete Fourier measurements.

    PubMed

    Patel, Vishal M; Maleh, Ray; Gilbert, Anna C; Chellappa, Rama

    2012-01-01

    A major problem in imaging applications such as magnetic resonance imaging and synthetic aperture radar is the task of trying to reconstruct an image with the smallest possible set of Fourier samples, every single one of which has a potential time and/or power cost. The theory of compressive sensing (CS) points to ways of exploiting inherent sparsity in such images in order to achieve accurate recovery using sub-Nyquist sampling schemes. Traditional CS approaches to this problem consist of solving total-variation (TV) minimization programs with Fourier measurement constraints or other variations thereof. This paper takes a different approach. Since the horizontal and vertical differences of a medical image are each more sparse or compressible than the corresponding TV image, CS methods will be more successful in recovering these differences individually. We develop an algorithm called GradientRec that uses a CS algorithm to recover the horizontal and vertical gradients and then estimates the original image from these gradients. We present two methods of solving the latter inverse problem, i.e., one based on least-square optimization and the other based on a generalized Poisson solver. After a thorough derivation of our complete algorithm, we present the results of various experiments that compare the effectiveness of the proposed method against other leading methods. PMID:21690011

  9. A new simple method to estimate fracture pressure gradient

    SciTech Connect

    Rocha, L.A.; Bourgoyne, A.T.

    1996-09-01

    Projecting safety and more economic wells calls for estimating correctly the fracture pressure gradient. On the other hand, a poor prediction of the fracture pressure gradient may lead to serious accidents, such as lost circulation followed by a kick. Although these kind of accidents can occur in any phase of the well, drilling shallow formations can offer additional dangers caused by shallow gas kicks because they have the potential of becoming a shallow gas blowout leading sometimes to the formation of craters. This paper presents a new method to estimate fracture pressure gradient. The proposed method has the advantage of (1) using only the knowledge of leakoff test data and (2) being independent of the pore pressure. The method is based on a new concept called pseudo-overburden pressure, defined as the overburden pressure a formation would exhibit if it were plastic. The method was applied in several areas of the world, such as the US Gulf Coast (Mississippi Canyon and Green Canyon), with very good results.

  10. Conjugation behaviours of CdTe quantum dots and antibody by a novel immunochromatographic method.

    PubMed

    Wang, Y; Bai, Y; Wei, X

    2011-03-01

    Three water-soluble CdTe quantum dots (QDs) (green-emitting, yellow-emitting and red-emitting) were synthesised for different refluxing time with 3-mercaptopropionic acid (MPA) as stabiliser. Then the red-emitting CdTe QDs and mouse immunoglobulin G (IgG) were taken as the representative to study the conjugation behaviour of QDs and antibody by a novel immunochromatographic method. After comparing with several methods, that is, direct conjugation, 1-ethyl-3(3-dimethylaminopropyl) carbodiimides hydrochloride (EDC)-mediated conjugation, N-hydroxysuccinimide (NHS)-mediated conjugation, EDC/NHS-mediated conjugation by immunochromatographic strips, EDC and NHS were selected together as coupling agents to conjugate QDs with antibody efficiently. Finally, the K562 leukaemia cells were incubated with the EDC/NHS-mediated conjugates to evaluate the performance in practical application, and the result from fluorescence images showed that it was successfully applied to label cells. The immunochromatographic strip was a superior method to study the conjugation of the fluorophore and antibody. PMID:21241157

  11. Method to conjugate polysaccharide antigens to surfaces for the detection of antibodies.

    PubMed

    Boas, Ulrik; Lind, Peter; Riber, Ulla

    2014-11-15

    A new generic method for the conjugation of lipopolysaccharide (LPS)-derived polysaccharide antigens from gram-negative bacteria has been developed using Salmonella as a model. After removal of lipid A from the LPS by mild acidolysis, the polysaccharide antigen was conjugated to polystyrene microbeads modified with N-alkyl hydroxylamine and N-alkyl-O-methyl hydroxylamine surface groups by incubation of antigen and beads for 16 h at 40 °C without the need for coupling agents. The efficiency of the new method was evaluated by flow cytometry in model samples and serum samples containing antibodies against Salmonella typhimurium and Salmonella dublin. The presented method was compared with a similar method for conjugation of Salmonella polysaccharide antigens to surfaces. Here, the new method showed higher antigen coupling efficiency by detecting low concentrations of antibodies. Furthermore, the polysaccharide-conjugated beads showed preserved bioactivity after 1 year of use. PMID:25076184

  12. New convergence results for the scaled gradient projection method

    NASA Astrophysics Data System (ADS)

    Bonettini, S.; Prato, M.

    2015-09-01

    The aim of this paper is to deepen the convergence analysis of the scaled gradient projection (SGP) method, proposed by Bonettini et al in a recent paper for constrained smooth optimization. The main feature of SGP is the presence of a variable scaling matrix multiplying the gradient, which may change at each iteration. In the last few years, extensive numerical experimentation showed that SGP equipped with a suitable choice of the scaling matrix is a very effective tool for solving large scale variational problems arising in image and signal processing. In spite of the very reliable numerical results observed, only a weak convergence theorem is provided establishing that any limit point of the sequence generated by SGP is stationary. Here, under the only assumption that the objective function is convex and that a solution exists, we prove that the sequence generated by SGP converges to a minimum point, if the scaling matrices sequence satisfies a simple and implementable condition. Moreover, assuming that the gradient of the objective function is Lipschitz continuous, we are also able to prove the {O}(1/k) convergence rate with respect to the objective function values. Finally, we present the results of a numerical experience on some relevant image restoration problems, showing that the proposed scaling matrix selection rule performs well also from the computational point of view.

  13. Multispectral face liveness detection method based on gradient features

    NASA Astrophysics Data System (ADS)

    Hou, Ya-Li; Hao, Xiaoli; Wang, Yueyang; Guo, Changqing

    2013-11-01

    Face liveness detection aims to distinguish genuine faces from disguised faces. Most previous works under visible light focus on classification of genuine faces and planar photos or videos. To handle the three-dimensional (3-D) disguised faces, liveness detection based on multispectral images has been shown to be an effective choice. In this paper, a gradient-based multispectral method has been proposed for face liveness detection. Three feature vectors are developed to reduce the influence of varying illuminations. The reflectance-based feature achieves the best performance, which has a true positive rate of 98.3% and a true negative rate of 98.7%. The developed methods are also tested on individual bands to provide a clue for band selection in the imaging system. Preliminary results on different face orientations are also shown. The contributions of this paper are threefold. First, a gradient-based multispectral method has been proposed for liveness detection, which considers the reflectance properties of all the distinctive regions in a face. Second, three illumination-robust features are studied based on a dataset with two-dimensional planar photos, 3-D mannequins, and masks. Finally, the performance of the method on different spectral bands and face orientations is also shown in the evaluations.

  14. Conjugate heat and mass transfer in the lattice Boltzmann equation method

    SciTech Connect

    Li, LK; Chen, C; Mei, RW; Klausner, JF

    2014-04-22

    An interface treatment for conjugate heat and mass transfer in the lattice Boltzmann equation method is proposed based on our previously proposed second-order accurate Dirichlet and Neumann boundary schemes. The continuity of temperature (concentration) and its flux at the interface for heat (mass) transfer is intrinsically satisfied without iterative computations, and the interfacial temperature (concentration) and their fluxes are conveniently obtained from the microscopic distribution functions without finite-difference calculations. The present treatment takes into account the local geometry of the interface so that it can be directly applied to curved interface problems such as conjugate heat and mass transfer in porous media. For straight interfaces or curved interfaces with no tangential gradient, the coupling between the interfacial fluxes along the discrete lattice velocity directions is eliminated and thus the proposed interface schemes can be greatly simplified. Several numerical tests are conducted to verify the applicability and accuracy of the proposed conjugate interface treatment, including (i) steady convection-diffusion in a channel containing two different fluids, (ii) unsteady convection-diffusion in the channel, (iii) steady heat conduction inside a circular domain with two different solid materials, and (iv) unsteady mass transfer from a spherical droplet in an extensional creeping flow. The accuracy and order of convergence of the simulated interior temperature (concentration) field, the interfacial temperature (concentration), and heat (mass) flux are examined in detail and compared with those obtained from the "half-lattice division" treatment in the literature. The present analysis and numerical results show that the half-lattice division scheme is second-order accurate only when the interface is fixed at the center of the lattice links, while the present treatment preserves second-order accuracy for arbitrary link fractions. For curved

  15. EVALUATION OF A METHOD TO MEASURE CONJUGAL TRANSFER OF RECOMBINANT DNA IN SOIL SLURRIES

    EPA Science Inventory

    Release of recombinant microbes into the environment necessitates an evaluation of their ability to transfer genetic material. he present report evaluates a method to detect conjugal DNA plasmid transfer in soil slurries under various environmental conditions. onor Pseudomonas ce...

  16. Streptavidin conjugation and quantification-a method evaluation for nanoparticles.

    PubMed

    Quevedo, Pablo Darío; Behnke, Thomas; Resch-Genger, Ute

    2016-06-01

    Aiming at the development of validated protocols for protein conjugation of nanomaterials and the determination of protein labeling densities, we systematically assessed the conjugation of the model protein streptavidin (SAv) to 100-, 500-, and 1000-nm-sized polystyrene and silica nanoparticles and dye-encoded polymer particles with two established conjugation chemistries, based upon achievable coupling efficiencies and labeling densities. Bioconjugation reactions compared included EDC/sulfo NHS ester chemistry for direct binding of the SAv to carboxyl groups at the particle surface and maleimide-thiol chemistry in conjunction with heterobifunctional PEG linkers and aminated nanoparticles (NPs). Quantification of the total and functional amounts of SAv on these nanomaterials and unreacted SAv in solution was performed with the BCA assay and the biotin-FITC (BF) titration, relying on different signal generation principles, which are thus prone to different interferences. Our results revealed a clear influence of the conjugation chemistry on the amount of NP crosslinking, yet under optimized reaction conditions, EDC/sulfo NHS ester chemistry and the attachment via heterobifunctional PEG linkers led to comparably efficient SAv coupling and good labeling densities. Particle size can obviously affect protein labeling densities and particularly protein functionality, especially for larger particles. For unstained nanoparticles, direct bioconjugation seems to be the most efficient strategy, whereas for dye-encoded nanoparticles, PEG linkers are to be favored for the prevention of dye-protein interactions which can affect protein functionality specifically in the case of direct SAv binding. Moreover, an influence of particle size on achievable protein labeling densities and protein functionality could be demonstrated. PMID:27038055

  17. Testing Method for Heat Resistance Under Temperature Gradient

    NASA Astrophysics Data System (ADS)

    Takagi, K.; Kawasaki, A.; Itoh, Y.; Harada, Y.; Ono, F.

    2007-12-01

    “Testing Method for Heat Resistance under Temperature Gradient” is a Japanese Industrial Standard (JIS) newly established by the Minister of Economy, Trade and Industry, after deliberations by the Japanese Industrial Standards Committee, in accordance with the Industrial Standardization Law. This standard specified the testing method for heat resistance under temperature gradient of materials and coated members of equipment exposed to high temperature, such as aircraft engines, gas turbines, and so on. This paper introduces the principle and overview of the established standard. In addition, taking the heat cycle test using the burner rig for instance, we specifically illustrate the acquirable data and their analysis in the standard. Monitoring of the effective thermal conductivity and acoustic emission particularly enables to the non-destructive evaluation of failure cycle.

  18. Method to create gradient index in a polymer

    DOEpatents

    Dirk, Shawn M; Johnson, Ross Stefan; Boye, Robert; Descour, Michael R; Sweatt, William C; Wheeler, David R; Kaehr, Bryan James

    2014-10-14

    Novel photo-writable and thermally switchable polymeric materials exhibit a refractive index change of .DELTA.n.gtoreq.1.0 when exposed to UV light or heat. For example, lithography can be used to convert a non-conjugated precursor polymer to a conjugated polymer having a higher index-of-refraction. Further, two-photon lithography can be used to pattern high-spatial frequency structures.

  19. A method to stabilize linear systems using eigenvalue gradient information

    NASA Technical Reports Server (NTRS)

    Wieseman, C. D.

    1985-01-01

    Formal optimization methods and eigenvalue gradient information are used to develop a stabilizing control law for a closed loop linear system that is initially unstable. The method was originally formulated by using direct, constrained optimization methods with the constraints being the real parts of the eigenvalues. However, because of problems in trying to achieve stabilizing control laws, the problem was reformulated to be solved differently. The method described uses the Davidon-Fletcher-Powell minimization technique to solve an indirect, constrained minimization problem in which the performance index is the Kreisselmeier-Steinhauser function of the real parts of all the eigenvalues. The method is applied successfully to solve two different problems: the determination of a fourth-order control law stabilizes a single-input single-output active flutter suppression system and the determination of a second-order control law for a multi-input multi-output lateral-directional flight control system. Various sets of design variables and initial starting points were chosen to show the robustness of the method.

  20. [Spectral discrimination method information divergence combined with gradient angle].

    PubMed

    Zhang, Xiu-bao; Yuan, Yan; Jing, Juan-juan; Sun, Cheng-ming; Wang, Qian

    2011-03-01

    The present paper proposes a spectral discrimination method combining spectral information divergence with spectral gradient angle (SID x tan(SGA(pi/2)) which overcomes the shortages of the existing methods which can not take the whole spectral shape and local characteristics into account simultaneously. Using the simulation spectra as input data, according to the interferogram acquirement principle and spectrum recovery algorithm of the temporally and spatially modulated Fourier transform imaging spectrometer (TSMFTIS), we simulated the distortion spectra recovery process of the TMSFTIS in different maximum mix ratio and distinguished the difference between the recovered spectra and the true spectrum by different spectral discrimination methods. The experiment results show that the SID x tan(SGA(pi/2)) can not only identify the similarity of the whole spectral shapes, but also distinguish local differences of the spectral characteristics. A comparative study was conducted among the different discrimination methods. The results have validated that the SID x tan(SGA(pi/2)) has a significant improvement in the discriminatory ability. PMID:21595255

  1. Absolute measurement of optical flat surface shape based on the conjugate differential method.

    PubMed

    Huang, Ya; Ma, Jun; Zhu, Rihong; Yuan, Caojin; Chen, Lei; Cai, Huijuan; Sun, Weiyuan

    2015-11-16

    In this paper the conjugate differential method is proposed to measure the absolute surface shape of the flat mirror using a phase-shifting interferometer. The conjugate differential method is derived from the differential method, which extracts absolute phase differences by introducing the slight transverse shifts of the optic. It employs the measurement schemes making transverse shifts on the orthogonally bilateral symmetry positions. So the measurement procedures have been changed into four-step tests to get the phase difference map instead of three-step tests for the differential method. The precision of the slope approximation is enhanced by reducing couplings between multi-step tests, and the reliability of the measurements can be improved. Several differential wavefront reconstruction methods, such as Fourier transform, Zernike polynomial fitting and Hudgin model method, can be applied to reconstruct the absolute surface shape from the differencing phase maps in four different simulation environment. They were also used to reconstruct the absolute surface shape with the conjugate differential method in the experiment. Our method accords with the classical three-flat test better than the traditional differential method, where the deviation of RMS value between the conjugate differential method and the three-flat test is less than 0.3 nm. PMID:26698450

  2. Estimation of Organ Activity using Four Different Methods of Background Correction in Conjugate View Method.

    PubMed

    Shanei, Ahmad; Afshin, Maryam; Moslehi, Masoud; Rastaghi, Sedighe

    2015-01-01

    To make an accurate estimation of the uptake of radioactivity in an organ using the conjugate view method, corrections of physical factors, such as background activity, scatter, and attenuation are needed. The aim of this study was to evaluate the accuracy of four different methods for background correction in activity quantification of the heart in myocardial perfusion scans. The organ activity was calculated using the conjugate view method. A number of 22 healthy volunteers were injected with 17-19 mCi of (99m)Tc-methoxy-isobutyl-isonitrile (MIBI) at rest or during exercise. Images were obtained by a dual-headed gamma camera. Four methods for background correction were applied: (1) Conventional correction (referred to as the Gates' method), (2) Buijs method, (3) BgdA subtraction, (4) BgdB subtraction. To evaluate the accuracy of these methods, the results of the calculations using the above-mentioned methods were compared with the reference results. The calculated uptake in the heart using conventional method, Buijs method, BgdA subtraction, and BgdB subtraction methods was 1.4 ± 0.7% (P < 0.05), 2.6 ± 0.6% (P < 0.05), 1.3 ± 0.5% (P < 0.05), and 0.8 ± 0.3% (P < 0.05) of injected dose (I.D) at rest and 1.8 ± 0.6% (P > 0.05), 3.1 ± 0.8% (P > 0.05), 1.9 ± 0.8% (P < 0.05), and 1.2 ± 0.5% (P < 0.05) of I.D, during exercise. The mean estimated myocardial uptake of (99m)Tc-MIBI was dependent on the correction method used. Comparison among the four different methods of background activity correction applied in this study showed that the Buijs method was the most suitable method for background correction in myocardial perfusion scan. PMID:26955568

  3. Using nonlinear kernels in seismic tomography: go beyond gradient methods

    NASA Astrophysics Data System (ADS)

    Wu, R.

    2013-05-01

    In quasi-linear inversion, a nonlinear problem is typically solved iteratively and at each step the nonlinear problem is linearized through the use of a linear functional derivative, the Fréchet derivative. Higher order terms generally are assumed to be insignificant and neglected. The linearization approach leads to the popular gradient method of seismic inversion. However, for the real Earth, the wave equation (and the real wave propagation) is strongly nonlinear with respect to the medium parameter perturbations. Therefore, the quasi-linear inversion may have a serious convergence problem for strong perturbations. In this presentation I will compare the convergence properties of the Taylor-Fréchet series and the renormalized Fréchet series, the De Wolf approximation, and illustrate the improved convergence property with numerical examples. I'll also discuss the application of nonlinear partial derivative to least-square waveform inversion. References: Bonnans, J., Gilbert, J., Lemarechal, C. and Sagastizabal, C., 2006, Numirical optmization, Springer. Wu, R.S. and Y. Zheng, 2012. Nonlinear Fréchet derivative and its De Wolf approximation, Expanded Abstracts of Society of Exploration Gephysicists, SI 8.1.

  4. A method of genetically engineering acidophilic, heterotrophic, bacteria by electroporation and conjugation

    SciTech Connect

    Roberto, F.F.; Glenn, A.W.; Ward, T.E.

    1990-08-07

    A method of genetically manipulating an acidophilic bacteria is provided by two different procedures. Using electroporation, chimeric and broad-host range plasmids are introduced into Acidiphilium. Conjugation is also employed to introduce broad-host range plasmids into Acidiphilium at neutral pH.

  5. A rapid on-line method for mass spectrometric confirmation of a cysteine-conjugated antibody-drug-conjugate structure using multidimensional chromatography

    PubMed Central

    Birdsall, Robert E; Shion, Henry; Kotch, Frank W; Xu, April; Porter, Thomas J; Chen, Weibin

    2015-01-01

    Cysteine-conjugated antibody-drug conjugates (ADCs) are manufactured using controlled partial reduction and conjugation chemistry with drug payloads that typically occur in intervals of 0, 2, 4, 6, and 8. Control of heterogeneity is of particular importance to the quality of ADC product because drug loading and distribution can affect the safety and efficacy of the ADC. Liquid chromatography ultra-violet (LC-UV)-based methods can be used to acquire the drug distribution profiles of cysteine-conjugated ADCs when analyzed using hydrophobic interaction chromatography (HIC). However, alternative analysis techniques are often required for structural identification when conjugated drugs do not possess discrete ultra-violet absorbance properties for precise assessment of the drug-to-antibody ratio (DAR). In this study, multidimensional chromatography was used as an efficient method for combining non-compatible techniques, such as HIC, with analysis by mass spectrometry (LC/LC/QTOF-MS) for rapid on-line structural elucidation of species observed in HIC distribution profiles of cysteine-conjugated ADCs. The methodology was tested using an IgG1 mAb modified by cysteine conjugation with a non-toxic drug mimic. Structural elucidation of peaks observed in the HIC analysis (1st dimension) were successfully identified based on their unique sub-unit masses via mass spectrometry techniques once dissociation occurred under denaturing reversed phase conditions (2nd dimension). Upon identification, the DAR values were determined to be 2.83, 4.44, and 5.97 for 3 drug load levels (low-, medium-, and high-loaded ADC batches), respectively, based on relative abundance from the LC-UV data. This work demonstrates that multidimensional chromatography coupled with MS, provides an efficient approach for on-line biotherapeutic characterization to ensure ADC product quality. PMID:26305867

  6. A rapid on-line method for mass spectrometric confirmation of a cysteine-conjugated antibody-drug-conjugate structure using multidimensional chromatography.

    PubMed

    Birdsall, Robert E; Shion, Henry; Kotch, Frank W; Xu, April; Porter, Thomas J; Chen, Weibin

    2015-01-01

    Cysteine-conjugated antibody-drug conjugates (ADCs) are manufactured using controlled partial reduction and conjugation chemistry with drug payloads that typically occur in intervals of 0, 2, 4, 6, and 8. Control of heterogeneity is of particular importance to the quality of ADC product because drug loading and distribution can affect the safety and efficacy of the ADC. Liquid chromatography ultra-violet (LC-UV)-based methods can be used to acquire the drug distribution profiles of cysteine-conjugated ADCs when analyzed using hydrophobic interaction chromatography (HIC). However, alternative analysis techniques are often required for structural identification when conjugated drugs do not possess discrete ultra-violet absorbance properties for precise assessment of the drug-to-antibody ratio (DAR). In this study, multidimensional chromatography was used as an efficient method for combining non-compatible techniques, such as HIC, with analysis by mass spectrometry (LC/LC/QTOF-MS) for rapid on-line structural elucidation of species observed in HIC distribution profiles of cysteine-conjugated ADCs. The methodology was tested using an IgG1 mAb modified by cysteine conjugation with a non-toxic drug mimic. Structural elucidation of peaks observed in the HIC analysis (1(st) dimension) were successfully identified based on their unique sub-unit masses via mass spectrometry techniques once dissociation occurred under denaturing reversed phase conditions (2(nd) dimension). Upon identification, the DAR values were determined to be 2.83, 4.44, and 5.97 for 3 drug load levels (low-, medium-, and high-loaded ADC batches), respectively, based on relative abundance from the LC-UV data. This work demonstrates that multidimensional chromatography coupled with MS, provides an efficient approach for on-line biotherapeutic characterization to ensure ADC product quality. PMID:26305867

  7. Optimization of the conjugation method for a serogroup B/C meningococcal vaccine.

    PubMed

    Fukasawa, Lucila O; Schenkman, Rocilda P F; Perciani, Catia T; Carneiro, Sylvia M; Dias, Waldely O; Tanizaki, Martha M

    2006-11-01

    A conjugate meningococcal vaccine against serogroup B/C consisting of capsular PS (polysaccharide) from serogroup C conjugated to OMV (outer membrane vesicle) from serogroup B would be a very useful vaccine in regions where there is a prevalence of both serogroups, for example in Brazil. For this purpose, the conjugation method that uses ADHy (adipic acid dihydrazide) as spacer and a carbodi-imide derivative, EDAC [1-ethyl-3-(3-dimethylaminopropyl)carbodi-imide], as catalyser was optimized looking for synthesis yield and maintenance of the antigenicity of both components. The best synthesis conditions preserving the vaccine immunogenicity resulted in a final yield of approx. 17%. Immunogenicity of the vaccine was highest when 10% of the sialic acid residues of the PS were occupied by the ADHy spacer. Sterilization of the conjugate by filtration through a 0.22-microm-pore-size membrane resulted in a low recovery of protein and PS (approximately 50%), although the vaccine immunogenicity was maintained. Using gamma irradiation on freeze-dried sample, it was possible to maintain the integrity of OMV structure and, consequently, its ability to induce bactericidal antibodies. PMID:16776648

  8. Refinement of the Diatom Episome Maintenance Sequence and Improvement of Conjugation-Based DNA Delivery Methods.

    PubMed

    Diner, Rachel E; Bielinski, Vincent A; Dupont, Christopher L; Allen, Andrew E; Weyman, Philip D

    2016-01-01

    Conjugation of episomal plasmids from bacteria to diatoms advances diatom genetic manipulation by simplifying transgene delivery and providing a stable and consistent gene expression platform. To reach its full potential, this nascent technology requires new optimized expression vectors and a deeper understanding of episome maintenance. Here, we present the development of an additional diatom vector (pPtPBR1), based on the parent plasmid pBR322, to add a plasmid maintained at medium copy number in Escherichia coli to the diatom genetic toolkit. Using this new vector, we evaluated the contribution of individual yeast DNA elements comprising the 1.4-kb tripartite CEN6-ARSH4-HIS3 sequence that enables episome maintenance in Phaeodactylum tricornutum. While various combinations of these individual elements enable efficient conjugation and high exconjugant yield in P. tricornutum, individual elements alone do not. Conjugation of episomes containing CEN6-ARSH4 and a small sequence from the low GC content 3' end of HIS3 produced the highest number of diatom exconjugant colonies, resulting in a smaller and more efficient vector design. Our findings suggest that the CEN6 and ARSH4 sequences function differently in yeast and diatoms, and that low GC content regions of greater than ~500 bp are a potential indicator of a functional diatom episome maintenance sequence. Additionally, we have developed improvements to the conjugation protocol including a high-throughput option utilizing 12-well plates and plating methods that improve exconjugant yield and reduce time and materials required for the conjugation protocol. The data presented offer additional information regarding the mechanism by which the yeast-derived sequence enables diatom episome maintenance and demonstrate options for flexible vector design. PMID:27551676

  9. Refinement of the Diatom Episome Maintenance Sequence and Improvement of Conjugation-Based DNA Delivery Methods

    PubMed Central

    Diner, Rachel E.; Bielinski, Vincent A.; Dupont, Christopher L.; Allen, Andrew E.; Weyman, Philip D.

    2016-01-01

    Conjugation of episomal plasmids from bacteria to diatoms advances diatom genetic manipulation by simplifying transgene delivery and providing a stable and consistent gene expression platform. To reach its full potential, this nascent technology requires new optimized expression vectors and a deeper understanding of episome maintenance. Here, we present the development of an additional diatom vector (pPtPBR1), based on the parent plasmid pBR322, to add a plasmid maintained at medium copy number in Escherichia coli to the diatom genetic toolkit. Using this new vector, we evaluated the contribution of individual yeast DNA elements comprising the 1.4-kb tripartite CEN6-ARSH4-HIS3 sequence that enables episome maintenance in Phaeodactylum tricornutum. While various combinations of these individual elements enable efficient conjugation and high exconjugant yield in P. tricornutum, individual elements alone do not. Conjugation of episomes containing CEN6-ARSH4 and a small sequence from the low GC content 3′ end of HIS3 produced the highest number of diatom exconjugant colonies, resulting in a smaller and more efficient vector design. Our findings suggest that the CEN6 and ARSH4 sequences function differently in yeast and diatoms, and that low GC content regions of greater than ~500 bp are a potential indicator of a functional diatom episome maintenance sequence. Additionally, we have developed improvements to the conjugation protocol including a high-throughput option utilizing 12-well plates and plating methods that improve exconjugant yield and reduce time and materials required for the conjugation protocol. The data presented offer additional information regarding the mechanism by which the yeast-derived sequence enables diatom episome maintenance and demonstrate options for flexible vector design. PMID:27551676

  10. Gradient index liquid crystal devices and method of fabrication thereof

    DOEpatents

    Lee, Jae-Cheul; Jacobs, Stephen

    1991-01-01

    Laser beam apodizers using cholesteric liquid crystals provides soft edge profile by use of two separate cholesteric liquid crystal mixtures with different selective reflection bands which in an overlap region have a gradient index where reflectivity changes as a function of position. The apodizers can be configured as a one-dimensional beam apod INTRODUCTION The U.S. government has rights in the invention under Contract No. DE-FC03-85DP40200 between the University of Rochester and the Department of Energy.

  11. Gradient index liquid crystal devices and method of fabrication thereof

    DOEpatents

    Lee, J.C.; Jacobs, S.

    1991-10-29

    Laser beam apodizers using cholesteric liquid crystals provides soft edge profile by use of two separate cholesteric liquid crystal mixtures with different selective reflection bands which in an overlap region have a gradient index where reflectivity changes as a function of position. The apodizers can be configured as a one-dimensional beam apod INTRODUCTION The U.S. government has rights in the invention under Contract No. DE-FC03-85DP40200 between the University of Rochester and the Department of Energy.

  12. Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method.

    PubMed

    Brorsen, Kurt R; Zahariev, Federico; Nakata, Hiroya; Fedorov, Dmitri G; Gordon, Mark S

    2014-12-01

    The equations for the response terms for the fragment molecular orbital (FMO) method interfaced with the density functional theory (DFT) gradient are derived and implemented. Compared to the previous FMO-DFT gradient, which lacks response terms, the FMO-DFT analytic gradient has improved accuracy for a variety of functionals, when compared to numerical gradients. The FMO-DFT gradient agrees with the fully ab initio DFT gradient in which no fragmentation is performed, while reducing the nonlinear scaling associated with standard DFT. Solving for the response terms requires the solution of the coupled perturbed Kohn-Sham (CPKS) equations, where the CPKS equations are solved through a decoupled Z-vector procedure called the self-consistent Z-vector method. FMO-DFT is a nonvariational method and the FMO-DFT gradient is unique compared to standard DFT gradients in that the FMO-DFT gradient requires terms from both DFT and time-dependent density functional theory (TDDFT) theories. PMID:26583213

  13. Group B Streptococcus capsular polysaccharide-cholera toxin B subunit conjugate vaccines prepared by different methods for intranasal immunization.

    PubMed

    Shen, X; Lagergård, T; Yang, Y; Lindblad, M; Fredriksson, M; Holmgren, J

    2001-01-01

    Group B Streptococcus (GBS) type III capsular polysaccharide (CPS III) was conjugated to recombinant cholera toxin B subunit (rCTB) using three different methods which employed (i) cystamine and N-succinimidyl-3-(2-pyridyldithio)propionate (SPDP), (ii) carbodiimide with adipic acid dihydrazide (ADH) as a spacer, or (iii) reductive amination (RA). The CPS III-rCTB conjugates were divided into large- and small-molecular-weight (M(r)) fractions, and the immunogenicities of the different preparations after intranasal (i.n.) immunization were studied in mice. Both large- and small-M(r) conjugates of CPS III-rCTB(RA) or CPS III-rCTB(ADH) induced high, almost comparable levels of CPS-specific immunoglobulin G (IgG) in serum, lungs, and vagina that were generally superior to those obtained with CPS III-rCTB(SPDP) conjugates or a CPS III and rCTB mixture. However, the smaller-M(r) conjugates of CPS III-rCTB(RA) or CPS III-rCTB(ADH) in most cases elicited a lower anti-CPS IgA immune response than the large-M(r) conjugates, and the highest anti-CPS IgA titers in both tissues and serum were obtained with the large-M(r) CPS III-rCTB(RA) conjugate. Serum IgG anti-CPS titers induced by the CPS III-rCTB(RA) conjugate had high levels of specific IgG1, IgG2a, IgG2b, and IgG3 antibodies. Based on the effectiveness of RA for coupling CPS III to rCTB, RA was also tested for conjugating GBS CPS Ia with rCTB. As for the CPS III-rCTB conjugates, the immunogenicity of CPS Ia was greatly increased by conjugation to rCTB. Intranasal immunization with a combination of CPS Ia-rCTB and CPS III-rCTB conjugates was shown to induce anti-CPS Ia and III immune responses in serum and lungs that were fully comparable with the responses to immunization with the monovalent CPS Ia-rCTB or CPS III-rCTB conjugates. These results suggest that the GBS CPS III-rCTB and CPS Ia-rCTB conjugates prepared by the RA method may be used in bivalent and possibly also in multivalent mucosal GBS conjugate vaccines. PMID

  14. Group B Streptococcus Capsular Polysaccharide-Cholera Toxin B Subunit Conjugate Vaccines Prepared by Different Methods for Intranasal Immunization

    PubMed Central

    Shen, Xuzhuang; Lagergård, Teresa; Yang, Yonghong; Lindblad, Marianne; Fredriksson, Margareta; Holmgren, Jan

    2001-01-01

    Group B Streptococcus (GBS) type III capsular polysaccharide (CPS III) was conjugated to recombinant cholera toxin B subunit (rCTB) using three different methods which employed (i) cystamine and N-succinimidyl-3-(2-pyridyldithio)propionate (SPDP), (ii) carbodiimide with adipic acid dihydrazide (ADH) as a spacer, or (iii) reductive amination (RA). The CPS III-rCTB conjugates were divided into large- and small-molecular-weight (Mr) fractions, and the immunogenicities of the different preparations after intranasal (i.n.) immunization were studied in mice. Both large- and small-Mr conjugates of CPS III-rCTBRA or CPS III-rCTBADH induced high, almost comparable levels of CPS-specific immunoglobulin G (IgG) in serum, lungs, and vagina that were generally superior to those obtained with CPS III-rCTBSPDP conjugates or a CPS III and rCTB mixture. However, the smaller-Mr conjugates of CPS III-rCTBRA or CPS III-rCTBADH in most cases elicited a lower anti-CPS IgA immune response than the large-Mr conjugates, and the highest anti-CPS IgA titers in both tissues and serum were obtained with the large-Mr CPS III-rCTBRA conjugate. Serum IgG anti-CPS titers induced by the CPS III-rCTBRA conjugate had high levels of specific IgG1, IgG2a, IgG2b, and IgG3 antibodies. Based on the effectiveness of RA for coupling CPS III to rCTB, RA was also tested for conjugating GBS CPS Ia with rCTB. As for the CPS III-rCTB conjugates, the immunogenicity of CPS Ia was greatly increased by conjugation to rCTB. Intranasal immunization with a combination of CPS Ia-rCTB and CPS III-rCTB conjugates was shown to induce anti-CPS Ia and III immune responses in serum and lungs that were fully comparable with the responses to immunization with the monovalent CPS Ia-rCTB or CPS III-rCTB conjugates. These results suggest that the GBS CPS III-rCTB and CPS Ia-rCTB conjugates prepared by the RA method may be used in bivalent and possibly also in multivalent mucosal GBS conjugate vaccines. PMID:11119518

  15. An improved method for covalently conjugating morpholino oligomers to antitumor antibodies.

    PubMed

    He, Jiang; Liu, Guozheng; Dou, Shuping; Gupta, Suresh; Rusckowski, Mary; Hnatowich, Donald

    2007-01-01

    Whether for conventional pretargeting, amplification pretargeting, or affinity enhancement pretargeting, it will be necessary to conjugate an antitumor antibody as the first injectate. This laboratory is investigating phosphorodiamidate morpholinos (MORFs) for pretargeting, and accordingly we are examining methods of attaching MORFs to antitumor antibodies that provide at least one group per molecule (gpm) without adversely influencing antibody properties. The aim of this investigation was to evaluate the commercial Hydralink for the conjugation of the anti-CEA MN14 antibody with an 18 mer amine-derivatized MORF. The conjugation was approached in both directions by first reacting MN14 with the NHS derivatives of 4-hydrozinonicotinate acetone hydrazone (SANH) or 4-formylbenzoate (SFB) and then combining with MORF that was previously reacted with SFB or SANH to yield MN14(SANH)-MORF and MN14(SFB)-MORF respectively. The storage stability, immunoreactive fraction, and the biodistribution in normal mice were compared for both conjugates. Thereafter, MN14(SANH)-MORF was used in a pretargeting study in tumored nude mice, and the results were compared to that obtained historically with MN14-MORF prepared by carbodiimide (EDC) coupling. Both new methods of conjugation provided between 1 and 2 gpm compared to 0.2 achieved previously by EDC. Furthermore, by repeat SE HPLC with and without CEA, both showed an unimpaired immunoreactive fraction. MN14(SANH)-MORF tolerated long-term storage best. More importantly, when labeled by hybridization with 99mTc-labeled complementary MORF (99mTc-cMORF), the biodistribution of MN14(SANH)-MORF was more favorable than that of MN14(SFB)-MORF in normal mice with lower liver (5.7 vs 9.4 %ID/g at 18 h) and spleen (3.5 vs 8.4 %ID/g) accumulations and higher blood levels (4.8 vs 3.4 %ID/g). Accordingly, only MN14(SANH)-MORF was used in a pretargeting study in tumored mice. When targeted with 99mTc-cMORF and at 2 days postinjection of antibody

  16. Gradient-free MCMC methods for dynamic causal modelling

    PubMed Central

    Sengupta, Biswa; Friston, Karl J.; Penny, Will D.

    2015-01-01

    In this technical note we compare the performance of four gradient-free MCMC samplers (random walk Metropolis sampling, slice-sampling, adaptive MCMC sampling and population-based MCMC sampling with tempering) in terms of the number of independent samples they can produce per unit computational time. For the Bayesian inversion of a single-node neural mass model, both adaptive and population-based samplers are more efficient compared with random walk Metropolis sampler or slice-sampling; yet adaptive MCMC sampling is more promising in terms of compute time. Slice-sampling yields the highest number of independent samples from the target density — albeit at almost 1000% increase in computational time, in comparison to the most efficient algorithm (i.e., the adaptive MCMC sampler). PMID:25776212

  17. Method for generation of spiral bevel gears with conjugate gear tooth surfaces

    NASA Technical Reports Server (NTRS)

    Litvin, F. L.; Coy, J. J.; Heine, C.; Tsung, Wei-Jiung

    1987-01-01

    A method for generation of spiral bevel gears is proposed that provides conjugate gear tooth surfaces. This method is based on a new principle for the performance of parallel motion of a straight line that slides along two mating ellipses with related dimensions and parameters of orientation. The parallel motion of the straight line, that is, the contact normal, is performed parallel to the line which passes through the foci of symmetry of the related ellipses. The manufacturing of gears can be performed with the existing Gleason's equipment.

  18. Comparison between pressure gradient method and MAC method on high Re calculation

    NASA Technical Reports Server (NTRS)

    Tan, C.-H.; Duh, J. C.

    1989-01-01

    A cavity flow driven by shear and buoyancy forces is used as a test problem in the application of a nonstaggered pressure gradient (PG) method in solving the two-dimensional incompressible Navier-Stokes equations. Twelve finite differencing schemes are used to solve the cavity flow problem. The schemes consist of various combinations of grid arrangements, upwinding treatments, and conservativeness of convection terms. An artificial source term is introduced, and the solutions are compared with those obtained by the conventional marker-and-cell (MAC) method. The comparisons favor the PG method. Numerical results obtained by the twelve schemes are compared with exact solutions in order to assess the stability and accuracy of each scheme.

  19. A modified micrometeorological gradient method for estimating O3 dry depositions over a forest canopy

    NASA Astrophysics Data System (ADS)

    Wu, Z. Y.; Zhang, L.; Wang, X. M.; Munger, J. W.

    2015-07-01

    Small pollutant concentration gradients between levels above a plant canopy result in large uncertainties in estimated air-surface exchange fluxes when using existing micrometeorological gradient methods, including the aerodynamic gradient method (AGM) and the modified Bowen ratio method (MBR). A modified micrometeorological gradient method (MGM) is proposed in this study for estimating O3 dry deposition fluxes over a forest canopy using concentration gradients between a level above and a level below the canopy top, taking advantage of relatively large gradients between these levels due to significant pollutant uptake in the top layers of the canopy. The new method is compared with the AGM and MBR methods and is also evaluated using eddy-covariance (EC) flux measurements collected at the Harvard Forest Environmental Measurement Site, Massachusetts, during 1993-2000. All three gradient methods (AGM, MBR, and MGM) produced similar diurnal cycles of O3 dry deposition velocity (Vd(O3)) to the EC measurements, with the MGM method being the closest in magnitude to the EC measurements. The multi-year average Vd(O3) differed significantly between these methods, with the AGM, MBR, and MGM method being 2.28, 1.45, and 1.18 times that of the EC, respectively. Sensitivity experiments identified several input parameters for the MGM method as first-order parameters that affect the estimated Vd(O3). A 10% uncertainty in the wind speed attenuation coefficient or canopy displacement height can cause about 10% uncertainty in the estimated Vd(O3). An unrealistic leaf area density vertical profile can cause an uncertainty of a factor of 2.0 in the estimated Vd(O3). Other input parameters or formulas for stability functions only caused an uncertainly of a few percent. The new method provides an alternative approach to monitoring/estimating long-term deposition fluxes of similar pollutants over tall canopies.

  20. A modified micrometeorological gradient method for estimating O3 dry deposition over a forest canopy

    NASA Astrophysics Data System (ADS)

    Wu, Z. Y.; Zhang, L.; Wang, X. M.; Munger, J. W.

    2015-01-01

    Small pollutant concentration gradients between levels above a plant canopy result in large uncertainties in estimated air-surface exchange fluxes when using existing micrometeorological gradient methods, including the aerodynamic gradient method (AGM) and the modified Bowen-Ratio method (MBR). A modified micrometeorological gradient method (MGM) is proposed in this study for estimating O3 dry deposition fluxes over a forest canopy using concentration gradients between a level above and a level below the canopy top, taking advantage of relatively large gradients between these levels due to significant pollutant uptake at top layers of the canopy. The new method is compared with the AGM and MBR methods and is also evaluated using eddy-covariance (EC) flux measurements collected at the Harvard Forest Environmental Measurement Site, Massachusetts during 1993-2000. All the three gradient methods (AGM, MBR and MGM) produced similar diurnal cycles of O3 dry deposition velocity (Vd(O3)) to the EC measurements, with the MGM method being the closest in magnitude to the EC measurements. The multi-year average Vd(O3) differed significantly between these methods, with the AGM, MBR and MGM method being 2.28, 1.45 and 1.18 times of that of the EC. Sensitivity experiments identified several input parameters for the MGM method as first-order parameters that affect the estimated Vd(O3). A 10% uncertainty in the wind speed attenuation coefficient or canopy displacement height can cause about 10% uncertainty in the estimated Vd(O3). An unrealistic leaf area density vertical profile can cause an uncertainty of a factor of 2.0 in the estimated Vd(O3). Other input parameters or formulas for stability functions only caused an uncertainly of a few percent. The new method provides an alternative approach in monitoring/estimating long-term deposition fluxes of similar pollutants over tall canopies.

  1. Development and application of a UPLC-MS/MS method for the pharmacokinetic study of 10-hydroxy camptothecin and hydroxyethyl starch conjugate in rats.

    PubMed

    Li, Guofei; Cai, Cuifang; Ren, Tianyang; Tang, Xing

    2014-01-01

    With the purpose to carry out the pharmacokinetic studies of 10-hydroxy camptothecin (10-HCPT) and hydroxyethyl starch (10-HCPT-HES) conjugate, an ultraperformance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) method has been developed and validated. The analytes, 10-HCPT and the internal standard, Diphenhydramine hydrochloride were extracted with ethyl acetate-isopropanol (95:5, v/v) and separated on an ACQUITY UPLC™ BEH C18 column using a mobile phase composed of acetonitrile and water (containing 0.1% formic acid) with a linear gradient program. With positive ion electrospray ionization (ESI), the analytes were monitored on a triple quadrupole mass spectrometer in the multiple reaction monitoring (MRM) mode. Linear calibration curves were obtained over the concentration ranges of 0.5-2500ng/mL. The intra- and inter-day precisions were less than 9.8% and 10.8%, respectively. The accuracy was within 12.1%. The mean recoveries of 10-HCPT at three concentrations of 2.5, 100, 2000ng/mL were higher than 87.2%. Commercial 10-HCPT injection and 10-HCPT-HES conjugate were administered intravenously at an equal dose of 10-HCPT at 0.5mg/kg. The biological half-life of conjugate was increased significantly from 10min to 3.15h and the bioavailability was 40 times higher than 10-HCPT injection. Consequently, the proposed UPLC-ESI-MS/MS method was proved to be sensitive, specific and reliable to analyze 10-HCPT in biological samples; 10-HCPT and HES conjugate is a promising strategy for delivery of 10-HCPT with prolonged half time and improved bioavailability. PMID:24140449

  2. Method for auto-alignment of digital optical phase conjugation systems based on digital propagation

    PubMed Central

    Jang, Mooseok; Ruan, Haowen; Zhou, Haojiang; Judkewitz, Benjamin; Yang, Changhuei

    2014-01-01

    Optical phase conjugation (OPC) has enabled many optical applications such as aberration correction and image transmission through fiber. In recent years, implementation of digital optical phase conjugation (DOPC) has opened up the possibility of its use in biomedical optics (e.g. deep-tissue optical focusing) due to its ability to provide greater-than-unity OPC reflectivity (the power ratio of the phase conjugated beam and input beam to the OPC system) and its flexibility to accommodate additional wavefront manipulations. However, the requirement for precise (pixel-to-pixel matching) alignment of the wavefront sensor and the spatial light modulator (SLM) limits the practical usability of DOPC systems. Here, we report a method for auto-alignment of a DOPC system by which the misalignment between the sensor and the SLM is auto-corrected through digital light propagation. With this method, we were able to accomplish OPC playback with a DOPC system with gross sensor-SLM misalignment by an axial displacement of up to~1.5 cm, rotation and tip/tilt of ~5∘, and in-plane displacement of ~5 mm (dependent on the physical size of the sensor and the SLM). Our auto-alignment method robustly achieved a DOPC playback peak-to-background ratio (PBR) corresponding to more than ~30 % of the theoretical maximum. As an additional advantage, the auto-alignment procedure can be easily performed at will and, as such, allows us to correct for small mechanical drifts within the DOPC systems, thus overcoming a previously major DOPC system vulnerability. We believe that this reported method for implementing robust DOPC systems will broaden the practical utility of DOPC systems. PMID:24977504

  3. Method for auto-alignment of digital optical phase conjugation systems based on digital propagation.

    PubMed

    Jang, Mooseok; Ruan, Haowen; Zhou, Haojiang; Judkewitz, Benjamin; Yang, Changhuei

    2014-06-16

    Optical phase conjugation (OPC) has enabled many optical applications such as aberration correction and image transmission through fiber. In recent years, implementation of digital optical phase conjugation (DOPC) has opened up the possibility of its use in biomedical optics (e.g. deep-tissue optical focusing) due to its ability to provide greater-than-unity OPC reflectivity (the power ratio of the phase conjugated beam and input beam to the OPC system) and its flexibility to accommodate additional wavefront manipulations. However, the requirement for precise (pixel-to-pixel matching) alignment of the wavefront sensor and the spatial light modulator (SLM) limits the practical usability of DOPC systems. Here, we report a method for auto-alignment of a DOPC system by which the misalignment between the sensor and the SLM is auto-corrected through digital light propagation. With this method, we were able to accomplish OPC playback with a DOPC system with gross sensor-SLM misalignment by an axial displacement of up to~1.5 cm, rotation and tip/tilt of ~5° and in-plane displacement of ~5 mm (dependent on the physical size of the sensor and the SLM). Our auto-alignment method robustly achieved a DOPC playback peak-to-background ratio (PBR) corresponding to more than ~30 % of the theoretical maximum. As an additional advantage, the auto-alignment procedure can be easily performed at will and, as such, allows us to correct for small mechanical drifts within the DOPC systems, thus overcoming a previously major DOPC system vulnerability. We believe that this reported method for implementing robust DOPC systems will broaden the practical utility of DOPC systems. PMID:24977504

  4. An analysis method for evaluating gradient-index fibers based on Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Yoshida, S.; Horiuchi, S.; Ushiyama, Z.; Yamamoto, M.

    2011-05-01

    We propose a numerical analysis method for evaluating gradient-index (GRIN) optical fiber using the Monte Carlo method. GRIN optical fibers are widely used in optical information processing and communication applications, such as an image scanner, fax machine, optical sensor, and so on. An important factor which decides the performance of GRIN optical fiber is modulation transfer function (MTF). The MTF of a fiber is swayed by condition of manufacturing process such as temperature. Actual measurements of the MTF of a GRIN optical fiber using this method closely match those made by conventional methods. Experimentally, the MTF is measured using a square wave chart, and is then calculated based on the distribution of output strength on the chart. In contrast, the general method using computers evaluates the MTF based on a spot diagram made by an incident point light source. But the results differ greatly from those by experiment. In this paper, we explain the manufacturing process which affects the performance of GRIN optical fibers and a new evaluation method similar to the experimental system based on the Monte Carlo method. We verified that it more closely matches the experimental results than the conventional method.

  5. A new gradient shimming method based on undistorted field map of B0 inhomogeneity.

    PubMed

    Bao, Qingjia; Chen, Fang; Chen, Li; Song, Kan; Liu, Zao; Liu, Chaoyang

    2016-04-01

    Most existing gradient shimming methods for NMR spectrometers estimate field maps that resolve B0 inhomogeneity spatially from dual gradient-echo (GRE) images acquired at different echo times. However, the distortions induced by B0 inhomogeneity that always exists in the GRE images can result in estimated field maps that are distorted in both geometry and intensity, leading to inaccurate shimming. This work proposes a new gradient shimming method based on undistorted field map of B0 inhomogeneity obtained by a more accurate field map estimation technique. Compared to the traditional field map estimation method, this new method exploits both the positive and negative polarities of the frequency encoded gradients to eliminate the distortions caused by B0 inhomogeneity in the field map. Next, the corresponding automatic post-data procedure is introduced to obtain undistorted B0 field map based on knowledge of the invariant characteristics of the B0 inhomogeneity and the variant polarity of the encoded gradient. The experimental results on both simulated and real gradient shimming tests demonstrate the high performance of this new method. PMID:26851711

  6. A new gradient shimming method based on undistorted field map of B0 inhomogeneity

    NASA Astrophysics Data System (ADS)

    Bao, Qingjia; Chen, Fang; Chen, Li; Song, Kan; Liu, Zao; Liu, Chaoyang

    2016-04-01

    Most existing gradient shimming methods for NMR spectrometers estimate field maps that resolve B0 inhomogeneity spatially from dual gradient-echo (GRE) images acquired at different echo times. However, the distortions induced by B0 inhomogeneity that always exists in the GRE images can result in estimated field maps that are distorted in both geometry and intensity, leading to inaccurate shimming. This work proposes a new gradient shimming method based on undistorted field map of B0 inhomogeneity obtained by a more accurate field map estimation technique. Compared to the traditional field map estimation method, this new method exploits both the positive and negative polarities of the frequency encoded gradients to eliminate the distortions caused by B0 inhomogeneity in the field map. Next, the corresponding automatic post-data procedure is introduced to obtain undistorted B0 field map based on knowledge of the invariant characteristics of the B0 inhomogeneity and the variant polarity of the encoded gradient. The experimental results on both simulated and real gradient shimming tests demonstrate the high performance of this new method.

  7. Methods for Fabricating Gradient Alloy Articles with Multi-Functional Properties

    NASA Technical Reports Server (NTRS)

    Hofmann, Douglas C. (Inventor); Borgonia, John Paul C. (Inventor); Dillon, Robert P. (Inventor); Suh, Eric J. (Inventor); Mulder, Jerry L. (Inventor); Gardner, Paul B. (Inventor)

    2015-01-01

    Systems and methods for fabricating multi-functional articles comprised of additively formed gradient materials are provided. The fabrication of multi-functional articles using the additive deposition of gradient alloys represents a paradigm shift from the traditional way that metal alloys and metal/metal alloy parts are fabricated. Since a gradient alloy that transitions from one metal to a different metal cannot be fabricated through any conventional metallurgy techniques, the technique presents many applications. Moreover, the embodiments described identify a broad range of properties and applications.

  8. Analyzing Longitudinal Magnetoresistance Asymmetry to Quantify Doping Gradients: Generalization of the van der Pauw Method.

    PubMed

    Zhou, Wang; Yoo, H M; Prabhu-Gaunkar, S; Tiemann, L; Reichl, C; Wegscheider, W; Grayson, M

    2015-10-30

    A longitudinal magnetoresistance asymmetry (LMA) between a positive and negative magnetic field is known to occur in both the extreme quantum limit and the classical Drude limit in samples with a nonuniform doping density. By analyzing the current stream function in van der Pauw measurement geometry, it is shown that the electron density gradient can be quantitatively deduced from this LMA in the Drude regime. Results agree with gradients interpolated from local densities calibrated across an entire wafer, establishing a generalization of the van der Pauw method to quantify density gradients. PMID:26565488

  9. Analyzing Longitudinal Magnetoresistance Asymmetry to Quantify Doping Gradients: Generalization of the van der Pauw Method

    NASA Astrophysics Data System (ADS)

    Zhou, Wang; Yoo, H. M.; Prabhu-Gaunkar, S.; Tiemann, L.; Reichl, C.; Wegscheider, W.; Grayson, M.

    2015-10-01

    A longitudinal magnetoresistance asymmetry (LMA) between a positive and negative magnetic field is known to occur in both the extreme quantum limit and the classical Drude limit in samples with a nonuniform doping density. By analyzing the current stream function in van der Pauw measurement geometry, it is shown that the electron density gradient can be quantitatively deduced from this LMA in the Drude regime. Results agree with gradients interpolated from local densities calibrated across an entire wafer, establishing a generalization of the van der Pauw method to quantify density gradients.

  10. Coherent gradient sensing method and system for measuring surface curvature

    NASA Technical Reports Server (NTRS)

    Rosakis, Ares J. (Inventor); Singh, Ramen P. (Inventor); Kolawa, Elizabeth (Inventor); Moore, Jr., Nicholas R. (Inventor)

    2000-01-01

    A system and method for determining a curvature of a specularly reflective surface based on optical interference. Two optical gratings are used to produce a spatial displacement in an interference field of two different diffraction components produced by one grating from different diffraction components produced by another grating. Thus, the curvature of the surface can be determined.

  11. Advantages of horizontal directional Theta method to detect the edges of full tensor gravity gradient data

    NASA Astrophysics Data System (ADS)

    Yuan, Yuan; Gao, Jin-Yao; Chen, Ling-Na

    2016-07-01

    Full tensor gravity gradient data contain nine signal components. They include higher frequency signals than traditional gravity data, which can extract the small-scale features of the sources. Edge detection has played an important role in the interpretation of potential-field data. There are many methods that have been proposed to detect and enhance the edges of geological bodies based on horizontal and vertical derivatives of potential-field data. In order to make full use of all the measured gradient components, we need to develop a new edge detector to process the full tensor gravity gradient data. We first define the directional Theta and use the horizontal directional Theta to define a new edge detector. This method was tested on synthetic and real full tensor gravity gradient data to validate its feasibility. Compared the results with other balanced detectors, the new detector can effectively delineate the edges and does not produce any additional false edges.

  12. An improved wavefront determination method based on phase conjugation for imaging through thin scattering medium

    NASA Astrophysics Data System (ADS)

    He, Hexiang; Wong, Kam Sing

    2016-08-01

    Wavefront shaping applied on scattering light is an efficient method for imaging through thin scattering layers. Normally, optimized modulation can be obtained by a liquid-crystal spatial light modulator (LCSLM) and CCD hardware iteration. In this paper, an improved method for such an optimization process is introduced. The core of the proposed method is to firstly detect the disturbed wavefront, and then to calculate the modulation phase pattern by computer simulation. Fast processing speed resulting in high quality images have been achieved with this new approach. Using supposition of conjugated phase of the scattering wavefront and a Fresnel phase scheme, more than two orders of magnitude improvement in processing speed for imaging restoration was shown compared to the LCSLM-CCD iteration method.

  13. A comparison of gradient estimation methods for volume rendering on unstructured meshes.

    PubMed

    Correa, Carlos D; Hero, Robert; Ma, Kwan-Liu

    2011-03-01

    This paper presents a study of gradient estimation methods for rendering unstructured-mesh volume data. Gradient estimation is necessary for rendering shaded isosurfaces and specular highlights, which provide important cues for shape and depth. Gradient estimation has been widely studied and deployed for regular-grid volume data to achieve local illumination effects, but has been, otherwise, for unstructured-mesh data. As a result, most of the unstructured-mesh volume visualizations made so far were unlit. In this paper, we present a comprehensive study of gradient estimation methods for unstructured meshes with respect to their cost and performance. Through a number of benchmarks, we discuss the effects of mesh quality and scalar function complexity in the accuracy of the reconstruction, and their impact in lighting-enabled volume rendering. Based on our study, we also propose two heuristic improvements to the gradient reconstruction process. The first heuristic improves the rendering quality with a hybrid algorithm that combines the results of the multiple reconstruction methods, based on the properties of a given mesh. The second heuristic improves the efficiency of its GPU implementation, by restricting the computation of the gradient on a fixed-size local neighborhood. PMID:21233515

  14. Development and Application of a Label-Free Fluorescence Method for Determining the Composition of Gold Nanoparticle–Protein Conjugates

    PubMed Central

    Sotnikov, Dmitriy V.; Zherdev, Anatoly V.; Dzantiev, Boris B.

    2014-01-01

    A method was developed for determining the composition of the conjugates between gold nanoparticles and proteins based on the intrinsic fluorescence of unbound protein molecules. The fluorescence was evaluated after separation of the conjugates from the reaction mixture by centrifugation. Gold nanoparticles obtained using the citrate technique (average diameter 24 nm) were conjugated at pH 5.4 with the following four proteins: human immunoglobulin G (IgG), bovine serum albumin (BSA), recombinant streptococcal protein G (protein G), and Kunitz-type soybean trypsin inhibitor (STI). The compositions of these conjugates were determined using the developed method. The conjugate compositions were dependent on the concentration of the added protein, and in all cases reached saturation. The equilibrium dissociation constants of the gold nanoparticle conjugates with IgG, BSA, protein G, STI in the initial section of the concentration dependence curve were 4, 6, 10, and 15 nM, respectively. Close to saturation, the corresponding values were 25, 76, 175, and 100 nM, respectively. The maximal binding capacities of a single gold nanoparticle for IgG, BSA, Protein G, and STI were 52, 90, 500, and 550, respectively, which agrees well with the hypothesis of monolayer immobilization. PMID:25561238

  15. HNO 3 fluxes to a deciduous forest derived using gradient and REA methods

    NASA Astrophysics Data System (ADS)

    Pryor, S. C.; Barthelmie, R. J.; Jensen, B.; Jensen, N. O.; Sørensen, L. L.

    Summertime nitric acid concentrations over a deciduous forest in the midwestern United States are reported, which range between 0.36 and 3.3 μg m -3. Fluxes to the forest are computed using the relaxed eddy accumulation technique and gradient methods. In accord with previous studies, the results indicate substantial uncertainties in the gradient-based calculations. The relaxed eddy accumulation (REA) derived fluxes are physically reasonable and are shown to be of similar magnitude to dry deposition estimates from gradient sampling. The REA derived mean deposition velocity is approximately 3 cm s -1, which is also comparable to growing season estimates derived by Meyers et al. for a similar deciduous forest. Occasional inverted concentration gradients and fluxes are observed but most are not statistically significant. Data are also presented that indicate substantial through canopy penetration of nitric acid.

  16. ILUBCG2-11: Solution of 11-banded nonsymmetric linear equation systems by a preconditioned biconjugate gradient routine

    NASA Astrophysics Data System (ADS)

    Chen, Y.-M.; Koniges, A. E.; Anderson, D. V.

    1989-10-01

    The biconjugate gradient method (BCG) provides an attractive alternative to the usual conjugate gradient algorithms for the solution of sparse systems of linear equations with nonsymmetric and indefinite matrix operators. A preconditioned algorithm is given, whose form resembles the incomplete L-U conjugate gradient scheme (ILUCG2) previously presented. Although the BCG scheme requires the storage of two additional vectors, it converges in a significantly lesser number of iterations (often half), while the number of calculations per iteration remains essentially the same.

  17. A simple method for MR elastography: a gradient-echo type multi-echo sequence.

    PubMed

    Numano, Tomokazu; Mizuhara, Kazuyuki; Hata, Junichi; Washio, Toshikatsu; Homma, Kazuhiro

    2015-01-01

    To demonstrate the feasibility of a novel MR elastography (MRE) technique based on a conventional gradient-echo type multi-echo MR sequence which does not need additional bipolar magnetic field gradients (motion encoding gradient: MEG), yet is sensitive to vibration. In a gradient-echo type multi-echo MR sequence, several images are produced from each echo of the train with different echo times (TEs). If these echoes are synchronized with the vibration, each readout's gradient lobes achieve a MEG-like effect, and the later generated echo causes a greater MEG-like effect. The sequence was tested for the tissue-mimicking agarose gel phantoms and the psoas major muscles of healthy volunteers. It was confirmed that the readout gradient lobes caused an MEG-like effect and the later TE images had higher sensitivity to vibrations. The magnitude image of later generated echo suffered the T2 decay and the susceptibility artifacts, but the wave image and elastogram of later generated echo were unaffected by these effects. In in vivo experiments, this method was able to measure the mean shear modulus of the psoas major muscle. From the results of phantom experiments and volunteer studies, it was shown that this method has clinical application potential. PMID:25311570

  18. Basic theory and experimental techniques of the strain-gradient method

    SciTech Connect

    Hecker, F.W.; Pindera, J.T.

    1987-09-01

    The theories of presently used experimental methods of stress and deformation analysis which employ radiant energy as a detector are based on the assumption that light propagates rectilinearly within both undeformed and deformed bodies which are initially homogeneous and isotropic when diffraction phenomena are negligible. This assumption is not correct: light propagation within deformed bodies is nonrectilinear in a general case. Although this has already been observed and applied practically by some researchers in photoelasticity, it has not so far been generally acknowledged and accepted in experimental mechanics. On the basis of empirical data produced in the period 1948-1983, theories and foundations are presented for a new experimental method which is based on the relations between stress/strain gradients and curvatures of light beams. This method is called the strain-gradient method or, less rigorously, gradient photoelasticity. 39 references.

  19. Refractive index gradient measurement across the thickness of a dielectric film by the prism coupling method

    SciTech Connect

    Sokolov, Viktor I; Panchenko, Vladislav Ya; Seminogov, V N

    2012-08-31

    A method is proposed for measuring the refractive index gradient n(z) in nonuniformly thick dielectric films. The method is based on the excitation of waveguide modes in a film using the prism coupling technique and on the calculation of n(z) and film thickness H{sub f} with the help of the angular positions of the TE or TM modes. The method can be used for an arbitrary shape of the index modulation over the film thickness in the limit of a small gradient [{Delta} n(z)/n(z) || 1]. (laser applications and other topics in quantum electronics)

  20. [Head and Neck Tumor Segmentation Based on Augmented Gradient Level Set Method].

    PubMed

    Zhang, Qiongmin; Zhang, Jing; Wang, Mintang; He, Ling; Men, Yi; Wei, Jun; Haung, Hua

    2015-08-01

    To realize the accurate positioning and quantitative volume measurement of tumor in head and neck tumor CT images, we proposed a level set method based on augmented gradient. With the introduction of gradient information in the edge indicator function, our proposed level set model is adaptive to different intensity variation, and achieves accurate tumor segmentation. The segmentation result has been used to calculate tumor volume. In large volume tumor segmentation, the proposed level set method can reduce manual intervention and enhance the segmentation accuracy. Tumor volume calculation results are close to the gold standard. From the experiment results, the augmented gradient based level set method has achieved accurate head and neck tumor segmentation. It can provide useful information to computer aided diagnosis. PMID:26710464

  1. Optimization with artificial neural network systems - A mapping principle and a comparison to gradient based methods

    NASA Technical Reports Server (NTRS)

    Leong, Harrison Monfook

    1988-01-01

    General formulae for mapping optimization problems into systems of ordinary differential equations associated with artificial neural networks are presented. A comparison is made to optimization using gradient-search methods. The performance measure is the settling time from an initial state to a target state. A simple analytical example illustrates a situation where dynamical systems representing artificial neural network methods would settle faster than those representing gradient-search. Settling time was investigated for a more complicated optimization problem using computer simulations. The problem was a simplified version of a problem in medical imaging: determining loci of cerebral activity from electromagnetic measurements at the scalp. The simulations showed that gradient based systems typically settled 50 to 100 times faster than systems based on current neural network optimization methods.

  2. Conjugation of R-Phycoerythrin to a Polyclonal Antibody and F (ab')2 Fragment of a Polyclonal Antibody by Two Different Methods.

    PubMed

    Mahmoudian, Jafar; Jeddi-Tehrani, Mahmood; Rabbani, Hodjattallah; Mahmoudi, Ahmad Reza; Akhondi, Mohammad Mehdi; Zarnani, Amir Hassan; Goli, Leila Balaei; Babaei, Mahdokht; Ghods, Roya

    2010-04-01

    R-Phycoerythrin (R-PE), a fluorescent protein from phycobiliprotein family, is isolated from red algae. Conjugation of antibodies to R-PE facilitates multiple fluorescent staining methods. In the present study polyclonal antibodies and polyclonal F(ab')2 fragment antibodies were conjugated to R-PE by two different methods. The efficiency of the methods was evaluated using Immunocytochemistry (ICC) and Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE). In the first conjugation method, PE was attached to SMCC linker followed by conjugation of antibody to PE-SMCC. In the second method, SH groups were added onto R-PE molecule, while the antibody was attached to SPDP linker. Then, the antibody-SPDP molecule was conjugated to R-PE. Our results showed that the two conjugation methods did not have any abrogative effects on the antibody binding activity. PMID:23407609

  3. Stable iteratively regularized gradient method for nonlinear irregular equations under large noise

    NASA Astrophysics Data System (ADS)

    Kokurin, Mihail Yu

    2006-02-01

    We consider an iteratively regularized version of the method of gradient descent for solving nonlinear irregular equations F(x) = 0 in a Hilbert space. When studying regularization methods for such equations with noisy operators F, traditional conditions on available approximations {\\skew3\\widetilde{F}} amount to error estimates of the form \\Vert {\\skew3\\widetilde{F}}(x)- F(x) \\Vert \\leq \\delta , for x from a neighbourhood of a solution. Convergence of the methods is usually established on the assumption that the error level δ → 0, i.e. that noisy elements {\\skew3\\widetilde{F}}(x) strongly converge to the exact value F(x). In this paper we analyse approximating properties of the regularized gradient method assuming that {\\skew3\\widetilde{F}}(x) may converge to F(x) only weakly. We suggest an a priori stopping rule for the gradient iteration and give error estimates for obtained approximate solutions in terms of levels of strong and weak perturbations of the original operator. The main theorem generalizes recent results of Bakushinsky and Kokurin (2004 Iterative Methods for Approximate Solution of Inverse Problems (Dordrecht: Springer)) on the stopping of regularized gradient method under strong perturbations of F.

  4. A new robust gradient-based method for detection of symmetry axis

    NASA Astrophysics Data System (ADS)

    Hu, Jing; Wan, Qinqi; Hu, Yongli

    2015-12-01

    Symmetry axis extraction is an important part of the image feature detection. So far, various classical symmetry axes extraction algorithms have been proposed, such as the minimum-inertia-axis-based method, the SIFT-based method. If the input image is blurry, or it's difficult to extract feature points or corner points from input images, however, the above algorithms are difficult to obtain satisfied results. This paper presents a gradient-based method that can robustly extract symmetry axis from visual pattern. The key points of our methods are gradient calculation, symmetric weight calculation, and Hough Transform. Our method was evaluated on several datasets, including both blurred and smooth-edged cases. Experimental results demonstrated that our method achieves a more robust performance than previous methods.

  5. Gradient Calculation Methods on Arbitrary Polyhedral Unstructured Meshes for Cell-Centered CFD Solvers

    NASA Technical Reports Server (NTRS)

    Sozer, Emre; Brehm, Christoph; Kiris, Cetin C.

    2014-01-01

    A survey of gradient reconstruction methods for cell-centered data on unstructured meshes is conducted within the scope of accuracy assessment. Formal order of accuracy, as well as error magnitudes for each of the studied methods, are evaluated on a complex mesh of various cell types through consecutive local scaling of an analytical test function. The tests highlighted several gradient operator choices that can consistently achieve 1st order accuracy regardless of cell type and shape. The tests further offered error comparisons for given cell types, leading to the observation that the "ideal" gradient operator choice is not universal. Practical implications of the results are explored via CFD solutions of a 2D inviscid standing vortex, portraying the discretization error properties. A relatively naive, yet largely unexplored, approach of local curvilinear stencil transformation exhibited surprisingly favorable properties

  6. Surface profile and stress field evaluation using digital gradient sensing method

    NASA Astrophysics Data System (ADS)

    Miao, C.; Sundaram, B. M.; Huang, L.; Tippur, H. V.

    2016-09-01

    Shape and surface topography evaluation from measured orthogonal slope/gradient data is of considerable engineering significance since many full-field optical sensors and interferometers readily output such a data accurately. This has applications ranging from metrology of optical and electronic elements (lenses, silicon wafers, thin film coatings), surface profile estimation, wave front and shape reconstruction, to name a few. In this context, a new methodology for surface profile and stress field determination based on a recently introduced non-contact, full-field optical method called digital gradient sensing (DGS) capable of measuring small angular deflections of light rays coupled with a robust finite-difference-based least-squares integration (HFLI) scheme in the Southwell configuration is advanced here. The method is demonstrated by evaluating (a) surface profiles of mechanically warped silicon wafers and (b) stress gradients near growing cracks in planar phase objects.

  7. Generalization of the van der Pauw Method: Analyzing Longitudinal Magnetoresistance Asymmetry to Quantify Doping Gradients

    NASA Astrophysics Data System (ADS)

    Grayson, M.; Zhou, Wang; Yoo, Heun-Mo; Prabhu-Gaunkar, S.; Tiemann, L.; Reichl, C.; Wegscheider, W.

    A longitudinal magnetoresistance asymmetry (LMA) between a positive and negative magnetic field is known to occur in both the extreme quantum limit and the classical Drude limit in samples with a nonuniform doping density. By analyzing the current stream function in van der Pauw measurement geometry, it is shown that the electron density gradient can be quantitatively deduced from this LMA in the Drude regime. Results agree with gradients interpolated from local densities calibrated across an entire wafer, establishing a generalization of the van der Pauw method to quantify density gradients. Results will be shown of various semoconductor systems where this method is applied, from bulk doped semiconductors, to exfoliated 2D materials. McCormick Catalyst Award from Northwestern University, EECS Bridge Funding, and AFOSR FA9550-15-1-0247.

  8. Microreactor and method for preparing a radiolabeled complex or a biomolecule conjugate

    SciTech Connect

    Reichert, David E; Kenis, Paul J. A.; Wheeler, Tobias D; Desai, Amit V; Zeng, Dexing; Onal, Birce C

    2015-03-17

    A microreactor for preparing a radiolabeled complex or a biomolecule conjugate comprises a microchannel for fluid flow, where the microchannel comprises a mixing portion comprising one or more passive mixing elements, and a reservoir for incubating a mixed fluid. The reservoir is in fluid communication with the microchannel and is disposed downstream of the mixing portion. A method of preparing a radiolabeled complex includes flowing a radiometal solution comprising a metallic radionuclide through a downstream mixing portion of a microchannel, where the downstream mixing portion includes one or more passive mixing elements, and flowing a ligand solution comprising a bifunctional chelator through the downstream mixing portion. The ligand solution and the radiometal solution are passively mixed while in the downstream mixing portion to initiate a chelation reaction between the metallic radionuclide and the bifunctional chelator. The chelation reaction is completed to form a radiolabeled complex.

  9. A method for controlling the synthesis of stable twisted two-dimensional conjugated molecules.

    PubMed

    Li, Yongjun; Jia, Zhiyu; Xiao, Shengqiang; Liu, Huibiao; Li, Yuliang

    2016-01-01

    Thermodynamic stabilization (π-electron delocalization through effective conjugation) and kinetic stabilization (blocking the most-reactive sites) are important considerations when designing stable polycyclic aromatic hydrocarbons displaying tunable optoelectronic properties. Here, we demonstrate an efficient method for preparing a series of stable two-dimensional (2D) twisted dibenzoterrylene-acenes. We investigated their electronic structures and geometries in the ground state through various experiments assisted by calculations using density functional theory. We find that the length of the acene has a clear effect on the photophysical, electrochemical, and magnetic properties. These molecules exhibit tunable ground-state structures, in which a stable open-shell quintet tetraradical can be transferred to triplet diradicals. Such compounds are promising candidates for use in nonlinear optics, field effect transistors and organic spintronics; furthermore, they may enable broader applications of 2D small organic molecules in high-performance electronic and optical devices. PMID:27181692

  10. A method for controlling the synthesis of stable twisted two-dimensional conjugated molecules

    PubMed Central

    Li, Yongjun; Jia, Zhiyu; Xiao, Shengqiang; Liu, Huibiao; Li, Yuliang

    2016-01-01

    Thermodynamic stabilization (π-electron delocalization through effective conjugation) and kinetic stabilization (blocking the most-reactive sites) are important considerations when designing stable polycyclic aromatic hydrocarbons displaying tunable optoelectronic properties. Here, we demonstrate an efficient method for preparing a series of stable two-dimensional (2D) twisted dibenzoterrylene-acenes. We investigated their electronic structures and geometries in the ground state through various experiments assisted by calculations using density functional theory. We find that the length of the acene has a clear effect on the photophysical, electrochemical, and magnetic properties. These molecules exhibit tunable ground-state structures, in which a stable open-shell quintet tetraradical can be transferred to triplet diradicals. Such compounds are promising candidates for use in nonlinear optics, field effect transistors and organic spintronics; furthermore, they may enable broader applications of 2D small organic molecules in high-performance electronic and optical devices. PMID:27181692

  11. Using the gradient method to measure soil gas fluxes: limitations and pitfalls

    NASA Astrophysics Data System (ADS)

    Martin, Martin; Schack-Kirchner, Helmer

    2015-04-01

    The gradient method (De Jong & Schappert,1974) can be used to determine gas efflux from the soil, representing an alternative to the widely used chamber methods. In addition, valuable information about the vertical distribution of the sources/sinks of gas (e.g. CO2, CH4) in the soil can be derived. Although the method seems to be simple, care must be taken whether all assumption and simplifications are made: (1) Diffusion only: Gas transport can be described by Fick's law. (2) 1D vertical gas diffusion: No horizontal concentration gradients. (3) Gas diffusion in the soil is at steady-state: Changes are negligible. If the preconditions are not met, the gradient method may yield unreliable results. We tried to address some of these and further issues in different studies. We identified the method used to interpolate the gas concentration profile between the measurement locations as an issue affecting substantially the calculated efflux and vertical partitioning. Another critical issue is deriving the correct soil gas diffusivity. The assumption of steady-state diffusion is not always justified, especially after rain, and may lead to substantial misinterpretation if ignored. We also observed that soil gas transport can be affected by turbulence-driven pressure-pumping, so that the effect of non-diffusive gas transport must be considered. The Temporal and spatial resolution must match the research question and gas species. The gradient method is a valuable tool , that, Ideally, the GM should be used on well aerated, horizontally homogeneous soils where gas exchange is entirely driven by diffusion. Here the gradient method promises to yield reliable results when soil respiration and methane consumption is studied. Substantial discrepancy in these conditions could lead to increasing uncertainty in the flux estimates

  12. Edge gradients evaluation for 2D hybrid finite volume method model

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this study, a two-dimensional depth-integrated hydrodynamic model was developed using FVM on a hybrid unstructured collocated mesh system. To alleviate the negative effects of mesh irregularity and non-uniformity, a conservative evaluation method for edge gradients based on the second-order Tayl...

  13. Maximum Power Point Tracking with Dichotomy and Gradient Method for Automobile Exhaust Thermoelectric Generators

    NASA Astrophysics Data System (ADS)

    Fang, W.; Quan, S. H.; Xie, C. J.; Tang, X. F.; Wang, L. L.; Huang, L.

    2016-03-01

    In this study, a direct-current/direct-current (DC/DC) converter with maximum power point tracking (MPPT) is developed to down-convert the high voltage DC output from a thermoelectric generator to the lower voltage required to charge batteries. To improve the tracking accuracy and speed of the converter, a novel MPPT control scheme characterized by an aggregated dichotomy and gradient (ADG) method is proposed. In the first stage, the dichotomy algorithm is used as a fast search method to find the approximate region of the maximum power point. The gradient method is then applied for rapid and accurate tracking of the maximum power point. To validate the proposed MPPT method, a test bench composed of an automobile exhaust thermoelectric generator was constructed for harvesting the automotive exhaust heat energy. Steady-state and transient tracking experiments under five different load conditions were carried out using a DC/DC converter with the proposed ADG and with three traditional methods. The experimental results show that the ADG method can track the maximum power within 140 ms with a 1.1% error rate when the engine operates at 3300 rpm@71 NM, which is superior to the performance of the single dichotomy method, the single gradient method and the perturbation and observation method from the viewpoint of improved tracking accuracy and speed.

  14. Cutting-edge mass spectrometry methods for the multi-level structural characterization of antibody-drug conjugates.

    PubMed

    Beck, Alain; Terral, Guillaume; Debaene, François; Wagner-Rousset, Elsa; Marcoux, Julien; Janin-Bussat, Marie-Claire; Colas, Olivier; Dorsselaer, Alain Van; Cianférani, Sarah

    2016-02-01

    Antibody drug conjugates (ADCs) are highly cytotoxic drugs covalently attached via conditionally stable linkers to monoclonal antibodies (mAbs) and are among the most promising next-generation empowered biologics for cancer treatment. ADCs are more complex than naked mAbs, as the heterogeneity of the conjugates adds to the inherent microvariability of the biomolecules. The development and optimization of ADCs rely on improving their analytical and bioanalytical characterization by assessing several critical quality attributes, namely the distribution and position of the drug, the amount of naked antibody, the average drug to antibody ratio, and the residual drug-linker and related product proportions. Here brentuximab vedotin (Adcetris®) and trastuzumab emtansine (Kadcyla®), the first and gold-standard hinge-cysteine and lysine drug conjugates, respectively, were chosen to develop new mass spectrometry (MS) methods and to improve multiple-level structural assessment protocols. PMID:26653789

  15. A projection gradient method for computing ground state of spin-2 Bose–Einstein condensates

    SciTech Connect

    Wang, Hanquan

    2014-10-01

    In this paper, a projection gradient method is presented for computing ground state of spin-2 Bose–Einstein condensates (BEC). We first propose the general projection gradient method for solving energy functional minimization problem under multiple constraints, in which the energy functional takes real functions as independent variables. We next extend the method to solve a similar problem, where the energy functional now takes complex functions as independent variables. We finally employ the method into finding the ground state of spin-2 BEC. The key of our method is: by constructing continuous gradient flows (CGFs), the ground state of spin-2 BEC can be computed as the steady state solution of such CGFs. We discretized the CGFs by a conservative finite difference method along with a proper way to deal with the nonlinear terms. We show that the numerical discretization is normalization and magnetization conservative and energy diminishing. Numerical results of the ground state and their energy of spin-2 BEC are reported to demonstrate the effectiveness of the numerical method.

  16. STABILIZATION OF A RACTOPAMINE ENZYME CONJUGATE IN AQUEOUS SOLUTION, A RAPID AND CONVENIENT IMMUNOASSAY METHOD FOR THE DETECTION OF RACTOPAMINE.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is an increasing demand for a sensitive screening method for ractopamine because of the zero tolerance policy in many countries. Most of the commercially available ractopamine ELISA kits require concentrated conjugate to be diluted prior to use. We have observed that the highly diluted racto...

  17. Simple Method To Prepare Oligonucleotide-Conjugated Antibodies and Its Application in Multiplex Protein Detection in Single Cells.

    PubMed

    Gong, Haibiao; Holcomb, Ilona; Ooi, Aik; Wang, Xiaohui; Majonis, Daniel; Unger, Marc A; Ramakrishnan, Ramesh

    2016-01-20

    The diversity of nucleic acid sequences enables genomics studies in a highly multiplexed format. Since multiplex protein detection is still a challenge, it would be useful to use genomics tools for this purpose. This can be accomplished by conjugating specific oligonucleotides to antibodies. Upon binding of the oligonucleotide-conjugated antibodies to their targets, the protein levels can be converted to oligonucleotide levels. In this report we describe a simple method for preparing oligonucleotide-conjugated antibodies and discuss this method's application in oligonucleotide extension reaction (OER) for multiplex protein detection. Conjugation is based on strain-promoted alkyne-azide cycloaddition (the Cu-free click reaction), in which the antibody is activated with a dibenzocyclooctyne (DBCO) moiety and subsequently linked covalently with an azide-modified oligonucleotide. In the functional test, the reaction conditions and purification processes were optimized to achieve maximum yield and best performance. The OER assay employs a pair of antibody binders (two antibodies, each conjugated with its own oligonucleotide) developed for each protein target. The two oligonucleotides contain unique six-base complementary regions at their 3' prime ends to allow annealing and extension by DNA synthesis enzymes to form a DNA template. Following preamplification, the DNA template is detected by qPCR. Distinct oligonucleotide sequences are assigned to different antibody binders to enable multiplex protein detection. When tested using recombinant proteins, some antibody binders, such as those specific to CSTB, MET, EpCAM, and CASP3, had dynamic ranges of 5-6 logs. The antibody binders were also used in a multiplexed format in OER assays, and the binders successfully detected their protein targets in cell lysates, and in single cells in combination with the C1 system. This click reaction-based antibody conjugation procedure is cost-effective, needs minimal hands-on time, and

  18. Interpretation of Gravity Anomalies with the Normalized Full Gradient (NFG) Method and an Example

    NASA Astrophysics Data System (ADS)

    Aydin, Ali

    2007-12-01

    The Normalized Full Gradient (NFG) method which was put forward about 50 years ago has been used for downward continuation of gravity potential data, especially in the former Union of Soviet Socialist Republics. This method nullifies perturbations due to the passage of mass depth during downward continuation. The method depends on the downwards analytical continuation of normalized full gradient values of gravity data. Analytical continuation discriminates certain structural anomalies which cannot be distinguished in the observed gravity field. This method has been used in various petroleum and tectonic studies. The Trapeze method was used for the determination of Fourier coefficients during the application of this method. No other techniques for calculating these coefficients have been used. However, the Filon method was used for the determination of Fourier coefficients during the application of the NFG method in this work. This method, rather than the Trapeze method, should be preferred for indicating abnormal mass resources at the lower harmonics. In this study, the NFG method using the Filon method has been applied the first time to theoretical models of gravity profiles as example field at the Hasankale-Horasan petroleum exploration province where successful results were achieved. Hydrocarbon presence was shown on the NFG sections by the application of NFG downward continuation operations on theoretical models. Important signs of hydrocarbon structure on the NFG section for field and model data at low harmonics are obtained more effectively using this method.

  19. Escherichia hermannii (ATCC 33651) polysaccharide-protein conjugates: comparison of two conjugation methods for the induction of humoral responses in mice.

    PubMed

    Jacques, I; Dubray, G

    1991-08-01

    Escherichia hermannii (ATCC 33651) LPS O-polysaccharide was covalently linked to a carrier (bovine serum albumin) to form conjugates either directly or with a spacer arm (adipic acid dihydrazide). The immunogenicity of both conjugates at three different doses was tested in mice. Antibodies to the conjugate were produced and were shown to react with free lipopolysaccharide. The directly-coupled conjugate was found to be more immunogenic than the indirect one (i.e. lower dose necessary for a similar response). The antibody response elicited by the directly coupled conjugate (1 microgram/animal) began at 21 days and was sustained for at least 4 months. The mouse model described here may be applicable to the testing of other conjugates composed of bacterial cell wall polysaccharides and LPS O-chains. PMID:1771969

  20. Dynamics of the adaptive natural gradient descent method for soft committee machines

    NASA Astrophysics Data System (ADS)

    Inoue, Masato; Park, Hyeyoung; Okada, Masato

    2004-05-01

    Adaptive natural gradient descent (ANGD) method realizes natural gradient descent (NGD) without needing to know the input distribution of learning data and reduces the calculation cost from a cubic order to a square order. However, no performance analysis of ANGD has been done. We have developed a statistical-mechanical theory of the simplified version of ANGD dynamics for soft committee machines in on-line learning; this method provides deterministic learning dynamics expressed through a few order parameters, even though ANGD intrinsically holds a large approximated Fisher information matrix. Numerical results obtained using this theory were consistent with those of a simulation, with respect not only to the learning curve but also to the learning failure. Utilizing this method, we numerically evaluated ANGD efficiency and found that ANGD generally performs as well as NGD. We also revealed the key condition affecting the learning plateau in ANGD.

  1. Evaluating angular deflections from the digital gradient sensing method with rigid-motion deleted

    NASA Astrophysics Data System (ADS)

    Zhang, Rui

    2016-06-01

    The digital gradient sensing method is used for measuring small angular deflections of light rays due to local stresses in transparent planar solids. The method is based on two-dimensional (2D) digital image correlation (DIC) to measure the angular deflection of light rays; however, when a specimen is subjected to loading, deformation measurement from DIC is not perfect because of the existence of small in-plane and out-of-plane motions of the test sample surface that occurred after loading. These disadvantages will lead to errors in the measured angular deflections. The influence of unavoidable in-plane and out-of-plane motions was discussed, and a method to eliminate the influence to show the pure stress gradient of polymethy methacrylate is demonstrated.

  2. Biconjugate gradient stabilized method in image deconvolution of a wavefront coding system

    NASA Astrophysics Data System (ADS)

    Liu, Peng; Liu, Qin-xiao; Zhao, Ting-yu; Chen, Yan-ping; Yu, Fei-hong

    2013-04-01

    The point spread function (PSF) is a non-rotational symmetric for the wavefront coding (WFC) system with a cubic phase mask (CPM). Antireflective boundary conditions (BCs) are used to eliminate the ringing effect on the border and vibration on the edge of the image. The Kronecker product approximation is used to reduce the computation consumption. The image-formation process of the WFC system is transformed into a matrix equation. In order to save storage space, biconjugate gradient (Bi-CG) and biconjugate gradient stabilized (Bi-CGSTAB) methods are used to solve the asymmetric matrix equation, which is a typical iteration algorithm of the Krylov subspace using the two-side Lanczos process. Simulation and experimental results illustrate the efficiency of the proposed algorithm for the image deconvolution. The result based on the Bi-CGSTAB method is smoother than the classic Wiener filter, while preserving more details than the Truncated Singular Value Decomposition (TSVD) method.

  3. Characterization and optimization of heroin hapten-BSA conjugates: method development for the synthesis of reproducible hapten-based vaccines.

    PubMed

    Torres, Oscar B; Jalah, Rashmi; Rice, Kenner C; Li, Fuying; Antoline, Joshua F G; Iyer, Malliga R; Jacobson, Arthur E; Boutaghou, Mohamed Nazim; Alving, Carl R; Matyas, Gary R

    2014-09-01

    A potential new treatment for drug addiction is immunization with vaccines that induce antibodies that can abrogate the addictive effects of the drug of abuse. One of the challenges in the development of a vaccine against drugs of abuse is the availability of an optimum procedure that gives reproducible and high yielding hapten-protein conjugates. In this study, a heroin/morphine surrogate hapten (MorHap) was coupled to bovine serum albumin (BSA) using maleimide-thiol chemistry. MorHap-BSA conjugates with 3, 5, 10, 15, 22, 28, and 34 haptens were obtained using different linker and hapten ratios. Using this optimized procedure, MorHap-BSA conjugates were synthesized with highly reproducible results and in high yields. The number of haptens attached to BSA was compared by 2,4,6-trinitrobenzenesulfonic acid (TNBS) assay, modified Ellman's test and matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Among the three methods, MALDI-TOF MS discriminated subtle differences in hapten density. The effect of hapten density on enzyme-linked immunosorbent assay (ELISA) performance was evaluated with seven MorHap-BSA conjugates of varying hapten densities, which were used as coating antigens. The highest antibody binding was obtained with MorHap-BSA conjugates containing 3-5 haptens. This is the first report that rigorously analyzes, optimizes and characterizes the conjugation of haptens to proteins that can be used for vaccines against drugs of abuse. The effect of hapten density on the ELISA detection of antibodies against haptens demonstrates the importance of careful characterization of the hapten density by the analytical techniques described. PMID:25084736

  4. Representing Matrix Cracks Through Decomposition of the Deformation Gradient Tensor in Continuum Damage Mechanics Methods

    NASA Technical Reports Server (NTRS)

    Leone, Frank A., Jr.

    2015-01-01

    A method is presented to represent the large-deformation kinematics of intraply matrix cracks and delaminations in continuum damage mechanics (CDM) constitutive material models. The method involves the additive decomposition of the deformation gradient tensor into 'crack' and 'bulk material' components. The response of the intact bulk material is represented by a reduced deformation gradient tensor, and the opening of an embedded cohesive interface is represented by a normalized cohesive displacement-jump vector. The rotation of the embedded interface is tracked as the material deforms and as the crack opens. The distribution of the total local deformation between the bulk material and the cohesive interface components is determined by minimizing the difference between the cohesive stress and the bulk material stress projected onto the cohesive interface. The improvements to the accuracy of CDM models that incorporate the presented method over existing approaches are demonstrated for a single element subjected to simple shear deformation and for a finite element model of a unidirectional open-hole tension specimen. The material model is implemented as a VUMAT user subroutine for the Abaqus/Explicit finite element software. The presented deformation gradient decomposition method reduces the artificial load transfer across matrix cracks subjected to large shearing deformations, and avoids the spurious secondary failure modes that often occur in analyses based on conventional progressive damage models.

  5. Limited-memory scaled gradient projection methods for real-time image deconvolution in microscopy

    NASA Astrophysics Data System (ADS)

    Porta, F.; Zanella, R.; Zanghirati, G.; Zanni, L.

    2015-04-01

    Gradient projection methods have given rise to effective tools for image deconvolution in several relevant areas, such as microscopy, medical imaging and astronomy. Due to the large scale of the optimization problems arising in nowadays imaging applications and to the growing request of real-time reconstructions, an interesting challenge to be faced consists in designing new acceleration techniques for the gradient schemes, able to preserve their simplicity and low computational cost of each iteration. In this work we propose an acceleration strategy for a state-of-the-art scaled gradient projection method for image deconvolution in microscopy. The acceleration idea is derived by adapting a step-length selection rule, recently introduced for limited-memory steepest descent methods in unconstrained optimization, to the special constrained optimization framework arising in image reconstruction. We describe how important issues related to the generalization of the step-length rule to the imaging optimization problem have been faced and we evaluate the improvements due to the acceleration strategy by numerical experiments on large-scale image deconvolution problems.

  6. Efficient gradient projection methods for edge-preserving removal of Poisson noise

    NASA Astrophysics Data System (ADS)

    Zanella, R.; Boccacci, P.; Zanni, L.; Bertero, M.

    2009-04-01

    Several methods based on different image models have been proposed and developed for image denoising. Some of them, such as total variation (TV) and wavelet thresholding, are based on the assumption of additive Gaussian noise. Recently the TV approach has been extended to the case of Poisson noise, a model describing the effect of photon counting in applications such as emission tomography, microscopy and astronomy. For the removal of this kind of noise we consider an approach based on a constrained optimization problem, with an objective function describing TV and other edge-preserving regularizations of the Kullback-Leibler divergence. We introduce a new discrepancy principle for the choice of the regularization parameter, which is justified by the statistical properties of the Poisson noise. For solving the optimization problem we propose a particular form of a general scaled gradient projection (SGP) method, recently introduced for image deblurring. We derive the form of the scaling from a decomposition of the gradient of the regularization functional into a positive and a negative part. The beneficial effect of the scaling is proved by means of numerical simulations, showing that the performance of the proposed form of SGP is superior to that of the most efficient gradient projection methods. An extended numerical analysis of the dependence of the solution on the regularization parameter is also performed to test the effectiveness of the proposed discrepancy principle.

  7. Analytical Energy Gradients for Excited-State Coupled-Cluster Methods

    NASA Astrophysics Data System (ADS)

    Wladyslawski, Mark; Nooijen, Marcel

    The equation-of-motion coupled-cluster (EOM-CC) and similarity transformed equation-of-motion coupled-cluster (STEOM-CC) methods have been firmly established as accurate and routinely applicable extensions of single-reference coupled-cluster theory to describe electronically excited states. An overview of these methods is provided, with emphasis on the many-body similarity transform concept that is the key to a rationalization of their accuracy. The main topic of the paper is the derivation of analytical energy gradients for such non-variational electronic structure approaches, with an ultimate focus on obtaining their detailed algebraic working equations. A general theoretical framework using Lagrange's method of undetermined multipliers is presented, and the method is applied to formulate the EOM-CC and STEOM-CC gradients in abstract operator terms, following the previous work in [P.G. Szalay, Int. J. Quantum Chem. 55 (1995) 151] and [S.R. Gwaltney, R.J. Bartlett, M. Nooijen, J. Chem. Phys. 111 (1999) 58]. Moreover, the systematics of the Lagrange multiplier approach is suitable for automation by computer, enabling the derivation of the detailed derivative equations through a standardized and direct procedure. To this end, we have developed the SMART (Symbolic Manipulation and Regrouping of Tensors) package of automated symbolic algebra routines, written in the Mathematica programming language. The SMART toolkit provides the means to expand, differentiate, and simplify equations by manipulation of the detailed algebraic tensor expressions directly. The Lagrangian multiplier formulation establishes a uniform strategy to perform the automated derivation in a standardized manner: A Lagrange multiplier functional is constructed from the explicit algebraic equations that define the energy in the electronic method; the energy functional is then made fully variational with respect to all of its parameters, and the symbolic differentiations directly yield the explicit

  8. Accelerating seismic interpolation with a gradient projection method based on tight frame property of curvelet

    NASA Astrophysics Data System (ADS)

    Cao, Jingjie; Wang, Yanfei; Wang, Benfeng

    2015-08-01

    Seismic interpolation, as an efficient strategy of providing reliable wavefields, belongs to large-scale computing problems. The rapid increase of data volume in high dimensional interpolation requires highly efficient methods to relieve computational burden. Most methods adopt the L1 norm as a sparsity constraint of solutions in some transformed domain; however, the L1 norm is non-differentiable and gradient-type methods cannot be applied directly. On the other hand, methods for unconstrained L1 norm optimisation always depend on the regularisation parameter which needs to be chosen carefully. In this paper, a fast gradient projection method for the smooth L1 problem is proposed based on the tight frame property of the curvelet transform that can overcome these shortcomings. Some smooth L1 norm functions are discussed and their properties are analysed, then the Huber function is chosen to replace the L1 norm. The novelty of the proposed method is that the tight frame property of the curvelet transform is utilised to improve the computational efficiency. Numerical experiments on synthetic and real data demonstrate the validity of the proposed method which can be used in large-scale computing.

  9. C 1 natural element method for strain gradient linear elasticity and its application to microstructures

    NASA Astrophysics Data System (ADS)

    Nie, Zhi-Feng; Zhou, Shen-Jie; Han, Ru-Jun; Xiao, Lin-Jing; Wang, Kai

    2012-02-01

    C 1 natural element method ( C 1 NEM) is applied to strain gradient linear elasticity, and size effects on microstructures are analyzed. The shape functions in C 1 NEM are built upon the natural neighbor interpolation (NNI), with interpolation realized to nodal function and nodal gradient values, so that the essential boundary conditions (EBCs) can be imposed directly in a Galerkin scheme for partial differential equations (PDEs). In the present paper, C 1 NEM for strain gradient linear elasticity is constructed, and several typical examples which have analytical solutions are presented to illustrate the effectiveness of the constructed method. In its application to microstructures, the size effects of bending stiffness and stress concentration factor (SCF) are studied for microspeciem and microgripper, respectively. It is observed that the size effects become rather strong when the width of spring for microgripper, the radius of circular perforation and the long axis of elliptical perforation for microspeciem come close to the material characteristic length scales. For the U-shaped notch, the size effects decline obviously with increasing notch radius, and decline mildly with increasing length of notch.

  10. Fixed and pulsed gradient diffusion methods in low-field core analysis.

    PubMed

    Leu, Gabriela; Fordham, Edmund J; Hürlimann, Martin D; Frulla, Phil

    2005-02-01

    We review diffusion-weighted relaxation protocols for two-dimensional diffusion/relaxation time (D, T(2)) distributions and their application to fluid-saturated sedimentary rocks at low fields typical of oil-well logging tools (< or = 2 MHz for 1H). Fixed field gradient (FFG) protocols may be implemented in logging tools and in the laboratory; there, pulsed field gradient (PFG) protocols are also available. In either category, direct or stimulated echoes may be used for the diffusion evolution periods. We compare the results of several variant FFG and PFG protocols obtained on liquids and two contrasting sedimentary rocks. For liquids and rocks of negligible internal gradients (g(int)), results are comparable, as expected, for all the studied protocols. For rocks of strong g(int), protocol-dependent artifacts are seen in the joint (D, T2) distributions, consistent with the effects of the internal fields. For laboratory petrophysics, the PFG methods offer several advantages: (a) significantly improved signal-to-noise ratio and acquisition times for repetitions over many samples; (b) freedom from heteronuclear contamination when fluorinated liquids are used in core holders; and (c) a palette of variants--one comparable with the FFG--for the study of rocks of significant g(int). Given suitable hardware, both PFG and FFG methods can be implemented in the same bench-top apparatus, providing a versatile test bed for application in a petrophysical laboratory. PMID:15833632

  11. A novel model-based hearing compensation design using a gradient-free optimization method.

    PubMed

    Chen, Zhe; Becker, Suzanna; Bondy, Jeff; Bruce, Ian C; Haykin, Simon

    2005-12-01

    We propose a novel model-based hearing compensation strategy and gradient-free optimization procedure for a learning-based hearing aid design. Motivated by physiological data and normal and impaired auditory nerve models, a hearing compensation strategy is cast as a neural coding problem, and a Neurocompensator is designed to compensate for the hearing loss and enhance the speech. With the goal of learning the Neurocompensator parameters, we use a gradient-free optimization procedure, an improved version of the ALOPEX that we have developed, to learn the unknown parameters of the Neurocompensator. We present our methodology, learning procedure, and experimental results in detail; discussion is also given regarding the unsupervised learning and optimization methods. PMID:16212766

  12. Batch gradient method with smoothing L1/2 regularization for training of feedforward neural networks.

    PubMed

    Wu, Wei; Fan, Qinwei; Zurada, Jacek M; Wang, Jian; Yang, Dakun; Liu, Yan

    2014-02-01

    The aim of this paper is to develop a novel method to prune feedforward neural networks by introducing an L1/2 regularization term into the error function. This procedure forces weights to become smaller during the training and can eventually removed after the training. The usual L1/2 regularization term involves absolute values and is not differentiable at the origin, which typically causes oscillation of the gradient of the error function during the training. A key point of this paper is to modify the usual L1/2 regularization term by smoothing it at the origin. This approach offers the following three advantages: First, it removes the oscillation of the gradient value. Secondly, it gives better pruning, namely the final weights to be removed are smaller than those produced through the usual L1/2 regularization. Thirdly, it makes it possible to prove the convergence of the training. Supporting numerical examples are also provided. PMID:24291693

  13. A gradient-free adaptation method for nonlinear active noise control

    NASA Astrophysics Data System (ADS)

    Spiriti, Emanuele; Morici, Simone; Piroddi, Luigi

    2014-01-01

    Active Noise Control (ANC) problems are often affected by nonlinear effects, such as saturation and distortion of microphones and loudspeakers. Nonlinear models and specific adaptation algorithms must be employed to properly account for these effects. The nonlinear structure of the problem complicates the application of gradient-based Least Mean Squares (LMS) algorithms, due to the fact that exact gradient calculation requires executing nonlinear recursive filtering operations, which pose computational and stability issues. One favored solution to this problem consists in neglecting recursive terms in the gradient calculation, an approximation which is not always without consequences on the convergence performance. Besides, an efficient application of nonlinear models cannot avoid some form of model structure selection, to avoid the well-known effects of overparametrization and to reduce the computational load on-line. Unfortunately, the standard ANC setting configures an indirect identification problem, due to the presence of the secondary path in the control loop. In the nonlinear case, this destroys the linear regression structure of the problem even if the control filter is linear-in-the-parameters, thereby making it impossible to apply the many existing model selection methods for linear regression problems. A simple and computationally wise low demanding approach is here proposed for parameter estimation and model structure selection that provides an answer to the mentioned issues. The proposed method avoids altogether the use of the error gradient and relies on direct cost function evaluations. A virtualization scheme is used to assess the accuracy improvements when the model is subject to parametric or structural modifications, without directly affecting the control performance. Several simulation examples are discussed to show the effectiveness of the proposed algorithms.

  14. Reconstruction of fluorescence molecular tomography via a nonmonotone spectral projected gradient pursuit method

    NASA Astrophysics Data System (ADS)

    Ye, Jinzuo; Du, Yang; An, Yu; Chi, Chongwei; Tian, Jie

    2014-12-01

    Fluorescence molecular tomography (FMT) is a promising imaging technique in preclinical research, enabling three-dimensional location of the specific tumor position for small animal imaging. However, FMT presents a challenging inverse problem that is quite ill-posed and ill-conditioned. Thus, the reconstruction of FMT faces various challenges in its robustness and efficiency. We present an FMT reconstruction method based on nonmonotone spectral projected gradient pursuit (NSPGP) with l1-norm optimization. At each iteration, a spectral gradient-projection method approximately minimizes a least-squares problem with an explicit one-norm constraint. A nonmonotone line search strategy is utilized to get the appropriate updating direction, which guarantees global convergence. Additionally, the Barzilai-Borwein step length is applied to build the optimal step length, further improving the convergence speed of the proposed method. Several numerical simulation studies, including multisource cases as well as comparative analyses, have been performed to evaluate the performance of the proposed method. The results indicate that the proposed NSPGP method is able to ensure the accuracy, robustness, and efficiency of FMT reconstruction. Furthermore, an in vivo experiment based on a heterogeneous mouse model was conducted, and the results demonstrated that the proposed method held the potential for practical applications of FMT.

  15. ABCD matrix of the human lens gradient-index profile: applicability of the calculation methods.

    PubMed

    Díaz, José Antonio

    2008-01-10

    The applicability of different approximate methods proposed to determine the paraxial properties of the gradient-index (GRIN) distribution resembling that of the human lens, by means of the system ABCD matrix, is tested. Thus, the parabolic-ray-path approximation has been extended to provide the ABCD matrix of a slab lens comprised of a rotationally GRIN medium. The results show that this method has good numerical stability, and it is also the easiest one in determining the Gaussian constants of the human lens GRIN profile. PMID:18188201

  16. I like your GRIN: Deign methods for gradient-index progressive addition lenses

    NASA Astrophysics Data System (ADS)

    Fischer, David J.; Moore, Duncan T.

    2002-12-01

    Progressive addition lenses (PALs) are vision correction lenses with a continuous change in power, used to treat the physical condition presbyopia. These lenses are currently fabricated using non-rotationally symmetric surfaces to achieve the focal power transition and aberration control. In this research, we consider the use of Gradient-Index (GRIN) designs for providing both power progression and aberration control. The use of B-Spline curves for GRIN representation is explained. Design methods and simulation results for GRIN PALs are presented. Possible uses for the design methods with other lenses, such as unifocal lenses and axicons, are also discussed.

  17. Accelerated Block Preconditioned Gradient method for large scale wave functions calculations in Density Functional Theory

    SciTech Connect

    Fattebert, J.-L.

    2010-01-20

    An Accelerated Block Preconditioned Gradient (ABPG) method is proposed to solve electronic structure problems in Density Functional Theory. This iterative algorithm is designed to solve directly the non-linear Kohn-Sham equations for accurate discretization schemes involving a large number of degrees of freedom. It makes use of an acceleration scheme similar to what is known as RMM-DIIS in the electronic structure community. The method is illustrated with examples of convergence for large scale applications using a finite difference discretization and multigrid preconditioning.

  18. A comparison of the Monte Carlo and the flux gradient method for atmospheric diffusion

    SciTech Connect

    Lange, R.

    1990-05-01

    In order to model the dispersal of atmospheric pollutants in the planetary boundary layer, various methods of parameterizing turbulent diffusion have been employed. The purpose of this paper is to use a three-dimensional particle-in-cell transport and diffusion model to compare the Markov chain (Monte Carlo) method of statistical particle diffusion with the deterministic flux gradient (K-theory) method. The two methods are heavily used in the study of atmospheric diffusion under complex conditions, with the Monte Carlo method gaining in popularity partly because of its more direct application of turbulence parameters. The basis of comparison is a data set from night-time drainage flow tracer experiments performed by the US Department of Energy Atmospheric Studies in Complex Terrain (ASCOT) program at the Geysers geothermal region in northern California. The Atmospheric Diffusion Particle-In-Cell (ADPIC) model used is the main model in the Lawrence Livermore National Laboratory emergency response program: Atmospheric Release Advisory Capability (ARAC). As a particle model, it can simulate diffusion in both the flux gradient and Monte Carlo modes. 9 refs., 6 figs.

  19. Gradients for the partitioned equation-of-motion coupled-cluster method

    SciTech Connect

    Gwaltney, S.R.; Bartlett, R.J.

    1996-12-31

    The Equation-of-Motion Coupled-Cluster method restricted to singles and doubles (EOM-CCSD) is a highly accurate method for calculating excited states of molecules. Errors of 0.1 to 0.3 eV are typical for excitation energies. But a major drawback is that EOM-CCSD is an iterative n{sup 6} method, and for large cases the cost can be prohibitive. For a partitioned EOM-CCSD calculation, the doubles-doubles block of the H matrix is replaced with Ho. Combined with truncating the H matrix at second order (i.e. basing the excited state calculation on a MBPT(2) ground state), the partitioning technique creates an iterative n{sup 5} method for excited states, the P-EOM-MBPT(2) method. In this poster we will present the theory and examples of P-EOM-MBPT(2) gradient calculations. The gradients provide an inexpensive way to look at potential energy surfaces of excited states of molecules.

  20. A Sea-Sky Line Detection Method for Unmanned Surface Vehicles Based on Gradient Saliency.

    PubMed

    Wang, Bo; Su, Yumin; Wan, Lei

    2016-01-01

    Special features in real marine environments such as cloud clutter, sea glint and weather conditions always result in various kinds of interference in optical images, which make it very difficult for unmanned surface vehicles (USVs) to detect the sea-sky line (SSL) accurately. To solve this problem a saliency-based SSL detection method is proposed. Through the computation of gradient saliency the line features of SSL are enhanced effectively, while other interference factors are relatively suppressed, and line support regions are obtained by a region growing method on gradient orientation. The SSL identification is achieved according to region contrast, line segment length and orientation features, and optimal state estimation of SSL detection is implemented by introducing a cubature Kalman filter (CKF). In the end, the proposed method is tested on a benchmark dataset from the "XL" USV in a real marine environment, and the experimental results demonstrate that the proposed method is significantly superior to other state-of-the-art methods in terms of accuracy rate and real-time performance, and its accuracy and stability are effectively improved by the CKF. PMID:27092503

  1. A Sea-Sky Line Detection Method for Unmanned Surface Vehicles Based on Gradient Saliency

    PubMed Central

    Wang, Bo; Su, Yumin; Wan, Lei

    2016-01-01

    Special features in real marine environments such as cloud clutter, sea glint and weather conditions always result in various kinds of interference in optical images, which make it very difficult for unmanned surface vehicles (USVs) to detect the sea-sky line (SSL) accurately. To solve this problem a saliency-based SSL detection method is proposed. Through the computation of gradient saliency the line features of SSL are enhanced effectively, while other interference factors are relatively suppressed, and line support regions are obtained by a region growing method on gradient orientation. The SSL identification is achieved according to region contrast, line segment length and orientation features, and optimal state estimation of SSL detection is implemented by introducing a cubature Kalman filter (CKF). In the end, the proposed method is tested on a benchmark dataset from the “XL” USV in a real marine environment, and the experimental results demonstrate that the proposed method is significantly superior to other state-of-the-art methods in terms of accuracy rate and real-time performance, and its accuracy and stability are effectively improved by the CKF. PMID:27092503

  2. A Robust Gradient Based Method for Building Extraction from LiDAR and Photogrammetric Imagery.

    PubMed

    Siddiqui, Fasahat Ullah; Teng, Shyh Wei; Awrangjeb, Mohammad; Lu, Guojun

    2016-01-01

    Existing automatic building extraction methods are not effective in extracting buildings which are small in size and have transparent roofs. The application of large area threshold prohibits detection of small buildings and the use of ground points in generating the building mask prevents detection of transparent buildings. In addition, the existing methods use numerous parameters to extract buildings in complex environments, e.g., hilly area and high vegetation. However, the empirical tuning of large number of parameters reduces the robustness of building extraction methods. This paper proposes a novel Gradient-based Building Extraction (GBE) method to address these limitations. The proposed method transforms the Light Detection And Ranging (LiDAR) height information into intensity image without interpolation of point heights and then analyses the gradient information in the image. Generally, building roof planes have a constant height change along the slope of a roof plane whereas trees have a random height change. With such an analysis, buildings of a greater range of sizes with a transparent or opaque roof can be extracted. In addition, a local colour matching approach is introduced as a post-processing stage to eliminate trees. This stage of our proposed method does not require any manual setting and all parameters are set automatically from the data. The other post processing stages including variance, point density and shadow elimination are also applied to verify the extracted buildings, where comparatively fewer empirically set parameters are used. The performance of the proposed GBE method is evaluated on two benchmark data sets by using the object and pixel based metrics (completeness, correctness and quality). Our experimental results show the effectiveness of the proposed method in eliminating trees, extracting buildings of all sizes, and extracting buildings with and without transparent roof. When compared with current state-of-the-art building

  3. A Robust Gradient Based Method for Building Extraction from LiDAR and Photogrammetric Imagery

    PubMed Central

    Siddiqui, Fasahat Ullah; Teng, Shyh Wei; Awrangjeb, Mohammad; Lu, Guojun

    2016-01-01

    Existing automatic building extraction methods are not effective in extracting buildings which are small in size and have transparent roofs. The application of large area threshold prohibits detection of small buildings and the use of ground points in generating the building mask prevents detection of transparent buildings. In addition, the existing methods use numerous parameters to extract buildings in complex environments, e.g., hilly area and high vegetation. However, the empirical tuning of large number of parameters reduces the robustness of building extraction methods. This paper proposes a novel Gradient-based Building Extraction (GBE) method to address these limitations. The proposed method transforms the Light Detection And Ranging (LiDAR) height information into intensity image without interpolation of point heights and then analyses the gradient information in the image. Generally, building roof planes have a constant height change along the slope of a roof plane whereas trees have a random height change. With such an analysis, buildings of a greater range of sizes with a transparent or opaque roof can be extracted. In addition, a local colour matching approach is introduced as a post-processing stage to eliminate trees. This stage of our proposed method does not require any manual setting and all parameters are set automatically from the data. The other post processing stages including variance, point density and shadow elimination are also applied to verify the extracted buildings, where comparatively fewer empirically set parameters are used. The performance of the proposed GBE method is evaluated on two benchmark data sets by using the object and pixel based metrics (completeness, correctness and quality). Our experimental results show the effectiveness of the proposed method in eliminating trees, extracting buildings of all sizes, and extracting buildings with and without transparent roof. When compared with current state-of-the-art building

  4. Multimode gradient high performance liquid chromatography mass spectrometry method applicable to metabolomics and environmental monitoring.

    PubMed

    Ammann, Adrian A; Suter, Marc J-F

    2016-07-22

    Metabolomics or environmental investigations generate samples containing very large numbers of small molecular weight analytes. A single mode chromatographic separation excludes a substantial part of such complex analyte mixtures. For instance, a reversed-phase separation would not retain ionic species, resulting in a correspondingly huge front peak. To address this problem, we used two commercially available mixed-mode ion-exchange reversed-phase columns (WAX-1 and WCX-1) in sequence in a novel multimode separation method. After trapping hydrophobics on a C18-trap in loop position, hydrophilics passing the trap are separated by a simultaneous gradient for HILIC, anion and cation exchange chromatography. This gradient ends in a washout phase with a high percentage of water, the correct starting conditions for a reversed-phase gradient eluting hydrophobics from the trap in a second step of the run. Amino acids (9), organic acids (2), sugars (8), fatty acid derived compounds (11), antioxidants (4), miscellanea (6) and xenobiotics (4) were analyzed. Compounds were separated after a single sample injection during a 50min run. Lipids derived small fatty acids up to a chain length of 12 carbons were also accessible within this run time. PMID:27324626

  5. Distortion Correction in EPI Using an Extended PSF Method with a Reversed Phase Gradient Approach

    PubMed Central

    In, Myung-Ho; Posnansky, Oleg; Beall, Erik B.; Lowe, Mark J.; Speck, Oliver

    2015-01-01

    In echo-planar imaging (EPI), such as commonly used for functional MRI (fMRI) and diffusion-tensor imaging (DTI), compressed distortion is a more difficult challenge than local stretching as spatial information can be lost in strongly compressed areas. In addition, the effects are more severe at ultra-high field (UHF) such as 7T due to increased field inhomogeneity. To resolve this problem, two EPIs with opposite phase-encoding (PE) polarity were acquired and combined after distortion correction. For distortion correction, a point spread function (PSF) mapping method was chosen due to its high correction accuracy and extended to perform distortion correction of both EPIs with opposite PE polarity thus reducing the PSF reference scan time. Because the amount of spatial information differs between the opposite PE datasets, the method was further extended to incorporate a weighted combination of the two distortion-corrected images to maximize the spatial information content of a final corrected image. The correction accuracy of the proposed method was evaluated in distortion-corrected data using both forward and reverse phase-encoded PSF reference data and compared with the reversed gradient approaches suggested previously. Further we demonstrate that the extended PSF method with an improved weighted combination can recover local distortions and spatial information loss and be applied successfully not only to spin-echo EPI, but also to gradient-echo EPIs acquired with both PE directions to perform geometrically accurate image reconstruction. PMID:25707006

  6. METHODS FOR STUDYING BACTERIAL GENE TRANSFER IN SOIL BY CONJUGATION AND TRANSDUCTION

    EPA Science Inventory

    The purpose of this document is to provide a series of protocols by which a trained technician can conduct studies on the transfer of genetic information by conjugation or transduction in soil, with emphasis on bacteria containing recombinant DNA. The level of the document is gea...

  7. A rapid biosensor-based method for quantification of free and glucose-conjugated salicylic acid

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Salicylic acid (SA) is an important signalling molecule in plant defenses against biotrophic pathogens. It is also involved in several other processes such as heat production, flowering, and germination. SA exists in the plant as free SA and as an inert glucose conjugate (salicylic acid 2-O-ß-D-...

  8. Estimating Effective Vertical Diffusivity in Shallow Ponds by a Constrained Flux-Gradient Method

    NASA Astrophysics Data System (ADS)

    Bean, J. R.; Torgersen, T.

    2004-12-01

    Shallow ponds have been used to mitigate the deleterious effects of storm water run-off by acting as detention/retention basins that sequester run-off associated pollutants in sediments. Studies show that the retention efficiency of these systems can decrease over time as a result of the internal loading of nutrients/contaminants from the sediments back to the water column where they are available for export downstream. Quantifying the vertical transport of gases (down) and sediment derived materials (up) is vital to the modeling and understanding of the processes that contribute to the magnitude of internal loading. A critical parameter is the effective vertical diffusion coefficient: Kz=Dmolecular +Deddy (cm2 sec-1). The flux gradient method for estimating effective vertical thermal diffusivity has been applied with success in large lakes which undergo stratification cycles on seasonal or longer time scales. We offer a constrained version of the flux-gradient method that has been adapted for use in a shallow pond with a daily stratification cycle. The method employs heat as a tracer and assumes that transport in the face of a stable gradient is diffusive. By shrinking the spatial and temporal resolution of measurement to scales appropriate to the system of interest and carefully accounting for internal source and sink terms of heat (e.g solar radiation and sediment heat fluxes) we are able to calculate Kz as a function of time and depth during periods of stable stratification, i.e when the pond is not vertically well-mixed. Results show the magnitude of Kz varies from ca. 10-3 to 10-1 (cm2 sec-1) under stratified conditions depending primarily on the strength of stratification.

  9. A Single-Lap Joint Adhesive Bonding Optimization Method Using Gradient and Genetic Algorithms

    NASA Technical Reports Server (NTRS)

    Smeltzer, Stanley S., III; Finckenor, Jeffrey L.

    1999-01-01

    A natural process for any engineer, scientist, educator, etc. is to seek the most efficient method for accomplishing a given task. In the case of structural design, an area that has a significant impact on the structural efficiency is joint design. Unless the structure is machined from a solid block of material, the individual components which compose the overall structure must be joined together. The method for joining a structure varies depending on the applied loads, material, assembly and disassembly requirements, service life, environment, etc. Using both metallic and fiber reinforced plastic materials limits the user to two methods or a combination of these methods for joining the components into one structure. The first is mechanical fastening and the second is adhesive bonding. Mechanical fastening is by far the most popular joining technique; however, in terms of structural efficiency, adhesive bonding provides a superior joint since the load is distributed uniformly across the joint. The purpose of this paper is to develop a method for optimizing single-lap joint adhesive bonded structures using both gradient and genetic algorithms and comparing the solution process for each method. The goal of the single-lap joint optimization is to find the most efficient structure that meets the imposed requirements while still remaining as lightweight, economical, and reliable as possible. For the single-lap joint, an optimum joint is determined by minimizing the weight of the overall joint based on constraints from adhesive strengths as well as empirically derived rules. The analytical solution of the sin-le-lap joint is determined using the classical Goland-Reissner technique for case 2 type adhesive joints. Joint weight minimization is achieved using a commercially available routine, Design Optimization Tool (DOT), for the gradient solution while an author developed method is used for the genetic algorithm solution. Results illustrate the critical design variables

  10. The dock-and-lock method combines recombinant engineering with site-specific covalent conjugation to generate multifunctional structures.

    PubMed

    Rossi, Edmund A; Goldenberg, David M; Chang, Chien-Hsing

    2012-03-21

    Advances in recombinant protein technology have facilitated the production of increasingly complex fusion proteins with multivalent, multifunctional designs for use in various in vitro and in vivo applications. In addition, traditional chemical conjugation remains a primary choice for linking proteins with polyethylene glycol (PEG), biotin, fluorescent markers, drugs, and others. More recently, site-specific conjugation of two or more interactive modules has emerged as a valid approach to expand the existing repertoires produced by either recombinant engineering or chemical conjugation alone, thus advancing the range of potential applications. Five such methods, each involving a specific binding event, are highlighted in this review, with a particular focus on the Dock-and-Lock (DNL) method, which exploits the natural interaction between the dimerization and docking domain (DDD) of cAMP-dependent protein kinase (PKA) and the anchoring domain (AD) of A-kinase anchoring proteins (AKAP). The various enablements of DNL to date include trivalent, tetravalent, pentavalent, and hexavalent antibodies of monospecificity or bispecificity; immnocytokines comprising multiple copies of interferon-alpha (IFNα); and site-specific PEGylation. These achievements attest to the power of the DNL platform technology to develop novel therapeutic and diagnostic agents from both proteins and nonproteins for unmet medical needs. PMID:22168393