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Sample records for conjugate gradient methods

  1. Conjugate gradient method - Electromagnetism applications

    NASA Astrophysics Data System (ADS)

    Mosig, Juan R.

    1987-10-01

    This paper presents a brief but rigorous description of the conjugate gradient technique as applied to the solution of algebraic linear systems with complex coefficients. The relationships between conjugate gradient techniques and other commonly used methods are established. A normalized algorithm is introduced which optimally exploits the computer capabilities. Its performance is compared with that of Gaussian elimination by numerical tests on Hilbert matrices of more than a thousand unknowns. As a practical application, the problem of electrostatic screening by a finite ground plane has been solved with this technique.

  2. 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.

  3. A new family of conjugate gradient methods

    NASA Astrophysics Data System (ADS)

    Shi, Zhen-Jun; Guo, Jinhua

    2009-02-01

    In this paper we develop a new class of conjugate gradient methods for unconstrained optimization problems. A new nonmonotone line search technique is proposed to guarantee the global convergence of these conjugate gradient methods under some mild conditions. In particular, Polak-Ribiére-Polyak and Liu-Storey conjugate gradient methods are special cases of the new class of conjugate gradient methods. By estimating the local Lipschitz constant of the derivative of objective functions, we can find an adequate step size and substantially decrease the function evaluations at each iteration. Numerical results show that these new conjugate gradient methods are effective in minimizing large-scale non-convex non-quadratic functions.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. The global convergence properties of a conjugate gradient method

    NASA Astrophysics Data System (ADS)

    Omer, Osman; Mamat, Mustafa; Abashar, Abdelrhaman; Rivaie, Mohd

    2014-06-01

    Conjugate gradient methods are the most famous methods for solving nonlinear unconstrained optimization problems, especially large scale problems. That is, for its simplicity and low memory requirement. The strong Wolfe line search are usually used in practice for the analyses and implementations of conjugate gradient methods. In this paper, we present a new method of nonlinear conjugate gradient method with strong Wolfe line search for unconstrained optimization problems. Under some assumptions, the sufficient descent property and the global convergence are given. The numerical results show that our new method is efficient for some unconstrained optimization problems.

  9. 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.

  10. A Spectral Conjugate Gradient Method for Unconstrained Optimization

    SciTech Connect

    Birgin, E. G. Martinez, J. M.

    2001-07-01

    A family of scaled conjugate gradient algorithms for large-scale unconstrained minimization is defined. The Perry, the Polak-Ribiere and the Fletcher-Reeves formulae are compared using a spectral scaling derived from Raydan's spectral gradient optimization method. The best combination of formula, scaling and initial choice of step-length is compared against well known algorithms using a classical set of problems. An additional comparison involving an ill-conditioned estimation problem in Optics is presented.

  11. 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.

  12. Conjugate Gradient Methods for Constrained Least Squares Problems

    DTIC Science & Technology

    1990-01-01

    TINO Hi!AGL . edi"o ar m m Conjugate Gradient Methods for Constrained Least Squares Problems by Douglas James A thesis 3ubmitted to the Graduate Faculty...Breakdown of Incomplete QR Factorizations The research which led to this dissertation began with a look at incomplete QR preconditioners for ordinary...AFIT/CI/CIA- 90-013D 6a. NAME OF PERFORMING ORGANIZATION 6b. OFFICE SYMBOL 7&. NAME OF MONITORING ORGANIZATION AFIT STUDENT AT (if applicable) AFIT/CIA

  13. Conjugate gradient methods with sufficient descent condition for large-scale unconstrained optimization

    NASA Astrophysics Data System (ADS)

    Ling, Mei Mei; Leong, Wah June

    2014-12-01

    In this paper, we make a modification to the standard conjugate gradient method so that its search direction satisfies the sufficient descent condition. We prove that the modified conjugate gradient method is globally convergent under Armijo line search. Numerical results show that the proposed conjugate gradient method is efficient compared to some of its standard counterparts for large-scale unconstrained optimization.

  14. A conjugate gradient method with descent direction for unconstrained optimization

    NASA Astrophysics Data System (ADS)

    Yuan, Gonglin; Lu, Xiwen; Wei, Zengxin

    2009-11-01

    A modified conjugate gradient method is presented for solving unconstrained optimization problems, which possesses the following properties: (i) The sufficient descent property is satisfied without any line search; (ii) The search direction will be in a trust region automatically; (iii) The Zoutendijk condition holds for the Wolfe-Powell line search technique; (iv) This method inherits an important property of the well-known Polak-Ribière-Polyak (PRP) method: the tendency to turn towards the steepest descent direction if a small step is generated away from the solution, preventing a sequence of tiny steps from happening. The global convergence and the linearly convergent rate of the given method are established. Numerical results show that this method is interesting.

  15. A new conjugate gradient method and its global convergence under the exact line search

    NASA Astrophysics Data System (ADS)

    Omer, Osman; Rivaie, Mohd; Mamat, Mustafa; Abdalla, Awad

    2014-12-01

    The conjugate gradient methods are numerously used for solving nonlinear unconstrained optimization problems, especially of large scale. Their wide applications are due to their simplicity and low memory requirement. To analyze conjugate gradient methods, two types of line searches are used; exact and inexact. In this paper, we present a new method of nonlinear conjugate gradient methods under the exact line search. The theoretical analysis shows that the new method generates a descent direction in each iteration and globally convergent under the exact line search. Moreover, numerical experiments based on comparing the new method with other well known conjugate gradient methods show that the new is efficient for some unconstrained optimization problems.

  16. A penalized linear and nonlinear combined conjugate gradient method for the reconstruction of fluorescence molecular tomography.

    PubMed

    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.

  17. Aerodynamic shape optimization using preconditioned conjugate gradient methods

    NASA Technical Reports Server (NTRS)

    Burgreen, Greg W.; Baysal, Oktay

    1993-01-01

    In an effort to further improve upon the latest advancements made in aerodynamic shape optimization procedures, a systematic study is performed to examine several current solution methodologies as applied to various aspects of the optimization procedure. It is demonstrated that preconditioned conjugate gradient-like methodologies dramatically decrease the computational efforts required for such procedures. The design problem investigated is the shape optimization of the upper and lower surfaces of an initially symmetric (NACA-012) airfoil in inviscid transonic flow and at zero degree angle-of-attack. The complete surface shape is represented using a Bezier-Bernstein polynomial. The present optimization method then automatically obtains supercritical airfoil shapes over a variety of freestream Mach numbers. Furthermore, the best optimization strategy examined resulted in a factor of 8 decrease in computational time as well as a factor of 4 decrease in memory over the most efficient strategies in current use.

  18. The proof of sufficient descent condition for a new type of conjugate gradient methods

    NASA Astrophysics Data System (ADS)

    Abashar, Abdelrhaman; Mamat, Mustafa; Rivaie, Mohd; Mohd, Ismail; Omer, Osman

    2014-06-01

    Conjugate gradient methods are effective in solving linear equations and solving non-linear optimization. In this work we compare our new conjugate gradient coefficient βk with classical formula under strong Wolfe line search; our method contains sufficient descent condition. Numerical results have shown that the new βk performs better than classical formula.

  19. A stable, rapidly converging conjugate gradient method for energy minimization

    SciTech Connect

    Watowich, S.J.; Meyer, E.S.; Hagstrom, R.; Josephs, R.

    1989-01-01

    We apply Shanno's conjugate gradient algorithm to the problem of minimizing the potential energy function associated with molecular mechanical calculations. Shanno's algorithm is stable with respect to roundoff errors and inexact line searches and converges rapidly to a minimum. Equally important, this algorithm can improve the rate of convergence to a minimum by a factor of 5 relative to Fletcher-Reeves or Polak-Ribiere minimizers when used within the molecular mechanics package AMBER. Comparable improvements are found for a limited number of simulations when the Polak-Ribiere direction vector is incorporated into the Shanno algorithm. 24 refs., 4 figs., 3 tabs.

  20. 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.

  1. 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.

  2. A new conjugate gradient method with sufficient descent without any line search for unconstrained optimization

    NASA Astrophysics Data System (ADS)

    Omer, Osman; Rivaie, Mohd; Mamat, Mustafa; Amani, Zahrahtul

    2015-02-01

    Conjugate gradient methods are one of the most used methods for solving nonlinear unconstrained optimization problems, especially of large scale. Their wide applications are due to their simplicity and low memory requirement. The sufficient descent property is an important issue in the analyses and implementations of conjugate gradient methods. In this paper, a new conjugate gradient method is proposed for unconstrained optimization problems. The theoretical analysis shows that the directions generated by the new method are always satisfy the sufficient descent property, and this property is independent of the line search used. Furthermore, a numerical experiment based on comparing the new method with other known conjugate gradient methods shows that the new is efficient for some unconstrained optimization problems.

  3. A three-term conjugate gradient method under the strong-Wolfe line search

    NASA Astrophysics Data System (ADS)

    Khadijah, Wan; Rivaie, Mohd; Mamat, Mustafa

    2017-08-01

    Recently, numerous studies have been concerned in conjugate gradient methods for solving large-scale unconstrained optimization method. In this paper, a three-term conjugate gradient method is proposed for unconstrained optimization which always satisfies sufficient descent direction and namely as Three-Term Rivaie-Mustafa-Ismail-Leong (TTRMIL). Under standard conditions, TTRMIL method is proved to be globally convergent under strong-Wolfe line search. Finally, numerical results are provided for the purpose of comparison.

  4. Application of the conjugate-gradient method to ground-water models

    USGS Publications Warehouse

    Manteuffel, T.A.; Grove, D.B.; Konikow, L.F.

    1984-01-01

    The conjugate-gradient method can solve efficiently and accurately finite-difference approximations to the ground-water flow equation. An aquifer-simulation model using the conjugate-gradient method was applied to a problem of ground-water flow in an alluvial aquifer at the Rocky Mountain Arsenal, Denver, Colorado. For this application, the accuracy and efficiency of the conjugate-gradient method compared favorably with other available methods for steady-state flow. However, its efficiency relative to other available methods depends on the nature of the specific problem. The main advantage of the conjugate-gradient method is that it does not require the use of iteration parameters, thereby eliminating this partly subjective procedure. (USGS)

  5. A new convergent conjugate gradient method under the exact line search

    NASA Astrophysics Data System (ADS)

    Omer, Osman; Mamat, Mustafa; Rivaie, Mohd

    2015-05-01

    Conjugate gradient methods are widely used for unconstrained optimization problems, especially large scale problems. That is, for its simplicity, low memory requirement, and global convergence properties. In this paper, we study the global convergence properties of a new conjugate gradient method under the exact line search. Under some assumptions, the proofs of the sufficient descent property and the global convergence are given. The numerical results show that our new method is efficient for some unconstrained optimization problems.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. A new conjugate gradient method for unconstrained optimization with sufficient descent

    NASA Astrophysics Data System (ADS)

    Yussoff, Nurul Hajar Mohd; Mamat, Mustafa; Rivaie, Mohd; Mohd, Ismail

    2014-06-01

    Conjugate gradient (CG) methods represent an important computational innovation in solving large-scaled unconstrained optimization problems. There are many different versions of CG methods. Although some methods are equivalent to each other, their performances are quite different. This paper presents a new CG method based on modification of the original CG methods. The important criteria of this new CG method are its global convergence properties. Numerical result shows that this new CG method performs better than the original CG methods.

  11. An Introduction to the Conjugate Gradient Method that Even an Idiot Can Understand

    DTIC Science & Technology

    1994-03-07

    and Jorge Nocedal , Global convergence properties of conjugate gradient methods for optimization, SIAM Journal of Optimization 2 (1992), no. 1, 21-42...line searches was analyzed by Daniel [3]. The choice of t3 for nonlinear CG is discussed by Gilbert and Nocedal [81.. A history and extensive

  12. 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.

  13. Steepest descent with momentum for quadratic functions is a version of the conjugate gradient method.

    PubMed

    Bhaya, Amit; Kaszkurewicz, Eugenius

    2004-01-01

    It is pointed out that the so called momentum method, much used in the neural network literature as an acceleration of the backpropagation method, is a stationary version of the conjugate gradient method. Connections with the continuous optimization method known as heavy ball with friction are also made. In both cases, adaptive (dynamic) choices of the so called learning rate and momentum parameters are obtained using a control Liapunov function analysis of the system.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. A family of derivative-free conjugate gradient methods for large-scale nonlinear systems of equations

    NASA Astrophysics Data System (ADS)

    Cheng, Wanyou; Xiao, Yunhai; Hu, Qing-Jie

    2009-02-01

    In this paper, we propose a family of derivative-free conjugate gradient methods for large-scale nonlinear systems of equations. They come from two modified conjugate gradient methods [W.Y. Cheng, A two term PRP based descent Method, Numer. Funct. Anal. Optim. 28 (2007) 1217-1230; L. Zhang, W.J. Zhou, D.H. Li, A descent modified Polak-Ribiére-Polyak conjugate gradient method and its global convergence, IMA J. Numer. Anal. 26 (2006) 629-640] recently proposed for unconstrained optimization problems. Under appropriate conditions, the global convergence of the proposed method is established. Preliminary numerical results show that the proposed method is promising.

  19. New hybrid conjugate gradient methods with the generalized Wolfe line search.

    PubMed

    Xu, Xiao; Kong, Fan-Yu

    2016-01-01

    The conjugate gradient method was an efficient technique for solving the unconstrained optimization problem. In this paper, we made a linear combination with parameters β k of the DY method and the HS method, and putted forward the hybrid method of DY and HS. We also proposed the hybrid of FR and PRP by the same mean. Additionally, to present the two hybrid methods, we promoted the Wolfe line search respectively to compute the step size α k of the two hybrid methods. With the new Wolfe line search, the two hybrid methods had descent property and global convergence property of the two hybrid methods that can also be proved.

  20. A conjugate gradient method with descent properties under strong Wolfe line search

    NASA Astrophysics Data System (ADS)

    Zull, N.; ‘Aini, N.; Shoid, S.; Ghani, N. H. A.; Mohamed, N. S.; Rivaie, M.; Mamat, M.

    2017-09-01

    The conjugate gradient (CG) method is one of the optimization methods that are often used in practical applications. The continuous and numerous studies conducted on the CG method have led to vast improvements in its convergence properties and efficiency. In this paper, a new CG method possessing the sufficient descent and global convergence properties is proposed. The efficiency of the new CG algorithm relative to the existing CG methods is evaluated by testing them all on a set of test functions using MATLAB. The tests are measured in terms of iteration numbers and CPU time under strong Wolfe line search. Overall, this new method performs efficiently and comparable to the other famous methods.

  1. 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.

  2. 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.

  3. Solving unconstrained optimization with a new type of conjugate gradient method

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    Conjugate gradient (CG) methods have been widely used as schemes to solve large-scale unconstrained optimization problems. Numerous studies and modifications have been done recently to improve this method. In this paper, we proposed a new type of CG coefficients (βk) by modification of Polak and Ribiere (PR) method. This new βk is shown to possess global convergence properties by using exact line searches. Performance comparisons are made with the four most common βk proposed by the early researches. Numerical results also show that this new βk performed better.

  4. 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.

  5. Iterative total least-squares image reconstruction algorithm for optical tomography by the conjugate gradient method.

    PubMed

    Zhu, W; Wang, Y; Yao, Y; Chang, J; Graber, H L; Barbour, R L

    1997-04-01

    We present an iterative total least-squares algorithm for computing images of the interior structure of highly scattering media by using the conjugate gradient method. For imaging the dense scattering media in optical tomography, a perturbation approach has been described previously [Y. Wang et al., Proc. SPIE 1641, 58 (1992); R. L. Barbour et al., in Medical Optical Tomography: Functional Imaging and Monitoring (Society of Photo-Optical Instrumentation Engineers, Bellingham, Wash., 1993), pp. 87-120], which solves a perturbation equation of the form W delta x = delta I. In order to solve this equation, least-squares or regularized least-squares solvers have been used in the past to determine best fits to the measurement data delta I while assuming that the operator matrix W is accurate. In practice, errors also occur in the operator matrix. Here we propose an iterative total least-squares (ITLS) method that minimizes the errors in both weights and detector readings. Theoretically, the total least-squares (TLS) solution is given by the singular vector of the matrix [W/ delta I] associated with the smallest singular value. The proposed ITLS method obtains this solution by using a conjugate gradient method that is particularly suitable for very large matrices. Simulation results have shown that the TLS method can yield a significantly more accurate result than the least-squares method.

  6. Non Linear Conjugate Gradient

    SciTech Connect

    Newman, Gregory A.; Commer, Michael

    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. 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.

  7. Finite elements and the method of conjugate gradients on a concurrent processor

    NASA Technical Reports Server (NTRS)

    Lyzenga, G. A.; Raefsky, A.; Hager, B. H.

    1984-01-01

    An algorithm for the iterative solution of finite element problems on a concurrent processor is presented. The method of conjugate gradients is used to solve the system of matrix equations, which is distributed among the processors of a MIMD computer according to an element-based spatial decomposition. This algorithm is implemented in a two-dimensional elastostatics program on the Caltech Hypercube concurrent processor. The results of tests on up to 32 processors show nearly linear concurrent speedup, with efficiencies over 90% for sufficiently large problems.

  8. Polarity for quadratic hypersurfaces and conjugate gradient method: Relation between degenerate and nondegenerate cases

    NASA Astrophysics Data System (ADS)

    Giovanni, Fasano; Silvio, Giove; Riccardo, Gusso

    2016-10-01

    In this paper we consider a geometric viewpoint to analyze the behaviour of the Conjugate Gradient (CG) method, for the solution of a symmetric linear system, when at current step a pivot breakdown possibly occurs (degenerate case). As well known this can occur when the system matrix is indefinite or singular. In the latter case the CG gets stuck, since the steplength along the current search direction cannot be computed. We show here that a simple geometric interpretation can be provided for the degenerate case, as long as some basics on projective geometry in the Euclidean space are considered.

  9. Multigrid preconditioned conjugate-gradient method for large-scale wave-front reconstruction.

    PubMed

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

    2002-09-01

    We introduce a multigrid preconditioned conjugate-gradient (MGCG) iterative scheme for computing open-loop wave-front reconstructors for extreme adaptive optics systems. We present numerical simulations for a 17-m class telescope with n = 48756 sensor measurement grid points within the aperture, which indicate that our MGCG method has a rapid convergence rate for a wide range of subaperture average slope measurement signal-to-noise ratios. The total computational cost is of order n log n. Hence our scheme provides for fast wave-front simulation and control in large-scale adaptive optics systems.

  10. Coordinate-space solver for superfluid many-fermion systems with the shifted conjugate-orthogonal conjugate-gradient method

    NASA Astrophysics Data System (ADS)

    Jin, Shi; Bulgac, Aurel; Roche, Kenneth; Wlazłowski, Gabriel

    2017-04-01

    Self-consistent approaches to superfluid many-fermion systems in three dimensions (and their subsequent use in time-dependent studies) require a large number of diagonalizations of very large dimension Hermitian matrices, which results in enormous computational costs. We present an approach based on the shifted conjugate-orthogonal conjugate-gradient (COCG) Krylov method for the evaluation of the Green's function, from which we subsequently extract various densities (particle number, spin, current, kinetic energy, anomalous, etc.) of a nuclear system. The approach eschews the determination of the quasiparticle wave functions and their corresponding quasiparticle energies, which never explicitly appear in the construction of a single-particle Hamiltonian or needed for the calculation of various static nuclear properties, which depend only on densities. As benchmarks we present calculations for nuclei with axial symmetry, including the ground state of spherical (magic or semimagic) and axially deformed nuclei, the saddle point in the 240Pu constrained fission path, and a vortex in the neutron star crust, and demonstrate the superior efficiency of the shifted COCG Krylov method over traditional approaches.

  11. The combined use of the Newton-Raphson method and the conjugate gradient method for solving elastoplastic problems

    NASA Astrophysics Data System (ADS)

    Movchan, A. A.; Brodskij, S. I.

    The paper is concerned with the elastic-plastic analysis of an axisymmetric bimetal joint under loading. A system of nonlinear equations describing this elastic-plastic problem are solved by using a modified version of the Newton-Raphson method. To increase the computational efficiency, a procedure is proposed whereby the Newton-Raphson method is combined with a version of the conjugate gradient method.

  12. Inexact Uzawa conjugate gradient method for the Stokes problem for incompressible fluid

    NASA Astrophysics Data System (ADS)

    Dementyeva, E.; Karepova, E.; Kireev, I.

    2016-10-01

    In this paper, the two-dimensional Stokes equations are considered for a viscous incompressible fluid in a channel. To construct a discrete problem, the Taylor-Hood finite elements are used. The obtained system of linear algebraic equations is of the saddle point type and is solved by a modified inexact Uzawa conjugate gradient method. Usually the Uzawa methods are considered for velocity-pressure unknowns. In our version, the problem is formulated in terms of velocity-pressure deviations from the desired saddle point of the discrete problem. This allows one to improve considerably the numerical efficiency of the method. The convergence of the method is studied numerically as well as theoretically.

  13. Conjugate-gradient optimization method for orbital-free density functional calculations.

    PubMed

    Jiang, Hong; Yang, Weitao

    2004-08-01

    Orbital-free density functional theory as an extension of traditional Thomas-Fermi theory has attracted a lot of interest in the past decade because of developments in both more accurate kinetic energy functionals and highly efficient numerical methodology. In this paper, we developed a conjugate-gradient method for the numerical solution of spin-dependent extended Thomas-Fermi equation by incorporating techniques previously used in Kohn-Sham calculations. The key ingredient of the method is an approximate line-search scheme and a collective treatment of two spin densities in the case of spin-dependent extended Thomas-Fermi problem. Test calculations for a quartic two-dimensional quantum dot system and a three-dimensional sodium cluster Na216 with a local pseudopotential demonstrate that the method is accurate and efficient.

  14. Conjugate-gradient preconditioning methods for shift-variant PET image reconstruction.

    PubMed

    Fessler, J A; Booth, S D

    1999-01-01

    Gradient-based iterative methods often converge slowly for tomographic image reconstruction and image restoration problems, but can be accelerated by suitable preconditioners. Diagonal preconditioners offer some improvement in convergence rate, but do not incorporate the structure of the Hessian matrices in imaging problems. Circulant preconditioners can provide remarkable acceleration for inverse problems that are approximately shift-invariant, i.e., for those with approximately block-Toeplitz or block-circulant Hessians. However, in applications with nonuniform noise variance, such as arises from Poisson statistics in emission tomography and in quantum-limited optical imaging, the Hessian of the weighted least-squares objective function is quite shift-variant, and circulant preconditioners perform poorly. Additional shift-variance is caused by edge-preserving regularization methods based on nonquadratic penalty functions. This paper describes new preconditioners that approximate more accurately the Hessian matrices of shift-variant imaging problems. Compared to diagonal or circulant preconditioning, the new preconditioners lead to significantly faster convergence rates for the unconstrained conjugate-gradient (CG) iteration. We also propose a new efficient method for the line-search step required by CG methods. Applications to positron emission tomography (PET) illustrate the method.

  15. Application of augmented-Lagrangian methods in meteorology: Comparison of different conjugate-gradient codes for large-scale minimization

    NASA Technical Reports Server (NTRS)

    Navon, I. M.

    1984-01-01

    A Lagrange multiplier method using techniques developed by Bertsekas (1982) was applied to solving the problem of enforcing simultaneous conservation of the nonlinear integral invariants of the shallow water equations on a limited area domain. This application of nonlinear constrained optimization is of the large dimensional type and the conjugate gradient method was found to be the only computationally viable method for the unconstrained minimization. Several conjugate-gradient codes were tested and compared for increasing accuracy requirements. Robustness and computational efficiency were the principal criteria.

  16. Application of augmented-Lagrangian methods in meteorology: Comparison of different conjugate-gradient codes for large-scale minimization

    NASA Technical Reports Server (NTRS)

    Navon, I. M.

    1984-01-01

    A Lagrange multiplier method using techniques developed by Bertsekas (1982) was applied to solving the problem of enforcing simultaneous conservation of the nonlinear integral invariants of the shallow water equations on a limited area domain. This application of nonlinear constrained optimization is of the large dimensional type and the conjugate gradient method was found to be the only computationally viable method for the unconstrained minimization. Several conjugate-gradient codes were tested and compared for increasing accuracy requirements. Robustness and computational efficiency were the principal criteria.

  17. A fast nonlinear conjugate gradient based method for 3D concentrated frictional contact problems

    NASA Astrophysics Data System (ADS)

    Zhao, Jing; Vollebregt, Edwin A. H.; Oosterlee, Cornelis W.

    2015-05-01

    This paper presents a fast numerical solver for a nonlinear constrained optimization problem, arising from 3D concentrated frictional shift and rolling contact problems with dry Coulomb friction. The solver combines an active set strategy with a nonlinear conjugate gradient method. One novelty is to consider the tractions of each slip element in a polar coordinate system, using azimuth angles as variables instead of conventional traction variables. The new variables are scaled by the diagonal of the underlying Jacobian. The fast Fourier transform (FFT) technique accelerates all matrix-vector products encountered, exploiting the matrix' Toeplitz structure. Numerical tests demonstrate a significant reduction of the computational time compared to existing solvers for concentrated contact problems.

  18. Preconditioning strategies for nonlinear conjugate gradient methods, based on quasi-Newton updates

    NASA Astrophysics Data System (ADS)

    Andrea, Caliciotti; Giovanni, Fasano; Massimo, Roma

    2016-10-01

    This paper reports two proposals of possible preconditioners for the Nonlinear Conjugate Gradient (NCG) method, in large scale unconstrained optimization. On one hand, the common idea of our preconditioners is inspired to L-BFGS quasi-Newton updates, on the other hand we aim at explicitly approximating in some sense the inverse of the Hessian matrix. Since we deal with large scale optimization problems, we propose matrix-free approaches where the preconditioners are built using symmetric low-rank updating formulae. Our distinctive new contributions rely on using information on the objective function collected as by-product of the NCG, at previous iterations. Broadly speaking, our first approach exploits the secant equation, in order to impose interpolation conditions on the objective function. In the second proposal we adopt and ad hoc modified-secant approach, in order to possibly guarantee some additional theoretical properties.

  19. Using Chebyshev polynomials and approximate inverse triangular factorizations for preconditioning the conjugate gradient method

    NASA Astrophysics Data System (ADS)

    Kaporin, I. E.

    2012-02-01

    In order to precondition a sparse symmetric positive definite matrix, its approximate inverse is examined, which is represented as the product of two sparse mutually adjoint triangular matrices. In this way, the solution of the corresponding system of linear algebraic equations (SLAE) by applying the preconditioned conjugate gradient method (CGM) is reduced to performing only elementary vector operations and calculating sparse matrix-vector products. A method for constructing the above preconditioner is described and analyzed. The triangular factor has a fixed sparsity pattern and is optimal in the sense that the preconditioned matrix has a minimum K-condition number. The use of polynomial preconditioning based on Chebyshev polynomials makes it possible to considerably reduce the amount of scalar product operations (at the cost of an insignificant increase in the total number of arithmetic operations). The possibility of an efficient massively parallel implementation of the resulting method for solving SLAEs is discussed. For a sequential version of this method, the results obtained by solving 56 test problems from the Florida sparse matrix collection (which are large-scale and ill-conditioned) are presented. These results show that the method is highly reliable and has low computational costs.

  20. A new family of Polak-Ribiere-Polyak conjugate gradient method with the strong-Wolfe line search

    NASA Astrophysics Data System (ADS)

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

    2017-08-01

    Conjugate gradient (CG) method is an important technique in unconstrained optimization, due to its effectiveness and low memory requirements. The focus of this paper is to introduce a new CG method for solving large scale unconstrained optimization. Theoretical proofs show that the new method fulfills sufficient descent condition if strong Wolfe-Powell inexact line search is used. Besides, computational results show that our proposed method outperforms to other existing CG methods.

  1. Conjugate gradient and approximate Newton methods for an optimal probablilistic neural network for food color classification

    NASA Astrophysics Data System (ADS)

    Chtioui, Younes; Panigrahi, Suranjan; Marsh, Ronald A.

    1998-11-01

    The probabilistic neural network (PNN) is based on the estimation of the probability density functions. The estimation of these density functions uses smoothing parameters that represent the width of the activation functions. A two-step numerical procedure is developed for the optimization of the smoothing parameters of the PNN: a rough optimization by the conjugate gradient method and a fine optimization by the approximate Newton method. The thrust is to compare the classification performances of the improved PNN and the standard back-propagation neural network (BPNN). Comparisons are performed on a food quality problem: french fry classification into three different color classes (light, normal, and dark). The optimized PNN correctly classifies 96.19% of the test data, whereas the BPNN classifies only 93.27% of the same data. Moreover, the PNN is more stable than the BPNN with regard to the random initialization. The optimized PNN requires 1464 s for training compared to only 71 s required by the BPNN.

  2. Ptychographic overlap constraint errors and the limits of their numerical recovery using conjugate gradient descent methods.

    PubMed

    Tripathi, Ashish; McNulty, Ian; Shpyrko, Oleg G

    2014-01-27

    Ptychographic coherent x-ray diffractive imaging is a form of scanning microscopy that does not require optics to image a sample. A series of scanned coherent diffraction patterns recorded from multiple overlapping illuminated regions on the sample are inverted numerically to retrieve its image. The technique recovers the phase lost by detecting the diffraction patterns by using experimentally known constraints, in this case the measured diffraction intensities and the assumed scan positions on the sample. The spatial resolution of the recovered image of the sample is limited by the angular extent over which the diffraction patterns are recorded and how well these constraints are known. Here, we explore how reconstruction quality degrades with uncertainties in the scan positions. We show experimentally that large errors in the assumed scan positions on the sample can be numerically determined and corrected using conjugate gradient descent methods. We also explore in simulations the limits, based on the signal to noise of the diffraction patterns and amount of overlap between adjacent scan positions, of just how large these errors can be and still be rendered tractable by this method.

  3. Solving groundwater flow problems by conjugate-gradient methods and the strongly implicit procedure

    USGS Publications Warehouse

    Hill, Mary C.

    1990-01-01

    The performance of the preconditioned conjugate-gradient method with three preconditioners is compared with the strongly implicit procedure (SIP) using a scalar computer. The preconditioners considered are the incomplete Cholesky (ICCG) and the modified incomplete Cholesky (MICCG), which require the same computer storage as SIP as programmed for a problem with a symmetric matrix, and a polynomial preconditioner (POLCG), which requires less computer storage than SIP. Although POLCG is usually used on vector computers, it is included here because of its small storage requirements. In this paper, published comparisons of the solvers are evaluated, all four solvers are compared for the first time, and new test cases are presented to provide a more complete basis by which the solvers can be judged for typical groundwater flow problems. Based on nine test cases, the following conclusions are reached: (1) SIP is actually as efficient as ICCG for some of the published, linear, two-dimensional test cases that were reportedly solved much more efficiently by ICCG; (2) SIP is more efficient than other published comparisons would indicate when common convergence criteria are used; and (3) for problems that are three-dimensional, nonlinear, or both, and for which common convergence criteria are used, SIP is often more efficient than ICCG, and is sometimes more efficient than MICCG.

  4. 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./.

  5. 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.

  6. 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.

  7. 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.

  8. Tomographic systems for the Helmholtz equation with extended Born field models using conjugate gradient inversion methods

    NASA Astrophysics Data System (ADS)

    Olsen, Scott Charles

    In this dissertation, new inverse scattering algorithms are derived for the Helmholtz equation using the Extended Born field model (eikonal rescattered field), and the angular spectrum (parabolic) layered field model. These two field models performed the 'best' of all the field models evaluated. Algorithms are solved with conjugate gradient methods. An advanced ultrasonic data acquisition system is also designed. Many different field models for use in a reconstruction algorithm are investigated. 'Layered' field models that mathematically partition the field calculation in layers in space possess the advantage that the field in layer n is calculated from the field in layer n - 1. Several of the 'layered' field models are investigated in terms of accuracy and computational complexity. Field model accuracy using field rescattering is also tested. The models investigated are the eikonal field model, the angular spectrum (AS) field model, and the parabolic field models known as the Split-Step Fast-Fourier Transform and the Crank-Nicolson algorithms. All of the 'layered' field models can be referred to as Extended Born field models since the 'layered' field models are more accurate than the Born approximated total field. The Rescattered Extended Born (eikonal rescattered field) Transmission Mode (REBTM) algorithm with the AS field model and the Nonrescattered AS Reconstruction (NASR) algorithm are tested with several types of objects: a single-layer cylinder, double-layer cylinders, two double-layer cylinders and the breast model. Both algorithms, REBTM and NASR work well; however, the NASR algorithm is faster and more accurate than the REBTM algorithm. The NASR algorithm is matched well with the requirements of breast model reconstructions. A major purpose of new scanner development is to collect both transmission and reflection data from multiple ultrasonic transducer arrays to test the next generation of reconstruction algorithms. The data acquisition system advanced

  9. Efficient spectral computation of the stationary states of rotating Bose-Einstein condensates by preconditioned nonlinear conjugate gradient methods

    NASA Astrophysics Data System (ADS)

    Antoine, Xavier; Levitt, Antoine; Tang, Qinglin

    2017-08-01

    We propose a preconditioned nonlinear conjugate gradient method coupled with a spectral spatial discretization scheme for computing the ground states (GS) of rotating Bose-Einstein condensates (BEC), modeled by the Gross-Pitaevskii Equation (GPE). We first start by reviewing the classical gradient flow (also known as imaginary time (IMT)) method which considers the problem from the PDE standpoint, leading to numerically solve a dissipative equation. Based on this IMT equation, we analyze the forward Euler (FE), Crank-Nicolson (CN) and the classical backward Euler (BE) schemes for linear problems and recognize classical power iterations, allowing us to derive convergence rates. By considering the alternative point of view of minimization problems, we propose the preconditioned steepest descent (PSD) and conjugate gradient (PCG) methods for the GS computation of the GPE. We investigate the choice of the preconditioner, which plays a key role in the acceleration of the convergence process. The performance of the new algorithms is tested in 1D, 2D and 3D. We conclude that the PCG method outperforms all the previous methods, most particularly for 2D and 3D fast rotating BECs, while being simple to implement.

  10. Solving a large scale nonlinear unconstrained optimization with exact line search direction by using new coefficient of conjugate gradient methods

    NASA Astrophysics Data System (ADS)

    Mohamed, Nur Syarafina; Mamat, Mustafa; Rivaie, Mohd

    2016-11-01

    Conjugate gradient (CG) methods are one of the tools in optimization. Due to its low computational memory requirement, this method is used in solving several of nonlinear unconstrained optimization problems from designs, economics, physics and engineering. In this paper, a new modification of CG family coefficient (βk) is proposed and posses global convergence under exact line search direction. Numerical experimental results based on the number of iterations and central processing unit (CPU) time show that the new βk performs better than some other well known CG methods under some standard test functions.

  11. Geometrical optics analysis of the structural imperfection of retroreflection corner cubes with a nonlinear conjugate gradient method.

    PubMed

    Kim, Hwi; Min, Sung-Wook; Lee, Byoungho

    2008-12-01

    Geometrical optics analysis of the structural imperfection of retroreflection corner cubes is described. In the analysis, a geometrical optics model of six-beam reflection patterns generated by an imperfect retroreflection corner cube is developed, and its structural error extraction is formulated as a nonlinear optimization problem. The nonlinear conjugate gradient method is employed for solving the nonlinear optimization problem, and its detailed implementation is described. The proposed method of analysis is a mathematical basis for the nondestructive optical inspection of imperfectly fabricated retroreflection corner cubes.

  12. Global convergence of the Polak-Ribiere-Polyak conjugate gradient method with an Armijo-type inexact line search for nonconvex unconstrained optimization problems

    NASA Astrophysics Data System (ADS)

    Wei, Zeng Xin; Li, Guo Yin; Qi, Li Qun

    2008-12-01

    We propose two algorithms for nonconvex unconstrained optimization problems that employ Polak-Ribiere-Polyak conjugate gradient formula and new inexact line search techniques. We show that the new algorithms converge globally if the function to be minimized has Lipschitz continuous gradients. Preliminary numerical results show that the proposed methods for particularly chosen line search conditions are very promising.

  13. Reduced-Shifted Conjugate-Gradient Method for a Green's Function: Efficient Numerical Approach in a Nano-Structured Superconductor

    NASA Astrophysics Data System (ADS)

    Nagai, Yuki; Shinohara, Yasushi; Futamura, Yasunori; Sakurai, Tetsuya

    2017-01-01

    We propose the reduced-shifted conjugate-gradient (RSCG) method, which is numerically efficient to calculate a matrix element of a Green's function defined as a resolvent of a Hamiltonian operator, by solving linear equations with a desired accuracy. This method does not calculate solution vectors of linear equations but does directly calculate a matrix element of the resolvent. The matrix elements with different frequencies are simultaneously obtained. Thus, it is easy to calculate the exception value expressed as a Matsubara summation of these elements. To illustrate a power of our method, we choose a nano-structured superconducting system with a mean-field Bogoliubov-de Gennes (BdG) approach. This method allows us to treat with the system with the fabrication potential, where one cannot effectively use the kernel-polynomial-based method. We consider the d-wave nano-island superconductor by simultaneously solving the linear equations with a large number (˜50000) of Matsubara frequencies.

  14. Two-step reconstruction method using global optimization and conjugate gradient for ultrasound-guided diffuse optical tomography.

    PubMed

    Tavakoli, Behnoosh; Zhu, Quing

    2013-01-01

    Ultrasound-guided diffuse optical tomography (DOT) is a promising method for characterizing malignant and benign lesions in the female breast. We introduce a new two-step algorithm for DOT inversion in which the optical parameters are estimated with the global optimization method, genetic algorithm. The estimation result is applied as an initial guess to the conjugate gradient (CG) optimization method to obtain the absorption and scattering distributions simultaneously. Simulations and phantom experiments have shown that the maximum absorption and reduced scattering coefficients are reconstructed with less than 10% and 25% errors, respectively. This is in contrast with the CG method alone, which generates about 20% error for the absorption coefficient and does not accurately recover the scattering distribution. A new measure of scattering contrast has been introduced to characterize benign and malignant breast lesions. The results of 16 clinical cases reconstructed with the two-step method demonstrates that, on average, the absorption coefficient and scattering contrast of malignant lesions are about 1.8 and 3.32 times higher than the benign cases, respectively.

  15. 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.

  16. A sensitivity function-based conjugate gradient method for optical tomography with the frequency-domain equation of radiative transfer

    NASA Astrophysics Data System (ADS)

    Kim, Hyun Keol; Charette, André

    2007-03-01

    The Sensitivity Function-based Conjugate Gradient Method (SFCGM) is described. This method is used to solve the inverse problems of function estimation, such as the local maps of absorption and scattering coefficients, as applied to optical tomography for biomedical imaging. A highly scattering, absorbing, non-reflecting, non-emitting medium is considered here and simultaneous reconstructions of absorption and scattering coefficients inside the test medium are achieved with the proposed optimization technique, by using the exit intensity measured at boundary surfaces. The forward problem is solved with a discrete-ordinates finite-difference method on the framework of the frequency-domain full equation of radiative transfer. The modulation frequency is set to 600 MHz and the frequency data, obtained with the source modulation, is used as the input data. The inversion results demonstrate that the SFCGM can retrieve simultaneously the spatial distributions of optical properties inside the medium within a reasonable accuracy, by significantly reducing a cross-talk between inter-parameters. It is also observed that the closer-to-detector objects are better retrieved.

  17. Block-preconditioned conjugate-gradient-like methods for numerical reservoir simulation

    SciTech Connect

    Eisenstat, S.C.; Elman, H.C.; Schultz, M.H.

    1985-02-01

    The authors describe a collection of block-preconditioners for use in solving large sparse linear systems of equations by iterative methods, and they compare their performance with several point-preconditioners in solving some systems arising in numerical reservoir simulation. They consider block-preconditioners that handle either lines or planes in an implicit manner, and pointwise incomplete LU factorizations combined with partial elimination preprocessors. Their conclusions are that the best of the pointwise methods are both more robust and faster, but that the best of the block methods are competitive for certain orderings of unknowns and require less storage.

  18. Krylov-Subspace Recycling via the POD-Augmented Conjugate-Gradient Method

    DOE PAGES

    Carlberg, Kevin; Forstall, Virginia; Tuminaro, Ray

    2016-01-01

    This paper presents a new Krylov-subspace-recycling method for efficiently solving sequences of linear systems of equations characterized by varying right-hand sides and symmetric-positive-definite matrices. As opposed to typical truncation strategies used in recycling such as deflation, we propose a truncation method inspired by goal-oriented proper orthogonal decomposition (POD) from model reduction. This idea is based on the observation that model reduction aims to compute a low-dimensional subspace that contains an accurate solution; as such, we expect the proposed method to generate a low-dimensional subspace that is well suited for computing solutions that can satisfy inexact tolerances. In particular, we proposemore » specific goal-oriented POD `ingredients' that align the optimality properties of POD with the objective of Krylov-subspace recycling. To compute solutions in the resulting 'augmented' POD subspace, we propose a hybrid direct/iterative three-stage method that leverages 1) the optimal ordering of POD basis vectors, and 2) well-conditioned reduced matrices. Numerical experiments performed on solid-mechanics problems highlight the benefits of the proposed method over existing approaches for Krylov-subspace recycling.« less

  19. Krylov-Subspace Recycling via the POD-Augmented Conjugate-Gradient Method

    SciTech Connect

    Carlberg, Kevin; Forstall, Virginia; Tuminaro, Ray

    2016-01-01

    This paper presents a new Krylov-subspace-recycling method for efficiently solving sequences of linear systems of equations characterized by varying right-hand sides and symmetric-positive-definite matrices. As opposed to typical truncation strategies used in recycling such as deflation, we propose a truncation method inspired by goal-oriented proper orthogonal decomposition (POD) from model reduction. This idea is based on the observation that model reduction aims to compute a low-dimensional subspace that contains an accurate solution; as such, we expect the proposed method to generate a low-dimensional subspace that is well suited for computing solutions that can satisfy inexact tolerances. In particular, we propose specific goal-oriented POD `ingredients' that align the optimality properties of POD with the objective of Krylov-subspace recycling. To compute solutions in the resulting 'augmented' POD subspace, we propose a hybrid direct/iterative three-stage method that leverages 1) the optimal ordering of POD basis vectors, and 2) well-conditioned reduced matrices. Numerical experiments performed on solid-mechanics problems highlight the benefits of the proposed method over existing approaches for Krylov-subspace recycling.

  20. 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.

  1. Conjugate Gradients Parallelized on the Hypercube

    NASA Astrophysics Data System (ADS)

    Basermann, Achim

    For the solution of discretized ordinary or partial differential equations it is necessary to solve systems of equations with coefficient matrices of different sparsity pattern, depending on the discretization method; using the finite element method (FE) results in largely unstructured systems of equations. A frequently used iterative solver for systems of equations is the method of conjugate gradients (CG) with different preconditioners. On a multiprocessor system with distributed memory, in particular the data distribution and the communication scheme depending on the used data struture are of greatest importance for the efficient execution of this method. Here, a data distribution and a communication scheme are presented which are based on the analysis of the column indices of the non-zero matrix elements. The performance of the developed parallel CG-method was measured on the distributed-memory-system INTEL iPSC/860 of the Research Centre Jülich with systems of equations from FE-models. The parallel CG-algorithm has been shown to be well suited for both regular and irregular discretization meshes, i.e. for coefficient matrices of very different sparsity pattern.

  2. 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.

  3. 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.

  4. Smoothed Analysis for the Conjugate Gradient Algorithm

    NASA Astrophysics Data System (ADS)

    Menon, Govind; Trogdon, Thomas

    2016-11-01

    The purpose of this paper is to establish bounds on the rate of convergence of the conjugate gradient algorithm when the underlying matrix is a random positive definite perturbation of a deterministic positive definite matrix. We estimate all finite moments of a natural halting time when the random perturbation is drawn from the Laguerre unitary ensemble in a critical scaling regime explored in Deift et al. (2016). These estimates are used to analyze the expected iteration count in the framework of smoothed analysis, introduced by Spielman and Teng (2001). The rigorous results are compared with numerical calculations in several cases of interest.

  5. Momentum-weighted conjugate gradient descent algorithm for gradient coil optimization.

    PubMed

    Lu, Hanbing; Jesmanowicz, Andrzej; Li, Shi-Jiang; Hyde, James S

    2004-01-01

    MRI gradient coil design is a type of nonlinear constrained optimization. A practical problem in transverse gradient coil design using the conjugate gradient descent (CGD) method is that wire elements move at different rates along orthogonal directions (r, phi, z), and tend to cross, breaking the constraints. A momentum-weighted conjugate gradient descent (MW-CGD) method is presented to overcome this problem. This method takes advantage of the efficiency of the CGD method combined with momentum weighting, which is also an intrinsic property of the Levenberg-Marquardt algorithm, to adjust step sizes along the three orthogonal directions. A water-cooled, 12.8 cm inner diameter, three axis torque-balanced gradient coil for rat imaging was developed based on this method, with an efficiency of 2.13, 2.08, and 4.12 mT.m(-1).A(-1) along X, Y, and Z, respectively. Experimental data demonstrate that this method can improve efficiency by 40% and field uniformity by 27%. This method has also been applied to the design of a gradient coil for the human brain, employing remote current return paths. The benefits of this design include improved gradient field uniformity and efficiency, with a shorter length than gradient coil designs using coaxial return paths.

  6. 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

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

    PubMed

    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.

  8. 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).

  9. Training feed-forward neural networks using conjugate gradients

    NASA Astrophysics Data System (ADS)

    Blue, James L.; Grother, Patrick J.

    1992-08-01

    Neural networks for optical character recognition are still being trained using back propagation, even though conjugate gradient methods have been shown to be much faster. Most multilayer perceptron network training results in the literature are obtained for small and unrealistic problems or from data sets that are proprietary and not available for comparison testing. We present results on a large realistic pattern set containing 2000 training and 1434 testing exemplars. Each pattern is composed of 32 Gabor coefficients obtained from a 32 by 32 pixel binary image of a handwritten digit segmented from the NIST Handwriting Image Data Base. These sets are believed to have approximately 1 segmentation errors. Comparative results for Moller''s scaled conjugate gradient method and for standard back propagation are presented for runs on a serial scientific workstation and a highly parallel computer. Typical training on a network with 32 inputs, 32 hidden nodes, and 10 output nodes gives a 98 recognition for the training set and 95 for the test set. Training with conjugate gradients requires fewer than 200 iterations; times are about 20 to 40 minutes on a scientific workstation and 6 minutes on the highly parallel computer. Testing (classification) is done at the rate of 600 to 1600 patterns per second on the scientific workstation and on the highly parallel computer respectively. These results suggest that commercial handwritten character recognition systems with great economic potential are feasible.

  10. 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.

  11. 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.

  12. 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

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

    DOE PAGES

    Yang, Xiaoli; Hofmann, Ralf; Dapp, Robin; ...

    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 o fin 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 numbermore » 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.« less

  14. 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 o fin 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.

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

    PubMed

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

    2015-03-09

    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.

  16. 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.

  17. Improved Conjugate Gradient Bundle Adjustment of Dunhuang Wall Painting Images

    NASA Astrophysics Data System (ADS)

    Hu, K.; Huang, X.; You, H.

    2017-09-01

    Bundle adjustment with additional parameters is identified as a critical step for precise orthoimage generation and 3D reconstruction of Dunhuang wall paintings. Due to the introduction of self-calibration parameters and quasi-planar constraints, the structure of coefficient matrix of the reduced normal equation is banded-bordered, making the solving process of bundle adjustment complex. In this paper, Conjugate Gradient Bundle Adjustment (CGBA) method is deduced by calculus of variations. A preconditioning method based on improved incomplete Cholesky factorization is adopt to reduce the condition number of coefficient matrix, as well as to accelerate the iteration rate of CGBA. Both theoretical analysis and experimental results comparison with conventional method indicate that, the proposed method can effectively conquer the ill-conditioned problem of normal equation and improve the calculation efficiency of bundle adjustment with additional parameters considerably, while maintaining the actual accuracy.

  18. 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.

  19. Effects of Conjugate Gradient Methods and Step-Length Formulas on the Multiscale Full Waveform Inversion in Time Domain: Numerical Experiments

    NASA Astrophysics Data System (ADS)

    Liu, Youshan; Teng, Jiwen; Xu, Tao; Badal, José; Liu, Qinya; Zhou, Bing

    2017-05-01

    We carry out full waveform inversion (FWI) in time domain based on an alternative frequency-band selection strategy that allows us to implement the method with success. This strategy aims at decomposing the seismic data within partially overlapped frequency intervals by carrying out a concatenated treatment of the wavelet to largely avoid redundant frequency information to adapt to wavelength or wavenumber coverage. A pertinent numerical test proves the effectiveness of this strategy. Based on this strategy, we comparatively analyze the effects of update parameters for the nonlinear conjugate gradient (CG) method and step-length formulas on the multiscale FWI through several numerical tests. The investigations of up to eight versions of the nonlinear CG method with and without Gaussian white noise make clear that the HS (Hestenes and Stiefel in J Res Natl Bur Stand Sect 5:409-436, 1952), CD (Fletcher in Practical methods of optimization vol. 1: unconstrained optimization, Wiley, New York, 1987), and PRP (Polak and Ribière in Revue Francaise Informat Recherche Opertionelle, 3e Année 16:35-43, 1969; Polyak in USSR Comput Math Math Phys 9:94-112, 1969) versions are more efficient among the eight versions, while the DY (Dai and Yuan in SIAM J Optim 10:177-182, 1999) version always yields inaccurate result, because it overestimates the deeper parts of the model. The application of FWI algorithms using distinct step-length formulas, such as the direct method ( Direct), the parabolic search method ( Search), and the two-point quadratic interpolation method ( Interp), proves that the Interp is more efficient for noise-free data, while the Direct is more efficient for Gaussian white noise data. In contrast, the Search is less efficient because of its slow convergence. In general, the three step-length formulas are robust or partly insensitive to Gaussian white noise and the complexity of the model. When the initial velocity model deviates far from the real model or the

  20. Comparative study of conjugate gradient algorithms performance on the example of steady-state axisymmetric heat transfer problem

    NASA Astrophysics Data System (ADS)

    Ocłoń, Paweł; Łopata, Stanisław; Nowak, Marzena

    2013-09-01

    The finite element method (FEM) is one of the most frequently used numerical methods for finding the approximate discrete point solution of partial differential equations (PDE). In this method, linear or nonlinear systems of equations, comprised after numerical discretization, are solved to obtain the numerical solution of PDE. The conjugate gradient algorithms are efficient iterative solvers for the large sparse linear systems. In this paper the performance of different conjugate gradient algorithms: conjugate gradient algorithm (CG), biconjugate gradient algorithm (BICG), biconjugate gradient stabilized algorithm (BICGSTAB), conjugate gradient squared algorithm (CGS) and biconjugate gradient stabilized algorithm with l GMRES restarts (BICGSTAB(l)) is compared when solving the steady-state axisymmetric heat conduction problem. Different values of l parameter are studied. The engineering problem for which this comparison is made is the two-dimensional, axisymmetric heat conduction in a finned circular tube.

  1. Global convergence analysis of a new nonlinear conjugate gradient coefficient with strong Wolfe line search

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    Nonlinear conjugate gradient (CG) methods are the most important method for solving large-scale unconstrained optimization problems. Many studies and modifications have been conducted recently to improve this method. In this paper, a new class of conjugate gradient coefficients (βk ) with a new parameter m =‖gk ‖ /‖gk -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 (αk>0 ) is a step size of CG methods. Numerical result shows that the new formula is superior and more efficient when compared to other CG coefficients.

  2. Pixel-based OPC optimization based on conjugate gradients.

    PubMed

    Ma, Xu; Arce, Gonzalo R

    2011-01-31

    Optical proximity correction (OPC) methods are resolution enhancement techniques (RET) used extensively in the semiconductor industry to improve the resolution and pattern fidelity of optical lithography. In pixel-based OPC (PBOPC), the mask is divided into small pixels, each of which is modified during the optimization process. Two critical issues in PBOPC are the required computational complexity of the optimization process, and the manufacturability of the optimized mask. Most current OPC optimization methods apply the steepest descent (SD) algorithm to improve image fidelity augmented by regularization penalties to reduce the complexity of the mask. Although simple to implement, the SD algorithm converges slowly. The existing regularization penalties, however, fall short in meeting the mask rule check (MRC) requirements often used in semiconductor manufacturing. This paper focuses on developing OPC optimization algorithms based on the conjugate gradient (CG) method which exhibits much faster convergence than the SD algorithm. The imaging formation process is represented by the Fourier series expansion model which approximates the partially coherent system as a sum of coherent systems. In order to obtain more desirable manufacturability properties of the mask pattern, a MRC penalty is proposed to enlarge the linear size of the sub-resolution assistant features (SRAFs), as well as the distances between the SRAFs and the main body of the mask. Finally, a projection method is developed to further reduce the complexity of the optimized mask pattern.

  3. Three-dimensional nonlinear conjugate gradient parallel inversion with full information of marine magnetotellurics

    NASA Astrophysics Data System (ADS)

    Zhang, Kun; Yan, Jiayong; Lü, Qingtian; Zhao, Jinhua; Hu, Hao

    2017-04-01

    A new inversion method using marine magnetotellurics is proposed based on previous studies using the nonlinear conjugate gradient method. A numerical example is used to verify the inversion algorithm and program. The inversion model and response resemble the synthetic model. Some technologies have been added to the inversion algorithm: parallel structure, terrain inversion and static shift correction.

  4. 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.

  5. 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.

  6. 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.

  7. The Modified HZ Conjugate Gradient Algorithm for Large-Scale Nonsmooth Optimization

    PubMed Central

    Yuan, Gonglin; Sheng, Zhou; Liu, Wenjie

    2016-01-01

    In this paper, the Hager and Zhang (HZ) conjugate gradient (CG) method and the modified HZ (MHZ) CG method are presented for large-scale nonsmooth convex minimization. Under some mild conditions, convergent results of the proposed methods are established. Numerical results show that the presented methods can be better efficiency for large-scale nonsmooth problems, and several problems are tested (with the maximum dimensions to 100,000 variables). PMID:27780245

  8. The Modified HZ Conjugate Gradient Algorithm for Large-Scale Nonsmooth Optimization.

    PubMed

    Yuan, Gonglin; Sheng, Zhou; Liu, Wenjie

    2016-01-01

    In this paper, the Hager and Zhang (HZ) conjugate gradient (CG) method and the modified HZ (MHZ) CG method are presented for large-scale nonsmooth convex minimization. Under some mild conditions, convergent results of the proposed methods are established. Numerical results show that the presented methods can be better efficiency for large-scale nonsmooth problems, and several problems are tested (with the maximum dimensions to 100,000 variables).

  9. Fast conjugate gradient algorithm extension for analyzer-based imaging reconstruction

    NASA Astrophysics Data System (ADS)

    Caudevilla, Oriol; Brankov, Jovan G.

    2016-04-01

    This paper presents an extension of the classic Conjugate Gradient Algorithm. Motivated by the Analyzer-Based Imaging inverse problem, the novel method maximizes the Poisson regularized log-likelihood with a non-linear transformation of parameter faster than other solutions. The new approach takes advantage of the special properties of the Poisson log-likelihood to conjugate each ascend direction with respect all the previous directions taken by the algorithm. Our solution is compared with the general solution for non-quadratic unconstrained problems: the Polak- Ribiere formula. Both methods are applied to the ABI reconstruction problem.

  10. 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.

  11. 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.

  12. 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.

  13. Conjugate and method for forming aminomethyl phosphorus conjugates

    SciTech Connect

    Katti, K.V.; Berning, D.E.; Volkert, W.A.; Ketring, A.R.; Churchill, R.

    1999-09-07

    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.

  14. 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.

  15. Conjugate-gradient-based decision feedback equalization with structured channel estimation for digital Television

    NASA Astrophysics Data System (ADS)

    Zoltowski, Michael D.; Hillery, William J.; Ozen, Serdar; Fimoff, Mark

    2002-06-01

    In this paper, we show how the convergence time of equalizers for 8-VSB based on the conjugate gradient (CG) algorithm can be considerably improved through initialization based on a channel estimate. We derive real and complex minimum mean-square error (MMSE) equalizers and implement them adaptively using the conjugate gradient, recursive least squares (RLS), and least mean squares (LMS) algorithms. We show that both CG and RLS have similar convergence times --- both are much faster than LMS. Since the CG algorithm is easily initialized, we compare several methods of initialization to determine how each affects convergence and then apply the best methods to initialize equalizers using channel estimates. We find that initializing the correlation matrices and filling the feedback taps with training symbols greatly speeds convergence of the CG adaptive equalizer, potentially approaching the rate of convergence when running the algorithm on the matrix equations using the actual channel.

  16. 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.

  17. 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.

  18. A modified conjugate gradient coefficient with inexact line search for unconstrained optimization

    NASA Astrophysics Data System (ADS)

    Aini, Nurul; Rivaie, Mohd; Mamat, Mustafa

    2016-11-01

    Conjugate gradient (CG) method is a line search algorithm mostly known for its wide application in solving unconstrained optimization problems. Its low memory requirements and global convergence properties makes it one of the most preferred method in real life application such as in engineering and business. In this paper, we present a new CG method based on AMR* and CD method for solving unconstrained optimization functions. The resulting algorithm is proven to have both the sufficient descent and global convergence properties under inexact line search. Numerical tests are conducted to assess the effectiveness of the new method in comparison to some previous CG methods. The results obtained indicate that our method is indeed superior.

  19. A forward model and conjugate gradient inversion technique for low-frequency ultrasonic imaging.

    PubMed

    van Dongen, Koen W A; Wright, William M D

    2006-10-01

    Emerging methods of hyperthermia cancer treatment require noninvasive temperature monitoring, and ultrasonic techniques show promise in this regard. Various tomographic algorithms are available that reconstruct sound speed or contrast profiles, which can be related to temperature distribution. The requirement of a high enough frequency for adequate spatial resolution and a low enough frequency for adequate tissue penetration is a difficult compromise. In this study, the feasibility of using low frequency ultrasound for imaging and temperature monitoring was investigated. The transient probing wave field had a bandwidth spanning the frequency range 2.5-320.5 kHz. The results from a forward model which computed the propagation and scattering of low-frequency acoustic pressure and velocity wave fields were used to compare three imaging methods formulated within the Born approximation, representing two main types of reconstruction. The first uses Fourier techniques to reconstruct sound-speed profiles from projection or Radon data based on optical ray theory, seen as an asymptotical limit for comparison. The second uses backpropagation and conjugate gradient inversion methods based on acoustical wave theory. The results show that the accuracy in localization was 2.5 mm or better when using low frequencies and the conjugate gradient inversion scheme, which could be used for temperature monitoring.

  20. Improved preconditioned conjugate gradient algorithm and application in 3D inversion of gravity-gradiometry data

    NASA Astrophysics Data System (ADS)

    Wang, Tai-Han; Huang, Da-Nian; Ma, Guo-Qing; Meng, Zhao-Hai; Li, Ye

    2017-06-01

    With the continuous development of full tensor gradiometer (FTG) measurement techniques, three-dimensional (3D) inversion of FTG data is becoming increasingly used in oil and gas exploration. In the fast processing and interpretation of large-scale high-precision data, the use of the graphics processing unit process unit (GPU) and preconditioning methods are very important in the data inversion. In this paper, an improved preconditioned conjugate gradient algorithm is proposed by combining the symmetric successive over-relaxation (SSOR) technique and the incomplete Choleksy decomposition conjugate gradient algorithm (ICCG). Since preparing the preconditioner requires extra time, a parallel implement based on GPU is proposed. The improved method is then applied in the inversion of noisecontaminated synthetic data to prove its adaptability in the inversion of 3D FTG data. Results show that the parallel SSOR-ICCG algorithm based on NVIDIA Tesla C2050 GPU achieves a speedup of approximately 25 times that of a serial program using a 2.0 GHz Central Processing Unit (CPU). Real airborne gravity-gradiometry data from Vinton salt dome (southwest Louisiana, USA) are also considered. Good results are obtained, which verifies the efficiency and feasibility of the proposed parallel method in fast inversion of 3D FTG data.

  1. A new nonlinear conjugate gradient coefficient under strong Wolfe-Powell line search

    NASA Astrophysics Data System (ADS)

    Mohamed, Nur Syarafina; Mamat, Mustafa; Rivaie, Mohd

    2017-08-01

    A nonlinear conjugate gradient method (CG) plays an important role in solving a large-scale unconstrained optimization problem. This method is widely used due to its simplicity. The method is known to possess sufficient descend condition and global convergence properties. In this paper, a new nonlinear of CG coefficient βk is presented by employing the Strong Wolfe-Powell inexact line search. The new βk performance is tested based on number of iterations and central processing unit (CPU) time by using MATLAB software with Intel Core i7-3470 CPU processor. Numerical experimental results show that the new βk converge rapidly compared to other classical CG method.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Efficient geostatistical inversion of transient groundwater flow using preconditioned nonlinear conjugate gradients

    NASA Astrophysics Data System (ADS)

    Klein, Ole; Cirpka, Olaf A.; Bastian, Peter; Ippisch, Olaf

    2017-04-01

    In the geostatistical inverse problem of subsurface hydrology, continuous hydraulic parameter fields, in most cases hydraulic conductivity, are estimated from measurements of dependent variables, such as hydraulic heads, under the assumption that the parameter fields are autocorrelated random space functions. Upon discretization, the continuous fields become large parameter vectors with O (104 -107) elements. While cokriging-like inversion methods have been shown to be efficient for highly resolved parameter fields when the number of measurements is small, they require the calculation of the sensitivity of each measurement with respect to all parameters, which may become prohibitive with large sets of measured data such as those arising from transient groundwater flow. We present a Preconditioned Conjugate Gradient method for the geostatistical inverse problem, in which a single adjoint equation needs to be solved to obtain the gradient of the objective function. Using the autocovariance matrix of the parameters as preconditioning matrix, expensive multiplications with its inverse can be avoided, and the number of iterations is significantly reduced. We use a randomized spectral decomposition of the posterior covariance matrix of the parameters to perform a linearized uncertainty quantification of the parameter estimate. The feasibility of the method is tested by virtual examples of head observations in steady-state and transient groundwater flow. These synthetic tests demonstrate that transient data can reduce both parameter uncertainty and time spent conducting experiments, while the presented methods are able to handle the resulting large number of measurements.

  8. 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.

  9. Conjugate gradient and steepest descent approach on quasi-Newton search direction

    NASA Astrophysics Data System (ADS)

    Sofi, A. Z. M.; Mamat, M.; Mohd, I.; Ibrahim, M. A. H.

    2014-07-01

    An approach of using conjugate gradient and classic steepest descent search direction onto quasi-Newton search direction had been proposed in this paper and we called it as 'scaled CGSD-QN' search direction. A new coefficient formula had been successfully constructed for being used in the 'scaled CGSD-QN' search direction and proven here that the coefficient formula is globally converge to the minimizer. The Hessian update formula that has been used in the quasi-Newton algorithm is DFP update formula. This new search direction approach was testes with some some standard unconstrained optimization test problems and proven that this new search direction approach had positively affect quasi-Newton method by using DFP update formula.

  10. Wavelet methods in multi-conjugate adaptive optics

    NASA Astrophysics Data System (ADS)

    Helin, T.; Yudytskiy, M.

    2013-08-01

    The next generation ground-based telescopes rely heavily on adaptive optics for overcoming the limitation of atmospheric turbulence. In the future adaptive optics modalities, like multi-conjugate adaptive optics (MCAO), atmospheric tomography is the major mathematical and computational challenge. In this severely ill-posed problem, a fast and stable reconstruction algorithm is needed that can take into account many real-life phenomena of telescope imaging. We introduce a novel reconstruction method for the atmospheric tomography problem and demonstrate its performance and flexibility in the context of MCAO. Our method is based on using locality properties of compactly supported wavelets, both in the spatial and frequency domains. The reconstruction in the atmospheric tomography problem is obtained by solving the Bayesian MAP estimator with a conjugate-gradient-based algorithm. An accelerated algorithm with preconditioning is also introduced. Numerical performance is demonstrated on the official end-to-end simulation tool OCTOPUS of European Southern Observatory.

  11. 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.

  12. A new modified conjugate gradient coefficient for solving system of linear equations

    NASA Astrophysics Data System (ADS)

    Hajar, N.; ‘Aini, N.; Shapiee, N.; Abidin, Z. Z.; Khadijah, W.; Rivaie, M.; Mamat, M.

    2017-09-01

    Conjugate gradient (CG) method is an evolution of computational method in solving unconstrained optimization problems. This approach is easy to implement due to its simplicity and has been proven to be effective in solving real-life application. Although this field has received copious amount of attentions in recent years, some of the new approaches of CG algorithm cannot surpass the efficiency of the previous versions. Therefore, in this paper, a new CG coefficient which retains the sufficient descent and global convergence properties of the original CG methods is proposed. This new CG is tested on a set of test functions under exact line search. Its performance is then compared to that of some of the well-known previous CG methods based on number of iterations and CPU time. The results show that the new CG algorithm has the best efficiency amongst all the methods tested. This paper also includes an application of the new CG algorithm for solving large system of linear equations

  13. 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

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

    PubMed

    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.

  15. 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

  16. 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.

  17. 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.

  18. Conjugate Gradient Parametric Detection of Multichannel Signals (Preprint)

    DTIC Science & Technology

    2012-05-01

    a block- Toeplitz matrix structure, preconditioning methods(e.g., [7], [8], [9]) can be employed, which are very effective in further speeding up the...convergence rate in CG iterations, while adding up only a modest computational overhead per iteration (due to the block- Toeplitz structure). Finally...rate. For PMF, the disturbance covariance matrix is a block- Toeplitz (BT) matrix. For such matrices, block-circulant (BC) preconditioners are often

  19. 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.

  20. 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).

  1. Active and passive computed tomography algorithm with a constrained conjugate gradient solution

    SciTech Connect

    Goodman, D.; Jackson, J. A.; Martz, H. E.; Roberson, G. P.

    1998-10-01

    An active and passive computed tomographic technique (A&PCT) has been developed at the Lawrence Livermore National Laboratory (LLNL). The technique uses an external radioactive source and active tomography to map the attenuation within a waste drum as a function of mono-energetic gamma-ray energy. Passive tomography is used to localize and identify specific radioactive waste within the same container. The passive data is corrected for attenuation using the active data and this yields a quantitative assay of drum activity. A&PCT involves the development of a detailed system model that combines the data from the active scans with the geometry of the imaging system. Using the system model, iterative optimization techniques are used to reconstruct the image from the passive data. Requirements for high throughput yield measured emission levels in waste barrels that are too low to apply optimization techniques involving the usual Gaussian statistics. In this situation a Poisson distribution, typically used for cases with low counting statistics, is used to create an effective maximum likelihood estimation function. An optimization algorithm, Constrained Conjugate Gradient (CCG), is used to determine a solution for A&PCT quantitative assay. CCG, which was developed at LLNL, has proven to be an efficient and effective optimization method to solve limited-data problems. A detailed explanation of the algorithms used in developing the model and optimization codes is given.

  2. 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.

  3. 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

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

    PubMed

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

    2013-10-01

    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. 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. At the same bias, the direct approach yielded significant relative reduction in standard deviation by 12%-29% and 32%-70% for 50 × 10(6) and 10 × 10(6) 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. 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.

  5. Fast conjugate phase image reconstruction based on a Chebyshev approximation to correct for B0 field inhomogeneity and concomitant gradients

    PubMed Central

    Chen, Weitian; Sica, Christopher T.; Meyer, Craig H.

    2008-01-01

    Off-resonance effects can cause image blurring in spiral scanning and various forms of image degradation in other MRI methods. Off-resonance effects can be caused by both B0 inhomogeneity and concomitant gradient fields. Previously developed off-resonance correction methods focus on the correction of a single source of off-resonance. This work introduces a computationally efficient method of correcting for B0 inhomogeneity and concomitant gradients simultaneously. The method is a fast alternative to conjugate phase reconstruction, with the off-resonance phase term approximated by Chebyshev polynomials. The proposed algorithm is well suited for semiautomatic off-resonance correction, which works well even with an inaccurate or low-resolution field map. The proposed algorithm is demonstrated using phantom and in vivo data sets acquired by spiral scanning. Semiautomatic off-resonance correction alone is shown to provide a moderate amount of correction for concomitant gradient field effects, in addition to B0 imhomogeneity effects. However, better correction is provided by the proposed combined method. The best results were produced using the semiautomatic version of the proposed combined method. PMID:18956462

  6. Hybrid conjugate gradient-Occam algorithms for inversion of multifrequency and multitransmitter EM data

    NASA Astrophysics Data System (ADS)

    Egbert, Gary D.

    2012-07-01

    We describe novel hybrid algorithms for inversion of electromagnetic geophysical data, combining the computational and storage efficiency of a conjugate gradient approach with an Occam scheme for regularization and step-length control. The basic algorithm is based on the observation that iterative solution of the symmetric (Gauss-Newton) normal equations with conjugate gradients effectively generates a sequence of sensitivities for different linear combinations of the data, allowing construction of the Jacobian for a projection of the original full data space. The Occam scheme can then be applied to this projected problem, with the tradeoff parameter chosen by assessing fit to the full data set. For EM geophysical problems with multiple transmitters (either multiple frequencies or source geometries) an extension of the basic hybrid algorithm is possible. In this case multiple forward and adjoint solutions (one each for each transmitter) are required for each step in the iterative normal equation solver, and each corresponds to the sensitivity for a separate linear combination of data. From the perspective of the hybrid approach, with conjugate gradients generating an approximation to the full Jacobian, it is advantageous to save all of the component sensitivities, and use these to solve the projected problem in a larger subspace. We illustrate the algorithms on a simple problem, 2-D magnetotelluric inversion, using synthetic data. Both the basic and modified hybrid schemes produce essentially the same result as an Occam inversion based on a full calculation of the Jacobian, and the modified scheme requires significantly fewer steps (relative to the basic hybrid scheme) to converge to an adequate solution to the normal equations. The algorithms are expected to be useful primarily for 3-D inverse problems for which the computational burden is heavily dominated by solution to the forward and adjoint problems.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Parallelization of the NAS Conjugate Gradient Benchmark Using the Global Arrays Shared Memory Programming Model

    SciTech Connect

    Zhang, Yeliang; Tipparaju, Vinod; Nieplocha, Jarek; Hariri, Salim

    2005-04-08

    The NAS Conjugate Gradient (CG) benchmark is an important scientific kernel used to evaluate machine performance and compare characteristics of different programming models. Global Arrays (GA) toolkit supports a shared memory programming paradigm— even on distributed memory systems— and offers the programmer control over the distribution and locality that are important for optimizing performance on scalable architectures. In this paper, we describe and compare two different parallelization strategies of the CG benchmark using GA and report performance results on a shared-memory system as well as on a cluster. Performance benefits of using shared memory for irregular/sparse computations have been demonstrated before in context of the CG benchmark using OpenMP. Similarly, the GA implementation outperforms the standard MPI implementation on shared memory system, in our case the SGI Altix. However, with GA these benefits are extended to distributed memory systems and demonstrated on a Linux cluster with Myrinet.

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

    NASA Astrophysics Data System (ADS)

    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.

  15. 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.

  16. On a concurrent element-by-element preconditioned conjugate gradient algorithm for multiple load cases

    NASA Technical Reports Server (NTRS)

    Watson, Brian; Kamat, M. P.

    1990-01-01

    Element-by-element preconditioned conjugate gradient (EBE-PCG) algorithms have been advocated for use in parallel/vector processing environments as being superior to the conventional LDL(exp T) decomposition algorithm for single load cases. Although there may be some advantages in using such algorithms for a single load case, when it comes to situations involving multiple load cases, the LDL(exp T) decomposition algorithm would appear to be decidedly more cost-effective. The authors have outlined an EBE-PCG algorithm suitable for multiple load cases and compared its effectiveness to the highly efficient LDL(exp T) decomposition scheme. The proposed algorithm offers almost no advantages over the LDL(exp T) algorithm for the linear problems investigated on the Alliant FX/8. However, there may be some merit in the algorithm in solving nonlinear problems with load incrementation, but that remains to be investigated.

  17. High-fidelity phase and amplitude control of phase-only computer generated holograms using conjugate gradient minimisation.

    PubMed

    Bowman, D; Harte, T L; Chardonnet, V; De Groot, C; Denny, S J; Le Goc, G; Anderson, M; Ireland, P; Cassettari, D; Bruce, G D

    2017-05-15

    We demonstrate simultaneous control of both the phase and amplitude of light using a conjugate gradient minimisation-based hologram calculation technique and a single phase-only spatial light modulator (SLM). A cost function, which incorporates the inner product of the light field with a chosen target field within a defined measure region, is efficiently minimised to create high fidelity patterns in the Fourier plane of the SLM. A fidelity of F = 0.999997 is achieved for a pattern resembling an LG10 mode with a calculated light-usage efficiency of 41.5%. Possible applications of our method in optical trapping and ultracold atoms are presented and we show uncorrected experimental realisation of our patterns with F = 0.97 and 7.8% light efficiency.

  18. High-fidelity phase and amplitude control of phase-only computer generated holograms using conjugate gradient minimisation

    NASA Astrophysics Data System (ADS)

    Bowman, D.; Harte, T. L.; Chardonnet, V.; De Groot, C.; Denny, S. J.; Le Goc, G.; Anderson, M.; Ireland, P.; Cassettari, D.; Bruce, G. D.

    2017-05-01

    We demonstrate simultaneous control of both the phase and amplitude of light using a conjugate gradient minimisation-based hologram calculation technique and a single phase-only spatial light modulator (SLM). A cost function which incorporates the inner product of the light field with a chosen target field within a defined measure region is efficiently minimised to create high fidelity patterns in the Fourier plane of the SLM. A fidelity of $F=0.999997$ is achieved for a pattern resembling an $LG^{0}_{1}$ mode with a calculated light-usage efficiency of $41.5\\%$. Possible applications of our method in optical trapping and ultracold atoms are presented and we show uncorrected experimental realisation of our patterns with $F = 0.97$ and $7.8\\%$ light efficiency.

  19. 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.

  20. Solution-processed bulk heterojunction photovoltaic cells from gradient pi-conjugated thienylene vinylene dendrimers.

    PubMed

    Wang, Jin-Liang; Zhong, Chengmei; Tang, Zheng-Ming; Wu, Hongbin; Ma, Yuguo; Cao, Yong; Pei, Jian

    2010-01-04

    A series of gradient pi-conjugated dendrimers and their corresponding models based on 5,5,10,10,15,15-hexahexyltruxene moieties as nodes and oligo(thienylene vinylene) (OTVs) units with different lengths as branching arms are synthesized in good yields through Wittig-Horner reactions. All new compounds are fully characterized by (1)H and (13)C NMR spectroscopy, elemental analysis, and MALDI-TOF MS or ESI-MS. Investigation of their photophysical properties reveals that the gradient dendritic scaffold not only results in a higher molar absorption coefficient and broader absorption region than those of their corresponding model compounds, but also improves the PL quantum yields relative to the corresponding OTVs. The suitable HOMO and LUMO levels as well as excellent film forming properties make these molecules potential candidates for organic solar cells. Solution-processed bulk heterojunction solar cells using these dendrimers as donor and [6,6]-phenyl-C(61) butyric acid methyl ester as acceptor are prepared and tested. The power conversion efficiency of the devices based on G0-4-2 is 0.40 % under illumination of air mass 1.5 and 100 mW cm(-2). This is the highest record value for OTV-based materials to date. Although the absorption band of dendrimer G0-4-2 is much narrower than that of poly(3-hexylthienylene vinylene) (P3HTV), the efficiency of its solar cell device is almost twice that of the device based on P3HTV. This result shows clearly the advantage of gradient dendritic structures as active materials for photovoltaic cells.

  1. Optimization using the gradient and simplex methods.

    PubMed

    Cerdà, Víctor; Cerdà, Juan Luis; Idris, Abubakr M

    2016-02-01

    Traditionally optimization of analytical methods has been conducted using a univariate method, varying each parameter one-by-one holding fixed the remaining. This means in many cases to reach only local minima and not get the real optimum. Among the various options for multivariate optimization, this paper highlights the gradient method, which involves the ability to perform the partial derivatives of a mathematical model, as well as the simplex method that does not require that condition. The advantages and disadvantages of those two multivariate optimization methods are discussed, indicating when they can be applied and the different forms that have been introduced. Different cases are described on the applications of these methods in analytical chemistry.

  2. 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.

  3. A numerical study of gradient-based nonlinear optimization methods for contrast enhanced optical tomography.

    PubMed

    Roy, R; Sevick-Muraca, E

    2001-07-02

    Numerical performance of two gradient-based methods, a truncated-Newton method with trust region (TN) and a nonlinear conjugate gradient (NCG), is studied and compared for a given data set and conditions specific for the contrast enhanced optical tomography problem. Our results suggest that the relative performance of the two methods depends upon the error functions, specific to the problem to be solved. The TN outperforms the NCG when maps of fluorescence lifetime are reconstructed while both methods performed well when the absorption coefficient constitutes the parameter set that is to be recovered.

  4. 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

  5. Optimization of the deflated Conjugate Gradient algorithm for the solving of elliptic equations on massively parallel machines

    NASA Astrophysics Data System (ADS)

    Malandain, Mathias; Maheu, Nicolas; Moureau, Vincent

    2013-04-01

    The discretization of Partial Differential Equations often leads to the need of solving large symmetric linear systems. In the case of the Navier-Stokes equations for incompressible flows, solving the elliptic pressure Poisson equation can represent the most important part of the computational time required for the massively parallel simulation of the flow. The need for efficiency that this issue induces is completed with a need for stability, in particular when dealing with unstructured meshes. Here, a stable and efficient variant of the Deflated Preconditioned Conjugate Gradient (DPCG) solver is first presented. This two-level method uses an arbitrary coarse grid to reduce the computational cost of the solving. However, in the massively parallel implementation of this technique for very large linear systems, the coarse grids generated can count up to millions of cells, which makes direct solvings on the coarse level impossible. The solving on the coarse grid, performed with a Preconditioned Conjugate Gradient (PCG) solver for this reason, may involve a large number of communications, which reduces dramatically the performances on massively parallel machines. To this effect, two methods developed in order to reduce the number of iterations on the coarse level are introduced, that is the creation of improved initial guesses and the adaptation of the convergence criterion. The design of these methods make them easy to implement in any already existing DPCG solver. The structural requirements for an efficient massively parallel unstructured solver and the implementation of this solver are described. The novel DPCG method is assessed for applications involving turbulence, heat transfers and two-phase flows, with grids up to 17.8 billion elements. Numerical results show a two- to 12-fold reduction of the number of iterations on the coarse level, which implies a reduction of the computational time of the Poisson solver up to 71% and a global reduction of the proportion

  6. 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.

  7. Evaluation of two conjugate gradient based algorithms for quantitation in cardiac SPECT imaging

    SciTech Connect

    Sire, P.; Grangeat, P.; Iovleff, S.; Mallon, L.A.

    1996-12-31

    Correction attenuation in SPECT is a very important issue in cardiac imaging. In this paper we evaluate two conjugate gradient (CG) based algorithms to reconstruct an attenuation compensated emission map. The first algorithm is a classic preconditioned CG approach, the second one uses the minimal residual (MR) algorithm. We discuss the emission reconstruction problem and the difficulty to get a good uniformity within the reconstructed cardiac wall. An evaluation on numerical and real phantoms shows that the point spread function (PSF) of the system strongly affects the uniformity. Thus, two essential improvements are made. First, the response of the reconstruction procedure is made isotropic by replacing the classic 1D apodized ramp reconstruction filter with a 2D filter. Second, to improve the spatial resolution, we apply a PSF deconvolution to the projections. A threshold parameter is used to prevent the deconvolution from amplifying high-frequency noise. Stabilization is also achieved by incorporating into the reconstruction algorithms a regularization, which is made spatially adaptive to preserve high contrast within the heart while smoothing the rest of the image. Results obtained on numerical and anatomic phantoms show that the proposed algorithms lead to fast, stabilized and more accurate attenuation compensation.

  8. The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces

    NASA Astrophysics Data System (ADS)

    Aviat, Félix; Lagardère, Louis; Piquemal, Jean-Philip

    2017-10-01

    In a recent paper [F. Aviat et al., J. Chem. Theory Comput. 13, 180-190 (2017)], we proposed the Truncated Conjugate Gradient (TCG) approach to compute the polarization energy and forces in polarizable molecular simulations. The method consists in truncating the conjugate gradient algorithm at a fixed predetermined order leading to a fixed computational cost and can thus be considered "non-iterative." This gives the possibility to derive analytical forces avoiding the usual energy conservation (i.e., drifts) issues occurring with iterative approaches. A key point concerns the evaluation of the analytical gradients, which is more complex than that with a usual solver. In this paper, after reviewing the present state of the art of polarization solvers, we detail a viable strategy for the efficient implementation of the TCG calculation. The complete cost of the approach is then measured as it is tested using a multi-time step scheme and compared to timings using usual iterative approaches. We show that the TCG methods are more efficient than traditional techniques, making it a method of choice for future long molecular dynamics simulations using polarizable force fields where energy conservation matters. We detail the various steps required for the implementation of the complete method by software developers.

  9. 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.

  10. 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.

  11. pi-Conjugated Gradient Copolymers Suppress Phase Separation and Improve Stability in Bulk Heterojunction Solar Cells

    DTIC Science & Technology

    2014-01-01

    discussion Polymer synthesis The gradient copolymers described herein were prepared using a living, chain-growth polymerization method known as catalyst...and C. S. Hsu, Adv. Funct. Mater., 2011, 21, 1723–1732; (d) V. A. Kostyanovsky, D. K. Susarova, A. S. Peregudov and P. A. Troshin, Thin Solid Films ...bromohexyl)thiophene (10 mol%) were synthesized by catalyst transfer polycondensation. Post- polymerization conversion of the side-chain bromides into azides

  12. Background field method in the gradient flow

    NASA Astrophysics Data System (ADS)

    Suzuki, Hiroshi

    2015-10-01

    In perturbative consideration of the Yang-Mills gradient flow, it is useful to introduce a gauge non-covariant term (“gauge-fixing term”) to the flow equation that gives rise to a Gaussian damping factor also for gauge degrees of freedom. In the present paper, we consider a modified form of the gauge-fixing term that manifestly preserves covariance under the background gauge transformation. It is shown that our gauge-fixing term does not affect gauge-invariant quantities as does the conventional gauge-fixing term. The formulation thus allows a background gauge covariant perturbative expansion of the flow equation that provides, in particular, a very efficient computational method of expansion coefficients in the small flow time expansion. The formulation can be generalized to systems containing fermions.

  13. High-performance conjugate-gradient benchmark: A new metric for ranking high-performance computing systems

    DOE PAGES

    Dongarra, Jack; Heroux, Michael A.; Luszczek, Piotr

    2015-08-17

    Here, we describe a new high-performance conjugate-gradient (HPCG) benchmark. HPCG is composed of computations and data-access patterns commonly found in scientific applications. HPCG strives for a better correlation to existing codes from the computational science domain and to be representative of their performance. Furthermore, HPCG is meant to help drive the computer system design and implementation in directions that will better impact future performance improvement.

  14. 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.

  15. Methods for determination of conjugated bilirubin in rat faeces.

    PubMed

    Saxerholt, H; Midtvedt, T; Gustafsson, B E

    1984-10-01

    Conjugated bilirubin was prepared from the faeces of germ-free (GF) rats by three different preparative methods. The bilirubin conjugate preparations were coupled with diazotized ethyl anthranilate and the formed ethyl anthranilate azopigments were quantified spectrophotometrically and separated by thin-layer chromatography (tlc). The most polar azopigment was purified by tlc and subjected to ammonolysis followed by tlc of the released saccaride. As a result of this procedure, only glucuronic acid was detected as the conjugating saccaride thus indicating that the most polar azopigment prepared from GF rat faeces was the delta ethyl anthranilate azopigment. Reference azopigments were prepared from GF rat small intestinal contents and subjected to separation by tlc. The azopigment pattern was very similar to the pattern obtained with the faecal azopigment preparations and a maximum of ten separated azopigment spots were detected. The findings indicated that, in addition to bilirubin glucuronides, other bilirubin conjugates with unknown structure are excreted with the faeces of GF rats. One of the preparative methods used for the preparation of conjugated bilirubin from GF rat faeces was tested on faeces from conventional (CONV) rats. From these preparations, no ethyl anthranilate azopigments were formed, thus indicating that faeces from CONV rats is devoid of conjugated bilirubin.

  16. Methods for conjugating antibodies to nanocarriers.

    PubMed

    Wagh, Anil; Law, Benedict

    2013-01-01

    Antibodies are one of the most commonly used targeting ligands for nanocarriers, mainly because they are specific, have a strong binding affinity, and are available for a number of disease biomarkers. The bioconjugation chemistry can be a crucial factor in determining the targeting efficiency of drug delivery and should be chosen on a case-by-case basis. An antibody consists of a number of functional groups which offer many flexible options for bioconjugation. This chapter focuses on discussing some of the approaches including periodate oxidation, carbodiimide, maleimide, and heterofunctional linkers, for conjugating antibodies to different nanocarriers. The advantages and limitations are described herein. Specific examples are selected to demonstrate the experimental procedures and to illustrate the potential for applying to other nanocarrier system.

  17. Iterative Method for Predistortion of MRI Gradient Waveforms

    PubMed Central

    Harkins, Kevin D.; Does, Mark D.; Grissom, William A.

    2014-01-01

    The purpose of this work is to correct for transient gradient waveform errors in magnetic resonance imaging (MRI), whether from eddy currents, group delay, or gradient amplifier nonlinearities, which are known to affect image quality. An iterative method is proposed to minimize error between desired and measured gradient waveforms, whose success does not depend on accurate knowledge of the gradient system impulse response. The method was applied to half-pulse excitation for 2-D ultra-short echo time (UTE) imaging on a small animal MRI system and to spiral 2-D excitation on a human 7T MRI system. Predistorted gradient waveforms reduced temporal signal variation caused by excitation gradient trajectory errors in 2-D UTE, and improved the quality of excitation patterns produced by spiral excitation pulses. Iterative gradient predistortion is useful for minimizing transient gradient errors without requiring accurate characterization of the gradient system impulse response. PMID:24801945

  18. Efficient Implementation of a Class of Preconditioned Conjugate Gradient Methods.

    DTIC Science & Technology

    1980-08-01

    Reservoir Simulation , pp. 127-132. Society of Petroleum Engineers of AIME, February 1979. (91 D. J. Evans. The analysis and application of sparse...equations. In Proceedins of_ theFourth Symposium on Reservoir Simulation , pp. 150-159. Society of Petroleum Engineers of AIME, February 1976. *ATE ,ILMED

  19. 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. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations

    PubMed Central

    2016-01-01

    We introduce a new class of methods, denoted as Truncated Conjugate Gradient(TCG), to solve the many-body polarization energy and its associated forces in molecular simulations (i.e. molecular dynamics (MD) and Monte Carlo). The method consists in a fixed number of Conjugate Gradient (CG) iterations. TCG approaches provide a scalable solution to the polarization problem at a user-chosen cost and a corresponding optimal accuracy. The optimality of the CG-method guarantees that the number of the required matrix-vector products are reduced to a minimum compared to other iterative methods. This family of methods is non-empirical, fully adaptive, and provides analytical gradients, avoiding therefore any energy drift in MD as compared to popular iterative solvers. Besides speed, one great advantage of this class of approximate methods is that their accuracy is systematically improvable. Indeed, as the CG-method is a Krylov subspace method, the associated error is monotonically reduced at each iteration. On top of that, two improvements can be proposed at virtually no cost: (i) the use of preconditioners can be employed, which leads to the Truncated Preconditioned Conjugate Gradient (TPCG); (ii) since the residual of the final step of the CG-method is available, one additional Picard fixed point iteration (“peek”), equivalent to one step of Jacobi Over Relaxation (JOR) with relaxation parameter ω, can be made at almost no cost. This method is denoted by TCG-n(ω). Black-box adaptive methods to find good choices of ω are provided and discussed. Results show that TPCG-3(ω) is converged to high accuracy (a few kcal/mol) for various types of systems including proteins and highly charged systems at the fixed cost of four matrix-vector products: three CG iterations plus the initial CG descent direction. Alternatively, T(P)CG-2(ω) provides robust results at a reduced cost (three matrix-vector products) and offers new perspectives for long polarizable MD as a production

  1. Fast inversion of gravity data using the symmetric successive over-relaxation (SSOR) preconditioned conjugate gradient algorithm

    NASA Astrophysics Data System (ADS)

    Meng, Zhaohai; Li, Fengting; Xu, Xuechun; Huang, Danian; Zhang, Dailei

    2017-02-01

    The subsurface three-dimensional (3D) model of density distribution is obtained by solving an under-determined linear equation that is established by gravity data. Here, we describe a new fast gravity inversion method to recover a 3D density model from gravity data. The subsurface will be divided into a large number of rectangular blocks, each with an unknown constant density. The gravity inversion method introduces a stabiliser model norm with a depth weighting function to produce smooth models. The depth weighting function is combined with the model norm to counteract the skin effect of the gravity potential field. As the numbers of density model parameters is NZ (the number of layers in the vertical subsurface domain) times greater than the observed gravity data parameters, the inverse density parameter is larger than the observed gravity data parameters. Solving the full set of gravity inversion equations is very time-consuming, and applying a new algorithm to estimate gravity inversion can significantly reduce the number of iterations and the computational time. In this paper, a new symmetric successive over-relaxation (SSOR) iterative conjugate gradient (CG) method is shown to be an appropriate algorithm to solve this Tikhonov cost function (gravity inversion equation). The new, faster method is applied on Gaussian noise-contaminated synthetic data to demonstrate its suitability for 3D gravity inversion. To demonstrate the performance of the new algorithm on actual gravity data, we provide a case study that includes ground-based measurement of residual Bouguer gravity anomalies over the Humble salt dome near Houston, Gulf Coast Basin, off the shore of Louisiana. A 3D distribution of salt rock concentration is used to evaluate the inversion results recovered by the new SSOR iterative method. In the test model, the density values in the constructed model coincide with the known location and depth of the salt dome.

  2. Optimization of non-linear gradient in hydrophobic interaction chromatography for the analytical characterization of antibody-drug conjugates.

    PubMed

    Bobály, Balázs; Randazzo, Giuseppe Marco; Rudaz, Serge; Guillarme, Davy; Fekete, Szabolcs

    2017-01-20

    The goal of this work was to evaluate the potential of non-linear gradients in hydrophobic interaction chromatography (HIC), to improve the separation between the different homologous species (drug-to-antibody, DAR) of commercial antibody-drug conjugates (ADC). The selectivities between Brentuximab Vedotin species were measured using three different gradient profiles, namely linear, power function based and logarithmic ones. The logarithmic gradient provides the most equidistant retention distribution for the DAR species and offers the best overall separation of cysteine linked ADC in HIC. Another important advantage of the logarithmic gradient, is its peak focusing effect for the DAR0 species, which is particularly useful to improve the quantitation limit of DAR0. Finally, the logarithmic behavior of DAR species of ADC in HIC was modelled using two different approaches, based on i) the linear solvent strength theory (LSS) and two scouting linear gradients and ii) a new derived equation and two logarithmic scouting gradients. In both cases, the retention predictions were excellent and systematically below 3% compared to the experimental values. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Modified2 gradient method and modified Born method for solving a two-dimensional inverse scattering problem

    NASA Astrophysics Data System (ADS)

    Belkebir, Kamal; Tijhuis, Anton G.

    2001-12-01

    This paper concerns the reconstruction of the complex relative permittivity of an inhomogeneous object from the measured scattered field. The parameter of interest is retrieved using iterative techniques. Four methods are considered, in which the permittivity is updated along the standard Polak-Ribière conjugate gradient directions of a cost functional. The difference lies in the update direction for the field, and the determination of the expansion coefficients. In the modified gradient method, the search direction is the conjugate gradient direction for the field, and the expansion coefficients for field and profile are determined simultaneously. In the Born method (BM) the field is considered as the fixed solution of the forward problem with the available estimate of the unknown permittivity, and only the profile coefficients are determined from the cost function. In the modified Born method, we use the same field direction as in the BM, but determine the coefficients for field and profile simultaneously. In the modified2 gradient method, we use both field directions, and again update all coefficients simultaneously. Examples of the reconstruction of either metal or dielectric cylinders from experimental data are presented and the methods are compared for a range of frequencies.

  4. 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.

  5. Conjugation of gold nanoparticles and recombinant human endostatin modulates vascular normalization via interruption of anterior gradient 2-mediated angiogenesis.

    PubMed

    Pan, Fan; Yang, Wende; Li, Wei; Yang, Xiao-Yan; Liu, Shuhao; Li, Xin; Zhao, Xiaoxu; Ding, Hui; Qin, Li; Pan, Yunlong

    2017-07-01

    Several studies have revealed the potential of normalizing tumor vessels in anti-angiogenic treatment. Recombinant human endostatin is an anti-angiogenic agent which has been applied in clinical tumor treatment. Our previous research indicated that gold nanoparticles could be a nanoparticle carrier for recombinant human endostatin delivery. The recombinant human endostatin-gold nanoparticle conjugates normalized vessels, which improved chemotherapy. However, the mechanism of recombinant human endostatin-gold nanoparticle-induced vascular normalization has not been explored. Anterior gradient 2 has been reported to be over-expressed in many malignant tumors and involved in tumor angiogenesis. To date, the precise efficacy of recombinant human endostatin-gold nanoparticles on anterior gradient 2-mediated angiogenesis or anterior gradient 2-related signaling cohort remained unknown. In this study, we aimed to explore whether recombinant human endostatin-gold nanoparticles could normalize vessels in metastatic colorectal cancer xenografts, and we further elucidated whether recombinant human endostatin-gold nanoparticles could interrupt anterior gradient 2-induced angiogenesis. In vivo, it was indicated that recombinant human endostatin-gold nanoparticles increased pericyte expression while inhibit vascular endothelial growth factor receptor 2 and anterior gradient 2 expression in metastatic colorectal cancer xenografts. In vitro, we uncovered that recombinant human endostatin-gold nanoparticles reduced cell migration and tube formation induced by anterior gradient 2 in human umbilical vein endothelial cells. Treatment with recombinant human endostatin-gold nanoparticles attenuated anterior gradient 2-mediated activation of MMP2, cMyc, VE-cadherin, phosphorylation of p38, and extracellular signal-regulated protein kinases 1 and 2 (ERK1/2) in human umbilical vein endothelial cells. Our findings demonstrated recombinant human endostatin-gold nanoparticles might normalize

  6. 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.

  7. 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

  8. Computer Subroutines for Analytic Rotation by Two Gradient Methods.

    ERIC Educational Resources Information Center

    van Thillo, Marielle

    Two computer subroutine packages for the analytic rotation of a factor matrix, A(p x m), are described. The first program uses the Flectcher (1970) gradient method, and the second uses the Polak-Ribiere (Polak, 1971) gradient method. The calculations in both programs involve the optimization of a function of free parameters. The result is a…

  9. A new method of determining moisture gradient in wood

    Treesearch

    Zhiyong Cai

    2008-01-01

    Moisture gradient in wood and wood composites is one of most important factors that affects both physical stability and mechanical performance. This paper describes a method for measuring moisture gradient in lumber and engineering wood composites as it varies across material thickness. This innovative method employs a collimated radiation beam (x rays or [gamma] rays...

  10. New method of underwater passive navigation based on gravity gradient

    NASA Astrophysics Data System (ADS)

    Wu, Lin; Gong, Jiaqi; Cheng, Hua; Ma, Jie; Tian, Jinwen

    2007-11-01

    A new method of underwater passive navigation based on gravity gradient is proposed in this paper. In comparison with some other geophysical characteristics such as gravity or gravity anomaly, gravity gradient which is the second derivative of gravitational potential has better spatial resolution and more sensitive to terrain changes. Through it, the digitally stored gravity gradient maps and real-time gravity gradient measurements can be taken as input information, with gravity gradient linearization techniques and extended Kalman filter, the navigation errors of INS are estimated by using gravity gradient error, therefore the output in the inertial navigation system are corrected. Simulation test has been done and the results show that, the method is effective and efficient for the positioning precision improvement.

  11. 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.

  12. Discrete gradient methods for solving variational image regularisation models

    NASA Astrophysics Data System (ADS)

    Grimm, V.; McLachlan, Robert I.; McLaren, David I.; Quispel, G. R. W.; Schönlieb, C.-B.

    2017-07-01

    Discrete gradient methods are well-known methods of geometric numerical integration, which preserve the dissipation of gradient systems. In this paper we show that this property of discrete gradient methods can be interesting in the context of variational models for image processing, that is where the processed image is computed as a minimiser of an energy functional. Numerical schemes for computing minimisers of such energies are desired to inherit the dissipative property of the gradient system associated to the energy and consequently guarantee a monotonic decrease of the energy along iterations, avoiding situations in which more computational work might lead to less optimal solutions. Under appropriate smoothness assumptions on the energy functional we prove that discrete gradient methods guarantee a monotonic decrease of the energy towards stationary states, and we promote their use in image processing by exhibiting experiments with convex and non-convex variational models for image deblurring, denoising, and inpainting.

  13. Analytic Gradients for the Effective Fragment Molecular Orbital Method.

    PubMed

    Bertoni, Colleen; Gordon, Mark S

    2016-10-11

    The analytic gradient for the Coulomb, polarization, exchange-repulsion, and dispersion terms of the fully integrated effective fragment molecular orbital (EFMO) method is derived and the implementation is discussed. The derivation of the EFMO analytic gradient is more complicated than that for the effective fragment potential (EFP) gradient, because the geometry of each EFP fragment is flexible (not rigid) in the EFMO approach. The accuracy of the gradient is demonstrated by comparing the EFMO analytic gradient with the numeric gradient for several systems, and by assessing the energy conservation during an EFMO NVE ensemble molecular dynamics simulation of water molecules. In addition to facilitating accurate EFMO geometry optimizations, this allows calculations with flexible EFP fragments to be performed.

  14. Numerical modeling of conjugate heat transfer on complex geometries with diagonal Cartesian method. Part 1: Methods

    SciTech Connect

    Lin, W.L.; Carlson, K.D.; Chen, C.J. |

    1999-05-01

    In this study, a diagonal Cartesian method for thermal analysis is developed for simulation of conjugate heat transfer over complex boundaries. This method uses diagonal line segments in addition to Cartesian coordinates. The velocity fields are also modeled using the diagonal Cartesian method. The transport equations are discretized with the finite analytic (FA) method. The current work is validated by simulating a rotated lid-driven cavity flow with conjugate heat transfer, and accurate results are obtained.

  15. A flux correction method for the conjugate heat transfer problem

    SciTech Connect

    He, M.; Bishop, P.J.; Minardi, A.; Kassab, A.J.

    1995-12-31

    A computational method, the flux correction method, is proposed to deal with the conjugate heat transfer problem, which uses a coupled FDM/BEM iteration scheme. The convective heat transfer in the fluid is solved using the BEM. The two solutions are coupled by enforcing continuity of temperature and heat flux at the solid-fluid interfaces. The proposed method is tested using available experimental data. For the considered cases of flow in a parallel plate channel subjected to constant heat flux or constant temperature, good agreements are observed.

  16. A projected preconditioned conjugate gradient algorithm for computing many extreme eigenpairs of a Hermitian matrix [A projected preconditioned conjugate gradient algorithm for computing a large eigenspace of a Hermitian matrix

    SciTech Connect

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

    2015-02-25

    Here, we present an iterative algorithm for computing an invariant subspace associated with the algebraically smallest eigenvalues of a large sparse or structured Hermitian matrix A. We are interested in the case in which the dimension of the invariant subspace is large (e.g., over several hundreds or thousands) even though it may still be small relative to the dimension of A. These problems arise from, for example, density functional theory (DFT) based electronic structure calculations for complex materials. The key feature of our algorithm is that it performs fewer Rayleigh–Ritz calculations compared to existing algorithms such as the locally 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.

  17. Gradient methods for variational optimization of projected entangled-pair states

    NASA Astrophysics Data System (ADS)

    Vanderstraeten, Laurens; Haegeman, Jutho; Corboz, Philippe; Verstraete, Frank

    2016-10-01

    We present a conjugate-gradient method for the ground-state optimization of projected entangled-pair states (PEPS) in the thermodynamic limit, as a direct implementation of the variational principle within the PEPS manifold. Our optimization is based on an efficient and accurate evaluation of the gradient of the global energy functional by using effective corner environments, and is robust with respect to the initial starting points. It has the additional advantage that physical and virtual symmetries can be straightforwardly implemented. We provide the tools to compute static structure factors directly in momentum space, as well as the variance of the Hamiltonian. We benchmark our method on Ising and Heisenberg models, and show a significant improvement on the energies and order parameters as compared to algorithms based on imaginary-time evolution.

  18. Gradient shape-persistent pi-conjugated dendrimers for light-harvesting: synthesis, photophysical properties, and energy funneling.

    PubMed

    Wang, Jin-Liang; Yan, Jing; Tang, Zheng-Ming; Xiao, Qi; Ma, Yuguo; Pei, Jian

    2008-07-30

    A new class of pi-conjugated dendrimers G0, G1, and G2 was developed through a double-stage divergent/convergent growth approach, in which 5,5,10,10,15,15-hexahexyltruxene was employed as the node and oligo(thienylethynylene)s (OTEs) with different lengths as the branching moieties. The dendrimers were fully characterized by (1)H and (13)C NMR, elemental analysis, gel permeation chromatography, and MALDI-TOF MS. Also, by using atomic force microscopy, it was observed that dendrimer G2 laid nearly flat on the mica surface as a single molecule. Dynamic light scattering results showed that the molecule retained its relatively flat shape in solution. To our best knowledge, dendrimer G2, with a radius approaching 10 nm and a molecular weight of 27 072 Da, was the largest among reported second generation dendrimers. The energy gradient in G2 was constructed by linking OTEs of increasing effective conjugation lengths from the dendritic rim to the core. The intramolecular energy transfer process was studied using steady-state UV-vis absorption and photoluminescent spectroscopies, as well as time-resolved fluorescence spectroscopy. Our structurally extended dendrimers showed an excellent energy funneling ability (their energy transfer efficiencies were all over 95%). All results demonstrate that these dendrimers are promising candidates as light-harvesting materials for optoelectronic devices.

  19. Gradient optimization and nonlinear control

    NASA Technical Reports Server (NTRS)

    Hasdorff, L.

    1976-01-01

    The book represents an introduction to computation in control by an iterative, gradient, numerical method, where linearity is not assumed. The general language and approach used are those of elementary functional analysis. The particular gradient method that is emphasized and used is conjugate gradient descent, a well known method exhibiting quadratic convergence while requiring very little more computation than simple steepest descent. Constraints are not dealt with directly, but rather the approach is to introduce them as penalty terms in the criterion. General conjugate gradient descent methods are developed and applied to problems in control.

  20. A note on spectral properties of some gradient methods

    NASA Astrophysics Data System (ADS)

    di Serafino, Daniela; Ruggiero, Valeria; Toraldo, Gerardo; Zanni, Luca

    2016-10-01

    Starting from the work by Barzilai and Borwein, gradient methods have gained a great amount of attention, and efficient low-cost schemes are available nowadays. The acceleration strategies used by these methods are based on the definition of effective steplength updating rules, which capture spectral properties of the Hessian of the objective function. The methods arising from this idea represent effective computational tools, extremely appealing for a variety of large-scale optimization problems arising in applications. In this work we discuss the spectral properties of some recently proposed gradient methods with the aim of providing insight into their computational effectiveness. Numerical experiments supporting and illustrating the theoretical analysis are provided.

  1. Separation of antibody drug conjugate species by RPLC: A generic method development approach.

    PubMed

    Fekete, Szabolcs; Molnár, Imre; Guillarme, Davy

    2017-04-15

    This study reports the use of modelling software for the successful method development of IgG1 cysteine conjugated antibody drug conjugate (ADC) in RPLC. The goal of such a method is to be able to calculate the average drug to antibody ratio (DAR) of and ADC product. A generic method development strategy was proposed including the optimization of mobile phase temperature, gradient profile and mobile phase ternary composition. For the first time, a 3D retention modelling was presented for large therapeutic protein. Based on a limited number of preliminary experiments, a fast and efficient separation of the DAR species of a commercial ADC sample, namely brentuximab vedotin, was achieved. The prediction offered by the retention model was found to be highly reliable, with an average error of retention time prediction always lower than 0.5% using a 2D or 3D retention models. For routine purpose, four to six initial experiments were required to build the 2D retention models, while 12 experiments were recommended to create the 3D model. At the end, RPLC can therefore be considered as a good method for estimating the average DAR of an ADC, based on the observed peak area ratios of RPLC chromatogram of the reduced ADC sample.

  2. Exploring chemical space with discrete, gradient, and hybrid optimization methods.

    PubMed

    Balamurugan, D; Yang, Weitao; Beratan, David N

    2008-11-07

    Discrete, gradient, and hybrid optimization methods are applied to the challenge of discovering molecules with optimized properties. The cost and performance of the approaches were studied using a tight-binding model to maximize the static first electronic hyperpolarizability of molecules. Our analysis shows that discrete branch and bound methods provide robust strategies for inverse chemical design involving diverse chemical structures. Based on the linear combination of atomic potentials, a hybrid discrete-gradient optimization strategy significantly improves the performance of the gradient methods. The hybrid method performs better than dead-end elimination and competes with branch and bound and genetic algorithms. The branch and bound methods for these model Hamiltonians are more cost effective than genetic algorithms for moderate-sized molecular optimization.

  3. 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.

  4. 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.

  5. 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.

  6. Absolute test for cylindrical surfaces using the conjugate differential method

    NASA Astrophysics Data System (ADS)

    Huang, Ya; Ma, Jun; Yuan, Caojin; Pruss, Christof; Sun, Weiyuan; Liu, Mincai; Zhu, Rihong; Gao, Zhishan; Osten, Wolfgang

    2016-11-01

    An absolute testing method for cylindrical surfaces is presented in a null test setup with a computer-generated hologram. The absolute test exploits the symmetry of cylinders, which allows us to introduce a certain shift of the test surface both parallel to and rotated about the centerline while the null test condition is still maintained. With two shifts of the cylindrical surface, four measurements belonging to two groups in conjugate positions can be accomplished to obtain the absolute differential map with the interferometer and null optics errors removed. The absolute surface can be obtained by wavefront reconstruction from local differential data. A simulation of the method is presented to estimate the error propagation. Experimental absolute test results of a concave cylindrical surface with 100-mm radius are given. The measured profiles are compared with those obtained from a commercial profiler, showing a difference of less than 15 nm (root-mean-square).

  7. A projected preconditioned conjugate gradient algorithm for computing many extreme eigenpairs of a Hermitian matrix [A projected preconditioned conjugate gradient algorithm for computing a large eigenspace of a Hermitian matrix

    DOE PAGES

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

    2015-02-25

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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Two dimension magnetotelluric modeling using finite element method, incomplete lu preconditioner and biconjugate gradient stabilized technique

    NASA Astrophysics Data System (ADS)

    Zukir, Muhammad; Srigutomo, Wahyu

    2016-08-01

    Magnetotelluric (MT) method is a passive geophysical exploration technique utilizing natural electromagnetic source to obtain variation of the electric field and magnetic field on the surface of the earth. The frequency range used in this modeling is 10-4 Hz to 102 Hz. The two-dimensional (2D) magnetotelluric modeling is aimed to determine the value of electromagnetic field in the earth, the apparent resistivity, and the impedance phase. The relation between the geometrical and physical parameters used are governed by the Maxwell's equations. These equations are used in the case of Transverse Electric polarization (TE) and Transverse Magnetic polarization (TM). To calculate the solutions of electric and magnetic fields in the entire domain, the modeling domain is discretized into smaller elements using the finite element method, whereas the assembled matrix of equation system is solved using the Biconjugate Gradient Stabilized (BiCGStab) technique combined with the Incomplete Lower - Upper (ILU) preconditioner. This scheme can minimize the iteration process (computational cost) and is more effective than the Biconjugate Gradient (BiCG) technique with LU preconditions and Conjugate Gradient Square (CGS).

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. An Adaptive Mesh Refined Gradient-Augmented Level Set Method

    NASA Astrophysics Data System (ADS)

    Nave, Jean-Christophe; Seibold, Benjamin; Rosales, Ruben

    2010-11-01

    The Gradient-Augmented Level Set method (GA-LS) was introduced at the 62^nd annual APS-DFD meeting by Nave et al. (arXiv:0905.3409). Leveraging the optimal locality and unconditional stability of the method, we present a natural extension to adaptive quad-tree meshes. The new method possesses many desirable features such as improved mass conservation, reduced computational effort, and is, due to the optimal locality property of the underlying GA-LS, very easy to implement. Several key benchmark tests will be presented to help demonstrate the benefits of the approach, and the overall simplicity of the algorithm.

  3. Dispersion serial dilution methods using the gradient diluter device.

    PubMed

    Walling, Leslie; Schulz, Craig; Johnson, Michael

    2012-12-01

    A solute aspirated into a prefilled tube of diluent undergoes a dilution effect known as dispersion. Traditionally the effects of dispersion have been considered a negative consequence of using liquid-filled fixed-tip liquid handlers. We present a novel device and technique that utilizes the effects of dispersion to the benefit of making dilutions. The device known as the Gradient Diluter extends the dilution range of practical serial dilutions to six orders of magnitude in final volumes as low as 10 μL. Presented are the device, dispersion methods, and validation tests using fluorescence detection of sulforhodamine and the high-performance liquid chromatography/ultraviolet detection of furosemide. In addition, a T-cell inhibition assay of a relevant downstream protein is used to demonstrate IC(50) curves made with the Gradient Diluter compare favorably with those generated by hand.

  4. Gradient-based optimum aerodynamic design using adjoint methods

    NASA Astrophysics Data System (ADS)

    Xie, Lei

    2002-09-01

    Continuous adjoint methods and optimal control theory are applied to a pressure-matching inverse design problem of quasi 1-D nozzle flows. Pontryagin's Minimum Principle is used to derive the adjoint system and the reduced gradient of the cost functional. The properties of adjoint variables at the sonic throat and the shock location are studied, revealing a log-arithmic singularity at the sonic throat and continuity at the shock location. A numerical method, based on the Steger-Warming flux-vector-splitting scheme, is proposed to solve the adjoint equations. This scheme can finely resolve the singularity at the sonic throat. A non-uniform grid, with points clustered near the throat region, can resolve it even better. The analytical solutions to the adjoint equations are also constructed via Green's function approach for the purpose of comparing the numerical results. The pressure-matching inverse design is then conducted for a nozzle parameterized by a single geometric parameter. In the second part, the adjoint methods are applied to the problem of minimizing drag coefficient, at fixed lift coefficient, for 2-D transonic airfoil flows. Reduced gradients of several functionals are derived through application of a Lagrange Multiplier Theorem. The adjoint system is carefully studied including the adjoint characteristic boundary conditions at the far-field boundary. A super-reduced design formulation is also explored by treating the angle of attack as an additional state; super-reduced gradients can be constructed either by solving adjoint equations with non-local boundary conditions or by a direct Lagrange multiplier method. In this way, the constrained optimization reduces to an unconstrained design problem. Numerical methods based on Jameson's finite volume scheme are employed to solve the adjoint equations. The same grid system generated from an efficient hyperbolic grid generator are adopted in both the Euler flow solver and the adjoint solver. Several

  5. A new noise reduction method for airborne gravity gradient data

    NASA Astrophysics Data System (ADS)

    Jirigalatu; Ebbing, Jörg; Sebera, Josef

    2016-09-01

    Airborne gravity gradient (AGG) measurements offer an increased resolution and accuracy compared to terrestrial measurements. But interpretation and processing of AGG data are often challenging as levelling errors and survey noise affect the data, and these effects are not easily recognised in the gradient components. We adopted the classic method of upward continuation in the noise reduction using the noise level estimates by the AGG system. By iteratively projecting the survey data to a lower level and upward continuing the data back to the survey height, parts of the high-frequency signal are suppressed. The filter, which is defined by this approach, is directly dependent on the noise level of the AGG data, the maximum number of iterations and the iterative step. We demonstrate the method by applying it to both synthetic data and real AGG data over Karasjok, Norway, and compare the results to the directional filtering method. The results show that the iterative filter can effectively reduce high-frequency noise in the data.

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

    PubMed

    Li, Like; Chen, Chen; Mei, Renwei; Klausner, James F

    2014-04-01

    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

  7. 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

  8. Conjugated carbon monolayer membranes: methods for synthesis and integration.

    PubMed

    Unarunotai, Sakulsuk; Murata, Yuya; Chialvo, Cesar E; Mason, Nadya; Petrov, Ivan; Nuzzo, Ralph G; Moore, Jeffrey S; Rogers, John A

    2010-03-12

    Monolayer membranes of conjugated carbon represent a class of nanomaterial with demonstrated uses in various areas of electronics, ranging from transparent, flexible, and stretchable thin film conductors, to semiconducting materials in moderate and high-performance field-effect transistors. Although graphene represents the most prominent example, many other more structurally and chemically diverse systems are also of interest. This article provides a review of demonstrated synthetic and integration strategies, and speculates on future directions for the field.

  9. 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.

  10. 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.

  11. Protein crystallization in low gravity by step gradient diffusion method

    NASA Astrophysics Data System (ADS)

    Sygusch, Jurgen; Coulombe, René; Cassanto, John M.; Sportiello, Michael G.; Todd, Paul

    1996-05-01

    Two-step crystallization experiments were conducted in low gravity employing a liquid-liquid diffusion method in an effort to eliminate problems associated with protein crystal growth under the supersaturating conditions required for nucleation. Experiments were performed in diffusion cells formed by the sliding of blocks on orbit. Step gradient diffusion experiments consisted of first exposing protein solutions in diffusion half-wells for brief periods to initiating buffer solutions of high precipitant concentrations to induce nucleation followed by exposure of the same protein solutions to solutions of lower precipitant concentration to promote growth of induced nuclei into crystals. To avoid convective disturbances that occur when solutions of discrepant densities are interfaced at normal gravity, crystallization of hen egg-white lysozyme and rabbit skeletal muscle aldolase by step gradient diffusion was investigated in low gravity on four NASA space shuttle flights. In general, the largest crystals of both proteins formed at the highest initiating precipitant concentration used, which is consistent with nuclei formation upon brief exposure to high precipitant concentration, and that these nuclei are competent for sustained growth at lower precipitant concentration. The two-step approach dissociates nucleation events from crystal growth allowing parameters affecting nucleation kinetics such as time, precipitant concentration and temperature of nucleation to be varied separately from conditions used for post-nucleation growth.

  12. 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.

  13. Using Elman recurrent neural networks with conjugate gradient algorithm in determining the anesthetic the amount of anesthetic medicine to be applied.

    PubMed

    Güntürkün, Rüştü

    2010-08-01

    In this study, Elman recurrent neural networks have been defined by using conjugate gradient algorithm in order to determine the depth of anesthesia in the continuation stage of the anesthesia and to estimate the amount of medicine to be applied at that moment. The feed forward neural networks are also used for comparison. The conjugate gradient algorithm is compared with back propagation (BP) for training of the neural Networks. The applied artificial neural network is composed of three layers, namely the input layer, the hidden layer and the output layer. The nonlinear activation function sigmoid (sigmoid function) has been used in the hidden layer and the output layer. EEG data has been recorded with Nihon Kohden 9200 brand 22-channel EEG device. The international 8-channel bipolar 10-20 montage system (8 TB-b system) has been used in assembling the recording electrodes. EEG data have been recorded by being sampled once in every 2 milliseconds. The artificial neural network has been designed so as to have 60 neurons in the input layer, 30 neurons in the hidden layer and 1 neuron in the output layer. The values of the power spectral density (PSD) of 10-second EEG segments which correspond to the 1-50 Hz frequency range; the ratio of the total power of PSD values of the EEG segment at that moment in the same range to the total of PSD values of EEG segment taken prior to the anesthesia.

  14. Gradient domain methods with application to 4D scene reconstruction

    NASA Astrophysics Data System (ADS)

    Di Martino, J. Matías; Fernández, Alicia; Ferrari, José A.

    2015-03-01

    In many applications such as Photometric Stereo, Shape from Shading, Differential 3D reconstruction and Image Editing in gradient domain it is important to integrate a retrieved gradient field. In most of the real experiments, the retrieved gradient fields correspond to nonintegrable fields (i.e. they are not irrotational on every point of the domain). Robust approaches have been proposed to deal with noisy nonintegrable gradient fields. In this work we extend some of these techniques for the case of dynamic scenes when the gradient field in the x - y domain can be estimated over time. We exploit temporal consistency in the scene to ensure integrability and improve the accuracy of the results. In addition, two known integration algorithms are reviewed and important implementation details are discussed. Experiments with synthetic and real data showing some potential applications for the proposed framework are presented.

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

    PubMed Central

    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 99mTc-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 99mTc-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

  16. 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.

  17. 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.

  18. Quantum mechanical calculation of nanomaterial-ligand interaction energies by molecular fractionation with conjugated caps method

    NASA Astrophysics Data System (ADS)

    Zhang, Dawei

    2017-03-01

    Molecular fractionation with conjugate caps (MFCC) method is introduced for the efficient estimation of quantum mechanical (QM) interaction energies between nanomaterial (carbon nanotube, fullerene, and graphene surface) and ligand (charged and neutral). In the calculations, nanomaterials are partitioned into small fragments and conjugated caps that are properly capped, and the interaction energies can be obtained through the summation of QM calculations of the fragments from which the contribution of the conjugated caps is removed. All the calculations were performed by density functional theory (DFT) and dispersion contributions for the attractive interactions were investigated by dispersion corrected DFT method. The predicted interaction energies by MFCC at each computational level are found to give excellent agreement with full system (FS) calculations with the mean energy deviation just a fractional kcal/mol. The accurate determination of nanomaterial-ligand interaction energies by MFCC suggests that it is an effective method for performing QM calculations on nanomaterial-ligand systems.

  19. Quantum mechanical calculation of nanomaterial-ligand interaction energies by molecular fractionation with conjugated caps method

    PubMed Central

    Zhang, Dawei

    2017-01-01

    Molecular fractionation with conjugate caps (MFCC) method is introduced for the efficient estimation of quantum mechanical (QM) interaction energies between nanomaterial (carbon nanotube, fullerene, and graphene surface) and ligand (charged and neutral). In the calculations, nanomaterials are partitioned into small fragments and conjugated caps that are properly capped, and the interaction energies can be obtained through the summation of QM calculations of the fragments from which the contribution of the conjugated caps is removed. All the calculations were performed by density functional theory (DFT) and dispersion contributions for the attractive interactions were investigated by dispersion corrected DFT method. The predicted interaction energies by MFCC at each computational level are found to give excellent agreement with full system (FS) calculations with the mean energy deviation just a fractional kcal/mol. The accurate determination of nanomaterial-ligand interaction energies by MFCC suggests that it is an effective method for performing QM calculations on nanomaterial-ligand systems. PMID:28300179

  20. Investigation of gradient structures prepared by laser ablation method

    NASA Astrophysics Data System (ADS)

    Ciosek, Jerzy; Budner, Boguslaw; Burdynska, Sylwia; Jedynski, Marcin; Minikayev, Roman; Prokopiuk, Artur; Mroz, Waldemar

    2010-12-01

    Gradient structures are very important for sensors, laser and wave-guide techniques, telecommunications and other techniques which employ radiation propagation and conversion. By varying admixture concentration, the stress occurring in the structure may increase or reduce, which is vital for charge carrier movement velocity. We discusse two kind of gradient structures of thin TiNx layer with a total thickness of approximately 22 nm deposited on the Si(100) substrate and multi-layer structures with a Si-Pd and Si-Mg bi-layer periods. The gradient structures were deposited using a laser ablation of target-compound materials. A Lambda Physics excimer laser (model LPX 305i; t ~ 15 ns, λ = 193 nm) with f = 5 Hz operating frequency was used for layer depositing. The analyses confirmed the presence of the gradient distribution of deposited materials. The gradient structures proved highly sensitive to both thermal effects and strong adsorption of ambient gases. The usefulness of titanium-containing structures for gas, especially hydrogen and oxygen, sensors was confirmed. Due to the strong gas adsorption, the gradient structures used in radiation conversion or waveguide technology should be adequately protected against ambient conditions.

  1. An adaptive precision gradient method for optimal control.

    NASA Technical Reports Server (NTRS)

    Klessig, R.; Polak, E.

    1973-01-01

    This paper presents a gradient algorithm for unconstrained optimal control problems. The algorithm is stated in terms of numerical integration formulas, the precision of which is controlled adaptively by a test that ensures convergence. Empirical results show that this algorithm is considerably faster than its fixed precision counterpart.-

  2. Methods for MAG3 conjugation and 99mTc radiolabeling of biomolecules.

    PubMed

    Wang, Yi; Liu, Guozheng; Hnatowich, Donald J

    2006-01-01

    The chelator mercaptoacetyltriglycine (MAG3) forms a single stable chelate with technetium-99m (99mTc) oxotechnetate. The bifunctional N-hydroxysuccinimidyl ester of mercaptoacetyltriglycine with S-acetyl protection of the sulfhydryl group may be used to conjugate MAG3 to primary amine functionalized biomolecules for the purpose of radiolabeling with 99mTc for gamma detection or single photon emission computed tomography imaging (SPECT). We report here an improved MAG3 conjugation and 99mTc radiolabeling method capable of generating high radiochemical yield and high specific radioactivity. Post-labeling purification will not be needed if the protocol is followed as presented. Apart from the preparation of reagents, the conjugation and purification requires about 4 h, while the labeling with 99mTc requires about an additional 30 min.

  3. 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.

  4. Solution-processable gradient red-emitting pi-conjugated dendrimers based on benzothiadiazole as core: synthesis, characterization, and device performances.

    PubMed

    Wang, Jin-Liang; Zhou, Yi; Li, Yongfang; Pei, Jian

    2009-10-02

    A family of gradient pi-conjugated dendrimers, in which the 5,5,10,10,15,15-hexahexyltruxene unit is employed as the node, oligo(thienylethynylene)s (OTEs) are employed as light-harvesting branching units, and a 4,7-diaryl-2,1,3-benzothiadiazole is employed as the core, have been developed through the Sonogashira reaction in good yields. All dendrimers were fully characterized by (1)H and (13)C NMR, elemental analysis, and MALDI-TOF MS. Investigation of their steady-state and time-resolved photophysical properties revealed that the gradient dendritic scaffold resulted in efficient energy transfer and strong red emission. On the basis of the good solubility and excellent film forming properties, single-layer red-emitting diodes using these dendrimers as the active materials were fabricated by a simple solution spin-coating process. The moderate device performance was achieved; for example, the maximum luminance of 1290 cd/m(2) with a maximum luminescence efficiency of 1.07 cd/A was performed from BTDyn.

  5. A new method for hydrolyzing sulfate and glucuronyl conjugates of steroids.

    PubMed

    Tang, P W; Crone, D L

    1989-11-01

    A new method for hydrolyzing steroid conjugates (both sulfates and glucuronides conjugates) that is efficient, effective, and inexpensive is described. This method comprises incubation of the conjugates--after salting-out into ethyl acetate or elution from a C18 cartridge--with anhydrous methanolic hydrogen chloride (methanolysis) for 10 min. It has been successfully applied to our routine radioimmunoassay screening and GC/MS confirmation studies of steroids in prerace and postrace equine urine samples. Comparative GC/MS studies on entire (male horse) urine samples showed that methanolysis gave amounts of free steroids (estrone, estradiols, testosterone, estrenediols, nandrolone, androstanediols) at least as large as those obtained by solvolysis. Similar studies on urine samples from a gelding that had been administered nandrolone phenylpropionate showed that methanolysis gave larger amounts of free steroids (nandrolone, estranediols) than Helix pomatia enzymatic hydrolysis or solvolysis. Also, TLC studies on methanolysis of corticosteroid conjugates such as hydrocortisone 21-sulfate and hydrocortisone 21-phosphate showed that free corticosteroid was released in 5 min.

  6. 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.

  7. 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.

  8. Systematic interpolation method predicts protein chromatographic elution with salt gradients, pH gradients and combined salt/pH gradients.

    PubMed

    Creasy, Arch; Barker, Gregory; Carta, Giorgio

    2017-03-01

    A methodology is presented to predict protein elution behavior from an ion exchange column using both individual or combined pH and salt gradients based on high-throughput batch isotherm data. The buffer compositions are first optimized to generate linear pH gradients from pH 5.5 to 7 with defined concentrations of sodium chloride. Next, high-throughput batch isotherm data are collected for a monoclonal antibody on the cation exchange resin POROS XS over a range of protein concentrations, salt concentrations, and solution pH. Finally, a previously developed empirical interpolation (EI) method is extended to describe protein binding as a function of the protein and salt concentration and solution pH without using an explicit isotherm model. The interpolated isotherm data are then used with a lumped kinetic model to predict the protein elution behavior. Experimental results obtained for laboratory scale columns show excellent agreement with the predicted elution curves for both individual or combined pH and salt gradients at protein loads up to 45 mg/mL of column. Numerical studies show that the model predictions are robust as long as the isotherm data cover the range of mobile phase compositions where the protein actually elutes from the column.

  9. A solid phase adsorption method for preparation of bovine serum albumin-bovine hemoglobin conjugate.

    PubMed

    Hu, Tao; Su, Zhiguo

    2003-02-13

    A solid phase adsorption method was proposed to prepare well-defined bovine serum albumin-bovine hemoglobin (Hb) conjugate. After adsorption by the solid phase, Q Sepharose Fast Flow media, bovine serum albumin (BSA) molecules were allowed to react with glutaraldehyde. The spacing out of BSA molecules on the solid phase was assumed to limit polymerization of BSA molecules, except some molecules bound closely on the solid phase resulting in minor dimer formation. Following the elution procedure, the activated monomeric BSA was separated from the dimers by gel filtration chromatography on Superdex 200 and then reacted with bovine Hb at 4 degrees C and pH 9.5. The 1:1 (BSA:Hb) conjugate was obtained with the yield of 64%. The P(50) values of the conjugates, prepared under anaerobic and aerobic conditions, were 19.1 and 14.2 mmHg, respectively. The dependence of the P(50) on chloride ions for the conjugate was slightly diminished, presumably due to covalent attachment of BSA to bovine Hb.

  10. Single fiber lignin distributions based on the density gradient column method

    Treesearch

    Brian Boyer; Alan W. Rudie

    2007-01-01

    The density gradient column method was used to determine the effects of uniform and non-uniform pulping processes on variation in individual fiber lignin concentrations of the resulting pulps. A density gradient column uses solvents of different densities and a mixing process to produce a column of liquid with a smooth transition from higher density at the bottom to...

  11. Gradient-free MCMC methods for dynamic causal modelling

    DOE PAGES

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

    2015-03-14

    Here, 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 comparisonmore » to the most efficient algorithm (i.e., the adaptive MCMC sampler).« less

  12. 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

  13. A New Discontinuous Galerkin Method for Convection-Diffusion Problems: The Gradient-Recovery DG Method

    NASA Astrophysics Data System (ADS)

    Johnson, Philip; Johnsen, Eric

    2016-11-01

    The Discontinuous Galerkin (DG) numerical method, while well-suited for hyperbolic PDE systems such as the Euler equations, is not naturally competitive for convection-diffusion systems, such as the Navier-Stokes equations. Where the DG weak form of the Euler equations depends only on the field variables for calculation of numerical fluxes, the traditional form of the Navier-Stokes equations requires calculation of the gradients of field variables for flux calculations. It is this latter task for which the standard DG discretization is ill-suited, and several approaches have been proposed to treat the issue. The most popular strategy for handling diffusion is the "mixed" approach, where the solution gradient is constructed from the primal as an auxiliary. We designed a new mixed approach, called Gradient-Recovery DG; it uses the Recovery concept of Van Leer & Nomura with the mixed approach to produce a scheme with excellent stability, high accuracy, and unambiguous implementation when compared to typical mixed approach concepts. In addition to describing the scheme, we will perform analysis with comparison to other DG approaches for diffusion. Gas dynamics examples will be presented to demonstrate the scheme's capabilities.

  14. 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

  15. Direct gradient reversed-phase high-performance liquid chromatographic determination of salicylic acid, with the corresponding glycine and glucuronide conjugates in human plasma and urine.

    PubMed

    Vree, T B; van Ewijk-Beneken Kolmer, E W; Verwey-van Wissen, C P; Hekster, Y A

    1994-02-11

    A gradient reversed-phase HPLC analysis for the direct measurement of salicylic acid (SA) with the corresponding glycine and glucuronide conjugates in plasma and urine of humans was developed. The glucuronides were isolated by preparative HPLC from human urine samples. The concentration of the glucuronides in the isolated fraction were determined after enzymatic hydrolysis. Salicylic acid acyl glucuronide (SAAG) was not present in plasma. No isoglucuronides were present in acidic and alkaline urine of the volunteer. The limits of quantitation in plasma are: SA 0.2 microgram/ml, salicyluric acid (SU) 0.1 microgram/ml, salicylic acid phenolic glucuronide (SAPG) 0.4 microgram/ml and salicyluric acid phenolic glucuronide (SUPG) 0.2 microgram/ml. The limit of quantitation in urine is for all compounds 5 micrograms/ml. Salicylic acid acyl glucuronide is stable in phosphate buffer pH 4.9 during 8 h at 37 degrees C; thereafter it declines to 80% after 24 h. The subject's urine was therefore acidified by the oral intake of 4 x 1.2 g of ammonium chloride/day. With acidic urine, hardly any salicylic acid is excreted unchanged (0.6%). It is predominantly excreted as salicyluric acid (68.7%).

  16. 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

  17. 3D full tensor gradient method improves subsalt interpretation

    SciTech Connect

    Coburn, G.W.

    1998-09-14

    Imagine you`re working the deepwater Gulf of Mexico, looking for potential subsalt prospects to guide your company`s bidding in an upcoming lease sale. There are no speculative 3D surveys in the area, just 2D seismic and a few well logs. So you obtain some regional 2D lines across a number of promising salt features and begin your initial structural interpretation. The top of salt is pretty easy to pick. But, not surprisingly, the base is fuzzy in many areas. Large shadow zones wipe out the image, making it difficult to tell how thick the salt may be and whether sediments continue beneath the salt or truncate at the edges. With the limited data you have available, you could pick the base of salt in several different places, all of them reasonable. How do you decide? One option is an expensive reprocessing job. But it would be nice to have another choice--a way to independently test your salt interpretation against high-quality data not derived from seismic. Three-dimensional full tensor gradient (FTG) data can provide such an alternative. This article focuses on an actual test study done on a regional 2D seismic line across the Green Canyon area of the Gulf of Mexico. The purpose of the study was to determine how well 3D FTG data could identify the base of salt, where standard seismic interpretation was ambiguous.

  18. Zonal matrix iterative method for wavefront reconstruction from gradient measurements.

    PubMed

    Panagopoulou, Sophia I; Neal, Daniel R

    2005-01-01

    To present an alternate method to Zemike decomposition (modal) of wavefront reconstruction using iterative implicit solution to the finite difference equations (zonal). Different reconstruction methods, modal and zonal, were compared and the advantages of each method were analyzed. Although the modal or Zemike method allows for quantitative interpretation of some of the aberrations, it is cumbersome for use with fine details and may lead to errors for eyes with keratoconus or other rapidly varying aberration. The zonal method produces a very high-resolution map that can be used for identifying irregular structures. The distinction between the two methods is useful to maintain, and the solution methods are generally different. In practice, both methods are useful and, with modern computers, both zonal and lower-order modal may be calculated rapidly. The difference between the wavefronts derived from the two methods may provide useful insight or interpretation of the infornation.

  19. Conjugate symplecticity of second-order linear multi-step methods

    NASA Astrophysics Data System (ADS)

    Feng, Quan-Dong; Jiao, Yan-Dong; Tang, Yi-Fa

    2007-06-01

    We review the two different approaches for symplecticity of linear multi-step methods (LMSM) by Eirola and Sanz-Serna, Ge and Feng, and by Feng and Tang, Hairer and Leone, respectively, and give a numerical example between these two approaches. We prove that in the conjugate relation with and being LMSMs, if is symplectic, then the B-series error expansions of , and of the form are equal to those of trapezoid, mid-point and Euler forward schemes up to a parameter [theta] (completely the same when [theta]=1), respectively, this also partially solves a problem due to Hairer. In particular we indicate that the second-order symmetric leap-frog scheme Z2=Z0+2[tau]J-1[backward difference]H(Z1) cannot be conjugate-symplectic via another LMSM.

  20. An improved equivalent magnetization current method applied to the design of local breast gradient coils

    NASA Astrophysics Data System (ADS)

    Lopez, Hector Sanchez; Poole, Michael; Crozier, Stuart

    2009-07-01

    Magnetic resonance imaging (MRI) is an important tool in the diagnosis of breast cancer. Increased gradient strengths and slew rates assist in terms of the potential to image with increased spatial and/or temporal resolution. Strong gradients also facilitate diffusion studies; one well-known method of increasing gradient strength is to design local gradient coils, those with reduced diameter where the gradient conductors are closer to the region of interest. In the case of breast imaging, this necessitates the use of coil geometries that lack the symmetry (e.g. cylindrical) required by some standard coil design techniques. Therefore a symmetry-free, inverse boundary element method (BEM) was employed to design a set of local breast gradient coils which would allow simultaneous imaging of both breasts. This BEM is a modified version of a previously reported equivalent magnetisation current method that now incorporates a piecewise-linear magnetisation rather than piecewise-constant. It is demonstrated that coil geometries more closely encompassing the sample shape, hence possessing wire windings located close the sample, produce superior coil performances. The use of two regions of interest instead one that covers the two samples produces superior high performance breast gradient coils. Additionally, it was demonstrated that this inverse BEM produced standard cylindrical coils with comparable properties and that the method is robust when challenged with difficult coil design problems in two other examples.

  1. Numerical modeling of conjugate heat transfer on complex geometries with diagonal Cartesian method. Part 2: Applications

    SciTech Connect

    Carlson, K.D.; Lin, W.L.; Chen, C.J. |

    1999-05-01

    Part 1 of this study discusses the diagonal Cartesian method for temperature analysis. The application of this method to the analysis of flow and conjugate heat transfer in a compact heat exchanger is given in Part 2. In addition to a regular (i.e., Cartesian-oriented) fin arrangement, two complex fin arrangements are modeled using the diagonal Cartesian method. The pressure drop and heat transfer characteristics of the different configurations are compared. It is found that enhanced heat transfer and reduced pressure drop can be obtained with the modified fin arrangements for this compact heat exchanger.

  2. Numerical simulation of magneto-acoustic Wave Phase Conjugation with the DG method in the CPR framework

    NASA Astrophysics Data System (ADS)

    Modarreszadeh, Seyedamirreza; Timofeev, Evgeny; Merlen, Alain; Matar, Olivier Bou; Pernod, Philippe

    2017-07-01

    The present paper is concerned with the numerical modeling of magneto-acoustic Wave Phase Conjugation (WPC) phenomena. Since ultrasonic waves in the WPC applications have short wavelengths relative to the traveling distances, high-order numerical methods in both space and time domains are required. The numerical scheme chosen for the current research is the Runge-Kutta Discontinuous Galerkin (RKDG) method incorporated into the Correction Procedure via Reconstruction (CPR) framework. In order to avoid non-physical oscillations near high-gradient regions, a Weighted Essentially Non-Oscillatory (WENO) limiter is used to reconstruct the solutions in the affected cells. After being assured that the numerical scheme has appropriate accuracy and performance, the WPC process is modeled in both linear and non-linear regimes. The results in the linear regime are in acceptable agreement with the analytical solution. The only significant deviation between the linear and non-linear results is at the sensor within the passive zone, where the mean pressure starts to grow gradually in the non-linear regime due to overtaking of the low-velocity pressure waves by the high-velocity ones.

  3. 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.

  4. 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.

  5. General implementation of the ERETIC method for pulsed field gradient probe heads.

    PubMed

    Ziarelli, Fabio; Viel, Stéphane; Caldarelli, Stefano; Sobieski, Daniel N; Augustine, Matthew P

    2008-10-01

    A capacitive coupling between a secondary radiofrequency (rf) channel and the gradient coil of a standard commercially available high resolution NMR spectrometer and probe head is described and used to introduce a low level exponentially damped rf signal near the frequency of the primary rf channel to serve as an external concentration standard, in analogy to the so-called ERETIC method. The stability of this inexpensive and simple to implement method, here referred to as the Pulse Into the Gradient (PIG) approach, is superb over a 14-h period and both gradient tailored water suppression and one-dimensional imaging applications are provided. Since the low level signal is introduced via the pulsed field gradient coil, the coupling is identical to that for a free induction signal and thus the method proves to be immune (within 5%) to sample ionic strength effects up to the 2M NaCl solutions explored here.

  6. Alpha Alumina Nanoparticle Conjugation to Cysteine Peptidase A and B: An Efficient Method for Autophagy Induction

    PubMed Central

    Beyzay, Fatemeh; Zavaran Hosseini, Ahmad; Soudi, Sara

    2017-01-01

    Background: Autophagy as a cellular pathway facilitates several immune responses against infection. It also eliminates invading pathogens through transferring content between the cytosol and the lysosomal vesicles and contributes to the cross-presentation of exogenous antigens to T lymphocytes via MHC class I pathway. Autophagy induction is one of the main targets for new drugs and future vaccine formulations. Nanoparticles are one of the candidates for autophagy induction. Cysteine Peptidase A (CPA) and Cysteine Peptidase B (CPB) are two members of papain family (Clan CA, family C1) enzyme that have been considered as a virulence factor of Leishmania (L.) major, making them suitable vaccine candidates. In this research, Leishmania major cysteine peptidase A and B (CPA and CPB) conjugation to alpha alumina nanoparticle was the main focus and their entrance efficacy to macrophages was assessed. Methods: For this purpose, CPA and CPB genes were cloned in expression vectors. Related proteins were extracted from transformed Escherichia coli (E. coli) and purified using Ni affinity column. Alpha alumina nanoparticles were conjugated to CPA/CPB proteins using Aldehyde/Hydrazine Reaction. Autophagy induction in macrophages was assessed using acridine orange staining. Results: CPA/CPB protein loading to nanoparticles was confirmed by Fourier Transform Infrared Spectroscopy. α-alumina conjugated CPA/CPB antigen uptake by macrophages at different concentrations was confirmed using fluorescence microscope and flowcytometry. Highly efficient CPA/CPB protein loading to α-alumina nanoparticles and rapid internalization to macrophages introduced these nanocarriers as a delivery tool. Acridine orange staining demonstrated higher autophagy induction in CPA/CPB protein conjugated with α-alumina nanoparticles. Conclusion: α-alumina nanoparticles may be a promising adjuvant in the development of therapeutic leishmania vaccines through antigen delivery to intracellular compartments

  7. 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.

  8. Development of a bioorthogonal and highly efficient conjugation method for quantum dots using tetrazine-norbornene cycloaddition.

    PubMed

    Han, Hee-Sun; Devaraj, Neal K; Lee, Jungmin; Hilderbrand, Scott A; Weissleder, Ralph; Bawendi, Moungi G

    2010-06-16

    We present a bioorthogonal and modular conjugation method for efficient coupling of organic dyes and biomolecules to quantum dots (QDs) using a norbornene-tetrazine cycloaddition. The use of noncoordinating functional groups combined with the rapid rate of the cycloaddition leads to highly efficient conjugation. We have applied this method to the in situ targeting of norbornene-coated QDs to live cancer cells labeled with tetrazine-modified proteins.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. A Simple Method for MR Gradient System Characterization and k-Space Trajectory Estimation

    PubMed Central

    Addy, Nii Okai; Wu, Holden H.; Nishimura, Dwight G.

    2014-01-01

    Fast imaging trajectories are employed in MRI to speed up the acquisition process, but imperfections in the gradient system create artifacts in the reconstructed images. Artifacts result from the deviation between k-space trajectories achieved on the scanner and their original prescription. Measuring or approximating actual k-space trajectories with predetermined gradient timing delays reduces the artifacts, but are generally based on a specific trajectory and scan orientation. A single linear time-invariant characterization of the gradient system, provides a method to predict k-space trajectories scanned in arbitrary orientations through convolution. This is done effciently, by comparing the the Fourier transforms of the input and measured waveforms of a single high-bandwidth test gradient waveform. This new method is tested for spiral, interleaved echo-planar, and 3D cones imaging, demonstrating its ability to reduce reconstructed image artifacts for various k-space trajectories. PMID:22189904

  16. Improving the accuracy of the gradient method for determining soil carbon dioxide efflux

    USDA-ARS?s Scientific Manuscript database

    Continuous soil CO2 efflux (Fsoil) estimates can be obtained by the gradient method (GM), but the utility of the method is hindered by uncertainties in the application of published models for the diffusion coefficient (Ds). We compared two in-situ methods for determining Ds, one based calibrating th...

  17. Non-overlapping domain decomposition method for a variational inequality with gradient constraints

    NASA Astrophysics Data System (ADS)

    Lapin, A.; Laitinen, E.; Lapin, S.

    2016-11-01

    Non-overlapping domain decomposition method is applied to a variational inequality with nonlinear diffusion-convection operator and gradient constraints. The method is based on the initial approximation of the problem and its subsequent splitting into subproblems. For the resulting constrained saddle point problem block relaxation-Uzawa iterative solution method is applied.

  18. Development and validation of a simple and direct ELISA method for the determination of conjugated (glucuronide) and non-conjugated testosterone excretion in urine.

    PubMed

    Al-Dujaili, Emad A S

    2006-02-01

    Several methods are now available to estimate urinary testosterone levels that can only be performed in established big laboratories using GC/MS techniques. In clinical practice or for research projects, an inexpensive method that does not require skilled technicians would be useful. A simple, rapid and accurate ELISA method has been developed and applied in our laboratory to measure urinary non-conjugated and total testosterone. High affinity anti-testosterone antibody and HRP-Donkey anti-sheep IgG (Horse Radish Peroxidase) as enzyme tracer were used to develop the ELISA method. The assay was evaluated for specificity, sensitivity, parallelism, accuracy and imprecision by the established methods on samples obtained from healthy volunteers. The results from the direct ELISA were compared to those after enzyme hydrolysis plus solvent extraction and HPLC or commercial kits. A satisfactory standard curve for the direct testosterone ELISA has been developed with good sensitivity. Cross-reactivity values of anti-testosterone antibody with major interfering steroids were minimal except for testosterone-3-glucuronide (58.8%). The validity of urinary testosterone assay was confirmed by the good correlation between the results obtained by the direct ELISA and those after enzyme hydrolysis and solvent extraction (Y = 0.987X + 0.398, R2 = 0.97). Accuracy studies, parallelism and imprecision data were determined and all found to be satisfactory. Urinary testosterone excretion values obtained by our direct ELISA from healthy volunteers were generally in agreement with those published by other workers. Male urinary total testosterone excretion (non-conjugated and testosterone glucuronide) ranged from 177.9 to 865.3 nmol/day, which was about 3-6 times more than the range for women urinary testosterone excretion (34.5-308.8 nmol/day). A direct, reliable, easy to perform, sensitive and highly specific ELISA type assay for the measurement of total testosterone in urine samples

  19. Gradient plasticity crack tip characterization by means of the extended finite element method

    NASA Astrophysics Data System (ADS)

    Martínez-Pañeda, E.; Natarajan, S.; Bordas, S.

    2017-01-01

    Strain gradient plasticity theories are being widely used for fracture assessment, as they provide a richer description of crack tip fields by incorporating the influence of geometrically necessary dislocations. Characterizing the behavior at the small scales involved in crack tip deformation requires, however, the use of a very refined mesh within microns to the crack. In this work a novel and efficient gradient-enhanced numerical framework is developed by means of the extended finite element method (X-FEM). A mechanism-based gradient plasticity model is employed and the approximation of the displacement field is enriched with the stress singularity of the gradient-dominated solution. Results reveal that the proposed numerical methodology largely outperforms the standard finite element approach. The present work could have important implications on the use of microstructurally-motivated models in large scale applications. The non-linear X-FEM code developed in MATLAB can be downloaded from http://www.empaneda.com/codes.

  20. Gradient plasticity crack tip characterization by means of the extended finite element method

    NASA Astrophysics Data System (ADS)

    Martínez-Pañeda, E.; Natarajan, S.; Bordas, S.

    2017-05-01

    Strain gradient plasticity theories are being widely used for fracture assessment, as they provide a richer description of crack tip fields by incorporating the influence of geometrically necessary dislocations. Characterizing the behavior at the small scales involved in crack tip deformation requires, however, the use of a very refined mesh within microns to the crack. In this work a novel and efficient gradient-enhanced numerical framework is developed by means of the extended finite element method (X-FEM). A mechanism-based gradient plasticity model is employed and the approximation of the displacement field is enriched with the stress singularity of the gradient-dominated solution. Results reveal that the proposed numerical methodology largely outperforms the standard finite element approach. The present work could have important implications on the use of microstructurally-motivated models in large scale applications. The non-linear X-FEM code developed in MATLAB can be downloaded from http://www.empaneda.com/codes.

  1. 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.

  2. Convergence analysis of a two-point gradient method for nonlinear ill-posed problems

    NASA Astrophysics Data System (ADS)

    Hubmer, Simon; Ramlau, Ronny

    2017-09-01

    We perform a convergence analysis of a two-point gradient method which is based on Landweber iteration and on Nesterov’s acceleration scheme. Additionally, we show the usefulness of this method via two numerical example problems based on a nonlinear Hammerstein operator and on the nonlinear inverse problem of single photon emission computed tomography.

  3. 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

  4. 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.

  5. 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.

  6. Fast recognition method for metallic topographies by the three-color selective stereo gradient method

    NASA Astrophysics Data System (ADS)

    Hossfeld, Michael; Chu, Weiyi; Eich, Manfred; Adameck, Markus

    2006-02-01

    A machine-vision system for real-time classification of moving objects with highly reflective metallic surfaces and complex 3D-structures is presented. As an application example of our Three-Color Selective Stereo Gradient Method (Three-Color SSGM) a classification system for the three main coin denominations of Euro coins is presented. The coins are quickly moving in a coin validation system. The objective is to decide only from comparison of measured 3D-surface properties with characteristic topographical data stored in a database whether a coin belongs to one of the reference classes or not. Under illumination of a three-color LED-ring a single image of the moving coin is captured by a CCD-camera. Exploiting the spectral properties of the illumination sources, which correspond to the special spectral characteristics of the camera, three independent subimages can be extracted from the first. Comparison between these subimages leads to a discrimination between a coin with real 3D-surface and a photographic image of a coin of the same type. After the coin has been located and segmented, grey value based rotation and translation invariant features are extracted from a normalized image. In combination with template matching methods, a coin can be classified. Statistical classification results will be reported.

  7. The Evaluation of Islet Purification Methods That Use Large Bottles to Create a Continuous Density Gradient

    PubMed Central

    Miyagi-Shiohira, Chika; Kobayashi, Naoya; Saitoh, Issei; Watanabe, Masami; Noguchi, Yasufumi; Matsushita, Masayuki; Noguchi, Hirofumi

    2017-01-01

    Islet purification is one of the most important steps of islet isolation for pancreatic islet transplantation. The most common method of islet purification is density gradient centrifugation using a COBE 2991 cell processor. However, this method can damage islets mechanically through its high shearing force. We recently reported that a new purification method using large plastic bottles effectively achieves a high yield of islets from the porcine pancreas. In the present study, we evaluated the methods of making a continuous density gradient. The gradient was produced with a gradient maker and two types of candy cane-shaped stainless steel pipes. One method was to use a “bent-tipped” stainless steel pipe and to load from a high-density solution to a low-density solution, uploading the stainless steel pipe. The other method was to use a regular stainless steel pipe and to load from a low-density solution to a high-density solution, leaving the stainless steel pipe in place. There were no significant differences between the two solutions in terms of the islet yield, rate of viability or purity, score, or the stimulation index after purification. Furthermore, there were no differences in the attainability or suitability of posttransplantation normoglycemia. Our study shows the equivalency of these two methods of islet purification. PMID:28174674

  8. A computationally efficient method for full-core conjugate heat transfer modeling of sodium fast reactors

    DOE PAGES

    Hu, Rui; Yu, Yiqi

    2016-09-08

    For efficient and accurate temperature predictions of sodium fast reactor structures, a 3-D full-core conjugate heat transfer modeling capability is developed for an advanced system analysis tool, SAM. The hexagon lattice core is modeled with 1-D parallel channels representing the subassembly flow, and 2-D duct walls and inter-assembly gaps. The six sides of the hexagon duct wall and near-wall coolant region are modeled separately to account for different temperatures and heat transfer between coolant flow and each side of the duct wall. The Jacobian Free Newton Krylov (JFNK) solution method is applied to solve the fluid and solid field simultaneouslymore » in a fully coupled fashion. The 3-D full-core conjugate heat transfer modeling capability in SAM has been demonstrated by a verification test problem with 7 fuel assemblies in a hexagon lattice layout. In addition, the SAM simulation results are compared with RANS-based CFD simulations. Very good agreements have been achieved between the results of the two approaches.« less

  9. A computationally efficient method for full-core conjugate heat transfer modeling of sodium fast reactors

    SciTech Connect

    Hu, Rui; Yu, Yiqi

    2016-09-08

    For efficient and accurate temperature predictions of sodium fast reactor structures, a 3-D full-core conjugate heat transfer modeling capability is developed for an advanced system analysis tool, SAM. The hexagon lattice core is modeled with 1-D parallel channels representing the subassembly flow, and 2-D duct walls and inter-assembly gaps. The six sides of the hexagon duct wall and near-wall coolant region are modeled separately to account for different temperatures and heat transfer between coolant flow and each side of the duct wall. The Jacobian Free Newton Krylov (JFNK) solution method is applied to solve the fluid and solid field simultaneously in a fully coupled fashion. The 3-D full-core conjugate heat transfer modeling capability in SAM has been demonstrated by a verification test problem with 7 fuel assemblies in a hexagon lattice layout. In addition, the SAM simulation results are compared with RANS-based CFD simulations. Very good agreements have been achieved between the results of the two approaches.

  10. Analytical method for determining relative chaperone activity using an ovalbumin-conjugated column.

    PubMed

    Hirano, Makoto; Kato, Yuki; Imagawa, Ayami; Totani, Kiichiro

    2015-01-02

    Investigating the relative efficiencies of molecular chaperones is important for understanding protein biosynthesis inside a cell. We developed an analytical method for estimating relative chaperone activity under physiological, multi-chaperone conditions using a protein-conjugated column. A chaperone mixture was subjected to chromatography on a column conjugated with denatured ovalbumin, and the elution positions of target chaperones were compared using western blotting to determine the relative affinity of each chaperone for the denatured protein. Because molecular chaperones should be eluted according to their strength of association with the denatured ovalbumin in the column, the elution position must accord with the chaperone activity and can be used as an indicator of relative chaperone activity. We found that the column procedure was effective in an assay of a mixture of calreticulin and BiP, the molecular chaperones in the endoplasmic reticulum; the assay showed that calreticulin associated with denatured ovalbumin more strongly than BiP. Copyright © 2014 Elsevier Inc. All rights reserved.

  11. Flexible method for conjugation of phenolic lignin model compounds to carrier proteins

    DOE PAGES

    Gao, Ruili; Lu, Fachuang; Zhu, Yimin; ...

    2016-10-03

    Linking lignin model compounds to carrier proteins is required either to raise antibodies to them or to structurally screen antibodies raised against lignins or models. This paper describes a flexible method to link phenolic compounds of interest to cationic bovine serum albumin (cBSA) without interfering with their important structural features. With the guaiacylglycerol- β-guaiacyl ether dimer, for example, the linking was accomplished in 89% yield with the number of dimers per carrier protein being as high as 50; NMR experiments on a 15N- and 13C-labeled conjugation product indicated that 13 dimers were added to the native lysine residues and themore » remainder (~37) to the amine moieties on the ethylenediamine linkers added to BSA; ~32% of the available primary amine groups on cBSA were therefore conjugated to the hapten. As a result, this loading is suitable for attempting to raise new antibodies to plant lignins and for screening.« less

  12. A computationally efficient method for full-core conjugate heat transfer modeling of sodium fast reactors

    SciTech Connect

    Hu, Rui; Yu, Yiqi

    2016-09-08

    For efficient and accurate temperature predictions of sodium fast reactor structures, a 3-D full-core conjugate heat transfer modeling capability is developed for an advanced system analysis tool, SAM. The hexagon lattice core is modeled with 1-D parallel channels representing the subassembly flow, and 2-D duct walls and inter-assembly gaps. The six sides of the hexagon duct wall and near-wall coolant region are modeled separately to account for different temperatures and heat transfer between coolant flow and each side of the duct wall. The Jacobian Free Newton Krylov (JFNK) solution method is applied to solve the fluid and solid field simultaneously in a fully coupled fashion. The 3-D full-core conjugate heat transfer modeling capability in SAM has been demonstrated by a verification test problem with 7 fuel assemblies in a hexagon lattice layout. In addition, the SAM simulation results are compared with RANS-based CFD simulations. Very good agreements have been achieved between the results of the two approaches.

  13. Surface Profile and Stress Field Evaluation using Digital Gradient Sensing Method

    SciTech Connect

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

    2016-08-09

    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 accurate data of that kind. 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.

  14. 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

  15. Communication: Analytic gradients for the complex absorbing potential equation-of-motion coupled-cluster method

    NASA Astrophysics Data System (ADS)

    Benda, Zsuzsanna; Jagau, Thomas-C.

    2017-01-01

    The general theory of analytic energy gradients is presented for the complex absorbing potential equation-of-motion coupled-cluster (CAP-EOM-CC) method together with an implementation within the singles and doubles approximation. Expressions for the CAP-EOM-CC energy gradient are derived based on a Lagrangian formalism with a special focus on the extra terms arising from the presence of the CAP. Our implementation allows for locating minima on high-dimensional complex-valued potential energy surfaces and thus enables geometry optimizations of resonance states of polyatomic molecules. The applicability of our CAP-EOM-CC gradients is illustrated by computations of the equilibrium structures and adiabatic electron affinities of the temporary anions of formaldehyde, formic acid, and ethylene. The results are compared to those obtained from standard EOM-CC calculations and the advantages of CAP methods are emphasized.

  16. 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.

  17. 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.

  18. Numerical methods for the design of gradient-index optical coatings.

    PubMed

    Anzengruber, Stephan W; Klann, Esther; Ramlau, Ronny; Tonova, Diana

    2012-12-01

    We formulate the problem of designing gradient-index optical coatings as the task of solving a system of operator equations. We use iterative numerical procedures known from the theory of inverse problems to solve it with respect to the coating refractive index profile and thickness. The mathematical derivations necessary for the application of the procedures are presented, and different numerical methods (Landweber, Newton, and Gauss-Newton methods, Tikhonov minimization with surrogate functionals) are implemented. Procedures for the transformation of the gradient coating designs into quasi-gradient ones (i.e., multilayer stacks of homogeneous layers with different refractive indices) are also developed. The design algorithms work with physically available coating materials that could be produced with the modern coating technologies.

  19. Surface Profile and Stress Field Evaluation using Digital Gradient Sensing Method

    DOE PAGES

    Miao, C.; Sundaram, B. M.; Huang, L.; ...

    2016-08-09

    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 accurate data of that kind. 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-squaresmore » 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.« less

  20. Surface Profile and Stress Field Evaluation using Digital Gradient Sensing Method

    SciTech Connect

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

    2016-08-09

    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 accurate data of that kind. 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.

  1. A method of congruent type for linear systems with conjugate-normal coefficient matrices

    NASA Astrophysics Data System (ADS)

    Ghasemi Kamalvand, M.; Ikramov, Kh. D.

    2009-02-01

    Minimal residual methods, such as MINRES and GMRES, are well-known iterative versions of direct procedures for reducing a matrix to special condensed forms. The method of reduction used in these procedures is a sequence of unitary similarity transformations, while the condensed form is a tridiagonal matrix (MINRES) or a Hessenberg matrix (GMRES). The algorithm CSYM proposed in the 1990s for solving systems with complex symmetric matrices was based on the tridiagonal reduction performed via unitary congruences rather than similarities. In this paper, we construct an extension of this algorithm to the entire class of conjugate-normal matrices. (Complex symmetric matrices are a part of this class.) Numerical results are presented. They show that, on many occasions, the proposed algorithm has a superior convergence rate compared to GMRES.

  2. Shape optimization of the turbomachine channel by a gradient method — Accuracy improvement

    NASA Astrophysics Data System (ADS)

    Rabiega, Marek

    2003-08-01

    An algorithm of the gradient method of the channel shape optimization has been built on the basis of 3D equations of mass, momentum and energy conservation in the fluid flow. The gradient of the functional that is posed for minimization has been calculated by two methods, via sensitivities and - for comparison - by the finite difference approximation. The equations for sensitivities have been generated through a differentiate-then-discretize approach. The exemplary optimization of the blade shape of the centrifugal compressor wheel has been carried out for the inviscid gas flow governed by Euler equations with a non-uniform mass flow distribution as the inlet boundary condition. Mixing losses have been minimized downstream the outlet of the centrifugal wheel in this exemplary optimization. The results of the optimization problem accomplished by the two above-mentioned methods have been presented. In the case sparse grids have been used, the method with the gradient approximated by finite differences has been found to be more consistent. The discretization accuracy has turned out to be crucial for the consistency of the gradient method via sensitivities.

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

    PubMed Central

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

    2010-01-01

    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

  4. 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.

  5. Development, evaluation and application of a modified micrometeorological gradient method for long-term estimation of gaseous dry deposition over forest canopies

    EPA Science Inventory

    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 Bowe...

  6. Bounded perturbation resilience and superiorization techniques for the projected scaled gradient method

    NASA Astrophysics Data System (ADS)

    Xu, Hong-Kun

    2017-04-01

    Bounded perturbation resilience and superiorization techniques for the projected scaled gradient (PSG) method are studied under the general Hilbert space setting. Weak convergence results of the (superiorized) PSG method and its relaxed version are proved under the assumption that the errors be summable. It is also shown that the PSG method converges in a sublinear rate and can be accelerated to the convergence rate O≤ft(\\tfrac{1}{{n}2}\\right). Applications to linear inverse problems and split feasibility problems are discussed.

  7. Improving the accuracy of the discrete gradient method in the one-dimensional case.

    PubMed

    Cieśliński, Jan L; Ratkiewicz, Bogusław

    2010-01-01

    We present two numerical schemes of high accuracy for one-dimensional dynamical systems. They are modifications of the discrete gradient method and keep its advantages, including stability and conservation of the energy integral. However, their accuracy is higher by several orders of magnitude.

  8. 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.

  9. Full QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method.

    PubMed

    Jin, Xinsheng; Zhang, John Z H; He, Xiao

    2017-03-30

    In this study, the electrostatically embedded generalized molecular fractionation with conjugate caps (concaps) method (EE-GMFCC) was employed for efficient linear-scaling quantum mechanical (QM) calculation of total energies of RNAs. In the EE-GMFCC approach, the total energy of RNA is calculated by taking a proper combination of the QM energy of each nucleotide-centric fragment with large caps or small caps (termed EE-GMFCC-LC and EE-GMFCC-SC, respectively) deducted by the energies of concaps. The two-body QM interaction energy between non-neighboring ribonucleotides which are spatially in close contact are also taken into account for the energy calculation. Numerical studies were carried out to calculate the total energies of a number of RNAs using the EE-GMFCC-LC and EE-GMFCC-SC methods at levels of the Hartree-Fock (HF) method, density functional theory (DFT), and second-order many-body perturbation theory (MP2), respectively. The results show that the efficiency of the EE-GMFCC-SC method is about 3 times faster than the EE-GMFCC-LC method with minimal accuracy sacrifice. The EE-GMFCC-SC method is also applied for relative energy calculations of 20 different conformers of two RNA systems using HF and DFT, respectively. Both single-point and relative energy calculations demonstrate that the EE-GMFCC method has deviations from the full system results of only a few kcal/mol.

  10. 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.

  11. Automated capillary Western dot blot method for the identity of a 15-valent pneumococcal conjugate vaccine.

    PubMed

    Hamm, Melissa; Ha, Sha; Rustandi, Richard R

    2015-06-01

    Simple Western is a new technology that allows for the separation, blotting, and detection of proteins similar to a traditional Western except in a capillary format. Traditionally, identity assays for biological products are performed using either an enzyme-linked immunosorbent assay (ELISA) or a manual dot blot Western. Both techniques are usually very tedious, labor-intensive, and complicated for multivalent vaccines, and they can be difficult to transfer to other laboratories. An advantage this capillary Western technique has over the traditional manual dot blot Western method is the speed and the automation of electrophoresis separation, blotting, and detection steps performed in 96 capillaries. This article describes details of the development of an automated identity assay for a 15-valent pneumococcal conjugate vaccine, PCV15-CRM197, using capillary Western technology. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. 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

  13. Molecular mechanics-valence bond method for planar conjugated hydrocarbon cations.

    PubMed

    Hall, Katherine F; Tokmachev, Andrei M; Bearpark, Michael J; Boggio-Pasqua, Martial; Robb, Michael A

    2007-10-07

    We present an extension of the molecular mechanics-valence bond (MMVB) hybrid method to study ground and excited states of planar conjugated hydrocarbon cations. Currently, accurate excited state calculations on these systems are limited to expensive ab initio studies of smaller systems: up to 15 active electrons in 16 pi orbitals with complete active space self-consistent field (CASSCF) theory using high symmetry. The new MMVB extension provides a faster, cheaper treatment to investigate larger cation systems with more than 24 active orbitals. Extension requires both new matrix elements and new parameters: In this paper we present both, for the limited planar case. The scheme is tested for the planar radical cations of benzene, naphthalene, anthracene, and phenanthrene. Calculated MMVB relative energies are in good agreement with CASSCF results for equilibrium geometries on the ground and first excited states, and conical intersections.

  14. 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.

  15. Automatic Classification of Staphylococci by Principal-Component Analysis and a Gradient Method1

    PubMed Central

    Hill, L. R.; Silvestri, L. G.; Ihm, P.; Farchi, G.; Lanciani, P.

    1965-01-01

    Hill, L. R. (Università Statale, Milano, Italy), L. G. Silvestri, P. Ihm, G. Farchi, and P. Lanciani. Automatic classification of staphylococci by principal-component analysis and a gradient method. J. Bacteriol. 89:1393–1401. 1965.—Forty-nine strains from the species Staphylococcus aureus, S. saprophyticus, S. lactis, S. afermentans, and S. roseus were submitted to different taxometric analyses; clustering was performed by single linkage, by the unweighted pair group method, and by principal-component analysis followed by a gradient method. Results were substantially the same with all methods. All S. aureus clustered together, sharply separated from S. roseus and S. afermentans; S. lactis and S. saprophyticus fell between, with the latter nearer to S. aureus. The main purpose of this study was to introduce a new taxometric technique, based on principal-component analysis followed by a gradient method, and to compare it with some other methods in current use. Advantages of the new method are complete automation and therefore greater objectivity, execution of the clustering in a space of reduced dimensions in which different characters have different weights, easy recognition of taxonomically important characters, and opportunity for representing clusters in three-dimensional models; the principal disadvantage is the need for large computer facilities. Images PMID:14293013

  16. Limited-memory fast gradient descent method for graph regularized nonnegative matrix factorization.

    PubMed

    Guan, Naiyang; Wei, Lei; Luo, Zhigang; Tao, Dacheng

    2013-01-01

    Graph regularized nonnegative matrix factorization (GNMF) decomposes a nonnegative data matrix X[Symbol:see text]R(m x n) to the product of two lower-rank nonnegative factor matrices, i.e.,W[Symbol:see text]R(m x r) and H[Symbol:see text]R(r x n) (r < min {m,n}) and aims to preserve the local geometric structure of the dataset by minimizing squared Euclidean distance or Kullback-Leibler (KL) divergence between X and WH. The multiplicative update rule (MUR) is usually applied to optimize GNMF, but it suffers from the drawback of slow-convergence because it intrinsically advances one step along the rescaled negative gradient direction with a non-optimal step size. Recently, a multiple step-sizes fast gradient descent (MFGD) method has been proposed for optimizing NMF which accelerates MUR by searching the optimal step-size along the rescaled negative gradient direction with Newton's method. However, the computational cost of MFGD is high because 1) the high-dimensional Hessian matrix is dense and costs too much memory; and 2) the Hessian inverse operator and its multiplication with gradient cost too much time. To overcome these deficiencies of MFGD, we propose an efficient limited-memory FGD (L-FGD) method for optimizing GNMF. In particular, we apply the limited-memory BFGS (L-BFGS) method to directly approximate the multiplication of the inverse Hessian and the gradient for searching the optimal step size in MFGD. The preliminary results on real-world datasets show that L-FGD is more efficient than both MFGD and MUR. To evaluate the effectiveness of L-FGD, we validate its clustering performance for optimizing KL-divergence based GNMF on two popular face image datasets including ORL and PIE and two text corpora including Reuters and TDT2. The experimental results confirm the effectiveness of L-FGD by comparing it with the representative GNMF solvers.

  17. Limited-Memory Fast Gradient Descent Method for Graph Regularized Nonnegative Matrix Factorization

    PubMed Central

    Guan, Naiyang; Wei, Lei; Luo, Zhigang; Tao, Dacheng

    2013-01-01

    Graph regularized nonnegative matrix factorization (GNMF) decomposes a nonnegative data matrix to the product of two lower-rank nonnegative factor matrices, i.e., and () and aims to preserve the local geometric structure of the dataset by minimizing squared Euclidean distance or Kullback-Leibler (KL) divergence between X and WH. The multiplicative update rule (MUR) is usually applied to optimize GNMF, but it suffers from the drawback of slow-convergence because it intrinsically advances one step along the rescaled negative gradient direction with a non-optimal step size. Recently, a multiple step-sizes fast gradient descent (MFGD) method has been proposed for optimizing NMF which accelerates MUR by searching the optimal step-size along the rescaled negative gradient direction with Newton's method. However, the computational cost of MFGD is high because 1) the high-dimensional Hessian matrix is dense and costs too much memory; and 2) the Hessian inverse operator and its multiplication with gradient cost too much time. To overcome these deficiencies of MFGD, we propose an efficient limited-memory FGD (L-FGD) method for optimizing GNMF. In particular, we apply the limited-memory BFGS (L-BFGS) method to directly approximate the multiplication of the inverse Hessian and the gradient for searching the optimal step size in MFGD. The preliminary results on real-world datasets show that L-FGD is more efficient than both MFGD and MUR. To evaluate the effectiveness of L-FGD, we validate its clustering performance for optimizing KL-divergence based GNMF on two popular face image datasets including ORL and PIE and two text corpora including Reuters and TDT2. The experimental results confirm the effectiveness of L-FGD by comparing it with the representative GNMF solvers. PMID:24204761

  18. Deflection monitoring for a box girder based on a modified conjugate beam method

    NASA Astrophysics Data System (ADS)

    Chen, Shi-Zhi; Wu, Gang; Xing, Tuo

    2017-08-01

    After several years of operation, a box girder bridge would commonly experience excessive deflection, which endangers the bridge’s life span as well as the safety of vehicles travelling on it. In order to avoid potential risks, it is essential to constantly monitor the defection of box girders. However, currently, the direct deflection monitoring methods are limited by the complicated environments beneath the bridges, such as rivers or other traffic lanes, which severely impede the layouts of the sensors. The other indirect deflection monitoring methods mostly do not thoroughly consider the inherent shear lag effect and shear deformation in the box girder, resulting in a rather large error. Under these circumstances, a deflection monitoring method suiting box girders is proposed in this article, based on the conjugate beam method and distributed long-gauge fibre Bragg grating (FBG) sensor. A lab experiment was conducted to verify the reliability and feasibility of this method under practical application. Further, the serviceability under different span-depth ratios and web thicknesses was examined through a finite element model.

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

    PubMed

    Defraia, Christopher T; Schmelz, Eric A; Mou, Zhonglin

    2008-12-31

    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-beta-D-glucoside or SAG). Recently, Huang et al. developed a bacterial biosensor that responds to free SA but not SAG, designated as Acinetobacter sp. ADPWH_lux. In this paper we describe an improved methodology for Acinetobacter sp. ADPWH_lux-based free SA quantification, enabling high-throughput analysis, and present an approach for the quantification of SAG from crude plant extracts. On the basis of the original biosensor-based method, we optimized extraction and quantification. SAG content was determined by treating crude extracts with beta-glucosidase, then measuring the released free SA with the biosensor. beta-glucosidase treatment released more SA in acetate buffer extract than in Luria-Bertani (LB) extract, while enzymatic hydrolysis in either solution released more free SA than acid hydrolysis. The biosensor-based method detected higher amounts of SA in pathogen-infected plants than did a GC/MS-based method. SA quantification of control and pathogen-treated wild-type and sid2 (SA induction-deficient) plants demonstrated the efficacy of the method described. Using the methods detailed here, we were able to detect as little as 0.28 mug SA/g FW. Samples typically had a standard deviation of up to 25% of the mean. The ability of Acinetobacter sp. ADPWH_lux to detect SA in a complex mixture, combined with the enzymatic hydrolysis of SAG in crude extract, allowed the development of a simple, rapid, and inexpensive method to simultaneously measure free and glucose-conjugated SA. This approach is amenable to a high-throughput format, which would further reduce the cost and time required for biosensor-based SA quantification. Possible applications of this approach include

  20. Aeromagnetic gradient compensation method for helicopter based on ɛ-support vector regression algorithm

    NASA Astrophysics Data System (ADS)

    Wu, Peilin; Zhang, Qunying; Fei, Chunjiao; Fang, Guangyou

    2017-04-01

    Aeromagnetic gradients are typically measured by optically pumped magnetometers mounted on an aircraft. Any aircraft, particularly helicopters, produces significant levels of magnetic interference. Therefore, aeromagnetic compensation is essential, and least square (LS) is the conventional method used for reducing interference levels. However, the LSs approach to solving the aeromagnetic interference model has a few difficulties, one of which is in handling multicollinearity. Therefore, we propose an aeromagnetic gradient compensation method, specifically targeted for helicopter use but applicable on any airborne platform, which is based on the ɛ-support vector regression algorithm. The structural risk minimization criterion intrinsic to the method avoids multicollinearity altogether. Local aeromagnetic anomalies can be retained, and platform-generated fields are suppressed simultaneously by constructing an appropriate loss function and kernel function. The method was tested using an unmanned helicopter and obtained improvement ratios of 12.7 and 3.5 in the vertical and horizontal gradient data, respectively. Both of these values are probably better than those that would have been obtained from the conventional method applied to the same data, had it been possible to do so in a suitable comparative context. The validity of the proposed method is demonstrated by the experimental result.

  1. Practical method development for the separation of monoclonal antibodies and antibody-drug-conjugate species in hydrophobic interaction chromatography, part 1: optimization of the mobile phase.

    PubMed

    Rodriguez-Aller, Marta; Guillarme, Davy; Beck, Alain; Fekete, Szabolcs

    2016-01-25

    The goal of this work is to provide some recommendations for method development in HIC using monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs) as model drug candidates. The effects of gradient steepness, mobile phase pH, salt concentration and type, as well as organic modifier were evaluated for tuning selectivity and retention in HIC. Except the nature of the stationary phase, which was not discussed in this study, the most important parameter for modifying selectivity was the gradient steepness. The addition of organic solvent (up to 15% isopropanol) in the mobile phase was also found to be useful for mAbs analysis, since it could provide some changes in elution order, in some cases. On the contrary, isopropanol was not beneficial with ADCs, since the most hydrophobic DAR species (DAR6 and DAR8) cannot be eluted from the stationary phase under these conditions. This study also illustrates the possibility to perform HIC method development using optimization software, such as Drylab. The optimum conditions suggested by the software were tested using therapeutic mAbs and commercial cysteine linked ADC (brentuximab-vedotin) and the average retention time errors between predicted and experimental retention times were ∼ 1%.

  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. A Modified Magnetic Gradient Contraction Based Method for Ferromagnetic Target Localization

    PubMed Central

    Wang, Chen; Zhang, Xiaojuan; Qu, Xiaodong; Pan, Xiao; Fang, Guangyou; Chen, Luzhao

    2016-01-01

    The Scalar Triangulation and Ranging (STAR) method, which is based upon the unique properties of magnetic gradient contraction, is a high real-time ferromagnetic target localization method. Only one measurement point is required in the STAR method and it is not sensitive to changes in sensing platform orientation. However, the localization accuracy of the method is limited by the asphericity errors and the inaccurate value of position leads to larger errors in the estimation of magnetic moment. To improve the localization accuracy, a modified STAR method is proposed. In the proposed method, the asphericity errors of the traditional STAR method are compensated with an iterative algorithm. The proposed method has a fast convergence rate which meets the requirement of high real-time localization. Simulations and field experiments have been done to evaluate the performance of the proposed method. The results indicate that target parameters estimated by the modified STAR method are more accurate than the traditional STAR method. PMID:27999322

  4. A simple LC/MRM-MS-based method to quantify free linker-payload in antibody-drug conjugate preparations.

    PubMed

    Zmolek, Wesley; Bañas, Stefanie; Barfield, Robyn M; Rabuka, David; Drake, Penelope M

    2016-10-01

    Antibody-drug conjugates represent a growing class of biologic drugs that use the targeted specificity of an antibody to direct the localization of a small molecule drug, often a cytotoxic payload. After conjugation, antibody-drug conjugate preparations typically retain a residual amount of free (unconjugated) linker-payload. Monitoring this free small molecule drug component is important due to the potential for free payload to mediate unintended (off-target) toxicity. We developed a simple RP-HPLC/MRM-MS-based assay that can be rapidly employed to quantify free linker-payload. The method uses low sample volumes and offers an LLOQ of 10nM with 370pg on column. This analytical approach was used to monitor free linker-payload removal during optimization of the tangential flow filtration manufacturing step.

  5. Utilization of nuclear methods for materials analysis and the determination of concentration gradients

    NASA Technical Reports Server (NTRS)

    Darras, R.

    1979-01-01

    The various types of nuclear chemical analysis methods are discussed. The possibilities of analysis through activation and direct observation of nuclear reactions are described. Such methods make it possible to analyze trace elements and impurities with selectivity, accuracy, and a high degree of sensitivity. Such methods are used in measuring major elements present in materials which are available for analysis only in small quantities. These methods are well suited to superficial analyses and to determination of concentration gradients; provided the nature and energy of the incident particles are chosen judiciously. Typical examples of steels, pure iron and refractory metals are illustrated.

  6. 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

  7. ANDUCT- VELOCITY GRADIENT METHOD FOR CALCULATING VELOCITIES IN AN AXISYMMETRIC ANNULAR DUCT

    NASA Technical Reports Server (NTRS)

    Katsanis, T.

    1994-01-01

    Turbomachinery components are often connected by ducts, which are usually annular. The configurations and aerodynamic characteristics of these ducts are crucial to the optimum performance of the turbomachinery blade rows. The ANDUCT computer program was developed to calculate the velocity distribution along an arbitrary line between the inner and outer walls of an annular duct with axisymmetric swirling flow. Although other programs are available for duct analysis, the use of the velocity gradient method makes the ANDUCT program fast and convenient while requiring only modest computer resources. A fast and easy method of analyzing the flow through a duct with axisymmetric flow is the velocity gradient method, also known as the stream filament or streamline curvature method. This method has been used extensively for blade passages but has not been widely used for ducts, except for the radial equilibrium equation. In ANDUCT, a velocity gradient equation derived from the momentum equation is used to determine the velocity variation along an arbitrary straight line between the inner and outer wall of an annular duct. The velocity gradient equation is used with an assumed variation of meridional streamline curvature. Upstream flow conditions may vary between the inner and outer walls, and an assumed total pressure distribution may be specified. ANDUCT works best for well-guided passages and where the curvature of the walls is small as compared to the width of the passage. The ANDUCT program is written in FORTRAN IV for batch execution and has been implemented on an IBM 370 series computer with a central memory requirement of approximately 60K of 8 bit bytes. The ANDUCT program was developed in 1982.

  8. The microstructure evolution of hydrogenated microcrystalline germanium promoted by power gradient method

    NASA Astrophysics Data System (ADS)

    Wang, Xinyu; Ni, Jian; Li, Chang; Sun, Xiaoxiang; Li, Zhenglong; Cai, Hongkun; Li, Juan; Zhang, Jianjun

    2016-12-01

    This paper studies the microstructure evolution of hydrogenated microcrystalline germanium (μc-Ge:H) thin films deposited by plasma enhanced chemical vapor deposition (PECVD). There is an amorphous incubation layer formed in the initial deposition stage of μc-Ge:H thin film. It is demonstrated that the thickness of incubation layer can be reduced by high hydrogen dilution and high discharge power method. However, at high hydrogen dilution, the deposition rate of μc-Ge:H appears a sharply decrease. Using a high discharge power can compensate the deposition rate decrease but lead to decrease of average grain size and appearance of micro-void in the μc-Ge:H thin film. In addition, by comparing two thickness groups of μc-Ge:H thin films deposited at different discharge powers, it is noticed that the evolution process relates to the formation of crystal nucleuses. Thus, a power gradient method is proposed to understand the mechanism of nucleation and crystal growth in the initial deposition process of μc-Ge:H films. Finally, by power gradient method, the incubation layer thickness of μc-Ge:H thin films has been decreased to less than 6 nm. Moreover, Raman scattering spectra shows a 38 nm μc-Ge:H film has a crystal fraction (XC) of 62.4%. Meanwhile, the mobility of TFT devices shows the improved electrical property of μc-Ge:H film deposited by power gradient method.

  9. 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.

  10. Recommended methods of fatty acid methylester preparation for conjugated dienes and trienes in food and biological samples.

    PubMed

    Igarashi, Miki; Tsuzuki, Tsuyoshi; Kambe, Tomoko; Miyazawa, Teruo

    2004-04-01

    In this study, we compared three acid-catalyzed methods and three base-catalyzed methods for the methylester preparation of conjugated dienoic fatty acids and conjugated trienoic fatty acids in food and biological samples. Among the six methods examined, the sodium methoxide/methanol (NaOCH3/MeOH) method and the tetramethylguanidine/ methanol (TMG/MeOH) method of methylester preparation from tung oil were most efficient in preventing the artificial isomerization of alpha-eleostearic acid (alpha-ESA; 9c,11t,13t-18:3) to beta-eleostearic acid (beta-ESA: 9t,11t,13t-18:3) and for avoiding the artificial generation of unknown byproducts. Hydrochloric acid/methanol (HCl/MeOH), sulfuric acid/methanol (H2SO4/MeOH) and AOCS (boron trifluoride/methanol (BF3/MeOH)) methods of methylester preparation from tung oil resulted in the breakdown of alpha-ESA due to their long reaction periods and high reaction temperatures. In addition, these three methods did not prevent the generation of beta-ESA. For the methylester preparation of tung oil free fatty acids, the BF3/MeOH method (30 min at room temperature) did not lead to artificial beta-ESA formation or byproducts, while the trimethylsilyldiazomethane (TMSN2CH3) method did form artifacts. For the methylation of conjugated linoleic acid (CLA, free fatty acid), the BF3/ MeOH and TMSN2CH3 methods completely suppressed artificial isomerization of c,t-CLA and t,c-CLA to t,t-CLA. The results indicated that the BF3/MeOH method for free fatty acids is the best method for the methylester preparation of both conjugated dienoic and trienoic fatty acids with respect to preventing artificial isomerization and the formation of byproducts. The BF3/MeOH method was applicable to both food and biological samples.

  11. On modification of certain methods of the conjugate direction type for solving rectangular systems of linear algebraic equations

    NASA Astrophysics Data System (ADS)

    Yukhno, L. F.

    2007-12-01

    The use of modifications of certain well-known methods of the conjugate direction type for solving systems of linear algebraic equations with rectangular matrices is examined. The modified methods are shown to be superior to the original versions with respect to the round-off accumulation; the advantage is especially large for ill-conditioned matrices. Examples are given of the efficient use of the modified methods for solving certain fairly large ill-conditioned problems.

  12. 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.

  13. 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.

  14. 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

  15. [A novel method of chromosome distribution analysis in saccharose density gradient].

    PubMed

    Kuznetsova, A V; Kravatskiĭ, Iu V; Aksenov, A D; Shatrova, A N; Zenin, V V; Poletaev, A I

    2001-01-01

    The human chromosomes distribution in a sucrose density gradient was studied using a new computer method of the quantitative analysis of flow karyotypes. The dual-parameter flow distributions of human chromosomes fluorescence intensities of the sucrose density gradient fractions were analyzed to obtain the quantity of each chromosome. The chromosomes were found to distribute over sucrose density gradient as follows: 1) fractions with low sucrose density mostly contain chromosomes 1-7, and their quantity is increased between 1.4- to 3.2-fold in comparison with the control unfractionated suspension; 2) medium density fractions are enriched with chromosomes 8-20 up to 2.4-fold; 3) fractions with a high sucrose density mostly contain small chromosomes 21-22 and fragments of broken chromosomes. So the new method of quantitative analysis of flow karyotypes allows one to determine the efficiency of enrichment and the maximally enriched fraction for any chosen chromosome. Maximally enriched fractions maximize the rate of preparative flow sorting of individual chromosomes for research or biotechnology purposes.

  16. 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.

  17. Local a posteriori estimates for pointwise gradient errors in finite element methods for elliptic problems

    NASA Astrophysics Data System (ADS)

    Demlow, Alan

    2007-03-01

    We prove local a posteriori error estimates for pointwise gradient errors in finite element methods for a second-order linear elliptic model problem. First we split the local gradient error into a computable local residual term and a weaker global norm of the finite element error (the ``pollution term''). Using a mesh-dependent weight, the residual term is bounded in a sharply localized fashion. In specific situations the pollution term may also be bounded by computable residual estimators. On nonconvex polygonal and polyhedral domains in two and three space dimensions, we may choose estimators for the pollution term which do not employ specific knowledge of corner singularities and which are valid on domains with cracks. The finite element mesh is only required to be simplicial and shape-regular, so that highly graded and unstructured meshes are allowed.

  18. Computational and mathematical methods for morphogenetic gradient analysis, boundary formation and axonal targeting.

    PubMed

    Reingruber, Jürgen; Holcman, David

    2014-11-01

    Morphogenesis and axonal targeting are key processes during development that depend on complex interactions at molecular, cellular and tissue level. Mathematical modeling is essential to bridge this multi-scale gap in order to understand how the emergence of large structures is controlled at molecular level by interactions between various signaling pathways. We summarize mathematical modeling and computational methods for time evolution and precision of morphogenetic gradient formation. We discuss tissue patterning and the formation of borders between regions labeled by different morphogens. Finally, we review models and algorithms that reveal the interplay between morphogenetic gradients and patterned activity for axonal pathfinding and the generation of the retinotopic map in the visual system. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. 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.

  20. 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.

  1. Numerical modeling of void migration in solids due to temperature gradient using the boundary element method

    SciTech Connect

    Dong, Y.; Tagavi, K.A.; Wu, T.W.; Chow, L.C.

    1996-09-01

    Voids (a kind of flaw) are not desired in the products of many industrial and manufacturing processes. In this article, the authors seek effective ways to remove the void by modeling the void migration and predicting the intermediate and the final shape of the cavity. The boundary element method (BEM) is applied to the quasi-steady state void migration process governed by Laplace`s equation. The conduction solution depends on the void shape, and the void shape depends on the conduction solution. Hence this is a conjugate problem. The analytical formulation and the numerical approach are outlined. The Overhauser spline elements are used in the BEM to ensure continuous first-order derivatives on the void boundary. Given the material properties, geometry of the physical model, and boundary conditions, this computer model can predict detailed information such as flux, velocity and direction of void motion, and temperature at any stage of the void migration. Different strategies for void removal are investigated.

  2. Buckling analysis of tapered nanobeams using nonlocal strain gradient theory and a generalized differential quadrature method

    NASA Astrophysics Data System (ADS)

    Bakhshi Khaniki, H.; Hosseini-Hashemi, Sh

    2017-06-01

    This paper presents the buckling behavior of tapered small-scale beams in the framework of nonlocal strain gradient theory. Three different types of cross-sectional variation are proposed—width variation, thickness variation and a combination of both. The Euler-Bernoulli beam model, nonlocal strain gradient theory and Hamilton’s principle are employed to achieve the governing equations of small-scale beams. A generalized differential quadrature method is used to solve the governing equations for all three nonuniformity models. In order to comprehend the influence of a nonuniform cross section, a parametric study is presented and the effects of strain gradient, nonlocal elasticity and all three types of nonuniformity on the critical buckling load are presented. It is shown that such nonuniformities have a significant effect on the buckling behavior of small-scale beams. Accordingly, with the wide application of tapered small-scale beams in many devices, this study could be a step forward in understanding, predicting and controlling such behaviors.

  3. 3D inversion of full magnetic gradient tensor data based on hybrid regularization method

    NASA Astrophysics Data System (ADS)

    Ji, Shuangxi; Zhang, Huai; Wang, Yanfei; Zhao, Lingling

    2017-04-01

    Recently, the magnetic tensor data can be directly measured due to the latest development of superconducting quantum interference device (SQUID) based sensors, which can collect five unique magnetic gradients components (partial H_x/ partial x , partial H_x/ partial y , partial H_x/ partial z , partial H_y/ partial z ,partial H_z/ partial z ). More measurement date will bring more useful information of observed magnetic anomaly, however it still bear the computational instability problem because of the intrinsic ill-posed property in the magnetic inverse problem. Furthermore, most of research on magnetic regularization inversion only concentrate on total magnetic field or magnetic vector field, rather than the magnetic gradient tensor field. Therefore we introduce a novel 3D hybrid regularization method by MS-TV stabilizer for inversion of magnetic gradient tensor data, which is designed mainly based on the minimum support functional (MS) and total variation functional (TV), and the final regularization functional can be described as the following form: J(κ)&=1/2(G(κ)-d,wd(G(κ)-d))ΩP+α((1-λ)φpMS(κ)+λφβ TV(κ)) &=1/2(G(κ)-d,wd(G(κ)-d))ΩP +α(1-λ/2\\intΩQ(κ-κprior)2/(κ-κprior)2+e2dΩQ &+λ\\intΩQ√{|\

  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. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    PubMed

    Wang, Bo; Su, Yumin; Wan, Lei

    2016-04-15

    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.

  6. 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

  7. 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

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

    PubMed

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

    2016-07-19

    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

  9. Distortion correction in EPI using an extended PSF method with a reversed phase gradient approach.

    PubMed

    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.

  10. Myocardial fractional flow reserve: a biplane angiocardiographic alternative to the pressure gradient method

    NASA Astrophysics Data System (ADS)

    Schrijver, Marc; Slump, Cornelis H.; Storm, Corstiaan J.

    2001-05-01

    Pijls and De Bruyne (1993) developed a method employing intravascular blood pressure gradients to calculate the Myocardial Fractional Flow Reserve (FFR). This flow reserve is a better indication of the functional severity of a coronary stenosis than percentage diameter or luminal area reduction as provided by traditional Quantitative Coronary Angiography (QCA). However, to use this method, all of the relevant artery segments have to be select intra-operatively. After the procedure, only the segments for which a pressure reading is available can be graded. We previously introduced another way to assess the functional severity of stenosis using angiographic projections: the Relative Coronary Flow Reserve (RCFR). It is based on standard densitometric blood velocity and flow reserve methods, but without the need to estimate the geometry of the artery. This paper demonstrates that this RCFR method yields -- in theory -- the same results as the FFR, and can be given an almost identical interpretation. This provides the opportunity to use the RCFR retrospectively, when pressure gradients are not available for the segment(s) of interest.

  11. A Mixed FE-Meshfree Method for Gradient Plasticity Continuum with Linear Complementary Model

    NASA Astrophysics Data System (ADS)

    Zhang, Junbo; Li, Xikui

    2010-05-01

    A mixed FE-meshfree method based on gradient plasticity and linear complementary problem (LCP) model is proposed. The plastic multiplier field is assumed and approximately interpolated in terms of its discretized values defined at the integration points with moving least-square (MLS) meshfree method. Whereas the displacement field is discretized in terms of its nodal values with FE interpolation approximations. The weak form of the equilibrium equation along with the non-local constitutive equation and gradient-dependent yield criterion locally enforced at each integration point are combined to educe a normal form of LCP which is solved by means of Lexico-Lemke algorithm. A consistent algorithm based on backward-Euler return mapping integration scheme is devised. There is no need to derive non-local consistent tangent elasto-plastic modulus matrix in the proposed method while the second convergence rate is still retained. Numerical results demonstrate the validity of the method in modeling strain localization problem due to strain softening.

  12. Ficoll-400 density gradient method as an effective sperm preparation technique for assisted reproductive techniques

    PubMed Central

    Highland, Hyacinth N.; Rishika, A. Sharma; Almira, S. Shaikh; Kanthi, P. Bansal

    2016-01-01

    BACKGROUND: Infertility being a burning issue, the male itself contributes about 40% as a cause, as evident by statistical data. However, Assisted Reproductive Technology (ART) has emerged as a powerful tool in the management of infertility. Sperm preparation techniques govern the selection procedure to separate functional spermatozoa which can then be used in IUI, IVF, and ART and for cryopreservation. AIM: The present study was aimed at evaluation of sperm preparation techniques for reliability, performance and to determine the most effective, feasible and economical technique. MATERIALS AND METHODS: The subjects under study includes males with normal proven fertility (n=40) and the males with unexplained infertility (n=40). Four sperm separation techniques, viz., Swim-up, Swim-down, Sucrose and Ficoll-400 density gradient techniques were evaluated for their efficacy in separation of good quality fraction of spermatozoa. Sperm viability, morphology and maturation status of spermatozoa were taken as evaluation parameters following the standard methods (WHO 2010). STATISTICAL ANALYSIS: Data was analyzed using student's t-test and the four selected techniques were compared with the normal semen samples for scoring the efficiency of the techniques. RESULTS AND DISCUSSION: Out of the several techniques used, Ficoll-400 was found to be more efficient method for separation of spermatozoa. The percentage of change in each parameter was calculated and taken as the index for recovery of potent sperm from the original sperm. Ficoll-400 density gradient yielded higher percentage of live, mature, morphologically normal spermatozoa in an isolated fraction as compared to other three techniques. CONCLUSION: It was observed that a combination of Ficoll-400 gradient separation with Swim-up technique could give quality spermatozoa which in-turn would directly have an impact on the success of IVF and other ART techniques. PMID:27803588

  13. Partial spectral projected gradient method with active-set strategy for linearly constrained optimization

    NASA Astrophysics Data System (ADS)

    Andretta, Marina; Birgin, Ernesto; Martínez, J.

    2010-01-01

    A method for linearly constrained optimization which modifies and generalizes recent box-constraint optimization algorithms is introduced. The new algorithm is based on a relaxed form of Spectral Projected Gradient iterations. Intercalated with these projected steps, internal iterations restricted to faces of the polytope are performed, which enhance the efficiency of the algorithm. Convergence proofs are given and numerical experiments are included and commented. Software supporting this paper is available through the Tango Project web page: http://www.ime.usp.br/˜egbirgin/tango/.

  14. Assessing composition gradients in multifilamentary superconductors by means of magnetometry methods

    NASA Astrophysics Data System (ADS)

    Baumgartner, T.; Hecher, J.; Bernardi, J.; Pfeiffer, S.; Senatore, C.; Eisterer, M.

    2017-01-01

    We present two magnetometry-based methods suitable for assessing gradients in the critical temperature and hence the composition of multifilamentary superconductors: AC magnetometry and scanning Hall probe microscopy. The novelty of the former technique lies in the iterative evaluation procedure we developed, whereas the strength of the latter is the direct visualization of the temperature dependent penetration of a magnetic field into the superconductor. Using the example of a PIT Nb3Sn wire, we demonstrate the application of these techniques, and compare the respective results to each other and to EDX measurements of the Sn distribution within the sub-elements of the wire.

  15. 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

  16. 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

  17. Exciton Absorption Spectra by Linear Response Methods: Application to Conjugated Polymers.

    PubMed

    Mosquera, Martín A; Jackson, Nicholas E; Fauvell, Thomas J; Kelley, Matthew S; Chen, Lin X; Schatz, George C; Ratner, Mark A

    2017-03-15

    The theoretical description of the time-evolution of excitons requires, as an initial step, the calculation of their spectra, which has been inaccessible to most users due to the high computational scaling of conventional algorithms and accuracy issues caused by common density functionals. Previously (J. Chem. Phys. 2016, 144, 204105), we developed a simple method that resolves these issues. Our scheme is based on a two-step calculation in which a linear-response TDDFT calculation is used to generate orbitals perturbed by the excitonic state, and then a second linear-response TDDFT calculation is used to determine the spectrum of excitations relative to the excitonic state. Herein, we apply this theory to study near-infrared absorption spectra of excitons in oligomers of the ubiquitous conjugated polymers poly(3-hexylthiophene) (P3HT), poly(2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene) (MEH-PPV), and poly(benzodithiophene-thieno[3,4-b]thiophene) (PTB7). For P3HT and MEH-PPV oligomers, the calculated intense absorption bands converge at the longest wavelengths for 10 monomer units, and show strong consistency with experimental measurements. The calculations confirm that the exciton spectral features in MEH-PPV overlap with those of the bipolaron formation. In addition, our calculations identify the exciton absorption bands in transient absorption spectra measured by our group for oligomers (1, 2, and 3 units) of PTB7. For all of the cases studied, we report the dominant orbital excitations contributing to the optically active excited state-excited state transitions, and suggest a simple rule to identify absorption peaks at the longest wavelengths. We suggest our methodology could be considered for further developments in theoretical transient spectroscopy to include nonadiabatic effects, coherences, and to describe the formation of species such as charge-transfer states and polaron pairs.

  18. Improving the accuracy of the gradient method for determining soil carbon dioxide efflux

    NASA Astrophysics Data System (ADS)

    Sánchez-Cañete, Enrique P.; Scott, Russell L.; Haren, Joost; Barron-Gafford, Greg A.

    2017-01-01

    Soil CO2 efflux (Fsoil) represents a significant source of ecosystem CO2 emissions that is rarely quantified with high-temporal-resolution data in carbon flux studies. Fsoil estimates can be obtained by the low-cost gradient method (GM), but the utility of the method is hindered by uncertainties in the application of published models for the diffusion coefficient. Therefore, to address and resolve these uncertainties, we compared Fsoil measured by 2 soil CO2 efflux chambers and Fsoil estimated by 16 gas transport models using the GM across 1 year. We used 14 published empirical gas diffusion models and 2 in situ models: (1) a gas transfer model called "Chamber model" obtained using a calibration between the chamber and the gradient method and (2) a diffusion model called "SF6 model" obtained through an interwell conservative tracer experiment. Most of the published models using the GM underestimated cumulative annual Fsoil by 55% to 361%, while the Chamber model closely approximated cumulative Fsoil (0.6% error). Surprisingly, the SF6 model combined with the GM underestimated Fsoil by 32%. Differences between in situ models could stem from the Chamber model implicitly accounting for production of soil CO2, while the conservative tracer model does not. Therefore, we recommend using the GM only after calibration with chamber measurements to generate reliable long-term ecosystem Fsoil measurements. Accurate estimates of Fsoil will improve our understanding of soil respiration's contribution to ecosystem fluxes.

  19. Ficoll-400 density gradient method as an effective sperm preparation technique for assisted reproductive techniques.

    PubMed

    Highland, Hyacinth N; Rishika, A Sharma; Almira, S Shaikh; Kanthi, P Bansal

    2016-01-01

    Infertility being a burning issue, the male itself contributes about 40% as a cause, as evident by statistical data. However, Assisted Reproductive Technology (ART) has emerged as a powerful tool in the management of infertility. Sperm preparation techniques govern the selection procedure to separate functional spermatozoa which can then be used in IUI, IVF, and ART and for cryopreservation. The present study was aimed at evaluation of sperm preparation techniques for reliability, performance and to determine the most effective, feasible and economical technique. The subjects under study includes males with normal proven fertility (n=40) and the males with unexplained infertility (n=40). Four sperm separation techniques, viz., Swim-up, Swim-down, Sucrose and Ficoll-400 density gradient techniques were evaluated for their efficacy in separation of good quality fraction of spermatozoa. Sperm viability, morphology and maturation status of spermatozoa were taken as evaluation parameters following the standard methods (WHO 2010). Data was analyzed using student's t-test and the four selected techniques were compared with the normal semen samples for scoring the efficiency of the techniques. Out of the several techniques used, Ficoll-400 was found to be more efficient method for separation of spermatozoa. The percentage of change in each parameter was calculated and taken as the index for recovery of potent sperm from the original sperm. Ficoll-400 density gradient yielded higher percentage of live, mature, morphologically normal spermatozoa in an isolated fraction as compared to other three techniques. It was observed that a combination of Ficoll-400 gradient separation with Swim-up technique could give quality spermatozoa which in-turn would directly have an impact on the success of IVF and other ART techniques.

  20. Probability density function method for variable-density pressure-gradient-driven turbulence and mixing

    SciTech Connect

    Bakosi, Jozsef; Ristorcelli, Raymond J

    2010-01-01

    Probability density function (PDF) methods are extended to variable-density pressure-gradient-driven turbulence. We apply the new method to compute the joint PDF of density and velocity in a non-premixed binary mixture of different-density molecularly mixing fluids under gravity. The full time-evolution of the joint PDF is captured in the highly non-equilibrium flow: starting from a quiescent state, transitioning to fully developed turbulence and finally dissipated by molecular diffusion. High-Atwood-number effects (as distinguished from the Boussinesq case) are accounted for: both hydrodynamic turbulence and material mixing are treated at arbitrary density ratios, with the specific volume, mass flux and all their correlations in closed form. An extension of the generalized Langevin model, originally developed for the Lagrangian fluid particle velocity in constant-density shear-driven turbulence, is constructed for variable-density pressure-gradient-driven flows. The persistent small-scale anisotropy, a fundamentally 'non-Kolmogorovian' feature of flows under external acceleration forces, is captured by a tensorial diffusion term based on the external body force. The material mixing model for the fluid density, an active scalar, is developed based on the beta distribution. The beta-PDF is shown to be capable of capturing the mixing asymmetry and that it can accurately represent the density through transition, in fully developed turbulence and in the decay process. The joint model for hydrodynamics and active material mixing yields a time-accurate evolution of the turbulent kinetic energy and Reynolds stress anisotropy without resorting to gradient diffusion hypotheses, and represents the mixing state by the density PDF itself, eliminating the need for dubious mixing measures. Direct numerical simulations of the homogeneous Rayleigh-Taylor instability are used for model validation.

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

    USDA-ARS?s Scientific Manuscript database

    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-...

  2. Visualizing dispersive features in 2D image via minimum gradient method

    DOE PAGES

    He, Yu; Wang, Yan; Shen, Zhi -Xun

    2017-07-24

    Here, we developed a minimum gradient based method to track ridge features in a 2D image plot, which is a typical data representation in many momentum resolved spectroscopy experiments. Through both analytic formulation and numerical simulation, we compare this new method with existing DC (distribution curve) based and higher order derivative based analyses. We find that the new method has good noise resilience and enhanced contrast especially for weak intensity features and meanwhile preserves the quantitative local maxima information from the raw image. An algorithm is proposed to extract 1D ridge dispersion from the 2D image plot, whose quantitative applicationmore » to angle-resolved photoemission spectroscopy measurements on high temperature superconductors is demonstrated.« less

  3. Visualizing dispersive features in 2D image via minimum gradient method

    NASA Astrophysics Data System (ADS)

    He, Yu; Wang, Yan; Shen, Zhi-Xun

    2017-07-01

    We developed a minimum gradient based method to track ridge features in a 2D image plot, which is a typical data representation in many momentum resolved spectroscopy experiments. Through both analytic formulation and numerical simulation, we compare this new method with existing DC (distribution curve) based and higher order derivative based analyses. We find that the new method has good noise resilience and enhanced contrast especially for weak intensity features and meanwhile preserves the quantitative local maxima information from the raw image. An algorithm is proposed to extract 1D ridge dispersion from the 2D image plot, whose quantitative application to angle-resolved photoemission spectroscopy measurements on high temperature superconductors is demonstrated.

  4. Automatic localization of pupil using eccentricity and iris using gradient based method

    NASA Astrophysics Data System (ADS)

    Khan, Tariq M.; Aurangzeb Khan, M.; Malik, Shahzad A.; Khan, Shahid A.; Bashir, Tariq; Dar, Amir H.

    2011-02-01

    This paper presents a novel approach for the automatic localization of pupil and iris. Pupil and iris are nearly circular regions, which are surrounded by sclera, eyelids and eyelashes. The localization of both pupil and iris is extremely important in any iris recognition system. In the proposed algorithm pupil is localized using Eccentricity based Bisection method which looks for the region that has the highest probability of having pupil. While iris localization is carried out in two steps. In the first step, iris image is directionally segmented and a noise free region (region of interest) is extracted. In the second step, angular lines in the region of interest are extracted and the edge points of iris outer boundary are found through the gradient of these lines. The proposed method is tested on CASIA ver 1.0 and MMU Iris databases. Experimental results show that this method is comparatively accurate.

  5. Does non-ionizing radiant energy affect determination of the evaporation rate by the gradient method?

    PubMed

    Kjartansson, S; Hammarlund, K; Oberg, P A; Sedin, G

    1991-01-01

    A study was performed to investigate whether measurements of the evaporation rate from the skin of newborn infants by the gradient method are affected by the presence of non-ionizing radiation from phototherapy equipment or a radiant heater. The evaporation rate was measured experimentally with the measuring sensors either exposed to or protected from non-ionizing radiation. Either blue light (phototherapy) or infrared light (radiant heater) was used; in the former case the evaporation rate was measured from a beaker of water covered with a semipermeable membrane, and in the latter case from the hand of an adult subject, aluminium foil or with the measuring probe in the air. No adverse effect on the determinations of the evaporation rate was found in the presence of blue light. Infrared radiation caused an error of 0.8 g/m2h when the radiant heater was set at its highest effect level or when the ambient humidity was high. At low and moderate levels the observed evaporation rate was not affected. It is concluded that when clinical measurements are made from the skin of newborn infants nursed under a radiant heater, the evaporation rate can appropriately be determined by the gradient method.

  6. Lysis gradient centrifugation: a flexible method for the isolation of nuclei from primary cells.

    PubMed

    Katholnig, Karl; Poglitsch, Marko; Hengstschläger, Markus; Weichhart, Thomas

    2015-01-01

    The isolation of nuclei from eukaryotic cells is essential for studying the composition and the dynamic changes of the nuclear proteome to gain insight into the mechanisms of gene expression and cell signalling. Primary cells are particularly challenging for standard nuclear isolation protocols due to low protein content, sample degradation, or nuclear clumping. Here, we describe a rapid and flexible protocol for the isolation of clean and intact nuclei, which results in the recovery of 90-95 % highly pure nuclei. The method, called lysis gradient centrifugation (LGC), is based on an iso-osmolar discontinuous iodixanol-based density gradient including a detergent-containing lysis layer. A single low g-force centrifugation step enables mild cell lysis and prevents extensive contact of the nuclei with the cytoplasmic environment. This fast method shows high reproducibility due to the relatively little cell manipulation required by the investigator. Further advantages are the low amount of starting material required, easy parallel processing of multiple samples, and isolation of nuclei and cytoplasm at the same time from the same sample.

  7. Gradient Augmented Level Set Method for Two Phase Flow Simulations with Phase Change

    NASA Astrophysics Data System (ADS)

    Anumolu, C. R. Lakshman; Trujillo, Mario F.

    2016-11-01

    A sharp interface capturing approach is presented for two-phase flow simulations with phase change. The Gradient Augmented Levelset method is coupled with the two-phase momentum and energy equations to advect the liquid-gas interface and predict heat transfer with phase change. The Ghost Fluid Method (GFM) is adopted for velocity to discretize the advection and diffusion terms in the interfacial region. Furthermore, the GFM is employed to treat the discontinuity in the stress tensor, velocity, and temperature gradient yielding an accurate treatment in handling jump conditions. Thermal convection and diffusion terms are approximated by explicitly identifying the interface location, resulting in a sharp treatment for the energy solution. This sharp treatment is extended to estimate the interfacial mass transfer rate. At the computational cell, a d-cubic Hermite interpolating polynomial is employed to describe the interface location, which is locally fourth-order accurate. This extent of subgrid level description provides an accurate methodology for treating various interfacial processes with a high degree of sharpness. The ability to predict the interface and temperature evolutions accurately is illustrated by comparing numerical results with existing 1D to 3D analytical solutions.

  8. Comparisons and Limitations of Gradient Augmented Level Set and Algebraic Volume of Fluid Methods

    NASA Astrophysics Data System (ADS)

    Anumolu, Lakshman; Ryddner, Douglas; Trujillo, Mario

    2014-11-01

    Recent numerical methods for implicit interface transport are generally presented as enjoying higher order of spatial-temporal convergence when compared to classical methods or less sophisticated approaches. However, when applied to test cases, which are designed to simulate practical industrial conditions, significant reduction in convergence is observed in higher-order methods, whereas for the less sophisticated approaches same convergence is achieved but a growth in the error norms occurs. This provides an opportunity to understand the underlying issues which causes this decrease in accuracy in both types of methods. As an example we consider the Gradient Augmented Level Set method (GALS) and a variant of the Volume of Fluid (VoF) method in our study. Results show that while both methods do suffer from a loss of accuracy, it is the higher order method that suffers more. The implication is a significant reduction in the performance advantage of the GALS method over the VoF scheme. Reasons for this lie in the behavior of the higher order derivatives, particular in situations where the level set field is highly distorted. For the VoF approach, serious spurious deformations of the interface are observed, albeit with a deceptive zero loss of mass.

  9. An optimization-based method for high order gradient calculation on unstructured meshes

    NASA Astrophysics Data System (ADS)

    Busatto, Alcides Dallanora

    A new implicit and compact optimization-based method is presented for high order derivative calculation for finite-volume numerical method on unstructured meshes. High-order approaches to gradient calculation are often based on variants of the Least-Squares (L-S) method, an explicit method that requires a stencil large enough to accommodate the necessary variable information to calculate the derivatives. The new scheme proposed here is applicable for an arbitrary order of accuracy (demonstrated here up to 3rd order), and uses just the first level of face neighbors to compute all derivatives, thus reducing stencil size and avoiding stiffness in the calculation matrix. Preliminary results for a static variable field example and solution of a simple scalar transport (advection) equation show that the proposed method is able to deliver numerical accuracy equivalent to (or better than) the nominal order of accuracy for both 2nd and 3rd order schemes in the presence of a smoothly distributed variable field (i.e., in the absence of discontinuities). This new Optimization-based Gradient REconstruction (herein denoted OGRE) scheme produces, for the simple scalar transport test case, lower error and demands less computational time (for a given level of required precision) for a 3rd order scheme when compared to an equivalent L-S approach on a two-dimensional framework. For three-dimensional simulations, where the L-S scheme fails to obtain convergence without the help of limiters, the new scheme obtains stable convergence and also produces lower error solution when compared to a third order MUSCL scheme. Furthermore, spectral analysis of results from the advection equation shows that the new scheme is better able to accurately resolve high wave number modes, which demonstrates its potential to better solve problems presenting a wide spectrum of wavelengths, for example unsteady turbulent flow simulations.

  10. A pH-gradient induced method for wetting metal-layer embedded nanopores

    NASA Astrophysics Data System (ADS)

    Balagurusamy, Venkat; Stolovitzky, Gustavo

    2015-03-01

    Solid-state nanopores made on a single layer of Silicon nitride are wet by a number of methods by different workers. Typically, they involve using some low-surface tension liquid like iso propyl alcohol for pre-wetting before filling with the electrolyte solution of interest e.g., a buffered KCl solution both sides of the chamber that partition the nanopore. These methods can also be preceded by a cleaning step which may involve either oxygen plasma or piranha treatment. However we found that these methods were not successful in wetting certain batches of nanopores drilled in a stack of Si3N4/SiO2/TiN/SiO2/TiN/SiO2/TiN/SiO2/Si3N4 layers. We found that applying buffer solutions at different pH on the two sides of the nanopore greatly accelerated the wetting process from days to few hours and resulted in nanopores with near linear I-V behavior for high salt concentration buffer solutions. We will describe this method and the results for a number of nanopores. Nanopores wet with this pH gradient method translocate DNA molecules like nanopores wet by other methods mentioned here. We believe that the actual mechanism of this wetting process is influenced strongly by the pH effect on SiO2 surface. Efforts are underway to understand the working of this wetting method by quantum computer simulation methods.

  11. Accurate gradient approximation for complex interface problems in 3D by an improved coupling interface method

    SciTech Connect

    Shu, Yu-Chen; Chern, I-Liang; Chang, Chien C.

    2014-10-15

    Most elliptic interface solvers become complicated for complex interface problems at those “exceptional points” where there are not enough neighboring interior points for high order interpolation. Such complication increases especially in three dimensions. Usually, the solvers are thus reduced to low order accuracy. In this paper, we classify these exceptional points and propose two recipes to maintain order of accuracy there, aiming at improving the previous coupling interface method [26]. Yet the idea is also applicable to other interface solvers. The main idea is to have at least first order approximations for second order derivatives at those exceptional points. Recipe 1 is to use the finite difference approximation for the second order derivatives at a nearby interior grid point, whenever this is possible. Recipe 2 is to flip domain signatures and introduce a ghost state so that a second-order method can be applied. This ghost state is a smooth extension of the solution at the exceptional point from the other side of the interface. The original state is recovered by a post-processing using nearby states and jump conditions. The choice of recipes is determined by a classification scheme of the exceptional points. The method renders the solution and its gradient uniformly second-order accurate in the entire computed domain. Numerical examples are provided to illustrate the second order accuracy of the presently proposed method in approximating the gradients of the original states for some complex interfaces which we had tested previous in two and three dimensions, and a real molecule ( (1D63)) which is double-helix shape and composed of hundreds of atoms.

  12. A new multi-object image thresholding method based on correlation between object class uncertainty and intensity gradient

    PubMed Central

    Liu, Yinxiao; Liang, Guoyuan; Saha, Punam K.

    2012-01-01

    Purpose: Image thresholding and gradient analysis have remained popular image preprocessing tools for several decades due to the simplicity and straight-forwardness of their definitions. Also, optimum selection of threshold and gradient strength values are hidden steps in many advanced medical imaging algorithms. A reliable method for threshold optimization may be a crucial step toward automation of several medical image based applications. Most automatic thresholding and gradient selection methods reported in literature primarily focus on image histograms ignoring a significant amount of information embedded in the spatial distribution of intensity values forming visible features in an image. Here, we present a new method that simultaneously optimizes both threshold and gradient values for different object interfaces in an image that is based on unification of information from both the histogram and spatial image features; also, the method works for unknown number of object regions. Methods: A new energy function is formulated by combining the object class uncertainty measure, a histogram-based feature, of each pixel with its image gradient measure, a spatial contextual feature in an image. The energy function is designed to measure the overall compliance of the theoretical premise that, in a probabilistic sense, image intensities with high class uncertainty are associated with high image gradients. Finally, it is expressed as a function of threshold and gradient parameters and optimum combinations of these parameters are sought by locating pits and valleys on the energy surface. A major strength of the algorithm lies in the fact that it does not require the number of object regions in an image to be predefined. Results: The method has been applied on several medical image datasets and it has successfully determined both threshold and gradient parameters for different object interfaces even when some of the thresholds are almost impossible to locate in the

  13. An online supervised learning method based on gradient descent for spiking neurons.

    PubMed

    Xu, Yan; Yang, Jing; Zhong, Shuiming

    2017-09-01

    The purpose of supervised learning with temporal encoding for spiking neurons is to make the neurons emit a specific spike train encoded by precise firing times of spikes. The gradient-descent-based (GDB) learning methods are widely used and verified in the current research. Although the existing GDB multi-spike learning (or spike sequence learning) methods have good performance, they work in an offline manner and still have some limitations. This paper proposes an online GDB spike sequence learning method for spiking neurons that is based on the online adjustment mechanism of real biological neuron synapses. The method constructs error function and calculates the adjustment of synaptic weights as soon as the neurons emit a spike during their running process. We analyze and synthesize desired and actual output spikes to select appropriate input spikes in the calculation of weight adjustment in this paper. The experimental results show that our method obviously improves learning performance compared with the offline learning manner and has certain advantage on learning accuracy compared with other learning methods. Stronger learning ability determines that the method has large pattern storage capacity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. A self-reference PRF-shift MR thermometry method utilizing the phase gradient.

    PubMed

    Langley, Jason; Potter, William; Phipps, Corey; Huang, Feng; Zhao, Qun

    2011-12-21

    In magnetic resonance (MR) imaging, the most widely used and accurate method for measuring temperature is based on the shift in proton resonance frequency (PRF). However, inter-scan motion and bulk magnetic field shifts can lead to inaccurate temperature measurements in the PRF-shift MR thermometry method. The self-reference PRF-shift MR thermometry method was introduced to overcome such problems by deriving a reference image from the heated or treated image, and approximates the reference phase map with low-order polynomial functions. In this note, a new approach is presented to calculate the baseline phase map in self-reference PRF-shift MR thermometry. The proposed method utilizes the phase gradient to remove the phase unwrapping step inherent to other self-reference PRF-shift MR thermometry methods. The performance of the proposed method was evaluated using numerical simulations with temperature distributions following a two-dimensional Gaussian function as well as phantom and in vivo experimental data sets. The results from both the numerical simulations and experimental data show that the proposed method is a promising technique for measuring temperature.

  15. Probability density based gradient projection method for inverse kinematics of a robotic human body model.

    PubMed

    Lura, Derek; Wernke, Matthew; Alqasemi, Redwan; Carey, Stephanie; Dubey, Rajiv

    2012-01-01

    This paper presents the probability density based gradient projection (GP) of the null space of the Jacobian for a 25 degree of freedom bilateral robotic human body model (RHBM). This method was used to predict the inverse kinematics of the RHBM and maximize the similarity between predicted inverse kinematic poses and recorded data of 10 subjects performing activities of daily living. The density function was created for discrete increments of the workspace. The number of increments in each direction (x, y, and z) was varied from 1 to 20. Performance of the method was evaluated by finding the root mean squared (RMS) of the difference between the predicted joint angles relative to the joint angles recorded from motion capture. The amount of data included in the creation of the probability density function was varied from 1 to 10 subjects, creating sets of for subjects included and excluded from the density function. The performance of the GP method for subjects included and excluded from the density function was evaluated to test the robustness of the method. Accuracy of the GP method varied with amount of incremental division of the workspace, increasing the number of increments decreased the RMS error of the method, with the error of average RMS error of included subjects ranging from 7.7° to 3.7°. However increasing the number of increments also decreased the robustness of the method.

  16. A gradient based facile HPLC method for simultaneous estimation of antioxidants extracted from tea powder.

    PubMed

    Nanjegowda, Shankara H; Papanna, Manasa G; Achar, Raghu Ram; Rangappa, Kanchugarakoppal S; Mallu, Puttaswamappa; Swamy, Shivananju Nanjunda

    2016-05-01

    A new simple, rapid and precise RP-HPLC method was developed for the extraction and quantitative estimation of caffeine (C), (-)-epigallocatechin gallate (EGCG), (+)-catechin(Ct), (-)-epicatechin(EC), and (-)-epicatechin gallate (ECG) (collectively named as Tea Powder Bioactives TPBAs) extracted from tea powder using different ratios of ethanol: water. The simultaneous determination of TPBAs was performed using the UV spectrophotometric method which employs the absorbance at 205 nm (λmax of caffeine and polyphenols). This method is a gradient based HPLC method with a flow rate of 0.8 mL/min using Inertsil ODS 100 × 4.6 mm, 3 μm column with methanol and ammonium dihydrogen phosphate (pH-2.8) as mobile phase. The method was validated in terms of specificity, precision, linearity, accuracy, limit of quantification (LOQ), and limit of detection (LOD). The linearity of the proposed method was investigated for concentration ranging between 0.5-60 μg/mL with regression co-efficient, R(2) = 0.999-1.0. This method estimates all the TPBAs simultaneously with enhanced precision and linearity as per the ICH guidelines. Also, to confirm the individual TPBA, the antioxidant property of the each TPBA was analyzed which was commensurate with that of the previous reports.

  17. Phase conjugation method and apparatus for an active retrodirective antenna array

    NASA Technical Reports Server (NTRS)

    Tausworthe, R. C.; Chernoff, R. C. (Inventor)

    1979-01-01

    An active retrodirective antenna array wherein a reference array element is used to generate a phase reference which is replicated at succeeding elements of the array. Each element of the array is associated with a phase regeneration circuit and the phase conjugation circuitry of an adjacent element. In one implementation, the phase reference circuit operates on the input signal at the reference element, a voltage controlled oscillator (VCO) output signal and the input pilot signal at the next array element received from a transmission line. By proper filtering and mixing, a phase component may be produced to which the VCO may be locked to produce the phase conjugate of the pilot signal at the next array element plus a transmission line delay. In another implementation, particularly suited for large arrays in space, two different input pilot frequencies are employed.

  18. [Haemolysis and turbidity influence on three analysis methods of quantitative determination of total and conjugated bilirubin on ADVIA 1650].

    PubMed

    Gobert De Paepe, E; Munteanu, G; Schischmanoff, P O; Porquet, D

    2008-01-01

    Plasma bilirubin testing is crucial to prevent the occurrence of neonatal kernicterus. Haemolysis may occur during sampling and interfere with bilirubin determination. Moreover, lipidic infusions may induce plasma lipemia and also interfere with bilirubin measurement. We evaluated the interference of haemolysis and lipemia with three methods of total and direct bilirubin measurement adaptated on an Advia 1650 analyser (Siemens Medical Solutions Diagnostics) : Synermed (Sofibel), Bilirubin 2 (Siemens) and Bilirubin Auto FS (Diasys). The measurement of total bilirubin was little affected by haemolysis with all three methods. The Bilirubin 2 (Siemens) method was the less sensitive to haemolysis even at low bilirubin levels. The measurement of conjugated bilirubin was significantly altered by low heamoglobin concentrations for Bilirubin Auto FS(R) (30 microM or 0,192 g/100 mL haemoglobin) and for Synermed (60 microM or 0,484 g/100 mL haemoglobin). In marked contrast, we found no haemoglobin interference with the Direct Bilirubin 2 reagent which complied with the method validation criteria from the French Society for Biological Chemistry. The lipemia up to 2 g/L of Ivelip did not affect neither the measurement of total bilirubin for all three methods nor the measurement of conjugated bilirubin with the Diasys and Siemens reagents. However, we observed a strong interference starting at 0,5 g/L of Ivelip with the Synermed reagent. Our data suggest that both Siemens and Diasys methods allow to measure accurately total and conjugated bilirubin in hemolytic and lipemic samples, nevertheless, the Siemens methodology is less affected by these interferences.

  19. Methods for strand-specific DNA detection with cationic conjugated polymers suitable for incorporation into DNA chips and microarrays.

    PubMed

    Liu, Bin; Bazan, Guillermo C

    2005-01-18

    A strand-specific DNA sensory method is described based on surface-bound peptide nucleic acids and water-soluble cationic conjugated polymers. The main transduction mechanism operates by taking advantage of the net increase in negative charge at the peptide nucleic acid surface that occurs upon single-stranded DNA hybridization. Electrostatic forces cause the oppositely charged cationic conjugated polymer to bind selectively to the "complementary" surfaces. This approach circumvents the current need to label the probe or target strands. The polymer used in these assays is poly[9,9'-bis(6''-N,N,N-trimethylammonium)hexyl)fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide], which was specifically designed and synthesized to be compatible with excitation sources used in commonly used DNA microarray readers. Furthermore, the utility of poly[9,9'-bis(6''-N,N,N-trimethylammonium)-hexyl)fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide] has been demonstrated in homogenous and solid-state assays that involve fluorescence resonance energy transfer to a reporter dye (Cy5) and that can benefit from the light harvesting properties observed in water-soluble conjugated polymers.

  20. One-step method for generating PEG-like plasma polymer gradients: chemical characterization and analysis of protein interactions.

    PubMed

    Menzies, Donna J; Cowie, Bruce; Fong, Celesta; Forsythe, John S; Gengenbach, Thomas R; McLean, Keith M; Puskar, Ljiljana; Textor, Marcus; Thomsen, Lars; Tobin, Mark; Muir, Benjamin W

    2010-09-07

    In this work we report a one-step method for the fabrication of poly(ethylene glycol) PEG-like chemical gradients, which were deposited via continuous wave radio frequency glow discharge plasma polymerization of diethylene glycol dimethyl ether (DG). A knife edge top electrode was used to produce the gradient coatings at plasma load powers of 5 and 30 W. The chemistry across the gradients was analyzed using a number of complementary techniques including spatially resolved synchrotron source grazing incidence FTIR microspectroscopy, X-ray photoelectron spectroscopy (XPS) and synchrotron source near edge X-ray absorption fine structure (NEXAFS) spectroscopy. Gradients deposited at lower load power retained a higher degree of monomer like functionality as did the central region directly underneath the knife edge electrode of each gradient film. Surface derivatization experiments were employed to investigate the concentration of residual ether units in the films. In addition, surface derivatization was used to investigate the reactivity of the gradient films toward primary amine groups in a graft copolymer of poly (L-lysine) and poly(ethylene glycol) (PLL-g-PEG copolymer) which was correlated to residual aldehyde, ketone and carboxylic acid functionalities within the films. The protein adsorption characteristics of the gradients were analyzed using three proteins of varying size and charge. Protein adsorption varied and was dependent on the chemistry and the physical properties (such as size and charge) of the proteins. A correlation between the concentration of ether functionality and the protein fouling characteristics along the gradient films was observed. The gradient coating technique developed in this work allows for the efficient and high-throughput study of biomaterial gradient coating interactions.

  1. DFT study of the interaction between the conjugated fluorescein and dabcyl system, using fluorescene quenching method.

    PubMed

    Alvarado-González, Mónica; Gallo, Marco; Lopez-Albarran, Pablo; Flores-Holguín, Norma; Glossman-Mitnik, Daniel

    2012-09-01

    Molecular beacon is a DNA probe containing a sequence complementary to the target that is flanked by self-complementary termini, and carries a fluorophore and a quencher at the ends. We used the fluorescein and dabcyl as fluorophore and quencher respectively, and studied with DFT calculations at the GGA/DNP level, and taking into account DFT dispersion corrections by the Grimme and Tkatchenko-Scheffler (TS) schemes, the distance, where the most favorable energetic interaction between the fluorophore and quencher in conjugated form occurs. This distance occurs at a separation distance of 29.451 Å between the centers of Dabcyl and fluorescein employing the TS DFT dispersion correction scheme, indicating FRET efficiency around 94.28 %. The calculated emission spectra of the conjugated pair in water indicated that the emission and absorption spectrum overlap completely and thus no fluorescence can be observed due to the fluorescence resonance energy transfer (FRET) effect. The DFT results confirmed the experimentally observing fluorescence quenching of the fluorescein-dabcyl conjugated system by FRET.

  2. Gradient and High-Throughput Methods for the Accelerated Development of Nanomaterials and Nanometrology

    NASA Astrophysics Data System (ADS)

    Fasolka, Michael J.

    2005-03-01

    Increasingly, new materials are highly tailored towards specific applications, are formulated from many components, and exhibit behavior governed by a multitude of physical, chemical and processing factors. Accordingly, the discovery and optimization of materials are met by considerable challenges inherent to the understanding of large, complex parameter spaces. In this respect, combinatorial and high-throughput (C&HT) approaches are advantageous, since they present the ability to rapidly assess materials properties over large parameter ranges. The NIST Combinatorial Methods Center (NCMC, see www.nist.gov/combi) specializes in the development of quantitative C&HT measurement methods for materials research. In large part, the NCMC concentrates on continuous gradient (CG) combinatorial methods, which involve the fabrication and HT measurement of systems that gradually vary parameters over a single specimen, and which offer an alternative to the (often costly) robotics-driven C&HT paradigm used by the pharmaceutical industry. CG techniques are particularly suited for materials science since they naturally produce thorough maps (e.g. continuous phase diagrams) that relate materials properties to chemical, compositional, physical and processing parameters. This presentation focuses on NCMC research applied to the advancement of polymer-based nanotechnology. Topics to be discussed include CG techniques for the design and optimization of self-assembled systems, ultra-thin films, and intelligent surfaces; and HT methods for measuring thin film morphology and mechanical properties. In addition, the application of CG methods to the advancement of nanometrology, specifically scanned probe microscopy, will be discussed.

  3. A density-adaptive SPH method with kernel gradient correction for modeling explosive welding

    NASA Astrophysics Data System (ADS)

    Liu, M. B.; Zhang, Z. L.; Feng, D. L.

    2017-05-01

    Explosive welding involves processes like the detonation of explosive, impact of metal structures and strong fluid-structure interaction, while the whole process of explosive welding has not been well modeled before. In this paper, a novel smoothed particle hydrodynamics (SPH) model is developed to simulate explosive welding. In the SPH model, a kernel gradient correction algorithm is used to achieve better computational accuracy. A density adapting technique which can effectively treat large density ratio is also proposed. The developed SPH model is firstly validated by simulating a benchmark problem of one-dimensional TNT detonation and an impact welding problem. The SPH model is then successfully applied to simulate the whole process of explosive welding. It is demonstrated that the presented SPH method can capture typical physics in explosive welding including explosion wave, welding surface morphology, jet flow and acceleration of the flyer plate. The welding angle obtained from the SPH simulation agrees well with that from a kinematic analysis.

  4. Method for utilization of oil field waste brine to develop a salt gradient solar pond

    SciTech Connect

    Manning, R. A.; Wisneski, T. P.

    1984-10-30

    A process and method is disclosed for utilizing oil field waste brine to develop and maintain a salt gradient solar pond which in turn provides thermal energy for doing work, including improved separation of oil/brine emulsions into waste brine, crude oil, and natural gas; hot brine from the storage layer of the developed solar pond provides heat to a process heat exchanger which is intended to elevate the temperature of a working fluid such as an emulsion of crude oil and brine coming from producing oil wells prior to a separation process within a conventional heater treater. Waste brine from the crude oil process is utilized to develop and maintain the solar pond rather than simply being disposed.

  5. Accelerated gradient methods for the x-ray imaging of solar flares

    NASA Astrophysics Data System (ADS)

    Bonettini, S.; Prato, M.

    2014-05-01

    In this paper we present new optimization strategies for the reconstruction of x-ray images of solar flares by means of the data collected by the Reuven Ramaty high energy solar spectroscopic imager. The imaging concept of the satellite is based on rotating modulation collimator instruments, which allow the use of both Fourier imaging approaches and reconstruction techniques based on the straightforward inversion of the modulated count profiles. Although in the last decade, greater attention has been devoted to the former strategies due to their very limited computational cost, here we consider the latter model and investigate the effectiveness of different accelerated gradient methods for the solution of the corresponding constrained minimization problem. Moreover, regularization is introduced through either an early stopping of the iterative procedure, or a Tikhonov term added to the discrepancy function by means of a discrepancy principle accounting for the Poisson nature of the noise affecting the data.

  6. Flow instability of a centrifugal pump determined using the energy gradient method

    NASA Astrophysics Data System (ADS)

    Li, Yi; Dong, Wenlong; He, Zhaohui; Huang, Yuanmin; Jiang, Xiaojun

    2015-02-01

    The stability of the centrifugal pump has not been well revealed because of the complexity of internal flow. To analyze the flow characteristics of a centrifugal pump operating at low capacity, methods of numerical simulation and experimental research were adopted in this paper. Characteristics of the inner flow were obtained. Standard k-ɛ turbulence models were used to calculate the inner flow of the pump under off-design conditions. The distribution of the energy gradient function K was obtained by three-dimensional numerical simulation at different flow rates. The relative velocity component was acquired from the absolute velocity obtained in particle image velocimetry. By comparing with experimental results, it was found that flow instability occurs at the position of maximum K. The flow stability reduces with an increasing flow rate. The research results provide a theoretical basis for the optimization design of a centrifugal pump.

  7. Method and means for a spatial and temporal probe for laser-generated plumes based on density gradients

    DOEpatents

    Yeung, E.S.; Chen, G.

    1990-05-01

    A method and means are disclosed for a spatial and temporal probe for laser generated plumes based on density gradients includes generation of a plume of vaporized material from a surface by an energy source. The probe laser beam is positioned so that the plume passes through the probe laser beam. Movement of the probe laser beam caused by refraction from the density gradient of the plume is monitored. Spatial and temporal information, correlated to one another, is then derived. 15 figs.

  8. Method and means for a spatial and temporal probe for laser-generated plumes based on density gradients

    DOEpatents

    Yeung, Edward S.; Chen, Guoying

    1990-05-01

    A method and means for a spatial and temporal probe for laser generated plumes based on density gradients includes generation of a plume of vaporized material from a surface by an energy source. The probe laser beam is positioned so that the plume passes through the probe laser beam. Movement of the probe laser beam caused by refraction from the density gradient of the plume is monitored. Spatial and temporal information, correlated to one another, is then derived.

  9. A Fast and Practical Yeast Transformation Method Mediated by Escherichia coli Based on a Trans-Kingdom Conjugal Transfer System: Just Mix Two Cultures and Wait One Hour

    PubMed Central

    Moriguchi, Kazuki; Yamamoto, Shinji; Ohmine, Yuta; Suzuki, Katsunori

    2016-01-01

    Trans-kingdom conjugation is a phenomenon by which DNA is transferred into a eukaryotic cell by a bacterial conjugal transfer system. Improvement in this method to facilitate the rapid co-cultivation of donor bacterial and recipient eukaryotic cell cultures could make it the simplest transformation method, requiring neither isolation of vector DNA nor preparation of competent recipient cells. To evaluate this potential advantage of trans-kingdom conjugation, we examined this simple transformation method using vector combinations, helper plasmids, and recipient Saccharomyces cerevisiae strains. Mixing donor Escherichia coli and recipient S. cerevisiae overnight cultures (50 μL each) consistently yielded on the order of 101 transformants using the popular experimental strain BY4742 derived from S288c and a shuttle vector for trans-kingdom conjugation. Transformation efficiency increased to the order of 102 using a high receptivity trans-kingdom conjugation strain. In addition, either increasing the amount of donor cells or pretreating the recipient cells with thiols such as dithiothreitol improved the transformation efficiency by one order of magnitude. This simple trans-kingdom conjugation-mediated transformation method could be used as a practical yeast transformation method upon enrichment of available vectors and donor E. coli strains. PMID:26849654

  10. A Simple Method for Noninvasive Quantification of Pressure Gradient Across the Pulmonary Valve

    PubMed Central

    Zhou, Xueying; Xing, Changyang; Feng, Yang; Duan, Yunyou; Zheng, Qiangsun; Wang, Zuojun; Liu, Jie; Cao, Tiesheng; Yuan, Lijun

    2017-01-01

    Pressure gradient across the pulmonary valve (PVPG) is an important hemodynamic variable used in the management of patients with cardiovascular and pulmonary disease. However, a reliable noninvasive method is unavailable. We hypothesized that a progressive Muller maneuver would elicit the pulmonary valve premature opening (PVPO) in diastole and that this event would be detectable by Doppler echocardiography. The intrathoracic pressure (ITP) decrease during this maneuver equals PVPG, which may be assessed with a custom airway pressure measurement device. A total of 102 subjects were enrolled in the study. At the earliest appearance of PVPO, the ITP decrease was recorded as the PVPG. PVPG was also simultaneously measured and compared by other two methods: right heart catheterization in 43 subjects, and routine Doppler echocardiography (pulmonary regurgitation jet) in the other 59 subjects. The results measured by different approaches were compared using the Bland-Altman analysis. PVPG assessed via PVPO showed strong agreement with PVPG measured by catheterization or routine Doppler echocardiography methods, with Lin concordance correlation coefficients of 0.91 and 0.70, respectively. In conclusion, PVPO provides a new noninvasive method of quantification of PVPG. PMID:28198458

  11. A Novel Ultrasonic Method for Characterizing Microstructural Gradients in Tubular Structures

    NASA Technical Reports Server (NTRS)

    Roth, Don J.; Carney, Dorothy V.; Baaklini, George Y.; Bodis, James R.; Rauser, Richard W.

    1998-01-01

    Ultrasonic velocity and time-of-flight (TOF) imaging that uses back surface reflections to gage volumetric material quality is highly suited for quantitative characterization of microstructural gradients including those due to pore fraction, density, fiber fraction, and chemical composition variations. However, a weakness of conventional pulse echo ultrasonic velocity and TOF imaging is that the image shows the effects of thickness as well as microstructural variations, unless the part is uniformly thick. This limits this imaging method's usefulness in practical applications. Prior studies have described a pulse echo TOF based ultrasonic imaging method that requires using a single transducer in combination with a reflector plate placed behind samples which, eliminates the effect of thickness variation in the image. In those studies, this method was successful at isolating ultrasonic variations due to material in plate like samples of silicon nitride, metal matrix composite, and polymer matrix composite. In this study, the method is engineered for inspection of more complex shaped structures- those having (hollow) tubular or curved geometry. The experimental inspection technique and results are described as applied to a polymer matrix composite "proof of concept" tube that contains machined patches of various depths and an as manufactured monolithic silicon nitride ceramic tube that might be used in "real world" applications.

  12. A Simple Method for Noninvasive Quantification of Pressure Gradient Across the Pulmonary Valve.

    PubMed

    Zhou, Xueying; Xing, Changyang; Feng, Yang; Duan, Yunyou; Zheng, Qiangsun; Wang, Zuojun; Liu, Jie; Cao, Tiesheng; Yuan, Lijun

    2017-02-15

    Pressure gradient across the pulmonary valve (PVPG) is an important hemodynamic variable used in the management of patients with cardiovascular and pulmonary disease. However, a reliable noninvasive method is unavailable. We hypothesized that a progressive Muller maneuver would elicit the pulmonary valve premature opening (PVPO) in diastole and that this event would be detectable by Doppler echocardiography. The intrathoracic pressure (ITP) decrease during this maneuver equals PVPG, which may be assessed with a custom airway pressure measurement device. A total of 102 subjects were enrolled in the study. At the earliest appearance of PVPO, the ITP decrease was recorded as the PVPG. PVPG was also simultaneously measured and compared by other two methods: right heart catheterization in 43 subjects, and routine Doppler echocardiography (pulmonary regurgitation jet) in the other 59 subjects. The results measured by different approaches were compared using the Bland-Altman analysis. PVPG assessed via PVPO showed strong agreement with PVPG measured by catheterization or routine Doppler echocardiography methods, with Lin concordance correlation coefficients of 0.91 and 0.70, respectively. In conclusion, PVPO provides a new noninvasive method of quantification of PVPG.

  13. A rapid and scalable density gradient purification method for Plasmodium sporozoites

    PubMed Central

    2012-01-01

    Background Malaria remains a major human health problem, with no licensed vaccine currently available. Malaria infections initiate when infectious Plasmodium sporozoites are transmitted by Anopheline mosquitoes during their blood meal. Investigations of the malaria sporozoite are, therefore, of clear medical importance. However, sporozoites can only be produced in and isolated from mosquitoes, and their isolation results in large amounts of accompanying mosquito debris and contaminating microbes. Methods Here is described a discontinuous density gradient purification method for Plasmodium sporozoites that maintains parasite infectivity in vitro and in vivo and greatly reduces mosquito and microbial contaminants. Results This method provides clear advantages over previous approaches: it is rapid, requires no serum components, and can be scaled to purify >107 sporozoites with minimal operator involvement. Moreover, it can be effectively applied to both human (Plasmodium falciparum, Plasmodium vivax) and rodent (Plasmodium yoelii) infective species with excellent recovery rates. Conclusions This novel method effectively purifies viable malaria sporozoites by greatly reducing contaminating mosquito debris and microbial burdens associated with parasite isolation. Large-scale preparations of purified sporozoites will allow for enhanced in vitro infections, proteomics, and biochemical characterizations. In conjunction with aseptic mosquito rearing techniques, this purification technique will also support production of live attenuated sporozoites for vaccination. PMID:23244590

  14. Semen preparation methods and sperm telomere length: density gradient centrifugation versus the swim up procedure

    PubMed Central

    Zhao, Feifei; Yang, Qingling; Shi, Senlin; Luo, Xiaoyan; Sun, Yingpu

    2016-01-01

    Previous studies have shown that both density gradient centrifugation (DGC) and swim up (SU) procedures can select spermatozoa with longer telomeres for assisted reproduction techniques (ART). However, it is unknown which approach is more effective. The aim of the present study was to compare the effects of these two methods on sperm telomere length (STL). A total of 150 normozoospermic subjects were recruited. STL, DNA fragmentation index (DFI), reactive oxygen species (ROS) content and progressive motility of semen samples were detected before and after the procedures of DGC and SU. When compared to raw semen, the average length of sperm telomeres was significantly longer after the two sperm preparation methods. However, no significant difference was found between the DGC and SU procedures. We also found that semen prepared by the two methods had lower DNA fragmentation, ROS content and sperm progressive motility. However, no significant difference was found in those parameters between the two procedures. This is the first study that compares the effects of the DGC and SU procedures on STL, and the results show that both methods can recover a sperm population with longer STL and better DNA integrity for ART. PMID:27958357

  15. An adaptive multiresolution gradient-augmented level set method for advection problems

    NASA Astrophysics Data System (ADS)

    Schneider, Kai; Kolomenskiy, Dmitry; Nave, Jean-Chtristophe

    2014-11-01

    Advection problems are encountered in many applications, such as transport of passive scalars modeling pollution or mixing in chemical engineering. In some problems, the solution develops small-scale features localized in a part of the computational domain. If the location of these features changes in time, the efficiency of the numerical method can be significantly improved by adapting the partition dynamically to the solution. We present a space-time adaptive scheme for solving advection equations in two space dimensions. The third order accurate gradient-augmented level set method using a semi-Lagrangian formulation with backward time integration is coupled with a point value multiresolution analysis using Hermite interpolation. Thus locally refined dyadic spatial grids are introduced which are efficiently implemented with dynamic quad-tree data structures. For adaptive time integration, an embedded Runge-Kutta method is employed. The precision of the new fully adaptive method is analysed and speed up of CPU time and memory compression with respect to the uniform grid discretization are reported.

  16. Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient.

    PubMed

    Trubl, Gareth; Solonenko, Natalie; Chittick, Lauren; Solonenko, Sergei A; Rich, Virginia I; Sullivan, Matthew B

    2016-01-01

    Permafrost stores approximately 50% of global soil carbon (C) in a frozen form; it is thawing rapidly under climate change, and little is known about viral communities in these soils or their roles in C cycling. In permafrost soils, microorganisms contribute significantly to C cycling, and characterizing them has recently been shown to improve prediction of ecosystem function. In other ecosystems, viruses have broad ecosystem and community impacts ranging from host cell mortality and organic matter cycling to horizontal gene transfer and reprogramming of core microbial metabolisms. Here we developed an optimized protocol to extract viruses from three types of high organic-matter peatland soils across a permafrost thaw gradient (palsa, moss-dominated bog, and sedge-dominated fen). Three separate experiments were used to evaluate the impact of chemical buffers, physical dispersion, storage conditions, and concentration and purification methods on viral yields. The most successful protocol, amended potassium citrate buffer with bead-beating or vortexing and BSA, yielded on average as much as 2-fold more virus-like particles (VLPs) g(-1) of soil than other methods tested. All method combinations yielded VLPs g(-1) of soil on the 10(8) order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g(-1) of soil among the soil types. This research provides much-needed guidelines for resuspending viruses from soils, specifically carbon-rich soils, paving the way for incorporating viruses into soil ecology studies.

  17. Mixed gradient-Tikhonov methods for solving nonlinear ill-posed problems in Banach spaces

    NASA Astrophysics Data System (ADS)

    Margotti, Fábio

    2016-12-01

    Tikhonov regularization is a very useful and widely used method for finding stable solutions of ill-posed problems. A good choice of the penalization functional as well as a careful selection of the topologies of the involved spaces is fundamental to the quality of the reconstructions. These choices can be combined with some a priori information about the solution in order to preserve desired characteristics like sparsity constraints for example. To prove convergence and stability properties of this method, one usually has to assume that a minimizer of the Tikhonov functional is known. In practical situations however, the exact computation of a minimizer is very difficult and even finding an approximation can be a very challenging and expensive task if the involved spaces have poor convexity or smoothness properties. In this paper we propose a method to attenuate this gap between theory and practice, applying a gradient-like method to a Tikhonov functional in order to approximate a minimizer. Using only available information, we explicitly calculate a maximal step-size which ensures a monotonically decreasing error. The resulting algorithm performs only finitely many steps and terminates using the discrepancy principle. In particular the knowledge of a minimizer or even its existence does not need to be assumed. Under standard assumptions, we prove convergence and stability results in relatively general Banach spaces, and subsequently, test its performance numerically, reconstructing conductivities with sparsely located inclusions and different kinds of noise in the 2D electrical impedance tomography.

  18. Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient

    PubMed Central

    Trubl, Gareth; Solonenko, Natalie; Chittick, Lauren; Solonenko, Sergei A.

    2016-01-01

    Permafrost stores approximately 50% of global soil carbon (C) in a frozen form; it is thawing rapidly under climate change, and little is known about viral communities in these soils or their roles in C cycling. In permafrost soils, microorganisms contribute significantly to C cycling, and characterizing them has recently been shown to improve prediction of ecosystem function. In other ecosystems, viruses have broad ecosystem and community impacts ranging from host cell mortality and organic matter cycling to horizontal gene transfer and reprogramming of core microbial metabolisms. Here we developed an optimized protocol to extract viruses from three types of high organic-matter peatland soils across a permafrost thaw gradient (palsa, moss-dominated bog, and sedge-dominated fen). Three separate experiments were used to evaluate the impact of chemical buffers, physical dispersion, storage conditions, and concentration and purification methods on viral yields. The most successful protocol, amended potassium citrate buffer with bead-beating or vortexing and BSA, yielded on average as much as 2-fold more virus-like particles (VLPs) g−1 of soil than other methods tested. All method combinations yielded VLPs g−1 of soil on the 108 order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g−1 of soil among the soil types. This research provides much-needed guidelines for resuspending viruses from soils, specifically carbon-rich soils, paving the way for incorporating viruses into soil ecology studies. PMID:27231649

  19. Attachment of rattlesnake venom myotoxin a to sarcoplasmic reticulum: peroxidase conjugated method.

    PubMed Central

    Tu, A. T.; Morita, M.

    1983-01-01

    Myotoxin a is a muscle-damaging toxin isolated from the venom of Crotalus atrox (western diamondback rattlesnake) and is composed of 42 amino acid residues. Earlier electron microscopic observation indicated that the toxin causes extensive swelling of the sarcoplasmic reticulum followed by disorganization of the sarcomers. In the present paper we describe the evidence for the attachment of peroxidase-conjugated myotoxin a to the membrane of sarcoplasmic reticulum of human muscle. It is thus suggested that the attachment of the toxin to the sarcoplasmic reticulum and the subsequent swelling are the first steps in myonecrosis induced by myotoxin a. Images Fig. 3 Fig. 4 Fig. 5 PMID:6661395

  20. Quantification of conjugated metabolites of drugs in biological matrices after the hydrolysis with β-glucuronidase and sufatase: a review of bio-analytical methods.

    PubMed

    Ding, Yue; Peng, Ming; Zhang, Tong; Tao, Jian-Sheng; Cai, Zhen-Zhen; Zhang, Yong

    2013-10-01

    Glucuronidation and sulfation represent two major pathways in phase II drug metabolism in humans and other mammalian species. The great majority of drugs, for example, polyphenols, flavonoids and anthraquinones, could be transformed into sulfated and glucuronidated conjugates simultaneously and extensively in vivo. The pharmacological activities of drug conjugations are normally decreased compared with those of their free forms. However, some drug conjugates may either bear biological activities themselves or serve as excellent sources of biologically active compounds. As the bioactivities of drugs are thought to be relevant to the kinetics of their conjugates, it is essential to study the pharmacokinetic behaviors of the conjugates in more detail. Unfortunately, the free forms of drugs cannot be detected directly in most cases if their glucuronides and sulfates are the predominant forms in biological samples. Nevertheless, an initial enzymatic hydrolysis step using β-glucuronidase and/or sulfatase is usually performed to convert the glucuronidated and/or sulfated conjugates to their free forms prior to the extraction, purification and other subsequent analysis steps in the literature. This review provides fundamental information on drug metabolism pathways, the bio-analytical strategies for the quantification of various drug conjugates, and the applications of the analytical methods to pharmacokinetic studies. Copyright © 2013 John Wiley & Sons, Ltd.

  1. A constrained-gradient method to control divergence errors in numerical MHD

    NASA Astrophysics Data System (ADS)

    Hopkins, Philip F.

    2016-10-01

    In numerical magnetohydrodynamics (MHD), a major challenge is maintaining nabla \\cdot {B}=0. Constrained transport (CT) schemes achieve this but have been restricted to specific methods. For more general (meshless, moving-mesh, ALE) methods, `divergence-cleaning' schemes reduce the nabla \\cdot {B} errors; however they can still be significant and can lead to systematic errors which converge away slowly. We propose a new constrained gradient (CG) scheme which augments these with a projection step, and can be applied to any numerical scheme with a reconstruction. This iteratively approximates the least-squares minimizing, globally divergence-free reconstruction of the fluid. Unlike `locally divergence free' methods, this actually minimizes the numerically unstable nabla \\cdot {B} terms, without affecting the convergence order of the method. We implement this in the mesh-free code GIZMO and compare various test problems. Compared to cleaning schemes, our CG method reduces the maximum nabla \\cdot {B} errors by ˜1-3 orders of magnitude (˜2-5 dex below typical errors if no nabla \\cdot {B} cleaning is used). By preventing large nabla \\cdot {B} at discontinuities, this eliminates systematic errors at jumps. Our CG results are comparable to CT methods; for practical purposes, the nabla \\cdot {B} errors are eliminated. The cost is modest, ˜30 per cent of the hydro algorithm, and the CG correction can be implemented in a range of numerical MHD methods. While for many problems, we find Dedner-type cleaning schemes are sufficient for good results, we identify a range of problems where using only Powell or `8-wave' cleaning can produce order-of-magnitude errors.

  2. Reduction of lateritic iron ore briquette using coal bed reductant by isothermal - temperature gradient method

    NASA Astrophysics Data System (ADS)

    Zulhan, Zulfiadi; Himawan, David Mangatur; Dimyati, Arbi

    2017-01-01

    In this study, isothermal-temperature gradient method was used to separate iron and alumina in lateritic iron ore as an alternative technique. The lateritic iron ore was ground to obtain grain size of less than 200 mesh and agglomerated in the form of cylindrical briquette using a press machine. The iron oxide in the briquette was reduced by addition of coal so that all surface of the briquette was covered by the coal. The temperature profile for the reduction process of the briquette was divided into three stages: the first stage was isothermal at 1000°C, the second stage was temperature gradient at varies heating rate of 5, 6.67 and 8.33°C/minutes from 1000 to 1400°C, and the final stage was isothermal at 1400°C. The effect of dehydroxylation of lateritic iron ore was studied as well. Aluminum distribution inside and outside the briquette was analyzed by scanning electron microscope with energy dispersive spectroscopy (SEM-EDS). The analysis results showed that the aluminum content increased from 8.01% at the outside of the briquette to 13.12% in the inside of the briquette. On contrary, iron content is higher at the outside of the briquette compared to that in the inside. These phenomena indicated that aluminum tends to migrate into the center of the briquette while iron moves outward to the surface of briquette. Furthermore, iron metallization of 91.03% could be achieved in the case of without dehydroxylation treatment. With the dehydroxylation treatment, iron metallization degree was increased up to 95.27%.

  3. A new method of edge detection based on the total horizontal derivative and the modulus of full tensor gravity gradient

    NASA Astrophysics Data System (ADS)

    Wu, Heyu; Li, Lu; Xing, Congcong; Zhang, Shuang

    2017-04-01

    With the rapid development of gravity gradient measurement, the full tensor gravity gradient data has been used more and more frequently in the edge detection. This article focuses on the problem that the effect of edge detection of deep geological body is not clear and false edges among positive and negative anomalies using the common edge detection method. We present a new edge detection method which is based on the total horizontal derivative and the modulus of full tensor gravity gradient. Comparing with the model experiments, it is proved that this method is clearer and more accurate in detecting the edges of geological body especially for the deep model with almost no false edge interference. Finally, the method is applied to the processing of the actual data in St. Georges Bay, Canada, and the edge results are satisfying.

  4. Analytical energy gradient based on spin-free infinite-order Douglas-Kroll-Hess method with local unitary transformation.

    PubMed

    Nakajima, Yuya; Seino, Junji; Nakai, Hiromi

    2013-12-28

    In this study, the analytical energy gradient for the spin-free infinite-order Douglas-Kroll-Hess (IODKH) method at the levels of the Hartree-Fock (HF), density functional theory (DFT), and second-order Møller-Plesset perturbation theory (MP2) is developed. Furthermore, adopting the local unitary transformation (LUT) scheme for the IODKH method improves the efficiency in computation of the analytical energy gradient. Numerical assessments of the present gradient method are performed at the HF, DFT, and MP2 levels for the IODKH with and without the LUT scheme. The accuracies are examined for diatomic molecules such as hydrogen halides, halogen dimers, coinage metal (Cu, Ag, and Au) halides, and coinage metal dimers, and 20 metal complexes, including the fourth-sixth row transition metals. In addition, the efficiencies are investigated for one-, two-, and three-dimensional silver clusters. The numerical results confirm the accuracy and efficiency of the present method.

  5. Gradient-augmented hybrid interface capturing method for incompressible two-phase flow

    NASA Astrophysics Data System (ADS)

    Zheng, Fu; Shi-Yu, Wu; Kai-Xin, Liu

    2016-06-01

    Motivated by inconveniences of present hybrid methods, a gradient-augmented hybrid interface capturing method (GAHM) is presented for incompressible two-phase flow. A front tracking method (FTM) is used as the skeleton of the GAHM for low mass loss and resources. Smooth eulerian level set values are calculated from the FTM interface, and are used for a local interface reconstruction. The reconstruction avoids marker particle redistribution and enables an automatic treatment of interfacial topology change. The cubic Hermit interpolation is employed in all steps of the GAHM to capture subgrid structures within a single spacial cell. The performance of the GAHM is carefully evaluated in a benchmark test. Results show significant improvements of mass loss, clear subgrid structures, highly accurate derivatives (normals and curvatures) and low cost. The GAHM is further coupled with an incompressible multiphase flow solver, Super CE/SE, for more complex and practical applications. The updated solver is evaluated through comparison with an early droplet research. Project supported by the National Natural Science Foundation of China (Grant Nos. 10972010, 11028206, 11371069, 11372052, 11402029, and 11472060), the Science and Technology Development Foundation of China Academy of Engineering Physics (CAEP), China (Grant No. 2014B0201030), and the Defense Industrial Technology Development Program of China (Grant No. B1520132012).

  6. Development of a temperature gradient focusing method for in situ extraterrestrial biomarker analysis.

    PubMed

    Danger, Grégoire; Ross, David

    2008-08-01

    Scanning temperature gradient focusing (TGF) is a recently described technique for the simultaneous concentration and separation of charged analytes. It allows for high analyte peak capacities and low LODs in microcolumn electrophoretic separations. In this paper, we present the application of scanning TGF for chiral separations of amino acids. Using a mixture of seven carboxyfluorescein succinimidyl ester-labeled amino acids (including five chiral amino acids) which constitute the Mars7 standard, we show that scanning TGF is a very simple and efficient method for chiral separations. The modulation of TGF separation parameters (temperature window, pressure scan rate, temperature range, and chiral selector concentration) allows optimization of peak efficiencies and analyte resolutions. The use of hydroxypropyl-beta-CD at low concentration (1-5 mmol/L) as a chiral selector, with an appropriate pressure scan rate ( -0.25 Pa/s) and with a low temperature range (3-25 degrees C over 1 cm) provided high resolution between enantiomers (Rs >1.5 for each pair of enantiomers) using a short, 4 cm long capillary. With these new results, the scanning TGF method appears to be a viable method for in situ trace biomarker analysis for future missions to Mars or other solar system bodies.

  7. Direct measurement of sub-surface mass change using the variable-baseline gravity gradient method

    USGS Publications Warehouse

    Kennedy, Jeffrey; Ferré, Ty P. A.; Güntner, Andreas; Abe, Maiko; Creutzfeldt, Benjamin

    2014-01-01

    Time-lapse gravity data provide a direct, non-destructive method to monitor mass changes at scales from cm to km. But, the effectively infinite spatial sensitivity of gravity measurements can make it difficult to isolate the signal of interest. The variable-baseline gravity gradient method, based on the difference of measurements between two gravimeters, is an alternative to the conventional approach of individually modeling all sources of mass and elevation change. This approach can improve the signal-to-noise ratio for many applications by removing the contributions of Earth tides, loading, and other signals that have the same effect on both gravimeters. At the same time, this approach can focus the support volume within a relatively small user-defined region of the subsurface. The method is demonstrated using paired superconducting gravimeters to make for the first time a large-scale, non-invasive measurement of infiltration wetting front velocity and change in water content above the wetting front.

  8. Structure optimization via free energy gradient method: Application to glycine zwitterion in aqueous solution

    NASA Astrophysics Data System (ADS)

    Okuyama-Yoshida, Naoto; Kataoka, Ken; Nagaoka, Masataka; Yamabe, Tokio

    2000-09-01

    The free energy gradient method was applied to the multidimensional geometry optimization of glycine zwitterion (ZW) in aqueous solution in order not only to demonstrate its applicability, but also to examine its efficiency. The method utilizes force on the free energy surface that can be directly calculated by the molecular dynamics method and the free energy perturbation theory. Then, the most stable ZW structure in aqueous solution was obtained within the tolerance assumed, and it was found that the free energy (FE) and enthalpy changes of stabilization from the initial geometry optimized in the gas phase are -0.9 and -3.5 kcal/mol, respectively, and the amino and carboxyl groups are spatially separated by each other due to their solvating with water molecules. Comparing the contributions of enthalpy and entropy to FE, the former is attributed to the main origin of FE stabilization during the optimization procedure, and it was found that solvation entropy prevents water molecules from solvating the ZW more strongly.

  9. Highly durable superhydrophobic coatings with gradient density by movable spray method

    NASA Astrophysics Data System (ADS)

    Tenjimbayashi, Mizuki; Shiratori, Seimei

    2014-09-01

    Superhydrophobic surface is expected to be applied in anti-fouling, anti-icing, and anti-bacterial. However, practical use is interrupted by low mechanical strength, time-consuming process, and limited coating substrate. Here highly durable superhydrophobic coatings were prepared by simple and novel spraying method, which sprays with changing the "spray distance between substrate and spray" (SD), named "movable spray method." We prepared the solution that changes wettability and durability with spraying distance by mixing SiO2 nanoparticles and ethyl alpha cyanoacrylate polymer (EAC). Then, we evaluated the chemical components and surface morphologies of each spraying distance coatings (0 ˜ 50 cm) by XPS, SEM, and laser scanning microscope. It revealed that surface roughness and SiO2/EAC ratio increased as the SD increases. Thus, durable superhydrophobic coatings were designed by spraying with increasing SD gradually. Glow discharge-optical emission spectrometry analysis revealed that designed coatings showed the gradual increase of SiO2/EAC ratio. As a result, coatings prepared on glass, wood, or aluminum substrates maintained their superhydrophobicity up to the abrasion at 40 kPa. This movable spray method is simple coating by the wet process and prepares robust hydrophobic coating on complex shape and large area substrates. The gradient functional surface was found to have mechanical durability and superhydrophobicity, and wide area applications will be expected.

  10. Flux measurements of volatile organic compounds at SMEAR II using surface layer gradient method

    NASA Astrophysics Data System (ADS)

    Rantala, P.; Taipale, R.; Ruuskanen, T. M.; Aalto, J.; Kajos, M. K.; Patokoski, J.; Schallhart, S.; Rinne, J.

    2012-04-01

    Volatile organic compounds (VOCs) are mostly emitted into atmosphere from natural sources. Some of the compounds, such as monoterpenes, are highly reactive and seem to have major contributions to aerosol particle formation and growth, thus these compounds are also connected to the global climate change. Approximately 50 % of the biogenic emissions is coming from the tropical rain forests, 15-20 % from the boreal forests and the rest from the other sources like fields and oceans. In order to understand seasonal and interannual changes in VOC emissions long term emission measurements would be of great importance. However, long-term VOC emission measurements are extremely sparse. Our aim is to develop reliable and feasible method to measure ecosystem scale VOC emissions by micrometeorological methods. In the past decade the disjunct eddy covariance method with proton transfer reaction quadrupole mass spectrometry (DEC/PTR-QMS) has been the method of choise for VOC flux measurements. However, automatically data post-processing, crucial for long term measurement, remains a challenge, especially in low flux conditions. To by-pass these problems we can apply a surface layer gradient technique with PTR-QMS (SLG/PTR-QMS) for long term VOC flux measurements. In this technique fluxes are obtained using measured vertical profiles on VOC concentrations with Monin-Obukhov similarity theory. Albeit more indirect method than DEC, this classical method holds promise for long term measurement. The measurements wer conducted in Hyytiälä at SMEAR II station (61° 51' N, 24° 17' E, 180 m a.m.s.l.) since summer 2010. Hyytiälä represents a typical boreal region with clear snow covered winters and annual average temperature has been approximately 3.3°C. Clear cumulative positive flux of methanol, acetaldehyde, ethanol/formic acid, acetone, MBO-fragment/isoprene, and monoterpenes were observed.

  11. Analytical method development for synthesized conjugated metabolites of trans-resveratrol, and application to pharmacokinetic studies

    PubMed Central

    Iwuchukwu, Otito F.; Sharan, Satish; Canney, Daniel J.; Nagar, Swati

    2011-01-01

    Trans -3,5,4′-trihydroxystilbene (trans-resveratrol, RES) exhibits very low bioavailability due to extensive conjugative metabolism. Whether RES metabolites exhibit pharmacologic activity is of great interest. The present study aimed at synthesis of monoconjugates of RES – the 3- and 4′ monosulfates (R3S and R4′S), and the 3- and 4′ monoglucuronides (R3G and R4′G). Synthesis, purification, and yield are described. Synthesized metabolites were utilized to develop a sensitive LC-MSn assay for direct quantitation of all analytes. The assay was validated for intra- and inter-day precision and accuracy. Synthesis of RES conjugates and development and validation of a sensitive bioanalytical assay were applied to pharmacokinetic evaluation of RES and its circulating monoconjugates in C57BL mice. The study is a first report of direct quantitation of RES monosulfates and monoglucuronides. These results will aid in characterizing the disposition of RES and its major or active metabolites in vivo. PMID:22342060

  12. Simple immunohistochemical staining method using large sized gold colloid conjugated secondary antibody.

    PubMed

    Lee, Eun Jung; Kim, Yonggoo; Lim, Jihyang; Kim, Myungshin; Kang, Chang Suk; Lee, Jae Hoon; Mok, Rak Sun; Park, Young Nam; Choi, Ha-Young; Han, Kyungja

    2007-01-01

    To test the feasibility of semiquantitative immunohistochemical staining (IHC) with large sized gold conjugated secondary antibody (gold-2 degrees Ab), we used beads covered with a known amount of primary antibody and a secondary antibody conjugated with gold colloid particles (20 and 40 nm in diameter), and we compared the results to those obtained by enzyme IHC. Beads coated with 6 graded amounts of mouse IgG molecules showed 6 levels of color intensity. The graded color intensities could readily be distinguished. The color developed as soon as we added gold-2 degrees Ab, and the intensities were stable for 1 wk. Enzyme IHC using identical beads showed dregs of pigment after incubation in DAB for 5 min. The large sized gold-2 degrees Ab showed strong signals on cell surfaces; application of the large sized gold-2 degrees Ab to paraffin-embedded tissue sections was also feasible. The color was bright red and was easier to differentiate from hemosiderin pigment than the color developed by enzyme IHC. In conclusion, gold IHC with large sized gold-2 degrees Ab is superior to enzyme IHC for quantification of antigens via IHC. Gold IHC is especially recommended for tissues with many macrophages, such as bone marrow and spleen.

  13. An enzymatic deconjugation method for the analysis of small molecule active drugs on antibody-drug conjugates

    PubMed Central

    Li, Yi; Gu, Christine; Gruenhagen, Jason; Yehl, Peter; Chetwyn, Nik P.; Medley, Colin D.

    2016-01-01

    ABSTRACT Antibody-drug conjugates (ADCs) are complex therapeutic agents that use the specific targeting properties of antibodies and the highly potent cytotoxicity of small molecule drugs to selectively eliminate tumor cells while limiting the toxicity to normal healthy tissues. Two critical quality attributes of ADCs are the purity and stability of the active small molecule drug linked to the ADC, but these are difficult to assess once the drug is conjugated to the antibody. In this study, we report a enzyme deconjugation approach to cleave small molecule drugs from ADCs, which allows the drugs to be subsequently characterized by reversed-phase high performance liquid chromatography. The model ADC we used in this study utilizes a valine-citrulline linker that is designed to be sensitive to endoproteases after internalization by tumor cells. We screened several proteases to determine the most effective enzyme. Among the 3 cysteine proteases evaluated, papain had the best efficiency in cleaving the small molecule drug from the model ADC. The deconjugation conditions were further optimized to achieve complete cleavage of the small molecule drug. This papain deconjugation approach demonstrated excellent specificity and precision. The purity and stability of the active drug on an ADC drug product was evaluated and the major degradation products of the active drug were identified. The papain deconjugation method was also applied to several other ADCs, with the results suggesting it could be applied generally to ADCs containing a valine-citrulline linker. Our results indicate that the papain deconjugation method is a powerful tool for characterizing the active small molecule drug conjugated to an ADC, and may be useful in ensuring the product quality, efficacy and the safety of ADCs. PMID:26891281

  14. A Rapid Detection Method of Brucella with Quantum Dots and Magnetic Beads Conjugated with Different Polyclonal Antibodies

    NASA Astrophysics Data System (ADS)

    Song, Dandan; Qu, Xiaofeng; Liu, Yushen; Li, Li; Yin, Dehui; Li, Juan; Xu, Kun; Xie, Renguo; Zhai, Yue; Zhang, Huiwen; Bao, Hao; Zhao, Chao; Wang, Juan; Song, Xiuling; Song, Wenzhi

    2017-03-01

    Brucella spp. are facultative intracellular bacteria that cause zoonotic disease of brucellosis worldwide. Traditional methods for detection of Brucella spp. take 48-72 h that does not meet the need of rapid detection. Herein, a new rapid detection method of Brucella was developed based on polyclonal antibody-conjugating quantum dots and antibody-modified magnetic beads. First, polyclonal antibodies IgG and IgY were prepared and then the antibody conjugated with quantum dots (QDs) and immunomagnetic beads (IMB), respectively, which were activated by N-(3-dimethylaminopropyl)- N'-ethylcar-bodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) to form probes. We used the IMB probe to separate the Brucella and labeled by the QD probe, and then detected the fluorescence intensity with a fluorescence spectrometer. The detection method takes 105 min with a limit of detection of 103 CFU/mL and ranges from 10 to 105 CFU/mL ( R 2 = 0.9983), and it can be well used in real samples.

  15. Calculation of the magnetic gradient tensor from total magnetic anomaly field based on regularized method in frequency domain

    NASA Astrophysics Data System (ADS)

    Yin, Gang; Zhang, Yingtang; Mi, Songlin; Fan, Hongbo; Li, Zhining

    2016-11-01

    To obtain accurate magnetic gradient tensor data, a fast and robust calculation method based on regularized method in frequency domain was proposed. Using the potential field theory, the transform formula in frequency domain was deduced in order to calculate the magnetic gradient tensor from the pre-existing total magnetic anomaly data. By analyzing the filter characteristics of the Vertical vector transform operator (VVTO) and Gradient tensor transform operator (GTTO), we proved that the conventional transform process was unstable which would zoom in the high-frequency part of the data in which measuring noise locate. Due to the existing unstable problem that led to a low signal-to-noise (SNR) for the calculated result, we introduced regularized method in this paper. By selecting the optimum regularization parameters of different transform phases using the C-norm approach, the high frequency noise was restrained and the SNR was improved effectively. Numerical analysis demonstrates that most value and characteristics of the calculated data by the proposed method compare favorably with reference magnetic gradient tensor data. In addition, calculated magnetic gradient tensor components form real aeromagnetic survey provided better resolution of the magnetic sources and original profile.

  16. Analytical energy gradient for the two-component normalized elimination of the small component method

    SciTech Connect

    Zou, Wenli; Filatov, Michael; Cremer, Dieter

    2015-06-07

    The analytical gradient for the two-component Normalized Elimination of the Small Component (2c-NESC) method is presented. The 2c-NESC is a Dirac-exact method that employs the exact two-component one-electron Hamiltonian and thus leads to exact Dirac spin-orbit (SO) splittings for one-electron atoms. For many-electron atoms and molecules, the effect of the two-electron SO interaction is modeled by a screened nucleus potential using effective nuclear charges as proposed by Boettger [Phys. Rev. B 62, 7809 (2000)]. The effect of spin-orbit coupling (SOC) on molecular geometries is analyzed utilizing the properties of the frontier orbitals and calculated SO couplings. It is shown that bond lengths can either be lengthened or shortened under the impact of SOC where in the first case the influence of low lying excited states with occupied antibonding orbitals plays a role and in the second case the jj-coupling between occupied antibonding and unoccupied bonding orbitals dominates. In general, the effect of SOC on bond lengths is relatively small (≤5% of the scalar relativistic changes in the bond length). However, large effects are found for van der Waals complexes Hg{sub 2} and Cn{sub 2}, which are due to the admixture of more bonding character to the highest occupied spinors.

  17. Comparison of Aura MLS stratospheric chemical gradients with north polar vortex edges calculated by two methods

    NASA Astrophysics Data System (ADS)

    Meek, C. E.; Manson, A. H.; Drummond, J. R.

    2017-10-01

    The edge of the winter polar vortex is thought to isolate chemistry between inside and outside. A way to test how accurately it is estimated is to examine chemical mixing ratios along a path that crosses its edge. Two edge methods are tested, one is the ;Q-edge; (Harvey et al., 2002), which chooses a specific streamline; the other is scaled potential vorticity, ;sPV;, which identifies an inner and outer edge depending on the local value of potential vorticity scaled according to the static stability (Manney et al., 1994). Aura MLS mixing ratios show that, statistically overall, sPV edge area agrees better with the N2O mixing ratio gradient below ∼700 K, albeit with more scatter. Finally direct comparison statistics on a few 10 day winter intervals show that the Q-edge is usually outside the sPV outer edge below potential temperature levels ∼400-500 K, agrees up to ∼700 K, and inside to ∼1200 K. Above that, both methods tend to agree again.

  18. A universal parameterized gradient-based method for photon beam field size determination.

    PubMed

    Lebron, Sharon; Yan, Guanghua; Li, Jonathan; Lu, Bo; Liu, Chihray

    2017-09-09

    To propose a universal, parameterized gradient-based method (PGM) for radiation field size determination. The PGM locates the beam profile's edge by parameterizing its penumbra region with a modified sigmoid function where the inflection point can be determined in a closed form. The parametrization was validated with filter-flattened (FF), flattening-filter-free (FFF) and wedged profiles measured on two Elekta linac models (Synergy and Versa HD). Gamma analysis with the delta dose function set to zero was used to quantitatively assess the parameterization accuracy. Field sizes of FF beams were calculated with the PGM and the full width at half maximum (FWHM) methods for comparison. To assess the consistency of the PGM and the FWHM method with geometric scaling across different depths, the calculated field size at a reference depth was scaled to other depths and compared with the field sizes calculated from the measured profiles. The method was also validated against a maximum-slope method (MSM) with wedge and FFF profiles. We also evaluated the robustness of the three methods with respect to measurement noise, varying scanning step sizes, detector characteristics and beam energy/modality. Small distance-to-agreement (0.02±0.02 mm) between the measured and parameterized penumbra region was observed for all profiles. The differences between the field sizes calculated with the FWHM method and the PGM were consistent (0.9±0.3 mm), with the FWHM method yielding larger values. With geometrical scaling, the PGM and the FWHM method produced maximum differences of 0.26 and 1.16 mm, respectively. For wedge and FFF beams, the mean differences relative to FF fields were 0.15±0.09 mm and 0.57±0.91 mm for the PGM and the MSM, respectively. The PGM was also found to produce more consistent results than the FWHM method and the MSM when measurement noise, scanning step size, detector characteristics and beam energy/modality changed. The proposed PGM is universally applicable to

  19. Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient

    DOE PAGES

    Trubl, Gareth; Solonenko, Natalie; Chittick, Lauren; ...

    2016-05-17

    Permafrost stores approximately 50% of global soil carbon (C) in a frozen form; it is thawing rapidly under climate change, and little is known about viral communities in these soils or their roles in C cycling. In permafrost soils, microorganisms contribute significantly to C cycling, and characterizing them has recently been shown to improve prediction of ecosystem function. In other ecosystems, viruses have broad ecosystem and community impacts ranging from host cell mortality and organic matter cycling to horizontal gene transfer and reprogramming of core microbial metabolisms. Here we developed an optimized protocol to extract viruses from three types ofmore » high organic-matter peatland soils across a permafrost thaw gradient (palsa, moss-dominated bog, and sedge-dominated fen). Three separate experiments were used to evaluate the impact of chemical buffers, physical dispersion, storage conditions, and concentration and purification methods on viral yields. The most successful protocol, amended potassium citrate buffer with bead-beating or vortexing and BSA, yielded on average as much as 2-fold more virus-like particles (VLPs) g–1of soil than other methods tested. All method combinations yielded VLPs g–1of soil on the 108order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g–1of soil among the soil types. In conclusion, this research provides much-needed guidelines for resuspending viruses from soils, specifically carbon-rich soils, paving the way for incorporating viruses into soil ecology studies.« less

  20. Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient

    SciTech Connect

    Trubl, Gareth; Solonenko, Natalie; Chittick, Lauren; Solonenko, Sergei A.; Rich, Virginia I.; Sullivan, Matthew B.

    2016-05-17

    Permafrost stores approximately 50% of global soil carbon (C) in a frozen form; it is thawing rapidly under climate change, and little is known about viral communities in these soils or their roles in C cycling. In permafrost soils, microorganisms contribute significantly to C cycling, and characterizing them has recently been shown to improve prediction of ecosystem function. In other ecosystems, viruses have broad ecosystem and community impacts ranging from host cell mortality and organic matter cycling to horizontal gene transfer and reprogramming of core microbial metabolisms. Here we developed an optimized protocol to extract viruses from three types of high organic-matter peatland soils across a permafrost thaw gradient (palsa, moss-dominated bog, and sedge-dominated fen). Three separate experiments were used to evaluate the impact of chemical buffers, physical dispersion, storage conditions, and concentration and purification methods on viral yields. The most successful protocol, amended potassium citrate buffer with bead-beating or vortexing and BSA, yielded on average as much as 2-fold more virus-like particles (VLPs) g–1of soil than other methods tested. All method combinations yielded VLPs g–1of soil on the 108order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g–1of soil among the soil types. In conclusion, this research provides much-needed guidelines for resuspending viruses from soils, specifically carbon-rich soils, paving the way for incorporating viruses into soil ecology studies.

  1. Quantitative planar imaging method for measurement of renal activity by using a conjugate-emission image and transmission data.

    PubMed

    Kojima, A; Ohyama, Y; Tomiguchi, S; Kira, M; Matsumoto, M; Takahashi, M; Motomura, N; Ichihara, T

    2000-03-01

    We are proposing a method to accurately measure renal activity in renography using Tc-99m labeled tracers. This method uses a conjugate-view image and transmission data for attenuation correction, the triple energy window (TEW) method for scatter correction, and background correction techniques that consider the source volume for accurate background activity correction. To examine this method in planar imaging, we performed two renal phantom studies with various uniform background activity concentrations. One study used two ideal box-shaped kidney phantoms with a thickness of 2 or 4 cm in a water tank and the other study employed two real kidney-shaped phantoms in a fillable abdominal cavity. For these studies the kidney phantom-to-background activity concentration ratio (S) was changed from 5 to infinity. The transmission data were obtained with an external Tc-99m line array source. The anterior- and posterior-view emission images were acquired with a dual-headed gamma camera simultaneously and the TEW method was used to correct scatter for the emission and transmission images. The results showed that this method with both the accurate background correction and scatter correction could give depth-independent count rates and could estimate the true count rate with errors of less than 5% for all S values. However, if either accurate background correction or scatter correction was performed alone, the absolute error increased to about 50% for the smaller S values. Our proposed method allows one to accurately and simply measure the renal radioactivity by planar imaging using the conjugate-emission image and transmission data.

  2. New application of a subcellular fractionation method to kidney and testis for the determination of conjugated linoleic acid in selected cell organelles of healthy and cancerous human tissues.

    PubMed

    Hoffmann, Kristina; Blaudszun, Jörg; Brunken, Claus; Höpker, Wilhelm-Wolfgang; Tauber, Roland; Steinhart, Hans

    2005-03-01

    To clarify the mechanism of the anticarcinogenic effect of conjugated linoleic acid (CLA), its intracellular distribution needs to be determined. Subcellular fractionation using centrifugation techniques is a method that is frequently used for isolation of cell organelles from different tissues. But as the size and density of the organelles differ, the method needs to be optimised for every type of tissue. The novelty of this study is the application of a subcellular fractionation method to human healthy and cancerous renal and testicular tissue. Separation of total tissue homogenate into nuclei, cytosol, and a mixture of mitochondria and plasma membranes was achieved by differential centrifugation. As mitochondria and plasma membranes seemed to be too similar in size and weight to be separated by differential centrifugation, discontinuous density-gradient centrifugation was carried out successfully. The purity of the subcellular fractions was checked by measuring the activity of marker enzymes. All fractions were highly enriched in their corresponding marker enzyme. However, the nuclear fractions of kidney and renal cell carcinoma were slightly contaminated with mitochondria and plasma membrane fractions of all tissues with lysosomes. The fraction designated the cytosolic fraction contained not only cytosol, but also microsomes and lysosomes. The CLA contents of the subcellular fractions were in the range 0.13-0.37% of total fatty acids and were lowest in the plasma membrane fractions of all types of tissue studied. C16:0, C18:0, C18:1 c9, C18:2 n-6, and C20:4 n-6 were found to be the major fatty acids in all the subcellular fractions studied. However, marked variations in fatty acid content between subcellular fractions and between types of tissue were detectable. Because of these differences between tissues, no general statement on characteristic fatty acid profiles of single subcellular fractions is possible.

  3. Biogenic volatile organic compound emissions during BEARPEX 2009 measured by eddy covariance and flux-gradient similarity methods

    NASA Astrophysics Data System (ADS)

    Park, J.-H.; Fares, S.; Weber, R.; Goldstein, A. H.

    2014-01-01

    The Biosphere Effects on AeRosols and Photochemistry EXperiment (BEARPEX) took place in Blodgett Forest, a Ponderosa pine forest in the Sierra Nevada of California, USA, during summer 2009. We deployed a proton transfer reaction-quadrupole mass spectrometer (PTR-QMS) to measure fluxes and concentrations of biogenic volatile organic compounds (BVOCs). Eighteen ion species, including the major BVOC expected at the site, were measured sequentially at 5 heights to observe their vertical gradient from the forest floor to above the canopy. Fluxes of the 3 dominant BVOCs methanol, 2-Methyl-3-butene-2-ol (MBO), and monoterpenes were measured above the canopy by the disjunct eddy covariance (EC) method. Canopy-scale fluxes were also determined by the flux-gradient similarity method (K-theory). A universal K (Kuniv) was determined as the mean of individual K's calculated from the measured fluxes divided by vertical gradients for methanol, MBO, and monoterpenes. This Kuniv was then multiplied by the gradients of each observed ion species to compute their fluxes. The flux-gradient similarity method showed very good agreement with the disjunct EC method. Fluxes are presented for all measured species and compared to historical measurements from the same site, and used to test emission algorithms used to model fluxes at the regional scale. MBO was the dominant emission observed, followed by methanol, monoterpenes, acetone, and acetaldehyde. The flux-gradient similarity method is shown to be tenable, and we recommend its use, especially in experimental conditions when fast measurement of BVOC species is not available.

  4. Method of diffusive gradients in thin films (DGT) compared with other soil testing methods to predict uranium phytoavailability.

    PubMed

    Vandenhove, H; Antunes, K; Wannijn, J; Duquène, L; Van Hees, M

    2007-02-15

    The measurement of diffusive gradients in thin films (DGT) has been proposed as a surrogate for metal uptake by plants. A small-scale experiment was performed to test the predictive capacity of the DGT method with respect to uranium availability and uptake by ryegrass. Correlation analyses were performed to compare the results obtained with the DGT device with more conventional bioavailability indices - concentration of uranium in pore water or in selective extracts. Six soils with different uranium contamination history and with distinct soil characteristics were used for the availability tests and the uptake experiment. The four uranium bioavailability indices screened were highly correlated, indicating that at least partially comparable uranium pools were assessed. The uranium concentration in the pore water was a better predictor for uranium uptake by ryegrass than amounts of uranium recovered following extraction with 0.11 M CH3COOH or 0.4 M MgCl2, the fractions considered exchangeable according to, respectively, the BCR or NIST standardized sequential extraction methods. The DGT measured concentration, C(DGT), was also highly correlated with plant uptake but the significance level was sensitive to the value of the diffusion coefficient (pH depend or not) used to calculate C(DGT). From the results obtained it could not be concluded that the DGT method would have an additional value in assessing uranium bioavailability.

  5. On the constrained minimization of smooth Kurdyka—Łojasiewicz functions with the scaled gradient projection method

    NASA Astrophysics Data System (ADS)

    Prato, Marco; Bonettini, Silvia; Loris, Ignace; Porta, Federica; Rebegoldi, Simone

    2016-10-01

    The scaled gradient projection (SGP) method is a first-order optimization method applicable to the constrained minimization of smooth functions and exploiting a scaling matrix multiplying the gradient and a variable steplength parameter to improve the convergence of the scheme. For a general nonconvex function, the limit points of the sequence generated by SGP have been proved to be stationary, while in the convex case and with some restrictions on the choice of the scaling matrix the sequence itself converges to a constrained minimum point. In this paper we extend these convergence results by showing that the SGP sequence converges to a limit point provided that the objective function satisfies the Kurdyka-Łojasiewicz property at each point of its domain and its gradient is Lipschitz continuous.

  6. Vision system for classification of metallic tokens using the selective stereo gradient method

    NASA Astrophysics Data System (ADS)

    Adameck, Markus; Hossfeld, Michael; Eich, Manfred

    2002-03-01

    This paper presents a vision system whose purpose is to detect topographies of high reflective, metallic surfaces of minted tokens. We call this technique 'Selective Stereo Gradient Method' (SSGM). The objective is to decide whether the token belongs to a reference class or not. The most important property of the SSGM is that the classification can not be deceived by a photographic image and hence yields high fraud protection. To achieve this a 3 sector 120# LED illumination is used for generating three images under different illumination directions. The comparison between these three sequentially taken images leads to a discrimination between a real object with 3 D topography and a photographic image. The experimental setup and special illumination conditions are described. Rotation and translation invariance of the recognition and classification process are implemented. This is achieved by image transformation into a suitable coordinate system. A specimen will be identified to belong to the class of interest if, in a subsequent template matching step, selected patterns taken from the class reference object, can be successfully identified. If a first pattern is found additional patterns will be searched for. The classification statistics results will be reported for metallic tokens.

  7. A Novel Method Of Gradient Forming and Fluid Manipulation in Reduced Gravity Environments

    NASA Technical Reports Server (NTRS)

    Ramachandran N.; Leslie, F.

    1999-01-01

    The use of magnetic fields to control the motion and position of non-conducting liquids has received growing interest in recent times. The possibility of using the forces exerted by a nonuniform magnetic field on a ferrofluid to not only achieve fluid manipulation but also to actively control fluid motion makes it an attractive candidate for applications such as heat transfer in space systems. Terrestrial heat transfer equipment often relies on the normal gravitational force to hold liquid in a desired position or to provide a buoyant force to enhance the heat transfer rate. The residual gravitational force present in a space environment may no longer serve these useful functions and other forces, such as surface tension, can play a significant role in determining heat transfer rates. Although typically overwhelmed by gravitational forces in terrestrial applications, the body force induced in a ferrofluid by a nonuniform magnetic field can help to achieve these objectives in a microgravity environment. This paper will address the fluid manipulation aspect and will comprise of results from model fluid experiments and numerical modeling of the problem. Results from a novel method of forming concentration gradients that are applicable to low gravity applications will be presented. The ground based experiments are specifically tailored to demonstrate the magnetic manipulation capability of a ferrofluid and show that gravitational effects can be countered in carefully designed systems. The development of governing equations for the system will be presented along with a sampling of numerical results.

  8. Synthesis and crystal growth of Mg2Si by the liquid encapsulated vertical gradient freezing method

    NASA Astrophysics Data System (ADS)

    Nakagawa, Reo; Katsumata, Hiroshi; Hashimoto, Satoshi; Sakuragi, Shiro

    2015-08-01

    The synthesis of Mg2Si bulk crystals was performed by the vertical gradient freezing method using a KCl-MgCl2 eutectic liquid encapsulant. Stoichiometric polycrystalline Mg2Si bulk crystals were successfully grown by changing the composition ratio of starting Mg and Si powders (Mg/Si) from 2.0 to 3.5. A chemical reaction between Mg2Si and the crucible materials was inhibited using encapsulant materials, and the contamination by K or Cl originating from the encapsulant materials was not detected in almost all the samples. However, Mg evaporation could not be prevented completely during the synthesis and crystal growth. The optical band-gap energy of Mg2Si bulk crystals became minimal (0.79 eV) at a Mg/Si ratio of 2.5, at which the maximum electron mobility of 202 cm2·V-1·s-1 was obtained. These results indicate that the composition ratio of Mg/Si = 2.5 for starting Mg and Si powders was optimal for synthesizing Mg2Si bulk crystals with high crystalline quality.

  9. Recovery of Manganese Ore Tailings by High-Gradient Magnetic Separation and Hydrometallurgical Method

    NASA Astrophysics Data System (ADS)

    Zhang, Xiufeng; Tan, Xiumin; Yi, Yuejun; Liu, Weizao; Li, Chun

    2017-08-01

    With the depletion of high-grade manganese ores, Mn ore tailings are considered valuable secondary resources. In this study, a process combining high-gradient magnetic separation (HGMS) with hydrometallurgical methods is proposed to recycle fine-grained Mn tailings. The Mn tailings were treated by HGMS at 12,500 G to obtain a Mn concentrate of 30% Mn with the recovery efficiency of 64%. The Mn concentrate could be used in the ferromanganese industry. To recover Mn further, the nonmagnetic fraction was leached by SO2 in an H2SO4 solution. Hydrogen peroxide was added to the leachate to oxidize Fe2+ to Fe3+, and the solution pH was adjusted to 5.0-5.5 with ammonia to remove Al, Fe, and Si impurities. The purified solution was reacted with NH4HCO3, and a saleable product of MnCO3 with 97.9% purity was obtained. The combined process can be applied to Mn recovery from finely dispersed weakly magnetic Mn ores or tailings.

  10. Gradients for two-component quasirelativistic methods. Application to dihalogenides of element 116

    NASA Astrophysics Data System (ADS)

    van Wüllen, Christoph; Langermann, Norbert

    2007-03-01

    The authors report the implementation of geometry gradients for quasirelativistic two-component Hartree-Fock and density functional methods using either the zero-order regular approximation Hamiltonian or spin-dependent effective core potentials. The computational effort of the resulting program is comparable to that of corresponding nonrelativistic calculations, as it is dominated by the evaluation of derivative two-electron integrals, which is the same for both types of calculations. Besides the implementation of derivatives of matrix elements of the one-particle Hamiltonian with respect to nuclear displacements, the calculation of the derivative exchange-correlation energy for the open shell case involves complicated expressions because of the noncollinear approach chosen to define the spin density. A pilot application to dihalogenides of element 116 shows how spin-orbit coupling strongly affects the chemistry of the superheavy p-block elements. While these molecules are bent at a scalar-relativistic level, spin-orbit coupling is so strong that only the 7p3/2 atomic orbitals of element 116 are involved in bonding, which favors linear molecular geometries for dihalogenides with heavy terminal halogen atoms.

  11. Determination of the concentration dependence of polyelectrolyte diffusion coefficients by application of the Boltzmann gradient method.

    PubMed

    Wagner, A T; Kohler, H-H

    2008-03-15

    The concentration dependence of a polyelectrolyte diffusion coefficient in aqueous low salt solution (KCl, 1 mM) is determined from a single dynamic gradient experiment. The Boltzmann method is applied to calculate the diffusion coefficient. A special diffusion cell is constructed that minimizes aberrations in the optical detection of the polyion concentration profile. Bovine serum albumin (BSA) is chosen as a model polyion. To get information about the diffusion process down to very small polyion concentrations, the BSA molecule is fluorescently labeled. The fluorescence intensity is used as a measure of the polyion concentration. The change of the polyion net charge caused by labeling is discussed. The cell is illuminated by an LED, and the fluorescence intensity profile is detected by a CCD camera. Experiments at 5 and 17 degrees C show that the diffusion coefficient of labeled BSA remains constant in the very low polyion concentration range below a threshold of about 1.5 g/l. This is in contradiction to the linear concentration dependence of polyion diffusion coefficients at very low concentrations often postulated in the literature without reference to direct experimental evidence. Our finding is confirmed by dynamic light scattering experiments published recently. An explanation for this behavior based on a modified Donnan osmotic compressibility approach is given.

  12. Development and application of a gradient method for solving differential games

    NASA Technical Reports Server (NTRS)

    Roberts, D. A.; Montgomery, R. C.

    1971-01-01

    A technique for solving n-dimensional games is developed and applied to two pursuit-evasion games. The first is a two-dimensional game similar to the homicidal chauffeur but modified to resemble an airplane-helicopter engagement. The second is a five-dimensional game of two airplanes at constant altitude and with thrust and turning controls. The performance function to be optimized by the pursuer and evader was the distance between the evader and a given target point in front of the pursuer. The analytic solution to the first game reveals that both unique and nonunique solutions exist. A comparison between the gradient results and the analytic solution shows a dependence on the nominal controls in regions where nonunique solutions exist. In the unique solution region, the results from the two methods agree closely. The results for the five-dimensional two-airplane game are also shown to be dependent on the nominal controls selected and indicate that initial conditions are in a region of nonunique solutions.

  13. A Novel Method Of Gradient Forming and Fluid Manipulation in Reduced Gravity Environments

    NASA Technical Reports Server (NTRS)

    Ramachandran N.; Leslie, F.

    1999-01-01

    The use of magnetic fields to control the motion and position of non-conducting liquids has received growing interest in recent times. The possibility of using the forces exerted by a nonuniform magnetic field on a ferrofluid to not only achieve fluid manipulation but also to actively control fluid motion makes it an attractive candidate for applications such as heat transfer in space systems. Terrestrial heat transfer equipment often relies on the normal gravitational force to hold liquid in a desired position or to provide a buoyant force to enhance the heat transfer rate. The residual gravitational force present in a space environment may no longer serve these useful functions and other forces, such as surface tension, can play a significant role in determining heat transfer rates. Although typically overwhelmed by gravitational forces in terrestrial applications, the body force induced in a ferrofluid by a nonuniform magnetic field can help to achieve these objectives in a microgravity environment. This paper will address the fluid manipulation aspect and will comprise of results from model fluid experiments and numerical modeling of the problem. Results from a novel method of forming concentration gradients that are applicable to low gravity applications will be presented. The ground based experiments are specifically tailored to demonstrate the magnetic manipulation capability of a ferrofluid and show that gravitational effects can be countered in carefully designed systems. The development of governing equations for the system will be presented along with a sampling of numerical results.

  14. Microfluidic gradient PCR (MG-PCR): a new method for microfluidic DNA amplification.

    PubMed

    Zhang, Chunsun; Xing, Da

    2010-02-01

    This study develops a new microfluidic DNA amplification strategy for executing parallel DNA amplification in the microfluidic gradient polymerase chain reaction (MG-PCR) device. The developed temperature gradient microfluidic system is generated by using an innovative fin design. The device mainly consists of modular thermally conductive copper flake which is attached onto a finned aluminum heat sink with a small fan. In our microfluidic temperature gradient prototype, a non-linear temperature gradient is produced along the gradient direction. On the copper flake of length 45 mm, width 40 mm and thickness 4 mm, the temperature gradient easily spans the range from 97 to 52 degrees Celsius. By making full use of the hot (90-97 degrees Celsius) and cold (60-70 degrees Celsius) regions on the temperature gradient device, the parallel, two-temperature MG-PCR amplification is feasible. As a demonstration, the MG-PCR from three parallel reactions of 112-bp Escherichia coli DNA fragment is performed in a continuous-flow format, in which the flow of the PCR reagent in the closed loop is induced by the buoyancy-driven nature convection. Although the prototype is not optimized, the MG-PCR amplification can be completed in less than 45 min. However, the MG-PCR thermocycler presented herein can be further scaled-down, and thus the amplification times and reagent consumption can be further reduced. In addition, the currently developed temperature gradient technology can be applied onto other continuous-flow MG-PCR systems or used for other analytical purposes such as parallel and combination measurements, and fluorescent melting curve analysis.

  15. Investigation of intermolecular interactions between single walled nanotubes and conjugated oligomers using the dispersion-corrected DFT methods

    NASA Astrophysics Data System (ADS)

    Lagowski, Jolanta B.; Aljohani, Suad; Khan, M. Zahidul H.; Zhao, Yuming

    The area of carbon nanotubes (CNT)-polymer composites has been progressing rapidly in recent years. Pure CNT and CNT-polymer composites have many useful (industry related) properties: ranging from electronic electrical conductivity to superior strength. However the full potential of using CNTs as reinforcements (in say a polymer matrix) has been severely limited because of complications associated with the dispersion of CNTs. CNTs tend to entangle with each other forming materials that have properties that fall short of the expectations. The goal of this work is to identify the type of conjugated oligomers that are best suited for the dispersion of single walled CNT (SWCNT). For this purpose, various methods of dispersion corrected density functional theory (DFT-D/B97D, /WB97XD, /CAM-B3LYP) have been used to investigate the interaction between the SWCNT and the organic conjugated oligomers with different end groups (aldehyde (ALD) and dithiafulvenyl (DTF)). We investigate the effect of intermolecular interactions on the structure, polarity and energetics of the oligomers and SWCNT combinations. The comparison of results obtained using different DFT approximations is made. Our results show that DFT-endcapped oligomer interact more strongly with CNT than ALD-endcapped oligomer. The financial support from NSERC, SACBC and Memorial University and the computational resources from Compute Canada were received.

  16. Convergence of the gradient projection method and Newton's method as applied to optimization problems constrained by intersection of a spherical surface and a convex closed set

    NASA Astrophysics Data System (ADS)

    Chernyaev, Yu. A.

    2016-10-01

    The gradient projection method and Newton's method are generalized to the case of nonconvex constraint sets representing the set-theoretic intersection of a spherical surface with a convex closed set. Necessary extremum conditions are examined, and the convergence of the methods is analyzed.

  17. Poblano v1.0 : a Matlab toolbox for gradient-based optimization.

    SciTech Connect

    Dunlavy, Daniel M.; Acar, Evrim; Kolda, Tamara Gibson

    2010-03-01

    We present Poblano v1.0, a Matlab toolbox for solving gradient-based unconstrained optimization problems. Poblano implements three optimization methods (nonlinear conjugate gradients, limited-memory BFGS, and truncated Newton) that require only first order derivative information. In this paper, we describe the Poblano methods, provide numerous examples on how to use Poblano, and present results of Poblano used in solving problems from a standard test collection of unconstrained optimization problems.

  18. Parameter estimation with a novel gradient-based optimization method for biological lattice-gas cellular automaton models.

    PubMed

    Mente, Carsten; Prade, Ina; Brusch, Lutz; Breier, Georg; Deutsch, Andreas

    2011-07-01

    Lattice-gas cellular automata (LGCAs) can serve as stochastic mathematical models for collective behavior (e.g. pattern formation) emerging in populations of interacting cells. In this paper, a two-phase optimization algorithm for global parameter estimation in LGCA models is presented. In the first phase, local minima are identified through gradient-based optimization. Algorithmic differentiation is adopted to calculate the necessary gradient information. In the second phase, for global optimization of the parameter set, a multi-level single-linkage method is used. As an example, the parameter estimation algorithm is applied to a LGCA model for early in vitro angiogenic pattern formation.

  19. Three-dimensional lattice Boltzmann method benchmarks between color-gradient and pseudo-potential immiscible multi-component models

    NASA Astrophysics Data System (ADS)

    Leclaire, Sébastien; Parmigiani, Andrea; Chopard, Bastien; Latt, Jonas

    In this paper, a lattice Boltzmann color-gradient method is compared with a multi-component pseudo-potential lattice Boltzmann model for two test problems: a droplet deformation in a shear flow and a rising bubble subject to buoyancy forces. With the help of these two problems, the behavior of the two models is compared in situations of competing viscous, capillary and gravity forces. It is found that both models are able to generate relevant scientific results. However, while the color-gradient model is more complex than the pseudo-potential approach, numerical experiments show that it is also more powerful and suffers fewer limitations.

  20. Conjugate Reinforcement.

    ERIC Educational Resources Information Center

    Lewis, Richard F.

    Conjugate reinforcement is a new attention measure which has emerged from experimental psychology. It can provide accurate measurement of a subject's attention to a stimulus. In conjugate reinforcement, the duration of the stimulus varies directly and immediately with the subject's rate of response. In this process, the subject must demonstrate…

  1. Microencapsulation of conjugated linolenic acid-rich pomegranate seed oil by an emulsion method.

    PubMed

    Sen Gupta, Surashree; Ghosh, Santinath; Maiti, Prabir; Ghosh, Mahua

    2012-12-01

    Controlled release of food ingredients and their protection from oxidation are the key functionality provided by microencapsulation. In the present study, pomegranate seed oil, rich in conjugated linolenic acid, was microencapsulated. As encapsulating agent, sodium alginate or trehalose was used. Calcium caseinate was used as the emulsifier. Performances of the two encapsulants were compared in respect of the rate of release of core material from the microcapsules and stability of microcapsules against harsh conditions. Microencapsulation was carried out by preparation of an emulsion containing calcium caseinate as the emulsion stabilizer and a water-soluble carbohydrate (either sodium alginate or trehalose) as the encapsulant. An oil-in-water emulsion was prepared with pomegranate seed oil as the inner core material. The emulsion was thereby freeze-dried and the dried product pulverized. External morphology of the microcapsules was studied under scanning electron microscope. Micrographs showed that both types of microcapsules had uneven surface morphology. Release rate of the microcapsules was studied using UV-spectrophotometer. Trehalose-based microcapsules showed higher release rate. On subjecting the microcapsules at 110 °C for specific time periods, it was observed that sodium alginate microcapsules retained their original properties. Hence, we can say that sodium alginate microcapsules are more heat resistant than trehalose microcapsules.

  2. Spectroscopic and molecular modeling methods to study the interaction between naphthalimide-polyamine conjugates and DNA.

    PubMed

    Tian, Zhiyong; Huang, Yingying; Zhang, Yan; Song, Lina; Qiao, Yan; Xu, Xuejun; Wang, Chaojie

    2016-05-01

    The effect of polyamine side chains on the interaction between naphthalimide-polyamine conjugates (1-7) and herring sperm DNA was studied by UV/vis absorption and fluorescent spectra under physiological conditions (pH=7.4). The diverse spectral data and further molecular docking simulation in silico indicated that the aromatic moiety of these compounds could intercalate into the DNA base pairs while the polyamine motif might simultaneously locate in the minor groove. The triamine compound 7 can interact more potently with DNA than the corresponding diamine compounds (1-6). The presence of the bulky terminal group in the diamine side chain reduced the binding strength of compound 1 with DNA, compared to other diamine compounds (2-6). In addition, the increasing methylene number in the diamine backbone generally results in the elevated binding constant of compounds-DNA complex. The fluorescent tests at different temperature revealed that the quenching mechanism was a static type. The binding constant and thermodynamic parameter showed that the binding strength and the type of interaction force, associated with the side chains, were mainly hydrogen bonding and hydrophobic force. And the calculated free binding energies of molecular docking are generally consistent with the stability of polyamine-DNA complexes. The circular dichroism assay about the impact of compounds 1-7 on DNA conformation testified the B to A-like conformational change. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Development of morin-conjugated Au nanoparticles: Exploring the interaction efficiency with BSA using spectroscopic methods

    NASA Astrophysics Data System (ADS)

    Yue, Hua-Li; Hu, Yan-Jun; Huang, Hong-Gui; Jiang, Shan; Tu, Bao

    2014-09-01

    In order to enhance its interaction efficiency with biomacromolecules for the usage as a therapeutic agent, we have conjugated morin, an antioxidant activity and anti-tumor drug, with citrate-coated Au nanoparticles (M-C-AuNPs). M-C-AuNPs were prepared by reducing chloroauric acid using trisodium citrate in the boiling condition, and the resulted M-C-AuNPs were characterized by UV-vis absorption spectroscopy, Transmission Electron Microscopy (TEM), X-ray diffraction (XRD) and FTIR analysis. In this article, UV-vis absorption spectroscopy in combination with fluorescence spectroscopy, and circular dichroism (CD) spectroscopy were employed to investigate the interactions between M-C-AuNPs and bovine serum albumin (BSA), C-AuNPs and BSA in a phosphate buffer at pH 7.4. By comparing the quenching constant KSV, effective quenching constant Ka, binding constant Kb and the number of binding sites n, it is clearly suggested that M-C-AuNPs could enhance the binding force of morin with BSA, which would pave the way for the design of nanotherapeutic agents with improved functionality.

  4. Study on the interaction of anthracenyl-methyl homospermidine conjugate (ANTMHspd) with DNA by spectroscopic methods.

    PubMed

    Tian, Zhiyong; Zhao, Luyao; Dong, Huanyang; Zhang, Yan; Zhang, Yijuan; Ren, Qianlei; Shao, Shuangyu; Huang, Yingying; Song, Lina; Guo, Tao; Xu, Xuejun; Wang, Chaojie

    2017-04-01

    The interaction between anthracenyl-methyl homospermidine conjugate (ANTMHspd) with herring sperm DNA was investigated by UV/vis absorption, fluorescent spectra, circular dichroism (CD) spectroscopy and (1)HNMR under physiological conditions (pH=7.4). The observed hypochromism effect and fluorescence quenching of ANTMHspd by DNA, and the displacement of EB from DNA-EB system by ANTMHspd suggested that ANTMHspd might interact with DNA by the combined mode of intercalation and groove binding. Further fluorescent tests at different temperatures revealed that the quenching mechanism was a static type. The quenching constant, binding constant and thermodynamic parameter obtained from fluorescence showed that the type of interaction force included mainly hydrogen bonding and van der Waals, which promoted the binding process. The CD test revealed that ANTMHspd could cause the B to A-like conformational change while ANTMHspd is not a typical DNA intercalator. The (1)H NMR tests showed that ANTMHspd partially intercalated DNA. The effect of NaCl and KI on ANTMHspd-DNA interaction provided additional evidences of intercalation. Molecular docking simulation was carried out and the docking model in silico suggested that the binding modes of ANTMHspd and DNA were groove binding and intercalation, with the anthracene moiety inserted in DNA base pairs and the polyamine chain embedded in the DNA groove. Copyright © 2017. Published by Elsevier B.V.

  5. Solvent effects in time-dependent self-consistent field methods. II. Variational formulations and analytical gradients

    SciTech Connect

    Bjorgaard, J. A.; Velizhanin, K. A.; Tretiak, S.

    2015-08-06

    This study describes variational energy expressions and analytical excited state energy gradients for time-dependent self-consistent field methods with polarizable solvent effects. Linear response, vertical excitation, and state-specific solventmodels are examined. Enforcing a variational ground stateenergy expression in the state-specific model is found to reduce it to the vertical excitation model. Variational excited state energy expressions are then provided for the linear response and vertical excitation models and analytical gradients are formulated. Using semiempiricalmodel chemistry, the variational expressions are verified by numerical and analytical differentiation with respect to a static external electric field. Lastly, analytical gradients are further tested by performing microcanonical excited state molecular dynamics with p-nitroaniline.

  6. Solvent effects in time-dependent self-consistent field methods. II. Variational formulations and analytical gradients

    DOE PAGES

    Bjorgaard, J. A.; Velizhanin, K. A.; Tretiak, S.

    2015-08-06

    This study describes variational energy expressions and analytical excited state energy gradients for time-dependent self-consistent field methods with polarizable solvent effects. Linear response, vertical excitation, and state-specific solventmodels are examined. Enforcing a variational ground stateenergy expression in the state-specific model is found to reduce it to the vertical excitation model. Variational excited state energy expressions are then provided for the linear response and vertical excitation models and analytical gradients are formulated. Using semiempiricalmodel chemistry, the variational expressions are verified by numerical and analytical differentiation with respect to a static external electric field. Lastly, analytical gradients are further tested by performingmore » microcanonical excited state molecular dynamics with p-nitroaniline.« less

  7. Nitric oxide fluxes from an agricultural soil using a flux-gradient method

    NASA Astrophysics Data System (ADS)

    Taylor, N. M.; Wagner-Riddle, C.; Thurtell, G. W.; Beauchamp, E. G.

    1999-05-01

    Soil emission of nitric oxide may be a significant source of NOx in rural areas. Agricultural practices may enhance these emissions by addition of nitrogen fertilizers. A system that enables continuous measurement of NO fluxes from agricultural surfaces using the flux-gradient method was developed. Hourly differences in NO concentrations in air sampled at two intake heights (0.6 and 1 m) were determined using a chemiluminescence analyzer. Eddy diffusivities were determined using wind profiles (cup anemometers), and stability corrections calculated using a 5 cm path sonic anemometer. Fast switching of sampling between air intake heights (every 30 s) and determination of concentration values at a frequency of 2 Hz minimized the errors due to fluctuations in background concentration. Low travel times for air samples in the tubing (˜8 s) were estimated to result in small errors in flux values (<0.5 ng N m-2 s-1) due to chemical reactions. The overall resolution of the system was estimated as ˜1 ng N m-2s-1. NO fluxes from a bare soil were measured quasi-continuously from January to June 1995 at Elora, Canada, comprising a total of 1833 hourly values. Daily NO fluxes before nitrogen fertilization were small, increasing after nitrogen fertilizer was added (>10 ng N m-2 s-1). Monthly NO fluxes estimated were similar to those observed in previous studies. The designed system could be easily modified to measure NOx and NO fluxes by using an additional chemiluminescence analyzer. The system also could be adapted to measure fluxes sequentially from various plots, enabling testing of agricultural practices on NO emissions.

  8. Can the hybrid meta GGA and DFT-D methods describe the stacking interactions in conjugated polymers?

    PubMed

    Dkhissi, Ahmed; Ducéré, Jean Marie; Blossey, Ralf; Pouchan, Claude

    2009-06-01

    Newly developed hybrid meta density functionals and density functionals augmented by a classical London dispersion term have been systematically applied for the description of stacking energy and intermolecular distance of thiophene dimer and substituted thiophene dimer. The performance of the various approaches is compared with the benchmark ab-initio calculations done with CCSD(T) (Tsuzuki et al., JACS 2002, 124, 12200). Our results indicate that, contrary to the previous DFT methods which are not reliable, the new generation of DFT performs better the stacking interactions. These functionals, and especially those with an empirical correction, are suitable for general application in conducting polymers and, in particular, the modeling of solid state in which the overlap of Pi-Pi interactions between the conjugated chains is important. 2008 Wiley Periodicals, Inc.

  9. Finite difference time domain (FDTD) method for modeling the effect of switched gradients on the human body in MRI.

    PubMed

    Zhao, Huawei; Crozier, Stuart; Liu, Feng

    2002-12-01

    Numerical modeling of the eddy currents induced in the human body by the pulsed field gradients in MRI presents a difficult computational problem. It requires an efficient and accurate computational method for high spatial resolution analyses with a relatively low input frequency. In this article, a new technique is described which allows the finite difference time domain (FDTD) method to be efficiently applied over a very large frequency range, including low frequencies. This is not the case in conventional FDTD-based methods. A method of implementing streamline gradients in FDTD is presented, as well as comparative analyses which show that the correct source injection in the FDTD simulation plays a crucial rule in obtaining accurate solutions. In particular, making use of the derivative of the input source waveform is shown to provide distinct benefits in accuracy over direct source injection. In the method, no alterations to the properties of either the source or the transmission media are required. The method is essentially frequency independent and the source injection method has been verified against examples with analytical solutions. Results are presented showing the spatial distribution of gradient-induced electric fields and eddy currents in a complete body model. Copyright 2002 Wiley-Liss, Inc.

  10. Data assimilation using a gradient descent method for estimation of intraoperative brain deformation.

    PubMed

    Ji, Songbai; Hartov, Alex; Roberts, David; Paulsen, Keith

    2009-10-01

    Biomechanical models that simulate brain deformation are gaining attention as alternatives for brain shift compensation. One approach, known as the "forced-displacement method", constrains the model to exactly match the measured data through boundary condition (BC) assignment. Although it improves model estimates and is computationally attractive, the method generates fictitious forces and may be ill-advised due to measurement uncertainty. Previously, we have shown that by assimilating intraoperatively acquired brain displacements in an inversion scheme, the Representer algorithm (REP) is able to maintain stress-free BCs and improve model estimates by 33% over those without data guidance in a controlled environment. However, REP is computationally efficient only when a few data points are used for model guidance because its costs scale linearly in the number of data points assimilated, thereby limiting its utility (and accuracy) in clinical settings. In this paper, we present a steepest gradient descent algorithm (SGD) whose computational complexity scales nearly invariantly with the number of measurements assimilated by iteratively adjusting the forcing conditions to minimize the difference between measured and model-estimated displacements (model-data misfit). Solutions of full linear systems of equations are achieved with a parallelized direct solver on a shared-memory, eight-processor Linux cluster. We summarize the error contributions from the entire process of model-updated image registration compensation and we show that SGD is able to attain model estimates comparable to or better than those obtained with REP, capturing about 74-82% of tumor displacement, but with a computational effort that is significantly less (a factor of 4-fold or more reduction relative to REP) and nearly invariant to the amount of sparse data involved when the number of points assimilated is large. Based on five patient cases, an average computational cost of approximately 2 min for

  11. Repeatability of gradient ultrahigh pressure liquid chromatography-tandem mass spectrometry methods in instrument-controlled thermal environments.

    PubMed

    Grinias, James P; Wong, Jenny-Marie T; Kennedy, Robert T

    2016-08-26

    The impact of viscous friction on eluent temperature and column efficiency in liquid chromatography is of renewed interest as the need for pressures exceeding 1000bar to use with columns packed with sub-2μm particles has grown. One way the development of axial and radial temperature gradients that arise due to viscous friction can be affected is by the thermal environment the column is placed in. In this study, a new column oven integrated into an ultrahigh pressure liquid chromatograph that enables both still-air and forced-air operating modes is investigated to find the magnitude of the effect of the axial thermal gradient that forms in 2.1×100mm columns packed with sub-2μm particles in these modes. Temperature increases of nearly 30K were observed when the generated power of the column exceeded 25W/m. The impact of the heating due to viscous friction on the repeatability of peak capacity, elution time, and peak area ratio to an internal standard for a gradient UHPLC-MS/MS method to analyze neurotransmitters was found to be limited. This result indicates that high speed UHPLC-MS/MS gradient methods under conditions of high viscous friction may be possible without the negative effects typically observed with isocratic separations under similar conditions.

  12. Gradient-index microlenses: numerical investigation of different spherical index profiles with the wave propagation method.

    PubMed

    Singer, W; Testorf, M; Brenner, K H

    1995-05-01

    Ion-exchange microlenses are available with different gradient-index profiles. We investigate the dependence of the imaging properties on the steepness of the index profiles. Therefore we model the index distribution by the Fermi function as radial distribution with spherical symmetry. The results are compared to index profiles according to the Doremus model.

  13. A new method for the level set equation using a hierarchical-gradient truncation and remapping technique

    NASA Astrophysics Data System (ADS)

    Kohno, Haruhiko; Nave, Jean-Christophe

    2013-06-01

    We present a novel numerical method for solving the advection equation for a level set function. The new method uses hierarchical-gradient truncation and remapping (H-GTaR) of the original partial differential equation (PDE). Our strategy reduces the original PDE to a set of decoupled linear ordinary differential equations with constant coefficients. Additionally, we introduce a remapping strategy to periodically guarantee solution accuracy for a deformation problem. The proposed scheme yields nearly an exact solution for a rigid body motion with a smooth function that possesses vanishingly small higher derivatives and calculates the gradient of the advected function in a straightforward way. We will evaluate our method in one- and two-dimensional domains and present results to several classical benchmark problems.

  14. Derivation of general analytic gradient expressions for density-fitted post-Hartree-Fock methods: An efficient implementation for the density-fitted second-order Møller–Plesset perturbation theory

    SciTech Connect

    Bozkaya, Uğur

    2014-09-28

    General analytic gradient expressions (with the frozen-core approximation) are presented for density-fitted post-HF methods. An efficient implementation of frozen-core analytic gradients for the second-order Møller–Plesset perturbation theory (MP2) with the density-fitting (DF) approximation (applying to both reference and correlation energies), which is denoted as DF-MP2, is reported. The DF-MP2 method is applied to a set of alkanes, conjugated dienes, and noncovalent interaction complexes to compare the computational cost of single point analytic gradients with MP2 with the resolution of the identity approach (RI-MP2) [F. Weigend and M. Häser, Theor. Chem. Acc. 97, 331 (1997); R. A. Distasio, R. P. Steele, Y. M. Rhee, Y. Shao, and M. Head-Gordon, J. Comput. Chem. 28, 839 (2007)]. In the RI-MP2 method, the DF approach is used only for the correlation energy. Our results demonstrate that the DF-MP2 method substantially accelerate the RI-MP2 method for analytic gradient computations due to the reduced input/output (I/O) time. Because in the DF-MP2 method the DF approach is used for both reference and correlation energies, the storage of 4-index electron repulsion integrals (ERIs) are avoided, 3-index ERI tensors are employed instead. Further, as in case of integrals, our gradient equation is completely avoid construction or storage of the 4-index two-particle density matrix (TPDM), instead we use 2- and 3-index TPDMs. Hence, the I/O bottleneck of a gradient computation is significantly overcome. Therefore, the cost of the generalized-Fock matrix (GFM), TPDM, solution of Z-vector equations, the back transformation of TPDM, and integral derivatives are substantially reduced when the DF approach is used for the entire energy expression. Further application results show that the DF approach introduce negligible errors for closed-shell reaction energies and equilibrium bond lengths.

  15. Derivation of general analytic gradient expressions for density-fitted post-Hartree-Fock methods: an efficient implementation for the density-fitted second-order Møller-Plesset perturbation theory.

    PubMed

    Bozkaya, Uğur

    2014-09-28

    General analytic gradient expressions (with the frozen-core approximation) are presented for density-fitted post-HF methods. An efficient implementation of frozen-core analytic gradients for the second-order Møller-Plesset perturbation theory (MP2) with the density-fitting (DF) approximation (applying to both reference and correlation energies), which is denoted as DF-MP2, is reported. The DF-MP2 method is applied to a set of alkanes, conjugated dienes, and noncovalent interaction complexes to compare the computational cost of single point analytic gradients with MP2 with the resolution of the identity approach (RI-MP2) [F. Weigend and M. Häser, Theor. Chem. Acc. 97, 331 (1997); R. A. Distasio, R. P. Steele, Y. M. Rhee, Y. Shao, and M. Head-Gordon, J. Comput. Chem. 28, 839 (2007)]. In the RI-MP2 method, the DF approach is used only for the correlation energy. Our results demonstrate that the DF-MP2 method substantially accelerate the RI-MP2 method for analytic gradient computations due to the reduced input/output (I/O) time. Because in the DF-MP2 method the DF approach is used for both reference and correlation energies, the storage of 4-index electron repulsion integrals (ERIs) are avoided, 3-index ERI tensors are employed instead. Further, as in case of integrals, our gradient equation is completely avoid construction or storage of the 4-index two-particle density matrix (TPDM), instead we use 2- and 3-index TPDMs. Hence, the I/O bottleneck of a gradient computation is significantly overcome. Therefore, the cost of the generalized-Fock matrix (GFM), TPDM, solution of Z-vector equations, the back transformation of TPDM, and integral derivatives are substantially reduced when the DF approach is used for the entire energy expression. Further application results show that the DF approach introduce negligible errors for closed-shell reaction energies and equilibrium bond lengths.

  16. Derivation of general analytic gradient expressions for density-fitted post-Hartree-Fock methods: An efficient implementation for the density-fitted second-order Møller-Plesset perturbation theory

    NASA Astrophysics Data System (ADS)

    Bozkaya, Uǧur

    2014-09-01

    General analytic gradient expressions (with the frozen-core approximation) are presented for density-fitted post-HF methods. An efficient implementation of frozen-core analytic gradients for the second-order Møller-Plesset perturbation theory (MP2) with the density-fitting (DF) approximation (applying to both reference and correlation energies), which is denoted as DF-MP2, is reported. The DF-MP2 method is applied to a set of alkanes, conjugated dienes, and noncovalent interaction complexes to compare the computational cost of single point analytic gradients with MP2 with the resolution of the identity approach (RI-MP2) [F. Weigend and M. Häser, Theor. Chem. Acc. 97, 331 (1997); R. A. Distasio, R. P. Steele, Y. M. Rhee, Y. Shao, and M. Head-Gordon, J. Comput. Chem. 28, 839 (2007)]. In the RI-MP2 method, the DF approach is used only for the correlation energy. Our results demonstrate that the DF-MP2 method substantially accelerate the RI-MP2 method for analytic gradient computations due to the reduced input/output (I/O) time. Because in the DF-MP2 method the DF approach is used for both reference and correlation energies, the storage of 4-index electron repulsion integrals (ERIs) are avoided, 3-index ERI tensors are employed instead. Further, as in case of integrals, our gradient equation is completely avoid construction or storage of the 4-index two-particle density matrix (TPDM), instead we use 2- and 3-index TPDMs. Hence, the I/O bottleneck of a gradient computation is significantly overcome. Therefore, the cost of the generalized-Fock matrix (GFM), TPDM, solution of Z-vector equations, the back transformation of TPDM, and integral derivatives are substantially reduced when the DF approach is used for the entire energy expression. Further application results show that the DF approach introduce negligible errors for closed-shell reaction energies and equilibrium bond lengths.

  17. Beta-carotene chemical stability in Nanoemulsions was improved by stabilized with beta-lactoglobulin-catechin conjugates through free radical method.

    PubMed

    Yi, Jiang; Zhang, Yuzhu; Liang, Rong; Zhong, Fang; Ma, Jianguo

    2015-01-14

    Beta-lactoglobulin (BLG)–catechin conjugates were prepared by a free radical method and investigated with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), electrospray ionization–mass spectrometry (ESI-MS), and far-UV circular dichroism (CD). Covalent binding between BLG and catechin were confirmed with SDS-PAGE and ESI-MS. About 93% of beta-lactoglobulin was conjugated with catechin or catecin fragments according to the gel intensity analysis software. Far-UV CD results showed that the content of β-sheet decreased with a corresponding increase in unordered structures after grafting. Both nanoemulsions with mean particle size between 160 and 170 nm were prepared. Both the rate of particle growth and the total beta-carotene (BC) loss at 50 °C were significantly greater than at 4 and 25 °C. The retention rates of BC in nanoemulsions were 27.8% and 48.6% for BLG and BLG–catechin conjugates, respectively, after 30 days of storage at 50 °C. The BC retention encapsulated in nanoemulsion was significantly improved using BLG–catechin conjugates, compared with BLG alone. The increase of BC retention in nanoemulsions encapsulated with BLG–catechin conjugates was due to the significant improvement of antioxidative properties (reducing power, free radical scavenging activity, and hydroxyl radical scavenging activity) of BLG after covalent binding with catechin. The results indicated that the proteins modified with polyphenols can be widely used in a labile bioactive compounds encapsulation delivery system.

  18. An automatic and accurate method of full heart segmentation from CT image based on linear gradient model

    NASA Astrophysics Data System (ADS)

    Yang, Zili

    2017-07-01

    Heart segmentation is an important auxiliary method in the diagnosis of many heart diseases, such as coronary heart disease and atrial fibrillation, and in the planning of tumor radiotherapy. Most of the existing methods for full heart segmentation treat the heart as a whole part and cannot accurately extract the bottom of the heart. In this paper, we propose a new method based on linear gradient model to segment the whole heart from the CT images automatically and accurately. Twelve cases were tested in order to test this method and accurate segmentation results were achieved and identified by clinical experts. The results can provide reliable clinical support.

  19. Accurate pKa calculation of the conjugate acids of alkanolamines, alkaloids and nucleotide bases by quantum chemical methods.

    PubMed

    Gangarapu, Satesh; Marcelis, Antonius T M; Zuilhof, Han

    2013-04-02

    The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS-MP2 and M11-L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pKa units, in all cases. Extending this method to the pKa calculation of 35 nitrogen-containing compounds spanning 12 pKa units showed an excellent correlation between experimental and computational pKa values of these 35 amines with the computationally low-cost SM8/M11-L density functional approach. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Optimising a parallel conjugate gradient solver

    SciTech Connect

    Field, M.R.

    1996-12-31

    This work arises from the introduction of a parallel iterative solver to a large structural analysis finite element code. The code is called FEX and it was developed at Hitachi`s Mechanical Engineering Laboratory. The FEX package can deal with a large range of structural analysis problems using a large number of finite element techniques. FEX can solve either stress or thermal analysis problems of a range of different types from plane stress to a full three-dimensional model. These problems can consist of a number of different materials which can be modelled by a range of material models. The structure being modelled can have the load applied at either a point or a surface, or by a pressure, a centrifugal force or just gravity. Alternatively a thermal load can be applied with a given initial temperature. The displacement of the structure can be constrained by having a fixed boundary or by prescribing the displacement at a boundary.

  1. Hyperbolic Method for Dispersive PDEs: Same High-Order of Accuracy for Solution, Gradient, and Hessian

    NASA Technical Reports Server (NTRS)

    Mazaheri, Alireza; Ricchiuto, Mario; Nishikawa, Hiroaki

    2016-01-01

    In this paper, we introduce a new hyperbolic first-order system for general dispersive partial differential equations (PDEs). We then extend the proposed system to general advection-diffusion-dispersion PDEs. We apply the fourth-order RD scheme of Ref. 1 to the proposed hyperbolic system, and solve time-dependent dispersive equations, including the classical two-soliton KdV and a dispersive shock case. We demonstrate that the predicted results, including the gradient and Hessian (second derivative), are in a very good agreement with the exact solutions. We then show that the RD scheme applied to the proposed system accurately captures dispersive shocks without numerical oscillations. We also verify that the solution, gradient and Hessian are predicted with equal order of accuracy.

  2. A sensitive multidimensional method for the detection, characterization, and quantification of trace free drug species in antibody-drug conjugate samples using mass spectral detection.

    PubMed

    Birdsall, Robert E; McCarthy, Sean M; Janin-Bussat, Marie Claire; Perez, Michel; Haeuw, Jean-François; Chen, Weibin; Beck, Alain

    2016-01-01

    Conjugation processes and stability studies associated with the production and shelf life of antibody-drug conjugates (ADCs) can result in free (non-conjugated) drug species. These free drug species can increase the risk to patients and reduce the efficacy of the ADC. Despite stringent purification steps, trace levels of free drug species may be present in formulated ADCs, reducing the therapeutic window. The reduction of sample preparation steps through the incorporation of multidimensional techniques has afforded analysts more efficient methods to assess trace drug species. Multidimensional methods coupling size-exclusion and reversed phase liquid chromatography with ultra-violet detection (SEC-RPLC/UV) have been reported, but offer limited sensitivity and can limit method optimization. The current study addresses these challenges with a multidimensional method that is specific, sensitive, and enables method control in both dimensions via coupling of an on-line solid phase extraction column to RPLC with mass spectral detection (SPE-RPLC/MS). The proposed method was evaluated using an antibody-fluorophore conjugate (AFC) as an ADC surrogate to brentuximab vedotin and its associated parent maleimide-val-cit-DSEA payload and the derived N-acetylcysteine adduct formed during the conjugation process. Assay sensitivity was found to be 2 orders more sensitive using MS detection in comparison to UV-based detection with a nominal limit of quantitation of 0.30 ng/mL (1.5 pg on-column). Free-drug species were present in an unadulterated ADC surrogate sample at concentrations below 7 ng/mL, levels not detectable by UV alone. The proposed SPE-RPLC/MS method provides a high degree of specificity and sensitivity in the assessment of trace free drug species and offers improved control over each dimension, enabling straightforward integration into existing or novel workflows.

  3. A sensitive multidimensional method for the detection, characterization, and quantification of trace free drug species in antibody-drug conjugate samples using mass spectral detection

    PubMed Central

    Birdsall, Robert E.; McCarthy, Sean M.; Janin-Bussat, Marie Claire; Perez, Michel; Haeuw, Jean-François; Chen, Weibin; Beck, Alain

    2016-01-01

    abstract Conjugation processes and stability studies associated with the production and shelf life of antibody-drug conjugates (ADCs) can result in free (non-conjugated) drug species. These free drug species can increase the risk to patients and reduce the efficacy of the ADC. Despite stringent purification steps, trace levels of free drug species may be present in formulated ADCs, reducing the therapeutic window. The reduction of sample preparation steps through the incorporation of multidimensional techniques has afforded analysts more efficient methods to assess trace drug species. Multidimensional methods coupling size-exclusion and reversed phase liquid chromatography with ultra-violet detection (SEC-RPLC/UV) have been reported, but offer limited sensitivity and can limit method optimization. The current study addresses these challenges with a multidimensional method that is specific, sensitive, and enables method control in both dimensions via coupling of an on-line solid phase extraction column to RPLC with mass spectral detection (SPE-RPLC/MS). The proposed method was evaluated using an antibody-fluorophore conjugate (AFC) as an ADC surrogate to brentuximab vedotin and its associated parent maleimide-val-cit-DSEA payload and the derived N-acetylcysteine adduct formed during the conjugation process. Assay sensitivity was found to be 2 orders more sensitive using MS detection in comparison to UV-based detection with a nominal limit of quantitation of 0.30 ng/mL (1.5 pg on-column). Free-drug species were present in an unadulterated ADC surrogate sample at concentrations below 7 ng/mL, levels not detectable by UV alone. The proposed SPE-RPLC/MS method provides a high degree of specificity and sensitivity in the assessment of trace free drug species and offers improved control over each dimension, enabling straightforward integration into existing or novel workflows. PMID:26651262

  4. Liquid crystal thermography. A method for monitoring temperature gradients in microtitration plates.

    PubMed

    Oliver, D G; Sanders, A H; Jang, L; Poy, D; Van Heuvelen, A

    1983-03-11

    Precise quantitative heat transfer information in microtitration plates can be obtained by filling the wells of a microtitration plate with cholesteric liquid crystals and incubating the plates at the desired temperature in different incubators. The liquid crystals indicate temperature by changes in discrete reproducible colors over various temperature ranges. With these instrumented plates, interwell thermal gradients may be documented visually and are in close agreement with results obtained by using wire thermocouple measuring techniques.

  5. Ordering Methods for Sparse Matrices and Vector Computers.

    DTIC Science & Technology

    1986-08-15

    H.D. Simon, "Incomplete LU Preconditioners for Conjugate-Gradient-Type Iterative Methods," Eighth SPE Symposium on Reservoir Simulation , Dallas, Texas...Computing). H. D. Simon, Incomplete LU Preconditioners for Conjugate-Gradient-Type Iterative Methods, Proceedings of the Eighth SPE Symposium on Reservoir ... Simulation , Dallas, Texas, February 1985. RECENT PRESENTATIONS AT PROFESSIONAL MEETINGS C. Ashcraft, "The Solution of Banded Systems of Equations in

  6. Beta-Carotene chemical stability in nanoemulsions was improved by stabilized with Beta-Lactoglobulin-Catechin conjugates through free radical method

    USDA-ARS?s Scientific Manuscript database

    Beta-lactoglobulin (BLG)-catechin conjugates were prepared by a free radical method and investigated with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), electrospray ionization-mass spectrometry (ESI-MS), and far-UV circular dichroism (CD). Covalent binding between BLG and cat...

  7. Influence of Rotor-Stator Interaction on Flow Stability in Centrifugal Pump Based on Energy Gradient Method

    NASA Astrophysics Data System (ADS)

    Zheng, Lu-Lu; Dou, Hua-Shu; Jiang, Wei; Chen, Xiaoping; Zhu, Zuchao; Cui, Baoling

    2016-12-01

    Numerical simulation is performed for the three-dimensional turbulent flow field in a centrifugal pump by solving the Reynolds-averaged Navier-Stokes equations and the RNG k-epsilon turbulent model. The finite volume method and the SIMPLE algorithm are employed for the solution of the system. All the parameters in the centrifugal pump at different blade angular positions are obtained by simulation. The flow structure is analyzed and the distributions of the energy gradient function K are calculated at different blade angular positions based on the energy gradient method. According to the energy gradient method, the location which has larger value of K is easier to cause instability and to be of high turbulence intensity. The result shows that the flow instability is easier to be excited nearing the tongue where the value of K is large. The unstable flow area nearing the tongue is also in agreement with the zone where the velocity decreases rapidly. The sudden variation of velocity contributes to the large value of K. The research result also indicates that the tongue has large impact only on the impeller passages passing the tongue.

  8. Spherical tensor gradient operator method for integral rotation: a simple, efficient, and extendable alternative to Slater-Koster tables.

    PubMed

    Giese, Timothy J; York, Darrin M

    2008-07-07

    We present a novel alternative to the use of Slater-Koster tables for the efficient rotation and gradient evaluation of two-center integrals used in tight-binding Hamiltonian models. The method recasts the problem into an exact, yet implicit, basis representation through which the properties of the spherical tensor gradient operator are exploited. These properties provide a factor of 3 to 4 speedup in the evaluation of the integral gradients and afford a compact code structure that easily extends to high angular momentum without loss in efficiency. Thus, the present work is important in improving the performance of tight-binding models in molecular dynamics simulations and has particular use for methods that require the evaluation of two-center integrals that involve high angular momentum basis functions. These advances have a potential impact for the design of new tight-binding models that incorporate polarization or transition metal basis functions and methods based on electron density fitting of molecular fragments.

  9. Determination of in situ gas diffusivity for the reliable estimation of soil fluxes through the gradient method

    NASA Astrophysics Data System (ADS)

    Perez Sanchez-Canete, Enrique; Scott, Russell L.; Barron-Gafford, Greg; van Haren, Joost

    2016-04-01

    Soil CO2 fluxes represent a major source of CO2 emissions, where small changes in their estimation provoke large changes in the quantification of the global carbon cycle. Recently, the gradient method that employs soil CO2 probes at multiple depths has been offered as a way to inexpensively and continuously measure soil CO2 flux. However, the use of the gradient method can yield inappropriate flux estimates due to the uncertainties mainly associated with the inappropriate determination of the soil diffusion coefficient. Therefore, in-situ methods to determine diffusion coefficient are necessary to obtain accurate CO2 fluxes. Here the data obtained during one year with two automatic soil CO2 chambers along with CO2 molar fraction data from 4 probes at 10 cm depth, were used to determine a model of soil diffusion coefficient (Ds), which was applied later to obtain the soil CO2 fluxes by the gradient method. Another Ds model was obtained by injection and sampling of SF6 during several campaigns with different soil water content levels. Both Ds models obtained in situ were compared with another 13 Ds models published. We addressed three questions: 1) Can we use a previously published model, or do we need to determine Ds in situ? 2) How accurate are the CO2 fluxes estimates obtained by the gradient method for different Ds models, compared with chamber-measured CO2 fluxes? 3) Can we take a limited number of chamber measurements to obtain a good Ds model, or we need longer calibration periods? Comparing the cumulative soil respiration for the different diffusion models, we found that the model with empirical calibration to the soil chambers had the best agreement with the chamber fluxes (<0.5% error). The SF6 model underestimated by chamber fluxes by 23% and the published models ranged from an underestimate of 78% to an overestimate of 14%. Most importantly, we found that a few days of measurements with a soil respiration chamber (with widely varying soil water content

  10. Improvement of the analysis of dansylated derivatives of polyamines and their conjugates by high-performance liquid chromatography.

    PubMed

    Fontaniella, B; Mateos, J L; Vicente, C; Legaz, M E

    2001-06-15

    The paper described a method for improving the hydrolysis of conjugated polyamines in PH fraction, isolated from the lichen Evernia prunastri, as well as the optimization of dansylation procedure of these polyamines on the basis of the pH value to which derivatization is achieved. Dansylated polyamines have been later separated by high-performance liquid chromatography (HPLC) using a gradient elution. Hydrolysis of conjugates requires acid treatment at room temperature rather than at 110 degrees C, as usually described. Dansylation is improved at high pH values, whereas removal of phenolics (mainly evernic acid), from the conjugates requires low pH values.

  11. Purification of SUMO conjugating enzymes and kinetic analysis of substrate conjugation

    PubMed Central

    Yunus, Ali A.; Lima, Christopher D.

    2009-01-01

    SUMO conjugation to protein substrates requires the concerted action of a dedicated E2 ubiquitin conjugation enzyme (Ubc9) and associated E3 ligases. Although Ubc9 can directly recognize and modify substrate lysine residues that occur within a consensus site for SUMO modification, E3 ligases can redirect specificity and enhance conjugation rates during SUMO conjugation in vitro and in vivo. In this chapter, we will describe methods utilized to purify SUMO conjugating enzymes and model substrates which can be used for analysis of SUMO conjugation in vitro. We will also describe methods to extract kinetic parameters during E3-dependent or E3-independent substrate conjugation. PMID:19107417

  12. Conjugation of Hot-Melt Extrusion with High-Pressure Homogenization: a Novel Method of Continuously Preparing Nanocrystal Solid Dispersions.

    PubMed

    Ye, Xingyou; Patil, Hemlata; Feng, Xin; Tiwari, Roshan V; Lu, Jiannan; Gryczke, Andreas; Kolter, Karl; Langley, Nigel; Majumdar, Soumyajit; Neupane, Dipesh; Mishra, Sanjay R; Repka, Michael A

    2016-02-01

    Over the past few decades, nanocrystal formulations have evolved as promising drug delivery systems owing to their ability to enhance the bioavailability and maintain the stability of poorly water-soluble drugs. However, conventional methods of preparing nanocrystal formulations, such as spray drying and freeze drying, have some drawbacks including high cost, time and energy inefficiency, traces of residual solvent, and difficulties in continuous operation. Therefore, new techniques for the production of nanocrystal formulations are necessary. The main objective of this study was to introduce a new technique for the production of nanocrystal solid dispersions (NCSDs) by combining high-pressure homogenization (HPH) and hot-melt extrusion (HME). Efavirenz (EFZ), a Biopharmaceutics Classification System class II drug, which is used for the treatment of human immunodeficiency virus (HIV) type I, was selected as the model drug for this study. A nanosuspension (NS) was first prepared by HPH using sodium lauryl sulfate (SLS) and Kollidon® 30 as a stabilizer system. The NS was then mixed with Soluplus® in the extruder barrel, and the water was removed by evaporation. The decreased particle size and crystalline state of EFZ were confirmed by scanning electron microscopy, zeta particle size analysis, and differential scanning calorimetry. The increased dissolution rate was also determined. EFZ NCSD was found to be highly stable after storage for 6 months. In summary, the conjugation of HPH with HME technology was demonstrated to be a promising novel method for the production of NCSDs.

  13. Validation and application of a method for the determination of buprenorphine, norbuprenorphine, and their glucuronide conjugates in human meconium.

    PubMed

    Kacinko, Sherri L; Shakleya, Diaa M; Huestis, Marilyn A

    2008-01-01

    A novel liquid chromatography tandem mass spectrometry method for quantification of buprenorphine, norbuprenorphine, and glucuronidated conjugates was developed and validated. Analytes were extracted from meconium using buffer, concentrated by solid-phase extraction and quantified within 13.5 min. In order to determine free and total concentrations, specimens were analyzed with and without enzyme hydrolysis. Calibration was achieved by linear regression with a 1/x weighting factor and deuterated internal standards. All analytes were linear from 20 to 2000 ng/g with a correlation of determination of >0.98. Accuracy was >or=85.7% with intra-assay and interassay imprecisionor=85.0%. There was suppression of ionization by the polar matrix; however, this did not interfere with sensitivity or analyte quantification due to inclusion of deuterated internal standards. Analytes were stable on the autosampler, at room temperature, at 4 degrees C, and when exposed to three freeze/thaw cycles. This sensitive and specific method can be used to monitor in utero buprenorphine exposure and to evaluate correlations, if any, between buprenorphine exposure and neonatal outcomes.

  14. Validation and Application of a Method for the Determination of Buprenorphine, Norbuprenorphine, and Their Glucuronide Conjugates in Human Meconium

    PubMed Central

    Kacinko, Sherri L.; Shakleya, Diaa M.; Huestis, Marilyn A.

    2009-01-01

    A novel liquid chromatography tandem mass spectrometry method for quantification of buprenorphine, norbuprenorphine, and glucuronidated conjugates was developed and validated. Analytes were extracted from meconium using buffer, concentrated by solid-phase extraction and quantified within 13.5 min. In order to determine free and total concentrations, specimens were analyzed with and without enzyme hydrolysis. Calibration was achieved by linear regression with a 1/x weighting factor and deuterated internal standards. All analytes were linear from 20 to 2000 ng/g with a correlation of determination of >0.98. Accuracy was ≥85.7% with intra-assay and interassay imprecision ≤13.9 and 12.4%, respectively. There was no interference from 70 licit and illicit drugs and metabolites. Buffer extraction followed by SPE yielded recoveries of ≥85.0%. There was suppression of ionization by the polar matrix; however, this did not interfere with sensitivity or analyte quantification due to inclusion of deuterated internal standards. Analytes were stable on the autosampler, at room temperature, at 4 °C, and when exposed to three freeze/thaw cycles. This sensitive and specific method can be used to monitor in utero buprenorphine exposure and to evaluate correlations, if any, between buprenorphine exposure and neonatal outcomes. PMID:18044957

  15. Preliminary Structural Design Using Topology Optimization with a Comparison of Results from Gradient and Genetic Algorithm Methods

    NASA Technical Reports Server (NTRS)

    Burt, Adam O.; Tinker, Michael L.

    2014-01-01

    In this paper, genetic algorithm based and gradient-based topology optimization is presented in application to a real hardware design problem. Preliminary design of a planetary lander mockup structure is accomplished using these methods that prove to provide major weight savings by addressing the structural efficiency during the design cycle. This paper presents two alternative formulations of the topology optimization problem. The first is the widely-used gradient-based implementation using commercially available algorithms. The second is formulated using genetic algorithms and internally developed capabilities. These two approaches are applied to a practical design problem for hardware that has been built, tested and proven to be functional. Both formulations converged on similar solutions and therefore were proven to be equally valid implementations of the process. This paper discusses both of these formulations at a high level.

  16. Analytic gradients for Mukherjee's multireference coupled-cluster method using two-configurational self-consistent-field orbitals

    NASA Astrophysics Data System (ADS)

    Jagau, Thomas-C.; Prochnow, Eric; Evangelista, Francesco A.; Gauss, Jürgen

    2010-04-01

    Analytic gradients for the state-specific multireference coupled-cluster method suggested by Mahapatra et al. [Mol. Phys. 94, 157 (1998)] (Mk-MRCC) are reported within the singles and doubles approximation using two-configurational self-consistent field (TCSCF) orbitals. The present implementation extends our previous work on Mk-MRCC gradients [E. Prochnow et al., J. Chem. Phys. 131, 064109 (2009)] which is based on restricted Hartree-Fock orbitals and consequently the main focus of the present paper is on the treatment of orbital relaxation at the TCSCF level using coupled-perturbed TCSCF theory. Geometry optimizations on m-arynes and nitrenes are presented to illustrate the influence of the orbitals on the computed equilibrium structures. The results are compared to those obtained at the single-reference coupled-cluster singles and doubles and at the Mk-MRCC singles and doubles level of theory when using restricted Hartree-Fock orbitals.

  17. Nonlinear gyrokinetic simulation of ion temperature gradient turbulence based on a numerical Lie-transform perturbation method

    NASA Astrophysics Data System (ADS)

    Xu, Yingfeng; Ye, Lei; Dai, Zongliang; Xiao, Xiaotao; Wang, Shaojie

    2017-08-01

    The electrostatic gyrokinetic nonlinear turbulence code NLT, which is based on a numerical Lie-transform perturbation method, is developed. For improving the computational efficiency and avoiding the numerical instabilities, field-aligned coordinates and a Fourier filter are adopted in the NLT code. Nonlinear tests of the ion temperature gradient driven turbulence with adiabatic electrons are performed for verifying the NLT code by comparing with other gyrokinetic codes. The time evolution of the ion heat diffusivity and the relation between the ion heat diffusivity and the ion temperature gradient are compared in the nonlinear tests. Good agreements are achieved from the nonlinear benchmarks between the NLT code and other codes. The mode structures of the perturbed electric potential representing different phases have been simulated.

  18. Linear and non-linear effects of gradient artifact filtering methods in simultaneous EEG-FMRI - biomed 2010.

    PubMed

    Cusenza, Monica; Accardo, Agostino; Monti, Fabrizio; Bramanti, Placido

    2010-01-01

    Simultaneous EEG-fMRI is a powerful emerging tool in functional neuroimaging that exploits the relationship between neuronal electrophysiological activity and its hemodynamic response. It has found application in the study of both spontaneous and evoked brain activity. Combining the complementary advantages of the two techniques it provides a measurement with high temporal and spatial resolution, allowing a reliable localization of event generators. However, EEG data recorded inside MRI scanner are heavily corrupted by different types of artifacts due to the interactions between the patient, EEG electrodes wires and the magnetic fields inside the scanner. In particular, gradient switching and RF pulses, necessary to acquire fMRI data, generate large artifacts that can completely obscure EEG signals. Many methods have been proposed to eliminate or at least reduce gradient artifact. In this paper both a qualitative and a quantitative evaluation of two different algorithms used for gradient artifact removal are presented. Linear and non-linear characteristics of EEG, such as power spectra, fractal dimension and beta scaling exponent, are evaluated for EEGs recorded outside and inside the scanner, in MR static and dynamic conditions. The study highlights how residual artifacts after correction and artifacts induced by correction itself could still considerably affect EEG signals. The results suggest that the quality of both these gradient artifact filtering methods is not yet sufficient to preserve EEG characteristics and thus it must be further improved. The aim of this study is to make neurophysiologists aware of the filtering effects that can compromise linear and non-linear analysis of EEG recorded during functional MRI.

  19. Stochastic gradient processes: A survey of convergence theory using Lyapunov second method

    SciTech Connect

    Nakonechnyi, A.N.

    1995-09-01

    In the present article, our aim is to provide a comprehensive survey and analysis of the convergence conditions of known gradient type algorithms described by process in terms of the Lyapunov function v(z) = min/y {element_of} Y {parallel} z - y {parallel}{sup 2}, where Y is a closed bounded subset in R{sup l}, i.e., the conditions that ensure the equality P (lim/k{r_arrow}{infinity} min/y{element_of}Y {parallel} z{sup k}-y{parallel}{sup 2} = O) = 1. Alongside qualitative results, the article also focuses on comparison of specific gradient type stochastic algorithms on test examples, practical evaluation of the accuracy of the results, and acceleration of convergence by the averaging operation on the trajectory, which is defined by the recurrence u{sup k+1}=u{sup {center_dot}k} + (z{sup k}-u{sup k})/k, k {ge} 1, u{sup 1} = z{sup 1}.

  20. Cell interaction study method using novel 3D silica nanoneedle gradient arrays

    PubMed Central

    Rajput, Deepak; Crowder, Spencer; Hofmeister, Lucas; Costa, Lino; Sung, Hak-Joon; Hofmeister, William

    2012-01-01

    Understanding cellular interactions with culture substrate features is important to advance cell biology and regenerative medicine. When surface topographical features are considerably larger in vertical dimension and are spaced at least one cell dimension apart, the features act as 3D physical barriers that can guide cell adhesion, thereby altering cell behavior. In the present study, we investigated competitive interactions of cells with neighboring cells and matrix using a novel nanoneedle gradient array. A gradient array of nanoholes was patterned at the surface of fused silica by single-pulse femtosecond laser machining. A negative replica of the pattern was extracted by nanoimprinting with a thin film of polymer. Silica was deposited on top of the polymer replica to form silica nanoneedles. NIH 3T3 fibroblasts were cultured on silica nanoneedles and their behavior was studied and compared with those cultured on a flat silica surface. The presence of silica nanoneedles was found to enhance the adhesion of fibroblasts while maintaining cell viability. The anisotropy in the arrangement of silica nanoneedles was found to affect the morphology and spreading of fibroblasts. Additionally, variations in nanoneedle spacing regulated cell-matrix and cell-cell interactions, effectively preventing cell aggregation in areas of tightly-packed nanoneedles. This proof-of-concept study provides a reproducible means for controlling competitive cell adhesion events and offers a novel system whose properties can be manipulated to intimately control cell behavior. PMID:23006558

  1. COLLECTION OF AIRBORNE PARTICLES BY A HIGH-GRADIENT PERMANENT MAGNETIC METHOD

    SciTech Connect

    Cheng, Mengdawn; Allman, Steve L; Ludtka, Gerard Michael; Avens, Larry R

    2014-01-01

    We report on the use of magnetic force in collection of airborne particles by a high- gradient permanent magnetic separation (HGPMS) device. Three aerosol particles of different magnetic susceptibility (NaCl, CuO, and Fe2O3) were generated in the electrical mobility size range of 10 to 200 nm and were used to study HGPMS collection. One HGPMS matrix element, made of stainless steel wool, was used in the device configuration. Three flow rates were selected to simulate the environmental wind speeds of interest to the study. Magnetic force was found to exhibit an insignificant effect on the separation of NaCl particles, even in the HGPMS configuration. Diffusion was a major mechanism in the removal of the diamagnetic particles; however, diffusion is insignificant under the influence of a high-gradient magnetic field for paramagnetic or ferromagnetic particles. The HGPMS showed high-performance collection (> 99%) of paramagnetic CuO and ferromagnetic Fe2O3 particles for particle sizes greater than or equal to 60 nm. As the wind speed increases, the influence of the magnetic force weakens, and the capability to remove particles from the gas stream diminishes. The results suggest that the HGPMS principle could be explored for development of an advanced miniaturized passive aerosol collector.

  2. Behavior Learning Based on a Policy Gradient Method: Separation of Environmental Dynamics and State-Values in Policies

    NASA Astrophysics Data System (ADS)

    Ishihara, Seiji; Igarashi, Harukazu

    Policy gradient methods are useful approaches to reinforcement learning. Applying the method to behavior learning, we can deal with each decision problem in different time-steps as a problem of minimizing an objective function. In this paper, we give the objective function consists of two types of parameters, which represent state-values and environmental dynamics. In order to separate the learning of the state-value from that of the environmental dynamics, we also give respective learning rules for each type of parameters. Furthermore, we show that the same set of state-values can be reused under different environmental dynamics.

  3. A new powerful association for immunoassay: organometallic label conjugated to solvent separation method.

    PubMed

    Mariet, F; Brossier, P

    1990-05-01

    The convenient use of solvents as a method to separate free (F) and bound (B) fractions in drug immunoassays which utilize organometallic moieties as labels, has been developed. Two types of drugs labelled with an organometallic complex and denominated metallohaptens (or metallotracers) are studied as model assays: desipramine (tricyclic antidepressant) and phenobarbital (antiepileptic agent). Different organic solvents have potentialities to extract these metallohaptens. To illustrate this solvent procedure we describe antiserum dilution curves and we compare the results with those obtained for the same samples using radiotracers in conjunction with dextran coated charcoal as separation agent. This immunoassay method which associates a metallotracer and B/F solvent separation appears to be fast, cheap, without the step of centrifugation.

  4. Critical evaluation of indirect methods for the determination of deoxynivalenol and its conjugated forms in cereals.

    PubMed

    Malachová, Alexandra; Štočková, Lenka; Wakker, Astrid; Varga, Elisabeth; Krska, Rudolf; Michlmayr, Herbert; Adam, Gerhard; Berthiller, Franz

    2015-08-01

    A critical assessment of three previously published indirect methods based on acidic hydrolysis using superacids for the determination of "free" and "total" deoxynivalenol (DON) was carried out. The modified mycotoxins DON-3-glucoside (D3G), 3-acetyl-DON (3ADON), and 15-acetyl-DON (15ADON) were chosen as model analytes. The initial experiments focused on the stability/degradation of DON under hydrolytic conditions and the ability to release DON from the modified forms. Acidic conditions that were capable of cleaving D3G, 3ADON, and 15ADON to DON were not found, raising doubts over the efficacy of previously published indirect methods for total DON determination. Validation of these indirect methods for wheat, maize, and barley using UHPLC-MS/MS was performed in order to test the accuracy of the generated results. Validation data for DON, D3G, 3ADON, and 15ADON in nonhydrolyzed and hydrolyzed matrices were obtained. Under the tested conditions, DON was not released from D3G, 3ADON, or 15ADON after hydrolysis and thus none of the published methods were able to cleave the modified forms of DON. In addition to acids, alkaline hydrolysis with KOH for an extended time and at elevated temperatures was also tested. 3ADON and 15ADON were cleaved under the alkaline pH caused by the addition of KOH or aqueous K2CO3 to "neutralize" the acidic sample extracts in the published studies. The published additional DON increase after hydrolysis may have been caused by huge differences in matrix effects and the recovery of DON in nonhydrolyzed and hydrolyzed matrices as well as by the alkaline cleavage of 3ADON or 15ADON after the neutralization of hydrolyzed extracts.

  5. Digital image multiplexing/demultiplexing method using spatial spectral diffusion and virtual phase conjugation technique for reduction of dynamic range consumption in holographic medium

    NASA Astrophysics Data System (ADS)

    Goto, Yuta; Okamoto, Atsushi; Takabayashi, Masanori; Ogawa, Kazuhisa; Tomita, Akihisa

    2017-09-01

    The recording density in holographic data storage (HDS) systems is determined by the dynamic range of the recording medium. If a hologram is recorded with a small exposure, the consumption amount of the dynamic range per hologram is reduced, and the recording density can be improved. In this report, we propose a digital image multiplexing/demultiplexing method using spatial spectral diffusion and a virtual phase conjugation technique to reduce the consumption amount of the dynamic range in a recording medium. In our method, multiple signals are simultaneously recorded in a medium by multiplexing those signals using a beam combiner before recording, unlike the general multiplexing method of HDS. Then, each original signal can be reproduced independently by utilizing the property of a random diffuser and a phase-conjugated light. In the simulation, we confirmed that our method can improve the recording density because the consumption of the dynamic range is reduced.

  6. Computerized detection of non-calcified plaques in coronary CT angiography: topological soft-gradient detection method for plaque prescreening

    NASA Astrophysics Data System (ADS)

    Wei, Jun; Zhou, Chuan; Chan, Heang-Ping; Chughtai, Aamer; Patel, Smita; Agarwal, Prachi; Kuriakose, Jean; Hadjiiski, Lubomir; Kazerooni, Ella

    2013-03-01

    Non-calcified plaque (NCP) detection in coronary CT angiography (cCTA) is challenging due to the low CT number of NCP, the large number of coronary arteries and multiple phase CT acquisition. We are developing computervision methods for automated detection of NCPs in cCTA. A data set of 62 cCTA scans with 87 NCPs was collected retrospectively from patient files. Multiscale coronary vessel enhancement and rolling balloon tracking were first applied to each cCTA volume to extract the coronary artery trees. Each extracted vessel was reformatted to a straightened volume composed of cCTA slices perpendicular to the vessel centerline. A new topological soft-gradient (TSG) detection method was developed to prescreen for both positive and negative remodeling candidates by analyzing the 2D topological features of the radial gradient field surface along the vessel wall. Nineteen features were designed to describe the relative location along the coronary artery, shape, distribution of CT values, and radial gradients of each NCP candidate. With a machine learning algorithm and a two-loop leave-one-case-out training and testing resampling method, useful features were selected and combined into an NCP likelihood measure to differentiate TPs from FPs. The detection performance was evaluated by FROC analysis. Our TSG method achieved a sensitivity of 96.6% with 35.4 FPs/scan at prescreening. Classification with the NCP likelihood measure reduced the FP rates to 13.1, 10.0 and 6.7 FPs/scan at sensitivities of 90%, 80%, and 70%, respectively. These results demonstrated that the new TSG method is useful for computerized detection of NCPs in cCTA.

  7. Photocatalytic activity and NIR laser response of polyaniline conjugated graphene nanocomposite prepared by a novel acid-less method.

    PubMed

    Neelgund, Gururaj M; Bliznyuk, Valery N; Oki, Aderemi

    2016-06-15

    Herein, we present a novel acid-less synthetic approach for in-situ polymerization of aniline synchronized with reduction of graphene oxide to graphene. This method provides uniform deposition of ordered polyaniline nanotubes over the surface of graphene nanosheets. The synthesized graphene-polyaniline nanocomposite has the ability of complete removal of harmful dyes commonly used in industry: such as methyl orange, methylene blue, and rhoadmine B from the waste water under the exposure to natural sunlight. The system can be used as an efficient solar energy operated photocatalyst due to effective suppression of recombination of the charge carriers. The unique spatial structure of the graphene-polyaniline nanocomposite has high chemical stability, can be recycled after photolysis, and allows using in multiple cycles without reduction in its photocatalytic activity. In addition, the graphene-polyaniline nanocomposite exhibits strong near-infrared (NIR) absorption, good photothermal stability, as well as shows substantial thermal energy generation under exposure to 808 or 980 nm NIR lasers. The electrical conductivity of polyaniline nanotubes is improved as a result of their conjugation with graphene nanosheets in the nanocomposite. Owing to its outstanding photocatalytic activity and chemical stability, the reported graphene-polyaniline nanocomposite has a great potential in purification of industrially generated waste water.

  8. Comparison of Experimentally Measured Temperature Gradient and Finite-Element-Method Simulations for Two Continuously Cast Bloom Heating Strategies

    NASA Astrophysics Data System (ADS)

    Kvíčala, M.; Frydrýšek, K.; Štamborská, M.

    2015-03-01

    This paper deals with the comparison of experimentally measured temperature gradients and finite-element-method (FEM) simulations of two heating strategies that were used for continuously cast bloom soaking. The temperature gradient between the bloom surface and center was measured by two thermocouples incorporated directly into the bloom. Scanning electron microscopy equipped by energy dispersive X-ray spectroscopy analysis, hot tensile tests, and interdendritic solidification software was used for modeling of steel thermophysical properties with respect to the alloying-elements macrosegregation. The model of the bloom was programmed in the Fortran language. The FEM software MARC/MENTAT 2012 was used for simulation of two heating strategies (plane strain formulation). The first heating model was fitted to the commonly used heating strategy when internal defects grew above the critical limit. The second heating model was a newly proposed strategy that consisted of slower heating up to 1073 K when the first warming-through period occurred. The FEM simulations included determinations of the temperature gradient, the equivalent of stress, the equivalent of elastic strain, the equivalent of plastic strain, and the equivalent of total strain. The simulation results were in good agreement with experimental observations. The new heating strategy based on the FEM simulations led to significantly lower occurrence of internal defects in hot-rolled billets that are used for cylinder production.

  9. A new 3-D ray tracing method based on LTI using successive partitioning of cell interfaces and traveltime gradients

    NASA Astrophysics Data System (ADS)

    Zhang, Dong; Zhang, Ting-Ting; Zhang, Xiao-Lei; Yang, Yan; Hu, Ying; Qin, Qian-Qing

    2013-05-01

    We present a new method of three-dimensional (3-D) seismic ray tracing, based on an improvement to the linear traveltime interpolation (LTI) ray tracing algorithm. This new technique involves two separate steps. The first involves a forward calculation based on the LTI method and the dynamic successive partitioning scheme, which is applied to calculate traveltimes on cell boundaries and assumes a wavefront that expands from the source to all grid nodes in the computational domain. We locate several dynamic successive partition points on a cell's surface, the traveltimes of which can be calculated by linear interpolation between the vertices of the cell's boundary. The second is a backward step that uses Fermat's principle and the fact that the ray path is always perpendicular to the wavefront and follows the negative traveltime gradient. In this process, the first-arriving ray path can be traced from the receiver to the source along the negative traveltime gradient, which can be calculated by reconstructing the continuous traveltime field with cubic B-spline interpolation. This new 3-D ray tracing method is compared with the LTI method and the shortest path method (SPM) through a number of numerical experiments. These comparisons show obvious improvements to computed traveltimes and ray paths, both in precision and computational efficiency.

  10. Development of methods for the decrease in instability of recycling water of conjugated closed-circuit cooling system of HPP

    NASA Astrophysics Data System (ADS)

    Chichirov, A. A.; Chichirova, N. D.; Vlasov, S. M.; Lyapin, A. I.; Misbakhov, R. Sh.; Silov, I. Yu.; Murtazin, A. I.

    2016-10-01

    On Russian HPPs, conjugated closed-circuit cooling systems, where purge water is used as initial for water-treatment facilities, are widespread. For this reason, it is impossible to use general methods for the stabilization treatment of recycling water in order to prevent scale formation in the units of a system, namely, turbine condensers and cooling towers. In this paper, the methods for the decrease in the instability of recycling water using the methods of chemical engineering, such as stabilization and synchronization of flows and organization of recycles, are suggested. The results of an industrial experiment on the implementation of stabilization treatment of recycling water by the organization of recycle are given. The experiment was carried out on Kazan CHPP-3. The flow scheme involved the recycle of chemically purified water (CPW) for the heat network make-up to the closed-circuit cooling system. The experiment was carried out at three stages with the gradual change of the consumption of the recycle, namely, 0, 50, and 100 t/h. According to the results of experiments, the reliable decrease in the rate of the sedimentation was recorded on the units of the system, namely, turbine condenser and chimney-type cooling tower. This is caused by two reasons. Firstly, this is periodic excessive concentration of recycling water due to the nonstationary character of inlet and outlet flows. Secondly, this is seasonal (particularly, in the summer period) exceeding of the evaporation coefficient. As a result of stabilization and synchronization of flows and organization of recycles, the quality of clarified and chemically purified water for the heat network make-up increases and the corrosion of iron- and copper-containing structural materials decreases. A natural decrease in temperature drop on the operating turbine condensers is mentioned.

  11. Experiment, monitoring, and gradient methods used to infer climate change effects on plant communities yield consistent patterns.

    PubMed

    Elmendorf, Sarah C; Henry, Gregory H R; Hollister, Robert D; Fosaa, Anna Maria; Gould, William A; Hermanutz, Luise; Hofgaard, Annika; Jónsdóttir, Ingibjörg S; Jónsdóttir, Ingibjörg I; Jorgenson, Janet C; Lévesque, Esther; Magnusson, Borgþór; Molau, Ulf; Myers-Smith, Isla H; Oberbauer, Steven F; Rixen, Christian; Tweedie, Craig E; Walker, Marilyn D; Walker, Marilyn

    2015-01-13

    Inference about future climate change impacts typically relies on one of three approaches: manipulative experiments, historical comparisons (broadly defined to include monitoring the response to ambient climate fluctuations using repeat sampling of plots, dendroecology, and paleoecology techniques), and space-for-time substitutions derived from sampling along environmental gradients. Potential limitations of all three approaches are recognized. Here we address the congruence among these three main approaches by comparing the degree to which tundra plant community composition changes (i) in response to in situ experimental warming, (ii) with interannual variability in summer temperature within sites, and (iii) over spatial gradients in summer temperature. We analyzed changes in plant community composition from repeat sampling (85 plant communities in 28 regions) and experimental warming studies (28 experiments in 14 regions) throughout arctic and alpine North America and Europe. Increases in the relative abundance of species with a warmer thermal niche were observed in response to warmer summer temperatures using all three methods; however, effect sizes were greater over broad-scale spatial gradients relative to either temporal variability in summer temperature within a site or summer temperature increases induced by experimental warming. The effect sizes for change over time within a site and with experimental warming were nearly identical. These results support the view that inferences based on space-for-time substitution overestimate the magnitude of responses to contemporary climate warming, because spatial gradients reflect long-term processes. In contrast, in situ experimental warming and monitoring approaches yield consistent estimates of the magnitude of response of plant communities to climate warming.

  12. Experiment, monitoring, and gradient methods used to infer climate change effects on plant communities yield consistent patterns

    PubMed Central

    Elmendorf, Sarah C.; Henry, Gregory H. R.; Hollister, Robert D.; Fosaa, Anna Maria; Gould, William A.; Hermanutz, Luise; Hofgaard, Annika; Jónsdóttir, Ingibjörg S.; Jorgenson, Janet C.; Lévesque, Esther; Magnusson, Borgþór; Molau, Ulf; Myers-Smith, Isla H.; Oberbauer, Steven F.; Rixen, Christian; Tweedie, Craig E.; Walker, Marilyn D.

    2015-01-01

    Inference about future climate change impacts typically relies on one of three approaches: manipulative experiments, historical comparisons (broadly defined to include monitoring the response to ambient climate fluctuations using repeat sampling of plots, dendroecology, and paleoecology techniques), and space-for-time substitutions derived from sampling along environmental gradients. Potential limitations of all three approaches are recognized. Here we address the congruence among these three main approaches by comparing the degree to which tundra plant community composition changes (i) in response to in situ experimental warming, (ii) with interannual variability in summer temperature within sites, and (iii) over spatial gradients in summer temperature. We analyzed changes in plant community composition from repeat sampling (85 plant communities in 28 regions) and experimental warming studies (28 experiments in 14 regions) throughout arctic and alpine North America and Europe. Increases in the relative abundance of species with a warmer thermal niche were observed in response to warmer summer temperatures using all three methods; however, effect sizes were greater over broad-scale spatial gradients relative to either temporal variability in summer temperature within a site or summer temperature increases induced by experimental warming. The effect sizes for change over time within a site and with experimental warming were nearly identical. These results support the view that inferences based on space-for-time substitution overestimate the magnitude of responses to contemporary climate warming, because spatial gradients reflect long-term processes. In contrast, in situ experimental warming and monitoring approaches yield consistent estimates of the magnitude of response of plant communities to climate warming. PMID:25548195

  13. Phase conjugation of the second harmonic of a focused ultrasound beam as a method for improving C-scan acoustical imaging in nonlinear inhomogeneous media

    NASA Astrophysics Data System (ADS)

    Krutyansky, Leonid M.; Brysev, Andrew P.; Klopotov, Roman V.; Pernod, Philippe J.; Preobrazhensky, Vladimir L.; Yan, Xiang; Hamilton, Mark F.

    2003-10-01

    Acoustical imaging in complex media (e.g., biological tissue) can be affected by phase aberrations introduced in a wave during propagation. Wave phase conjugation (WPC) of ultrasound is known for its ability to compensate for phase distortions due to inhomogeneity of the propagation medium, and it can be used for improvement of acoustical imaging under these conditions. In a nonlinear medium harmonics are generated during propagation of an intense beam of ultrasound, and this principle is used in tissue harmonic imaging. The parametric method of WPC permits phase conjugation of a selected frequency component of the probe beam. In this way the peculiarities of WPC can be combined with advantages of harmonic imaging. Automated WPC-focusing of the conjugated second-harmonic component of a focused nonlinear probe beam is studied experimentally and theoretically for the case of a homogeneous medium, and experimentally for a medium with pseudo-random inhomogeneities. The generated conjugate wave can also be sufficiently intense to generate higher-order harmonics, which display enhanced focusing. Improvement of a C-scan harmonic imaging system operating in an inhomogeneous medium is provided as an example.

  14. Conjugate symplectic B-series

    NASA Astrophysics Data System (ADS)

    Hairer, Ernst; Zbinden, Christophe J.

    2012-09-01

    For the long-time integration of Hamiltonian differential equations the use of symplectic methods is recommended. In practice it is often sufficient to apply a method that is conjugate (up to a sufficiently high order) to a symplectic integrator. This article gives a criterion on the conjugate symplecticity of methods that can be represented as a B-series. It allows to characterize the conjugate symplecticity of a large class of numerical integrators including Lobatto IIIA and Lobatto IIIB methods, as well as energy-preserving collocation methods.

  15. The application of inverse-dispersion and gradient methods to estimate ammonia emissions from a penguin colony

    NASA Astrophysics Data System (ADS)

    Theobald, Mark R.; Crittenden, Peter D.; Tang, Y. Sim; Sutton, Mark A.

    2013-12-01

    Penguin colonies represent some of the most concentrated sources of ammonia emissions to the atmosphere in the world. The ammonia emitted into the atmosphere can have a large influence on the nitrogen cycling of ecosystems near the colonies. However, despite the ecological importance of the emissions, no measurements of ammonia emissions from penguin colonies have been made. The objective of this work was to determine the ammonia emission rate of a penguin colony using inverse-dispersion modelling and gradient methods. We measured meteorological variables and mean atmospheric concentrations of ammonia at seven locations near a colony of Adélie penguins in Antarctica to provide input data for inverse-dispersion modelling. Three different atmospheric dispersion models (ADMS, LADD and a Lagrangian stochastic model) were used to provide a robust emission estimate. The Lagrangian stochastic model was applied both in ‘forwards’ and ‘backwards’ mode to compare the difference between the two approaches. In addition, the aerodynamic gradient method was applied using vertical profiles of mean ammonia concentrations measured near the centre of the colony. The emission estimates derived from the simulations of the three dispersion models and the aerodynamic gradient method agreed quite well, giving a mean emission of 1.1 g ammonia per breeding pair per day (95% confidence interval: 0.4-2.5 g ammonia per breeding pair per day). This emission rate represents a volatilisation of 1.9% of the estimated nitrogen excretion of the penguins, which agrees well with that estimated from a temperature-dependent bioenergetics model. We found that, in this study, the Lagrangian stochastic model seemed to give more reliable emission estimates in ‘forwards’ mode than in ‘backwards’ mode due to the assumptions made.

  16. Antibody-gold cluster conjugates

    DOEpatents

    Hainfeld, J.F.

    1988-06-28

    Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be about 5.0 nm. Methods and reagents are disclosed in which antibodies or Fab' fragments thereof are covalently bound to a stable cluster of gold atoms. 2 figs.

  17. A novel gradient HPLC method for simultaneous determination of ranitidine, methylparaben and propylparaben in oral liquid pharmaceutical formulation.

    PubMed

    Kokoletsi, Magdalene Xenou; Kafkala, Stella; Tsiaganis, Michael

    2005-07-15

    A selective and accurate high-performance liquid chromatographic method has been developed and validated for the simultaneous determination of ranitidine, methylparaben (MP) and propylparaben (PP) in oral liquids. Samples were purified by solid-phase extraction (SPE) using a copolymeric [poly(divinylbenzene-co-N-vinylpyrrolidone)] sorbent. The chromatographic separation was achieved by HPLC using a mixture of ammonium acetate solution (0.5 M), acetonitrile and methanol as the mobile phase with gradient elution, a Nucleosil C18 column and UV detection at 254 nm. The method was validated with respect to linearity, precision, accuracy, selectivity, and robustness. All the parameters examined met the current recommendations for bioanalytical method validation. The method was found to be applicable to routine analysis (assays and stability tests) of active compound (ranitidine) and preservatives (MP and PP).

  18. On the convergence of the conditional gradient method as applied to the optimization of an elliptic equation

    NASA Astrophysics Data System (ADS)

    Chernov, A. V.

    2015-02-01

    The optimal control of a second-order semilinear elliptic diffusion-reaction equation is considered. Sufficient conditions for the convergence of the conditional gradient method are obtained without using assumptions (traditional for optimization theory) that ensure the Lipschitz continuity of the objective functional derivative. The total (over the entire set of admissible controls) preservation of solvability, a pointwise estimate of solutions, and the uniqueness of a solution to the homogeneous Dirichlet problem for a controlled elliptic equation are proved as preliminary results, which are of interest on their own.

  19. Are there any alternative methods to hepatic venous pressure gradient in portal hypertension assessment?

    PubMed

    Procopeţ, Bogdan; Tantau, Marcel; Bureau, Christophe

    2013-03-01

    Portal hypertension is a major consequence of any chronic liver disease and it represents the main mechanism of complication occurrence. Therefore, the assessment of portal hypertension presence is one of the most important steps in the management of any chronic liver diseases. The most accurate tool for portal pressure assessment is hepatic venous pressure gradient (HVPG) measurement, which has diagnostic and prognostic relevance. In this paper we review the methodology of HVPG measuring, together with the clinical relevance of this technique. Portal hypertension is defined as a HVPG higher than 5 mmHg, but clinically significant portal hypertension that predisposes to clinical decompensation is defined as HVPG higher than 10 mmHg. HVPG is useful for portal hypertension treatment monitoring. A decrease in HVPG greater than 20% or under the threshold of 12 mmHg is considered to be protective against portal hypertension-related events. Even if HVPG measurement is a safe procedure, it is still considered an invasive technique and not widely available. Therefore, non-invasive markers of portal hypertension were searched for. Until now only liver stiffness measurement by transient elastography has proved to be sufficiently accurate but there is still heterogeneity among the cut-off values for portal hypertension diagnosis.

  20. Can the gradient method improve our ability to predict soil respiration?

    NASA Astrophysics Data System (ADS)

    Phillips, Claire; Nickerson, Nicholas; Risk, Dave

    2015-04-01

    Soil surface flux measurements integrate respiration across steep vertical gradients of soil texture, moisture, temperature, and carbon substrates. Although there are benefits to integrating complex soil processes in a single surface measure, i.e. for constructing soil carbon budgets, one serious drawback of studying only surface respiration is the difficulty in generating predictive relationships from environmental drivers. For example, the relationship between depth-integrated soil respiration and temperature measured at a single discreet depth (apparent temperature sensitivity) can bear little resemblance to the temperature sensitivity of soil respiration within soil layers (actual temperature sensitivity). Here we present several examples of how the inferred environmental sensitivity of soil respiration can be improved from observations of CO2 flux profiles in contrast to surface fluxes alone. We present a theoretical approach for estimating the temperature sensitivity of soil respiration in situ, called the weighted heat flux approach, which avoids much of the hysteresis produced by typical respiration-temperature comparisons. The weighted heat flux approach gives more accurate estimates of within-soil temperature sensitivity, and is arguably the most theoretically robust analytical temperature model available. We also show how soil drying influences the effectiveness of the weighted heat flux approach, as well as the relative activity of discreet soil layers and specific soil organisms, such as mycorrhizal fungi. The additional information provided by within-soil flux profiles can improve the fidelity of both probabilistic and mechanistic soil respiration models