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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. 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...Methods for Constrained Least uares Problems (directed by Robert J . Plemmons). Nreiw• 1\\ . ’iu 1988, Barlow, Nichols, and Plemmons proposed order...typical). The blocks 13 element j / F __- . F= %.GEi ,,,mo node Figure 2.4: Matrices for Static Structurem Prcblem associated with t’e planar square

  12. 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.

  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. 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.

  17. 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.

  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. 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.

  20. 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.

  1. 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.

  2. 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)

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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./.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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).

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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).

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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).

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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…

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

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

    DOEpatents

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

    2002-01-01

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

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

    DOEpatents

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

    2007-03-20

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

  16. 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.

  17. 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.

  18. 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).

  19. 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.

  20. 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.

  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. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  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. 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.

  18. 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

  19. 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.

  20. 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.

  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. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

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

    DOEpatents

    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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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%.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

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

    PubMed Central

    Wang, Bo; Su, Yumin; Wan, Lei

    2016-01-01

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

  2. A 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.

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

    PubMed Central

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

    2016-01-01

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

  4. 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

  5. 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.

  6. 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

  7. 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/.

  8. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1999-01-01

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

  10. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. [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.

  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. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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

  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. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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%.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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).

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  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. 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

  17. 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.

  18. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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}.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  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. 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.

  18. 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

  19. 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.

  20. 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.

  1. Conjugation in "Escherichia coli"

    ERIC Educational Resources Information Center

    Phornphisutthimas, Somkiat; Thamchaipenet, Arinthip; Panijpan, Bhinyo

    2007-01-01

    Bacterial conjugation is a genetic transfer that involves cell-to-cell between donor and recipient cells. With the current method used to teach students in genetic courses at the undergraduate level, the transconjugants are identified using bacterial physiology and/or antibiotic resistance. Using physiology, however, is difficult for both…

  2. 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.

  3. 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

  4. Optimization of ion exchange sigmoidal gradients using hybrid models: Implementation of quality by design in analytical method development.

    PubMed

    Joshi, Varsha S; Kumar, Vijesh; Rathore, Anurag S

    2017-03-31

    Thorough product understanding is one of the basic tenets for successful implementation of Quality by Design (QbD). Complexity encountered in analytical characterization of biotech therapeutics such as monoclonal antibodies (mAbs) requires novel, simpler, and generic approaches towards product characterization. This paper presents a methodology for implementation of QbD for analytical method development. Optimization of an analytical cation exchange high performance liquid chromatography (CEX-HPLC) method utilizing a sigmoidal gradient has been performed using a hybrid mechanistic model that is based on Design of experiment (DOE) based studies. Since sigmodal gradients are much more complex than the traditional linear gradients and have a large number of input parameters (five) for optimization, the number of DOE experiments required for a full factorial design to estimate all the main effects as well as the interactions would be too large (243). To address this problem, a mechanistic model was used to simulate the analytical separation for the DOE and then the results were used to build an empirical model. The mechanistic model used in this work is a more versatile general rate model in combination of modified Langmuir binding kinetics. The modified Langmuir model is capable of modelling the impact of nonlinear changes in the concentration of the salt modifier. Further, to get the input and output profiles of mAb and salts/buffers, the HPLC system, consisting of the mixer, detectors, and tubing was modelled as a sequence of dispersed plug flow reactors and continuous stirred tank reactors (CSTR). The experimental work was limited to calibration of the HPLC system and finding the model parameters through three linear gradients. To simplify the optimization process, only three peaks in the centre of the profile (main product and the adjacent acidic and basic variants) were chosen to determine the final operating condition. The regression model made from the DoE data

  5. Evaluation of an alternate method for sampling benthic macroinvertebrates in low-gradient streams sampled as part of the National Rivers and Streams Assessment.

    PubMed

    Flotemersch, Joseph E; North, Sheila; Blocksom, Karen A

    2014-02-01

    Benthic macroinvertebrates are sampled in streams and rivers as one of the assessment elements of the US Environmental Protection Agency's National Rivers and Streams Assessment. In a 2006 report, the recommendation was made that different yet comparable methods be evaluated for different types of streams (e.g., low gradient vs. high gradient). Consequently, a research element was added to the 2008-2009 National Rivers and Streams Assessment to conduct a side-by-side comparison of the standard macroinvertebrate sampling method with an alternate method specifically designed for low-gradient wadeable streams and rivers that focused more on stream edge habitat. Samples were collected using each method at 525 sites in five of nine aggregate ecoregions located in the conterminous USA. Methods were compared using the benthic macroinvertebrate multimetric index developed for the 2006 Wadeable Streams Assessment. Statistical analysis did not reveal any trends that would suggest the overall assessment of low-gradient streams on a regional or national scale would change if the alternate method was used rather than the standard sampling method, regardless of the gradient cutoff used to define low-gradient streams. Based on these results, the National Rivers and Streams Survey should continue to use the standard field method for sampling all streams.

  6. A capillary zone electrophoretic method for the study of formation of a covalent conjugate between microcystin LR and protein phosphatase 2A.

    PubMed

    Hu, S; Li, P C

    2001-07-01

    The study of conjugate formation between microcystin (MCYST)-LR and protein phosphatase (PP) 2A, which was isolated from bovine kidney and mouse brain, was achieved by using a highly efficient capillary zone electrophoretic (CZE) separation method. The MCYST-LR-PP2A conjugate (from bovine kidney) was resolved from its precursor after just 15 min of incubation. Moreover, the migration time, and, hence, the total analysis time, was less than 5 min. While the present findings of the time lag between conjugate formation and full inhibition are not novel, the CZE method does provide an alternative tool to HPLC with a higher separation efficiency to yield data for kinetic and mechanistic studies of the enzyme-toxin interaction. The CZE data reported here were found not to be adequately described by a first-order kinetic model. Moreover, the CZE method, which involves the use of a low ionic strength aqueous buffer, does not suffer from the drawback of the use of denaturing organic solvents such as those used in HPLC.

  7. Combination of density gradient centrifugation and swim-up methods effectively decreases morphologically abnormal sperms

    PubMed Central

    YAMANAKA, Masaya; TOMITA, Kazuhisa; HASHIMOTO, Shu; MATSUMOTO, Hiroshi; SATOH, Manabu; KATO, Hiromi; HOSOI, Yoshihiko; INOUE, Masayasu; NAKAOKA, Yoshiharu; MORIMOTO, Yoshiharu

    2016-01-01

    Density gradient centrifugation (DGC) and swim-up techniques have been reported for semen preparation in assisted reproductive techniques in humans. We investigated whether semen preparation using a combination of DGC and swim-up techniques could effectively decrease morphologically abnormal human sperms at the ultrastructural level. Semen samples were obtained from 16 infertile males and fractionated by swim-up following DGC. Ultrastructural abnormalities of sperms obtained from original semen, lower layer of swim-up following DGC, and upper layer of swim-up following DGC were analyzed by transmission electron microscopy. The correlation among ultrastructural head abnormality in sperms from the upper layer of swim-up, fertilization in in vitro fertilization, and pregnancy after embryo transfer was also investigated. Furthermore, sperms with DNA fragmentation in the samples processed via a combination of DGC and swim-up was assessed in a sperm chromatin structure assay. Ultrastructural abnormalities in sperm heads and tails in the upper layer after swim-up following DGC was the lowest among the three groups. Sperms with nuclear vacuoles were the most difficult to eliminate using a combination of DGC and swim-up in all types of head abnormalities. A negative correlation was confirmed between the fertilization rates of intracytoplasmic sperm injection and head abnormality of sperms obtained from the upper layer of the swim-up following DGC. Sperms with DNA fragmentation were effectively decreased using the combination of two techniques. In conclusion, the combination of DGC and swim-up effectively decreased the number of sperms with ultrastructural abnormalities both in the head and in the tail. However, sperms with ultrastructural abnormalities that cannot be completely decreased using a combination of DGC and swim-up may impair fertilization in some cases of intracytoplasmic sperm injection. PMID:27616283

  8. A comparison of methods for computing the sigma-coordinate pressure gradient force for flow over sloped terrain in a hybrid theta-sigma model

    NASA Technical Reports Server (NTRS)

    Johnson, D. R.; Uccellini, L. W.

    1983-01-01

    In connection with the employment of the sigma coordinates introduced by Phillips (1957), problems can arise regarding an accurate finite-difference computation of the pressure gradient force. Over steeply sloped terrain, the calculation of the sigma-coordinate pressure gradient force involves computing the difference between two large terms of opposite sign which results in large truncation error. To reduce the truncation error, several finite-difference methods have been designed and implemented. The present investigation has the objective to provide another method of computing the sigma-coordinate pressure gradient force. Phillips' method is applied for the elimination of a hydrostatic component to a flux formulation. The new technique is compared with four other methods for computing the pressure gradient force. The work is motivated by the desire to use an isentropic and sigma-coordinate hybrid model for experiments designed to study flow near mountainous terrain.

  9. Gradient Matching Methods for Computational Inference in Mechanistic Models for Systems Biology: A Review and Comparative Analysis.

    PubMed

    Macdonald, Benn; Husmeier, Dirk

    2015-01-01

    Parameter inference in mathematical models of biological pathways, expressed as coupled ordinary differential equations (ODEs), is a challenging problem in contemporary systems biology. Conventional methods involve repeatedly solving the ODEs by numerical integration, which is computationally onerous and does not scale up to complex systems. Aimed at reducing the computational costs, new concepts based on gradient matching have recently been proposed in the computational statistics and machine learning literature. In a preliminary smoothing step, the time series data are interpolated; then, in a second step, the parameters of the ODEs are optimized, so as to minimize some metric measuring the difference between the slopes of the tangents to the interpolants, and the time derivatives from the ODEs. In this way, the ODEs never have to be solved explicitly. This review provides a concise methodological overview of the current state-of-the-art methods for gradient matching in ODEs, followed by an empirical comparative evaluation based on a set of widely used and representative benchmark data.

  10. Preparation of doxorubicin-hydrochloride nanoliposomes by ethanol injection-pH gradient method and their safety evaluation.

    PubMed

    Xie, Ming; Chen, Yuxiang; Wu, Lixiang

    2013-01-01

    A new type of ethanol injection-pH gradient method was established to produce Doxorubicin-Hydrochloride Nanoliposome (DHNP). The characteristics of DHNP were examined by Zetasizer. The acute toxicity and chronic toxicity trials were conducted in Kuming mice with different doses of DHNP. The results showed that the DHNP had the uniform distribution size, diameter ranged in 140-170 nm, its entrapment rate could reach as high as 99.85%, and it was relatively stable in low temperature. The LD50 of the DHNP is 31.69 mg/kg. In the chronic toxicity study, body weight, hematocrit, the mean red blood cell volume, platelets counts and percentage of eosinophil at the dose of 6 mg/kg and 9 mg/kg groups were significantly different (p < 0.05) compared with control group, while the other parameters had no significantly difference. In the tissue analysis, pathological change was found in the lung at the treated group, and its pathological degree increased as the dose increased, while there were no other pathological changes detected in other tissues. This study demonstrates that the DHNP prepared by ethanol injection-pH gradient method possesses the advantage of uniform distribution size, high encapsulation efficiency, big drug loading rate, and its toxicity is lower than free doxorubicin.

  11. Improving the accuracy of convexity splitting methods for gradient flow equations

    NASA Astrophysics Data System (ADS)

    Glasner, Karl; Orizaga, Saulo

    2016-06-01

    This paper introduces numerical time discretization methods which significantly improve the accuracy of the convexity-splitting approach of Eyre (1998) [7], while retaining the same numerical cost and stability properties. A first order method is constructed by iteration of a semi-implicit method based upon decomposing the energy into convex and concave parts. A second order method is also presented based on backwards differentiation formulas. Several extrapolation procedures for iteration initialization are proposed. We show that, under broad circumstances, these methods have an energy decreasing property, leading to good numerical stability. The new schemes are tested using two evolution equations commonly used in materials science: the Cahn-Hilliard equation and the phase field crystal equation. We find that our methods can increase accuracy by many orders of magnitude in comparison to the original convexity-splitting algorithm. In addition, the optimal methods require little or no iteration, making their computation cost similar to the original algorithm.

  12. Performance of quantitative vegetation sampling methods across gradients of cover in Great Basin plant communities

    USGS Publications Warehouse

    Pilliod, David S.; Arkle, Robert S.

    2013-01-01

    Resource managers and scientists need efficient, reliable methods for quantifying vegetation to conduct basic research, evaluate land management actions, and monitor trends in habitat conditions. We examined three methods for quantifying vegetation in 1-ha plots among different plant communities in the northern Great Basin: photography-based grid-point intercept (GPI), line-point intercept (LPI), and point-quarter (PQ). We also evaluated each method for within-plot subsampling adequacy and effort requirements relative to information gain. We found that, for most functional groups, percent cover measurements collected with the use of LPI, GPI, and PQ methods were strongly correlated. These correlations were even stronger when we used data from the upper canopy only (i.e., top “hit” of pin flags) in LPI to estimate cover. PQ was best at quantifying cover of sparse plants such as shrubs in early successional habitats. As cover of a given functional group decreased within plots, the variance of the cover estimate increased substantially, which required more subsamples per plot (i.e., transect lines, quadrats) to achieve reliable precision. For GPI, we found that that six–nine quadrats per hectare were sufficient to characterize the vegetation in most of the plant communities sampled. All three methods reasonably characterized the vegetation in our plots, and each has advantages depending on characteristics of the vegetation, such as cover or heterogeneity, study goals, precision of measurements required, and efficiency needed.

  13. A fluorogenic method for measuring enteropeptidase activity: spectral shift in the emission of GD4K-conjugated 7-amino-4-methylcoumarin.

    PubMed

    Choi, Mal-Gi; Lee, Eungyeong; Chung, Hye-Shin; Jang, Sei-Heon; Lee, ChangWoo

    2011-07-01

    Enteropeptidase is a serine protease secreted by the pancreas and converts inactive trypsinogen to active trypsin. Enteropeptidase cleaves the C-terminal end of the substrate recognition sequence Asp-Asp-Asp-Asp-Lys (D(4)K). The assay for enteropeptidase has utilized GD(4)K-conjugated 2-naphthylamine (GD(4)K-NA) as a fluorogenic probe over the last 30 years. However, no other D(4)K-conjugated fluorogenic substrates of enteropeptidase have been reported. Furthermore, naphthalene is known as carcinogenic to humans. In this study, we used shift in the emission spectrum of GD(4)K-conjugated 7-amino-4-methylcoumarin (GD(4)K-AMC) as a fluorogenic method to measure enteropeptidase activity. The kinetic analysis revealed that enteropeptidase has a K(M) of 0.025 mM and a k(cat) of 65 sec(-1) for GD(4)K-AMC, whereas it has a K(M) of 0.5 to 0.6 mM and a k(cat) of 25 sec(-1) for GD(4)K-NA. The optimum pH of GD(4)K-AMC hydrolysis was pH 8.0. Our data indicate that GD(4)K-AMC is more suitable as a substrate for enteropeptidase than GD(4)K-NA.

  14. Improvement of the variable storage coefficient method with water surface gradient as a variable

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The variable storage coefficient (VSC) method has been used for streamflow routing in continuous hydrological simulation models such as the Agricultural Policy/Environmental eXtender (APEX) and the Soil and Water Assessment Tool (SWAT) for more than 30 years. APEX operates on a daily time step and ...

  15. Novel, cyclic heat dissipation method for the correction of natural temperature gradients in sap flow measurements. Part 2. Laboratory validation.

    PubMed

    Reyes-Acosta, J Leonardo; Vandegehuchte, Maurits W; Steppe, Kathy; Lubczynski, Maciek W

    2012-07-01

    Sap flow measurements conducted with thermal dissipation probes (TDPs) are vulnerable to natural temperature gradient (NTG) bias. Few studies, however, attempted to explain the dynamics underlying the NTG formation and its influence on the sensors' signal. This study focused on understanding how the TDP signals are affected by negative and positive temperature influences from NTG and tested the novel cyclic heat dissipation (CHD) method to filter out the NTG bias. A series of three experiments were performed in which gravity-driven water flow was enforced on freshly cut stem segments of Fagus sylvatica L., while an artificial temperature gradient (ATG) was induced. The first experiment sought to confirm the incidence of the ATG on sensors. The second experiment established the mis-estimations caused by the biasing effect of the ATG on standard TDP measurements. The third experiment tested the accuracy of the CHD method to account for the ATG biasing effect, as compared with other cyclic correction methods. During experiments, sap flow measured by TDP was assessed against gravimetric measurements. The results show that negative and positive ATGs were comparable in pattern but substantially larger than field NTGs. Second, the ATG bias caused an overestimation of the standard TDP sap flux density of ∼17 cm(3) cm(-2) h(-1) by 76%, and the sap flux density of ∼2 cm(3) cm(-2) h(-1) by over 800%. Finally, the proposed CHD method successfully reduced the max. ATG bias to 25% at ∼11 cm(3) cm(-2) h(-1) and to 40% at ∼1 cm(3) cm(-2) h(-1). We concluded that: (i) the TDP method is susceptible to NTG especially at low flows; (ii) the CHD method successfully corrected the TDP signal and resulted in generally more accurate sap flux density estimates (mean absolute percentage error ranging between 11 and 21%) than standard constant power TDP method and other cyclic power methods; and (iii) the ATG enforcing system is a suitable way of re-creating NTG for future tests.

  16. The Spectrophotometric Method of Determining the Transmission of Solar Energy in Salt Gradient Solar Ponds

    NASA Technical Reports Server (NTRS)

    Giulianelli, J.

    1984-01-01

    In order to predict the thermal efficiency of a solar pond it is necessary to know total average solar energy reaching the storage layer. One method for determining this energy for water containing dissolved colored species is based upon spectral transmission measurements using a laboratory spectrophotometer. This method is examined and some of the theoretical ground work needed to discuss the measurement of transmission of light water. Results of in situ irradiance measurements from oceanography research are presented and the difficulties inherent in extrapolating laboratory data obtained with ten centimeter cells to real three dimensional pond situations is discussed. Particular emphasis is put on the need to account for molecular and particulate scattering in measurements done on low absorbing solutions. Despite these considerations it is expected that attenuation calculations based upon careful measurements using a dual beam spectrophotometer technique combined with known attenuation coefficients will be useful in solar pond modeling and monitoring for color buildup. Preliminary results using the CSM method are presented.

  17. Fabrication of gradient refractive index ball lenses using the method of combination of ion exchanging and sagging

    NASA Astrophysics Data System (ADS)

    Hao, Lv; Bangren, Shi; Jijiang, Wu; Lijun, Guo; Aimei, Liu

    2007-08-01

    Based on the Fick's diffusion equations, the distribution function of refractive index of a gradient refractive index ball lens (GRIN ball lens/GBL) is derived. Lithium containing silicate glass is fabricated and GRIN ball lenses (GBLs) which diameters are from 0.3 mm to 3.0 mm are made by the method of combination of Ion exchanging and sagging in sodium nitrate. Refractive index profiles of these GBLs are measured by interferometer, and the performances such as effective focal length (EFL), back focal length (BFL) and numerical aperture (NA) between GBLs and homogeneous ball lenses (HBLs) are compared. Results show that the distribution of the index of refraction is parabolic curve and its Δn is about 0.0002, the performances of the former are super to the latter.

  18. Double phase conjugation in tungsten bronze crystals.

    PubMed

    Sharp, E J; Clark Iii, W W; Miller, M J; Wood, G L; Monson, B; Salamo, G J; Neurgaonkar, R R

    1990-02-20

    In this paper we report a new method for double phase conjugation particularly suited to the tungsten bronze crystal strontium barium niobate. It has also been observed to produce conjugate waves in BaTiO(3) and BSKNN. This new arrangement is called the bridge conjugator because the two beams enter opposing [100] crystal faces and fan together to form a bridge without reflection off a crystal face. Our measurements indicate that the bridge conjugator is competitive with previously reported double phase conjugate mirrors in reflectivity, response time, ease of alignment, and fidelity.

  19. Predicting resist sensitivity to chemical flare effects though use of exposure density gradient method

    NASA Astrophysics Data System (ADS)

    Hyatt, Michael; DeVilliers, Anton; Jain, Kaveri

    2011-04-01

    Chemical flare has been shown to be a process limiter for patterns that are surrounded by areas of unexposed resist for certain chemically amplified resists. Using a pattern known to be susceptible to chemical flare effect a method was developed and tested on several materials. Details of the testing patterns, consisting of placements of small and large pattern density areas set to provide multiple degrees of resist loading; and a second level of loading variation achieved by selective exposure locations of those patterns across the wafer are given. Descriptions of the determination of slopes from linear trend-lines of the critical dimensions responses can be used to provide a gauge for internal evaluations as well as feedback to the vendors for chemical flare sensitivity.

  20. Comparison of gradient methods for gain tuning of a PD controller applied on a quadrotor system

    NASA Astrophysics Data System (ADS)

    Kim, Jinho; Wilkerson, Stephen A.; Gadsden, S. Andrew

    2016-05-01

    Many mechanical and electrical systems have utilized the proportional-integral-derivative (PID) control strategy. The concept of PID control is a classical approach but it is easy to implement and yields a very good tracking performance. Unmanned aerial vehicles (UAVs) are currently experiencing a significant growth in popularity. Due to the advantages of PID controllers, UAVs are implementing PID controllers for improved stability and performance. An important consideration for the system is the selection of PID gain values in order to achieve a safe flight and successful mission. There are a number of different algorithms that can be used for real-time tuning of gains. This paper presents two algorithms for gain tuning, and are based on the method of steepest descent and Newton's minimization of an objective function. This paper compares the results of applying these two gain tuning algorithms in conjunction with a PD controller on a quadrotor system.

  1. New method to estimate paleoprecipitation using fossil amphibians and reptiles and the middle and late Miocene precipitation gradients in Europe

    NASA Astrophysics Data System (ADS)

    Böhme, M.; Ilg, A.; Ossig, A.; Küchenhoff, H.

    2006-06-01

    Existing methods for determining paleoprecipitation are subject to large errors (±350 400 mm or more using mammalian proxies), or are restricted to wet climate systems due to their strong facies dependence (paleobotanical proxies). Here we describe a new paleoprecipitation tool based on an indexing of ecophysiological groups within herpetological communities. In recent communities these indices show a highly significant correlation to annual precipitation (r2 = 0.88), and yield paleoprecipitation estimates with average errors of ±250 280 mm. The approach was validated by comparison with published paleoprecipitation estimates from other methods. The method expands the application of paleoprecipitation tools to dry climate systems and in this way contributes to the establishment of a more comprehensive paleoprecipitation database. This method is applied to two high-resolution time intervals from the European Neogene: the early middle Miocene (early Langhian) and the early late Miocene (early Tortonian). The results indicate that both periods show significant meridional precipitation gradients in Europe, these being stronger in the early Langhian (threefold decrease toward the south) than in the early Tortonian (twofold decrease toward the south). This pattern indicates a strengthening of climatic belts during the middle Miocene climatic optimum due to Southern Hemisphere cooling and an increased contribution of Arctic low-pressure cells to the precipitation from the late Miocene onward due to Northern Hemisphere cooling.

  2. Full-field measurement of surface topographies and thin film stresses at elevated temperatures by digital gradient sensing method.

    PubMed

    Zhang, Changxing; Qu, Zhe; Fang, Xufei; Feng, Xue; Hwang, Keh-Chih

    2015-02-01

    Thin film stresses in thin film/substrate systems at elevated temperatures affect the reliability and safety of such structures in microelectronic devices. The stresses result from the thermal mismatch strain between the film and substrate. The reflection mode digital gradient sensing (DGS) method, a real-time, full-field optical technique, measures deformations of reflective surface topographies. In this paper, we developed this method to measure topographies and thin film stresses of thin film/substrate systems at elevated temperatures. We calibrated and compensated for the air convection at elevated temperatures, which is a serious problem for optical techniques. We covered the principles for surface topography measurements by the reflection mode DGS method at elevated temperatures and the governing equations to remove the air convection effects. The proposed method is applied to successfully measure the full-field topography and deformation of a NiTi thin film on a silicon substrate at elevated temperatures. The evolution of thin film stresses obtained by extending Stoney's formula implies the "nonuniform" effect the experimental results have shown.

  3. Computerized detection of noncalcified plaques in coronary CT angiography: Evaluation of topological soft gradient prescreening method and luminal analysis

    SciTech Connect

    Wei, Jun Zhou, Chuan; Chan, Heang-Ping; Chughtai, Aamer; Agarwal, Prachi; Kuriakose, Jean; Hadjiiski, Lubomir; Patel, Smita; Kazerooni, Ella

    2014-08-15

    Purpose: The buildup of noncalcified plaques (NCPs) that are vulnerable to rupture in coronary arteries is a risk for myocardial infarction. Interpretation of coronary CT angiography (cCTA) to search for NCP is a challenging task for radiologists due to the low CT number of NCP, the large number of coronary arteries, and multiple phase CT acquisition. The authors conducted a preliminary study to develop machine learning method for automated detection of NCPs in cCTA. Methods: With IRB approval, a data set of 83 ECG-gated contrast enhanced cCTA scans with 120 NCPs was collected retrospectively from patient files. A multiscale coronary artery response and rolling balloon region growing (MSCAR-RBG) method was applied to each cCTA volume to extract the coronary arterial trees. Each extracted vessel was reformatted to a straightened volume composed of cCTA slices perpendicular to the vessel centerline. A topological soft-gradient (TSG) detection method was developed to prescreen for NCP candidates by analyzing the 2D topological features of the radial gradient field surface along the vessel wall. The NCP candidates were then characterized by a luminal analysis that used 3D geometric features to quantify the shape information and gray-level features to evaluate the density of the NCP candidates. With machine learning techniques, useful features were identified and combined into an NCP score to differentiate true NCPs from false positives (FPs). To evaluate the effectiveness of the image analysis methods, the authors performed tenfold cross-validation with the available data set. Receiver operating characteristic (ROC) analysis was used to assess the classification performance of individual features and the NCP score. The overall detection performance was estimated by free response ROC (FROC) analysis. Results: With our TSG prescreening method, a prescreening sensitivity of 92.5% (111/120) was achieved with a total of 1181 FPs (14.2 FPs/scan). On average, six features

  4. An automated method for producing synoptic regional maps of river gradient variation: Procedure, accuracy tests, and comparison with other knickpoint mapping methods

    NASA Astrophysics Data System (ADS)

    Gonga-Saholiariliva, Nahossio; Gunnell, Yanni; Harbor, David; Mering, Catherine

    2011-11-01

    The study of abrupt changes in longitudinal river profiles, or knickpoints, is currently approached through an empirical power law: the slope-area relationship. Results based on digital elevation model (DEM) analyses and stream extractions are generally intended to determine crustal uplift rates and identify transient landscape conditions. In this article, we present an alternative geomorphometric method for locating knickpoints and knickzones based on local slope gradient and curvature attributes. Intended as a rapid, regional scale, automated knickpoint detection technique, the accuracy of this slope-curvature method is tested on two digital elevation grids, NASA's SRTM (ground resolution of 90 m, resampled here to 75 m) and the ASTER DEM (15 m) in the Sierra Nacimiento (New Mexico, USA), a basement-cored mountain range recently exhumed by waves of headward drainage integration in response to remote tectonic deformation in the adjacent Rio Grande rift. Out of every 10 gradient anomalies detected by the SRTM-derived numeric routine, up to 8 are certifiable knickpoints recognized among a population of georeferenced occurrences surveyed in the field. An independent comparison with the slope-area method provided a further accuracy test, which was particularly useful at sites that could not be validated in the field for practical reasons. Given the low tectonic activity of the study area, the majority of knickpoints was also found to coincide with lithologic boundaries, making it difficult without further geomorphological data to single out dynamic knickpoints directly caused by the upstream propagation of channel instabilities relating to base level change.

  5. Direct method of design and stress analysis of rotating disks with temperature gradient

    NASA Technical Reports Server (NTRS)

    Manson, S S

    1950-01-01

    A method is presented for the determination of the contour of disks, typified by those of aircraft gas turbines, to incorporate arbitrary elastic-stress distributions resulting from either centrifugal or combined centrifugal and thermal effects. The specified stress may be radial, tangential, or any combination of the two. Use is made of the finite-difference approach in solving the stress equations, the amount of computation necessary in the evolution of a design being greatly reduced by the judicious selection of point stations by the aid of a design chart. Use of the charts and of a preselected schedule of point stations is also applied to the direct problem of finding the elastic and plastic stress distribution in disks of a given design, thereby effecting a great reduction in the amount of calculation. Illustrative examples are presented to show computational procedures in the determination of a new design and in analyzing an existing design for elastic stress and for stresses resulting from plastic flow.

  6. RP-LC gradient elution method for simultaneous determination of thiocolchicoside, aceclofenac and related impurities in tablet formulation

    PubMed Central

    Karbhari, Pradnya A.; Joshi, Sneha J.; Bhoir, Suvarna I.

    2014-01-01

    Objective: The aim of the present study is to develop a simple and precise HPLC method for simultaneous determination of thiocolchicoside, aceclofenac and related impurities in a tablet formulation and validate as per ICH guidelines. The aim of study extends to perform forced degradation study to trace the degradation pathways of potential degradant impurities. Materials and Methods: The separation was achieved on a 4.6 mm × 100 mm, 3 μm C18 column at 40°C with the mobile phase containing 0.1 M ammonium acetate buffer and methanol in a gradient mode at a flow rate of 1.0 mL min−1. The UV detection was carried out at 257 nm. Results: Acelofenac, thiocolchicoside and their related compounds were well separated from each other with good resolution and symmetry factor without interference of excipients. The method for assay was linear in the range of 10-200 μg mL−1 for aceclofenac and 0.4 to 8 μg mL−1 for thiocolchicoside. Conclusion: The method was validated according to ICH guidelines and the acceptance criteria for accuracy, precision, linearity, specificity, robustness, ruggedness and system suitability were met in all cases. The method was highly specific, as two related compounds of thiocolchicoside and nine related compounds of aceclofenac were well separated from each other. Stress study ensured the specificity of the method as the unknown degradation products formed during stress studies did not interfere with the determination of thiocolchicoside and aceclofenac, thus proving the stability indicating capacity of the method. PMID:25400407

  7. Method to predict the bandwidth of elution profile under the linear gradient elution in reversed-phase HPLC.

    PubMed

    Lee, Ju Weon; Row, Kyung Ho

    2009-01-01

    Solute migration in a chromatographic column is an important consideration when designing batch or continuous chromatographic separation processes. Most design methods for the chromatographic processes are based on the equilibrium theory which concerns only the migration velocity of the solute. However, in real cases, it is important to predict the zone spreading which occurs by axial dispersion and mass transfer resistance. To predict the actual solute profiles in the column or effluent stream, numerical methods to solve nonlinear partial differential equations have been used. However, these methods involve much time and expense. In this work, two different rate factors are considered to predict the characteristics of the solute profiles. The first is solute migration velocity and the second is the zone spreading rate. The zone spreading rate can be estimated by the apparent axial dispersion coefficient which is obtained from the height of the equivalent theoretical plate in particular. Four benzene derivatives (benzene, toluene, p-xylene, and acetophenone) were used as model solutes, and two mobile phase systems, water/methanol and water/ACN, were used in RP-HPLC. The bandwidths and retention times of the solutes were predicted under several linear gradient conditions. The predicted and experimental bandwidths and retention times showed good agreement.

  8. Sequential measurements of conjugate observables

    NASA Astrophysics Data System (ADS)

    Carmeli, Claudio; Heinosaari, Teiko; Toigo, Alessandro

    2011-07-01

    We present a unified treatment of sequential measurements of two conjugate observables. Our approach is to derive a mathematical structure theorem for all the relevant covariant instruments. As a consequence of this result, we show that every Weyl-Heisenberg covariant observable can be implemented as a sequential measurement of two conjugate observables. This method is applicable both in finite- and infinite-dimensional Hilbert spaces, therefore covering sequential spin component measurements as well as position-momentum sequential measurements.

  9. A rational transformation conjugated to the Arnold-Thom Cat map. An application of the Schröder method to hyperbolic toral maps

    NASA Astrophysics Data System (ADS)

    Luévano, J.-R.

    2014-12-01

    We compute a vector-valued rational map conjugated to the Arnold-Thom Cat map by means of Schröder's method. The corresponding invariant density and the spectrum of Rényi information are analytically determined. We show that for the analogous n-dimensional case the invariant density is the product of n Cauchy densities. Hence, the spectrum of Rényi information is n times the corresponding Rényi information of a Cauchy density. We also work out two three-dimensional linear toral maps as an example of the general case.

  10. A novel prefractionation method combining protein and peptide isoelectric focusing in immobilized pH gradient strips.

    PubMed

    Pernemalm, Maria; Lehtiö, Janne

    2013-02-01

    To increase sensitivity and analytical depth in shotgun proteomics, prefractionation of complex samples is often used. Here we describe a novel prefractionation method, Sandwich high resolution isoelectric focusing, which combines both protein and peptide isoelectric focusing. In the first step, intact proteins are separated on the basis of isoelectric point (pI) using traditional immobilized pH gradient (IPG) strips. Segments in the IPG-strip containing proteins of interest are subsequently cut out and applied to in-strip digestion, without subsequent peptide elution. In the second peptide isoelectric focusing step, the strip segments are used as loading bridges. The peptides are thereby directly applied to the peptide isoelectric focusing, without an intermediate elution step, and separated on narrow range IPG strips to reduce the complexity on the peptide level. In the final step, the peptides are eluted into 96-well plates and analyzed with mass spectrometry. In a proof of principle experiment, using this method to zoom in on pI regions of interest in human plasma, we identify over 800 proteins, with concentrations spanning over 6 orders of magnitude.

  11. A generalized gradient projection method based on a new working set for minimax optimization problems with inequality constraints.

    PubMed

    Ma, Guodong; Zhang, Yufeng; Liu, Meixing

    2017-01-01

    Combining the techniques of the working set identification and generalized gradient projection, we present a new generalized gradient projection algorithm for minimax optimization problems with inequality constraints. In this paper, we propose a new optimal identification function, from which we provide a new working set. At each iteration, the improved search direction is generated by only one generalized gradient projection explicit formula, which is simple and could reduce the computational cost. Under some mild assumptions, the algorithm possesses the global and strong convergence. Finally, the numerical results show that the proposed algorithm is promising.

  12. Method and apparatus for fabrication of high gradient insulators with parallel surface conductors spaced less than one millimeter apart

    SciTech Connect

    Sanders, David M.; Decker, Derek E.

    1999-01-01

    Optical patterns and lithographic techniques are used as part of a process to embed parallel and evenly spaced conductors in the non-planar surfaces of an insulator to produce high gradient insulators. The approach extends the size that high gradient insulating structures can be fabricated as well as improves the performance of those insulators by reducing the scale of the alternating parallel lines of insulator and conductor along the surface. This fabrication approach also substantially decreases the cost required to produce high gradient insulators.

  13. Method and apparatus for fabrication of high gradient insulators with parallel surface conductors spaced less than one millimeter apart

    SciTech Connect

    Sanders, D.M.; Decker, D.E.

    1999-09-21

    Optical patterns and lithographic techniques are used as part of a process to embed parallel and evenly spaced conductors in the non-planar surfaces of an insulator to produce high gradient insulators. The approach extends the size that high gradient insulating structures can be fabricated as well as improves the performance of those insulators by reducing the scale of the alternating parallel lines of insulator and conductor along the surface. This fabrication approach also substantially decreases the cost required to produce high gradient insulators.

  14. Bacteriophage-nanocomposites: an easy and reproducible method for the construction, handling, storage and transport of conjugates for deployment of bacteriophages active against Pseudomonas aeruginosa.

    PubMed

    Cooper, Ian R; Illsley, Matthew; Korobeinyk, Alina V; Whitby, Raymond L D

    2015-04-01

    The purpose of this work was proof of concept to develop a novel, cost effective protocol for the binding of bacteriophages to a surface without loss of function, after storage in various media. The technology platform involved covalently bonding bacteriophage 13 (a Pseudomonas aeruginosa bacteriophage) to two magnetised multiwalled carbon nanotube scaffolds using a series of buffers; bacteriophage-nanotube (B-N) conjugates were efficacious after storage at 20 °C for six weeks. B-N conjugates were added to human cell culture in vitro for 9 days without causing necrosis and apoptosis. B-N conjugates were frozen (-20 °C) in cell culture media for several weeks, after which recovery from the human cell culture medium was possible using a simple magnetic separation technique. The retention of viral infective potential was demonstrated by subsequent spread plating onto lawns of susceptible P. aeruginosa. Analysis of the human cell culture medium revealed the production of interleukins by the human fibroblasts upon exposure to the bacteriophage. One day after exposure, IL-8 levels transitorily increased between 60 and 100 pg/mL, but this level was not found on any subsequent days, suggesting an initial but not long lasting response. This paper outlines the development of a method to deliver antimicrobial activity to a surface that is small enough to be combined with other materials. To our knowledge at time of publication, this is the first report of magnetically coupled bacteriophages specific to human pathogens which can be recovered from test systems, and could represent a novel means to conditionally deploy antibacterial agents into living eukaryotic systems without the risks of some antibiotic therapies.

  15. Alternative methods for the design of jet engine control systems

    NASA Technical Reports Server (NTRS)

    Sain, M. K.; Leake, R. J.; Basso, R.; Gejji, R.; Maloney, A.; Seshadri, V.

    1976-01-01

    Various alternatives to linear quadratic design methods for jet engine control systems are discussed. The main alternatives are classified into two broad categories: nonlinear global mathematical programming methods and linear local multivariable frequency domain methods. Specific studies within these categories include model reduction, the eigenvalue locus method, the inverse Nyquist method, polynomial design, dynamic programming, and conjugate gradient approaches.

  16. Increases in Water Potential Gradient Reduce Xylem Conductivity in Whole Plants. Evidence from a Low-Pressure Conductivity Method1

    PubMed Central

    Brodribb, Tim J.; Hill, Robert S.

    2000-01-01

    A new method using hydrostatic suctions (less than 0.02 MPa) was used to measure whole-root conductivity (Kr) in saplings of two angiosperm pioneer trees (Eucalyptus regnans and Toona australis) and two rainforest conifers (Dacrycarpus dacrydioides and Nageia fleurii). The resultant Kr was combined with measurements of stem and leaf hydraulic conductivity to calculate whole-plant conductivity and to predict leaf water potential (Ψl) during transpiration. At normal soil temperatures there was good agreement between measured and predicted Ψl during transpiration in all species. Changes in the soil-to-leaf water potential gradient were produced by root chilling, and in three of the four species, changes in Ψl corresponded to those expected by the effect of increased water viscosity on Kr. In one species, however, root chilling produced severe plant wilting and a decline in Ψl significantly below the predicted value. In this species Ψl decreased to a value close to, or below, the Ψl at 50% xylem cavitation. It is concluded that decreased whole-plant conductivity in T. australis resulted from a decrease in xylem conductivity due to stress-induced cavitation. PMID:10889251

  17. Comparative assessment of density functional methods for evaluating essential parameters to simulate SERS spectra within the excited state energy gradient approximation

    NASA Astrophysics Data System (ADS)

    Mohammadpour, Mozhdeh; Jamshidi, Zahra

    2016-05-01

    The prospect of challenges in reproducing and interpretation of resonance Raman properties of molecules interacting with metal clusters has prompted the present research initiative. Resonance Raman spectra based on the time-dependent gradient approximation are examined in the framework of density functional theory using different methods for representing the exchange-correlation functional. In this work the performance of different XC functionals in the prediction of ground state properties, excitation state energies, and gradients are compared and discussed. Resonance Raman properties based on time-dependent gradient approximation for the strongly low-lying charge transfer states are calculated and compared for different methods. We draw the following conclusions: (1) for calculating the binding energy and ground state geometry, dispersion-corrected functionals give the best performance in comparison to ab initio calculations, (2) GGA and meta GGA functionals give good accuracy in calculating vibrational frequencies, (3) excited state energies determined by hybrid and range-separated hybrid functionals are in good agreement with EOM-CCSD calculations, and (4) in calculating resonance Raman properties GGA functionals give good and reasonable performance in comparison to the experiment; however, calculating the excited state gradient by using the hybrid functional on the hessian of GGA improves the results of the hybrid functional significantly. Finally, we conclude that the agreement of charge-transfer surface enhanced resonance Raman spectra with experiment is improved significantly by using the excited state gradient approximation.

  18. Binding energy of transition-metal complexes with large pi-conjugate systems. Density functional theory vs post-Hartree-Fock methods.

    PubMed

    Ikeda, Atsushi; Nakao, Yoshihide; Sato, Hirofumi; Sakaki, Shigeyoshi

    2007-08-02

    We systematically evaluated the binding energies of d10, d8, and d6 transition-metal complexes with various pi-conjugate systems such as Pt(PH3)2{C2H4-n(CH=CH2)n}, Pd(PH3)2{C2H4-n(CH=CH2)n}, [PtCl3{C2H4-n-(CH=CH2)n}]-, [PdCl3{C2H4-n(CH=CH2)n}]-, and [PtCl5{C2H4-n(CH=CH2)n}]- (n = 0-4) using the MP2 to MP4, CCSD(T), and density functional theory (DFT) methods. The MP4(SDQ) and CCSD(T) methods present a reliable binding energy, whereas the DFT method significantly underestimates the binding energy when the size of the pi-conjugate system is large. The underestimation occurs independently of the coordinate bonding nature; the pi-back-donation is stronger than the sigma-donation in the Pt(0) complexes, as expected, they are comparable in the Pt(II) complexes, and only the sigma-donation participates in the coordinate bond of the Pt(IV) complexes. The DFT method provides moderately stronger charge-transfer (CT) interaction than the MP4(SDQ) method, suggesting that the underestimation of the binding energy by the DFT method does not arise from the insufficient description of the CT interaction. From theoretical investigation of several model systems, it is concluded that the underestimation arises from the insufficient description of electron correlation effects.

  19. Computer-aided detection of lung nodules: false positive reduction using a 3D gradient field method

    NASA Astrophysics Data System (ADS)

    Ge, Zhanyu; Sahiner, Berkman; Chan, Heang-Ping; Hadjiiski, Lubomir M.; Wei, Jun; Bogot, Naama; Cascade, Philip N.; Kazerooni, Ella A.; Zhou, Chuan

    2004-05-01

    We are developing a computer-aided detection system to aid radiologists in diagnosing lung cancer in thoracic computed tomographic (CT) images. The purpose of this study was to improve the false-positive (FP) reduction stage of our algorithm by developing and incorporating a gradient field technique. This technique extracts 3D shape information from the gray-scale values within a volume of interest. The gradient field feature values are higher for spherical objects, and lower for elongated and irregularly-shaped objects. A data set of 55 thin CT scans from 40 patients was used to evaluate the usefulness of the gradient field technique. After initial nodule candidate detection and rule-based first stage FP reduction, there were 3487 FP and 65 true positive (TP) objects in our data set. Linear discriminant classifiers with and without the gradient field feature were designed for the second stage FP reduction. The accuracy of these classifiers was evaluated using the area Az under the receiver operating characteristic (ROC) curve. The Az values were 0.93 and 0.91 with and without the gradient field feature, respectively. The improvement with the gradient field feature was statistically significant (p=0.01).

  20. Gradient networks

    NASA Astrophysics Data System (ADS)

    Toroczkai, Zoltán; Kozma, Balázs; Bassler, Kevin E.; Hengartner, N. W.; Korniss, G.

    2008-04-01

    Gradient networks are defined (Toroczkai and Bassler 2004 Nature 428 716) as directed graphs formed by local gradients of a scalar field distributed on the nodes of a substrate network G. We present the derivation for some of the general properties of gradient graphs and give an exact expression for the in-degree distribution R(l) of the gradient network when the substrate is a binomial (Erd{\\;\\kern -0.10em \\raise -0.35ex \\{{^{^{\\prime\\prime}}}}\\kern -0.57em \\o} s-Rényi) random graph, G_{N,p} , and the scalars are independent identically distributed (i.i.d.) random variables. We show that in the limit N \\to \\infty, p \\to 0, z = pN = \\mbox{const} \\gg 1, R(l)\\propto l^{-1} for l < l_c = z , i.e., gradient networks become scale-free graphs up to a cut-off degree. This paper presents the detailed derivation of the results announced in Toroczkai and Bassler (2004 Nature 428 716).

  1. Kinetic models of conjugated metabolic cycles

    NASA Astrophysics Data System (ADS)

    Ershov, Yu. A.

    2016-01-01

    A general method is developed for the quantitative kinetic analysis of conjugated metabolic cycles in the human organism. This method is used as a basis for constructing a kinetic graph and model of the conjugated citric acid and ureapoiesis cycles. The results from a kinetic analysis of the model for these cycles are given.

  2. A biconjugate gradient type algorithm on massively parallel architectures

    NASA Technical Reports Server (NTRS)

    Freund, Roland W.; Hochbruck, Marlis

    1991-01-01

    The biconjugate gradient (BCG) method is the natural generalization of the classical conjugate gradient algorithm for Hermitian positive definite matrices to general non-Hermitian linear systems. Unfortunately, the original BCG algorithm is susceptible to possible breakdowns and numerical instabilities. Recently, Freund and Nachtigal have proposed a novel BCG type approach, the quasi-minimal residual method (QMR), which overcomes the problems of BCG. Here, an implementation is presented of QMR based on an s-step version of the nonsymmetric look-ahead Lanczos algorithm. The main feature of the s-step Lanczos algorithm is that, in general, all inner products, except for one, can be computed in parallel at the end of each block; this is unlike the other standard Lanczos process where inner products are generated sequentially. The resulting implementation of QMR is particularly attractive on massively parallel SIMD architectures, such as the Connection Machine.

  3. Development and validation of an ultra-high-performance liquid chromatography tandem mass spectrometric method for the simultaneous determination of free and conjugated Alternaria toxins in cereal-based foodstuffs.

    PubMed

    Walravens, Jeroen; Mikula, Hannes; Rychlik, Michael; Asam, Stefan; Ediage, Emmanuel Njumbe; Di Mavungu, José Diana; Van Landschoot, Anita; Vanhaecke, Lynn; De Saeger, Sarah

    2014-10-31

    A UPLC-ESI(+/-)-MS/MS method for the simultaneous determination of free (alternariol, alternariol monomethyl ether, altenuene, tenuazonic acid, tentoxin, altertoxin-I) and conjugated (sulfates and glucosides of alternariol and alternariol monomethyl ether) Alternaria toxins in cereals and cereal products (rice, oat flakes and barley) was developed. Optimization of the sample preparation and extraction methodology was achieved through experimental design, using full factorial design for extraction solvent composition optimization and fractional factorial design to identify the critical factors in the sample preparation protocol, which were in turn subjected to optimization. Final extracts were analysed using an Waters Acquity UPLC system coupled to a Quattro Premier XE mass spectrometer equipped with an electrospray interface operated in both positive and negative ionization mode. Chromatographic separation was achieved using an Acquity UPLC HSS T3 column, and the applied gradient elution programme allowed for the simultaneous determination of 10 Alternaria toxins in a one-step chromatographic run with a total run time of only 7min. Subsequently, the method, applying isotopically labelled internal standards ([(2)H4]-alternariol monomethyl ether and [(13)C6,(15)N]-tenuazonic acid), was validated for several parameters such as linearity, apparent recovery, limit of detection, limit of quantification, precision, measurement uncertainty and specificity (in agreement with the criteria mentioned in Commission Regulation No. 401/2006/EC and Commission Decision No. 2002/657/EC). During validation, quality of the bioanalytical data was improved by counteracting the observed heteroscedasticity through the application of weighted least squares linear regression (WLSLR). Finally, 24 commercially available cereal-based foodstuffs were subjected to analysis, revealing the presence of tenuazonic acid in both rice and oat flake samples (

  4. Gradient-based Electrical Properties Tomography (gEPT): a Robust Method for Mapping Electrical Properties of Biological Tissues In Vivo Using Magnetic Resonance Imaging

    PubMed Central

    Liu, Jiaen; Zhang, Xiaotong; Schmitter, Sebastian; Van de Moortele, Pierre-Francois; He, Bin

    2014-01-01

    Purpose To develop high-resolution electrical properties tomography (EPT) methods and investigate a gradient-based EPT (gEPT) approach which aims to reconstruct the electrical properties (EP), including conductivity and permittivity, of an imaged sample from experimentally measured B1 maps with improved boundary reconstruction and robustness against measurement noise. Theory and Methods Using a multi-channel transmit/receive stripline head coil, with acquired B1 maps for each coil element, by assuming negligible Bz component compared to transverse B1 components, a theory describing the relationship between B1 field, EP value and their spatial gradient has been proposed. The final EP images were obtained through spatial integration over the reconstructed EP gradient. Numerical simulation, physical phantom and in vivo human experiments at 7 T have been conducted to evaluate the performance of the proposed methods. Results Reconstruction results were compared with target EP values in both simulations and phantom experiments. Human experimental results were compared with EP values in literature. Satisfactory agreement was observed with improved boundary reconstruction. Importantly, the proposed gEPT method proved to be more robust against noise when compared to previously described non-gradient-based EPT approaches. Conclusion The proposed gEPT approach holds promises to improve EP mapping quality by recovering the boundary information and enhancing robustness against noise. PMID:25213371

  5. Susceptibility gradient mapping (SGM): a new postprocessing method for positive contrast generation applied to superparamagnetic iron oxide particle (SPIO)-labeled cells.

    PubMed

    Dahnke, Hannes; Liu, Wei; Herzka, Daniel; Frank, Joseph A; Schaeffter, Tobias

    2008-09-01

    Local susceptibility gradients result in a dephasing of the precessing magnetic moments and thus in a fast decay of the NMR signals. In particular, cells labeled with superparamagnetic iron oxide particles (SPIOs) induce hypointensities, making the in vivo detection of labeled cells from such a negative image contrast difficult. In this work, a new method is proposed to selectively turn this negative contrast into a positive contrast. The proposed method calculates the susceptibility gradient and visualizes it in a parametric map directly from a regular gradient-echo image dataset. The susceptibility gradient map is determined in a postprocessing step, requiring no dedicated pulse sequences or adaptation of the sequence before and during image acquisition. Phantom experiments demonstrated that local susceptibility differences can be quantified. In vivo experiments showed the feasibility of the method for tracking of SPIO-labeled cells. The method bears the potential also for usage in other applications, including the detection of contrast agents and interventional devices as well as metal implants.

  6. Fast Gradient Elution Reversed-Phase HPLC with Diode-Array Detection as a High Throughput Screening Method for Drugs of Abuse

    SciTech Connect

    Peter W. Carr; K.M. Fuller; D.R. Stoll; L.D. Steinkraus; M.S. Pasha; Glenn G. Hardin

    2005-12-30

    A new approach has been developed by modifying a conventional gradient elution liquid chromatograph for the high throughput screening of biological samples to detect the presence of regulated intoxicants. The goal of this work was to improve the speed of a gradient elution screening method over current approaches by optimizing the operational parameters of both the column and the instrument without compromising the reproducibility of the retention times, which are the basis for the identification. Most importantly, the novel instrument configuration substantially reduces the time needed to re-equilibrate the column between gradient runs, thereby reducing the total time for each analysis. The total analysis time for each gradient elution run is only 2.8 minutes, including 0.3 minutes for column reequilibration between analyses. Retention times standard calibration solutes are reproducible to better than 0.002 minutes in consecutive runs. A corrected retention index was adopted to account for day-to-day and column-to-column variations in retention time. The discriminating power and mean list length were calculated for a library of 47 intoxicants and compared with previous work from other laboratories to evaluate fast gradient elution HPLC as a screening tool.

  7. Surfactant gradient methods using mixed systems of cethyltrimethylammonium chloride and nonionic surfactants possessing polyoxyethylene chains for electrokinetic separation of benzoate anions as model analytes.

    PubMed

    Esaka, Yukihiro; Sawamura, Mika; Murakami, Hiroya; Uno, Bunji

    2006-12-01

    Surfactant gradient methods for electrokinetic separation of 10 benzoates as model organic anions were investigated using mixed micellar solutions of cetyltrimethylammonium chloride (CTAC) and nonionic surfactants possessing polyoxyethylene chains, polyoxyethylene sorbitan monolaurate (Tween 20) or polyoxyethylene lauryl ether (Brij 35). Electroosmotic flow (EOF) was eliminated virtually by a coating of the inner wall of the capillaries, and then the benzoates were detected fundamentally in the order of their hydrophobicity. In a pure CTAC system, the synergistic influences of attractive electrostatic and hydrophobic interactions gave rise to quite large retention factors of many of the benzoate anions, resulting in their coelution. Addition of an adequate amount of Tween 20 to the pure CTAC system decreased the electrostatic interaction significantly to give remarkably improved separation of the analytes, but long analysis time was required. A surfactant gradient method would be useful to decrease analysis time and to improve separation simultaneously. Under slight EOF, the micelles in the inlet reservoir can pass through and, thus, interact with all of the analytes before they were detected. In the present system, surfactant gradient separations could be performed simply by changing compositions of the surfactant solutions in the inlet reservoir during a single run. Additionally, we carried out continuous gradient separation using a simple device. Brij 35 gave an effect parallel to that by Tween 20 in migration behavior of the analytes. A practically negligible change in the level of the baseline was observed in a stepwise gradient elution with the CTAC/Brij 35 system because of the small absorbance at the detection wavelength, while that with the CTAC/Tween 20 was considerable. All the benzoates were separated completely within reasonable analysis times using both stepwise and continuous gradient programs for the concentrations of Tween 20 or Brij 35 in the

  8. Application of machine learning methods to describe the effects of conjugated equine estrogens therapy on region-specific brain volumes.

    PubMed

    Casanova, Ramon; Espeland, Mark A; Goveas, Joseph S; Davatzikos, Christos; Gaussoin, Sarah A; Maldjian, Joseph A; Brunner, Robert L; Kuller, Lewis H; Johnson, Karen C; Mysiw, W Jerry; Wagner, Benjamin; Resnick, Susan M

    2011-05-01

    Use of conjugated equine estrogens (CEE) has been linked to smaller regional brain volumes in women aged ≥65 years; however, it is unknown whether this results in a broad-based characteristic pattern of effects. Structural magnetic resonance imaging was used to assess regional volumes of normal tissue and ischemic lesions among 513 women who had been enrolled in a randomized clinical trial of CEE therapy for an average of 6.6 years, beginning at ages 65-80 years. A multivariate pattern analysis, based on a machine learning technique that combined Random Forest and logistic regression with L(1) penalty, was applied to identify patterns among regional volumes associated with therapy and whether patterns discriminate between treatment groups. The multivariate pattern analysis detected smaller regional volumes of normal tissue within the limbic and temporal lobes among women that had been assigned to CEE therapy. Mean decrements ranged as high as 7% in the left entorhinal cortex and 5% in the left perirhinal cortex, which exceeded the effect sizes reported previously in frontal lobe and hippocampus. Overall accuracy of classification based on these patterns, however, was projected to be only 54.5%. Prescription of CEE therapy for an average of 6.6 years is associated with lower regional brain volumes, but it does not induce a characteristic spatial pattern of changes in brain volumes of sufficient magnitude to discriminate users and nonusers.

  9. Use of passive diffusion sampling method for defining NO2 concentrations gradient in São Paulo, Brazil

    PubMed Central

    da Silva, Agnes Soares; Cardoso, Maria Regina; Meliefste, Kees; Brunekreef, Bert

    2006-01-01

    Background Air pollution in São Paulo is constantly being measured by the State of Sao Paulo Environmental Agency, however there is no information on the variation between places with different traffic densities. This study was intended to identify a gradient of exposure to traffic-related air pollution within different areas in São Paulo to provide information for future epidemiological studies. Methods We measured NO2 using Palmes' diffusion tubes in 36 sites on streets chosen to be representative of different road types and traffic densities in São Paulo in two one-week periods (July and August 2000). In each study period, two tubes were installed in each site, and two additional tubes were installed in 10 control sites. Results Average NO2 concentrations were related to traffic density, observed on the spot, to number of vehicles counted, and to traffic density strata defined by the city Traffic Engineering Company (CET). Average NO2concentrations were 63μg/m3 and 49μg/m3 in the first and second periods, respectively. Dividing the sites by the observed traffic density, we found: heavy traffic (n = 17): 64μg/m3 (95% CI: 59μg/m3 – 68μg/m3); local traffic (n = 16): 48μg/m3 (95% CI: 44μg/m3 – 52μg/m3) (p < 0.001). Conclusion The differences in NO2 levels between heavy and local traffic sites are large enough to suggest the use of a more refined classification of exposure in epidemiological studies in the city. Number of vehicles counted, traffic density observed on the spot and traffic density strata defined by the CET might be used as a proxy for traffic exposure in São Paulo when more accurate measurements are not available. PMID:16772044

  10. Preparation and in vitro evaluation of ethosomal total alkaloids of Sophora alopecuroides loaded by a transmembrane pH-gradient method.

    PubMed

    Zhou, Yan; Wei, Yuhui; Liu, Huanxiang; Zhang, Guoqiang; Wu, Xin'an

    2010-09-01

    A novel transmembrane pH gradient active loading method to prepare alkaloids binary ethosomes was developed in this work. Using this novel method, binary ethosomes containing total alkaloids extracted from Sophora alopecuroides (TASA) were prepared successfully at the temperature below the phase transition temperature (Tc) of the phosphatidyl choline (PC). Several factors affecting this method were investigated. The qualities of the TASA binary ethosomes were characterized by the shape, particle size, and encapsulation efficiency (EE). The percutaneous absorption study of TASA binary ethosomes was performed using confocal laser scanning microscopy and Franz diffusion cells. The results showed that more than 90% sophoridine, 47% matrine, 35% sophocarpine, and 32% lemannine in TASA were entrapped within 1 h at 40°C, with an efficiency improvement of 8.87, 8.10, 7.63, and 7.78-fold than those observed in passive loading method. Transdermal experiments showed that the penetration depth and fluorescence intensity of Rhodamine B from binary ethosome prepared by pH gradient active loading method were much greater than that from binary ethosome prepared by passive loading method or hydroalcoholic solution. These results suggested transmembrane pH gradient active loading method may be an effective method to prepare alkaloids ethosomal systems at the temperatures below the Tc of PC.

  11. Internally mounted thin-liquid-film skin-friction meter - Comparison with floating element method with and without pressure gradient

    NASA Technical Reports Server (NTRS)

    Hornung, Hans; Seto, Jeffrey

    1991-01-01

    A new, robust oil film skin friction meter was designed and constructed. This enables skin friction measurements remotely and from within the model, as well as avoiding the need to know the location of the leading edge of the film. The instrument was tested by comparing measurements with those given by a floating element gage in a zero pressure gradient flat plate turbulent boundary layer. Both instruments agreed satisfactorily with the well-known curve for this case. Significant discrepancies between the two instruments were observed in the case of adverse and favorable pressure gradients. The discrepancies were of opposite sign for opposite-sign pressure gradients as is consistent with the error expected from floating-element gages. Additional confidence in the oil film technique is supplied by the good agreement of the behavior of the film profile with predictions from lubrication theory.

  12. Engineering spatial gradients of signaling proteins using magnetic nanoparticles.

    PubMed

    Bonnemay, L; Hostachy, S; Hoffmann, C; Gautier, J; Gueroui, Z

    2013-11-13

    Intracellular biochemical reactions are often localized in space and time, inducing gradients of enzymatic activity that may play decisive roles in determining cell's fate and functions. However, the techniques available to examine such enzymatic gradients of activity remain limited. Here, we propose a new method to engineer a spatial gradient of signaling protein concentration within Xenopus egg extracts using superparamagnetic nanoparticles. We show that, upon the application of a magnetic field, a concentration gradient of nanoparticles with a tunable length extension is established within confined egg extracts. We then conjugate the nanoparticles to RanGTP, a small G-protein controlling microtubule assembly. We found that the generation of an artificial gradient of Ran-nanoparticles modifies the spatial positioning of microtubule assemblies. Furthermore, the spatial control of the level of Ran concentration allows us to correlate the local fold increase in Ran-nanoparticle concentration with the spatial positioning of the microtubule-asters. Our assay provides a bottom-up approach to examine the minimum ingredients generating polarization and symmetry breaking within cells. More generally, these results show how magnetic nanoparticles and magnetogenetic tools can be used to control the spatiotemporal dynamics of signaling pathways.

  13. New Langevin and gradient thermostats for rigid body dynamics.

    PubMed

    Davidchack, R L; Ouldridge, T E; Tretyakov, M V

    2015-04-14

    We introduce two new thermostats, one of Langevin type and one of gradient (Brownian) type, for rigid body dynamics. We formulate rotation using the quaternion representation of angular coordinates; both thermostats preserve the unit length of quaternions. The Langevin thermostat also ensures that the conjugate angular momenta stay within the tangent space of the quaternion coordinates, as required by the Hamiltonian dynamics of rigid bodies. We have constructed three geometric numerical integrators for the Langevin thermostat and one for the gradient thermostat. The numerical integrators reflect key properties of the thermostats themselves. Namely, they all preserve the unit length of quaternions, automatically, without the need of a projection onto the unit sphere. The Langevin integrators also ensure that the angular momenta remain within the tangent space of the quaternion coordinates. The Langevin integrators are quasi-symplectic and of weak order two. The numerical method for the gradient thermostat is of weak order one. Its construction exploits ideas of Lie-group type integrators for differential equations on manifolds. We numerically compare the discretization errors of the Langevin integrators, as well as the efficiency of the gradient integrator compared to the Langevin ones when used in the simulation of rigid TIP4P water model with smoothly truncated electrostatic interactions. We observe that the gradient integrator is computationally less efficient than the Langevin integrators. We also compare the relative accuracy of the Langevin integrators in evaluating various static quantities and give recommendations as to the choice of an appropriate integrator.

  14. Effects of temperature gradient in the growth of Si0.5Ge0.5 crystals by the traveling liquidus-zone method on board the International Space Station

    NASA Astrophysics Data System (ADS)

    Kinoshita, K.; Arai, Y.; Inatomi, Y.; Tsukada, T.; Miyata, H.; Tanaka, R.

    2016-12-01

    Si0.5Ge0.5 crystals were grown at two different temperature gradients on board the International Space Station (ISS) using the traveling liquidus-zone (TLZ) method and effects of temperature gradient on crystal quality were investigated. Although average axial Ge concentration profile was not affected by the temperature gradient, crystal quality was affected greatly. Single crystal length was shortened and constitutional supercooling (CS) is shown to occur more easily at higher temperature gradient. The calculated degree of CS based on the solute concentration profile in the melt and phase diagram data is about 4 times larger when the temperature gradient is twice, which supports the experimental results. Instability at high temperature gradient is unique to the TLZ method and is not common to other crystal growth methods such as the directional solidification method and Czochralski method.

  15. The method of common search direction of joint inversion

    NASA Astrophysics Data System (ADS)

    Zhao, C.; Tang, R.

    2013-12-01

    In geophysical inversion, the first step is to construct an objective function. The second step is using the optimization algorithm to minimize the objective function, such as the gradient method and the conjugate gradient method. Compared with the former, the conjugate gradient method can find a better direction to make the error decreasing faster and has been widely used for a long time. At present, the joint inversion is generally using the conjugate gradient method. The most important thing of joint inversion is to construct the partial derivative matrix with respect to different physical properties. Then we should add the constraints among different physical properties into the integrated matrix and also use the cross gradient as constrained of joint inversion. There are two ways to apply the cross gradient into inverse process that can be added to the data function or the model function. One way is adding the cross gradient into data function. The partial derivative matrix will grow two times, meanwhile it's also requested to calculate the cross gradient of each grid and bring great computation cost.

  16. Auxin conjugated to fluorescent dyes--a tool for the analysis of auxin transport pathways.

    PubMed

    Sokołowska, K; Kizińska, J; Szewczuk, Z; Banasiak, A

    2014-09-01

    Auxin is a small molecule involved in most processes related to plant growth and development. Its effect usually depends on the distribution in tissues and the formation of concentration gradients. Until now there has been no tool for the direct tracking of auxin transport at the cellular and tissue level; therefore the majority of studies have been based on various indirect methods. However, due to their various restrictions, relatively little is known about the relationship between various pathways of auxin transport and specific developmental processes. We present a new research tool: fluorescently labelled auxin in the form of a conjugate with two different fluorescent tracers, FITC and RITC, which allows direct observation of auxin transport in plant tissues. Chemical analysis and biological tests have shown that our conjugates have auxin-like biological activity and transport; therefore they can be used in all experimental systems as an alternative to IAA. In addition, the conjugates are a universal tool that can be applied in studies of all plant groups and species. The conjugation procedure presented in this paper can be adapted to other fluorescent dyes, which are constantly being improved. In our opinion, the conjugates greatly expand the possibilities of research concerning the role of auxin and its transport in different developmental processes in plants.

  17. A cell-centred finite volume method for the Poisson problem on non-graded quadtrees with second order accurate gradients

    NASA Astrophysics Data System (ADS)

    Batty, Christopher

    2017-02-01

    This paper introduces a two-dimensional cell-centred finite volume discretization of the Poisson problem on adaptive Cartesian quadtree grids which exhibits second order accuracy in both the solution and its gradients, and requires no grading condition between adjacent cells. At T-junction configurations, which occur wherever resolution differs between neighboring cells, use of the standard centred difference gradient stencil requires that ghost values be constructed by interpolation. To properly recover second order accuracy in the resulting numerical gradients, prior work addressing block-structured grids and graded trees has shown that quadratic, rather than linear, interpolation is required; the gradients otherwise exhibit only first order convergence, which limits potential applications such as fluid flow. However, previous schemes fail or lose accuracy in the presence of the more complex T-junction geometries arising in the case of general non-graded quadtrees, which place no restrictions on the resolution of neighboring cells. We therefore propose novel quadratic interpolant constructions for this case that enable second order convergence by relying on stencils oriented diagonally and applied recursively as needed. The method handles complex tree topologies and large resolution jumps between neighboring cells, even along the domain boundary, and both Dirichlet and Neumann boundary conditions are supported. Numerical experiments confirm the overall second order accuracy of the method in the L∞ norm.

  18. Gradient refractive index of the crystalline lens of the Black Oreo Dory (Allocyttus Niger): comparison of magnetic resonance imaging (MRI) and laser ray-trace methods.

    PubMed

    Garner, L F; Smith, G; Yao, S; Augusteyn, R C

    2001-04-01

    The gradient refractive index of the crystalline lens in the Black Oreo Dory (Allocyttus Niger) was determined using two methods; an optimisation program based on finite ray-tracing and the path of laser beams through the lens, and magnetic resonance imaging (MRI) and the linear relationship between refractive index and nuclear transverse relaxation rates. The methods showed good agreement in the cortical zone of the lens, but the lack of free water in the core of the lens made MRI measurement impossible in this region. The laser-optimisation method gave mean values of 1.368 and 1.543 for the surface and core refractive indices respectively, with a radial distribution for the gradient refractive index given by n(r)=1.543-0.121r2-0.033r4-0.021r6.

  19. A study of numerical methods of solution of the equations of motion of a controlled satellite under the influence of gravity gradient torque

    NASA Technical Reports Server (NTRS)

    Thompson, J. F.; Mcwhorter, J. C.; Siddiqi, S. A.; Shanks, S. P.

    1973-01-01

    Numerical methods of integration of the equations of motion of a controlled satellite under the influence of gravity-gradient torque are considered. The results of computer experimentation using a number of Runge-Kutta, multi-step, and extrapolation methods for the numerical integration of this differential system are presented, and particularly efficient methods are noted. A large bibliography of numerical methods for initial value problems for ordinary differential equations is presented, and a compilation of Runge-Kutta and multistep formulas is given. Less common numerical integration techniques from the literature are noted for further consideration.

  20. SU-C-BRA-02: Gradient Based Method of Target Delineation On PET/MR Image of Head and Neck Cancer Patients

    SciTech Connect

    Dance, M; Chera, B; Falchook, A; Das, S; Lian, J

    2015-06-15

    Purpose: Validate the consistency of a gradient-based segmentation tool to facilitate accurate delineation of PET/CT-based GTVs in head and neck cancers by comparing against hybrid PET/MR-derived GTV contours. Materials and Methods: A total of 18 head and neck target volumes (10 primary and 8 nodal) were retrospectively contoured using a gradient-based segmentation tool by two observers. Each observer independently contoured each target five times. Inter-observer variability was evaluated via absolute percent differences. Intra-observer variability was examined by percentage uncertainty. All target volumes were also contoured using the SUV percent threshold method. The thresholds were explored case by case so its derived volume matched with the gradient-based volume. Dice similarity coefficients (DSC) were calculated to determine overlap of PET/CT GTVs and PET/MR GTVs. Results: The Levene’s test showed there was no statistically significant difference of the variances between the observer’s gradient-derived contours. However, the absolute difference between the observer’s volumes was 10.83%, with a range from 0.39% up to 42.89%. PET-avid regions with qualitatively non-uniform shapes and intensity levels had a higher absolute percent difference near 25%, while regions with uniform shapes and intensity levels had an absolute percent difference of 2% between observers. The average percentage uncertainty between observers was 4.83% and 7%. As the volume of the gradient-derived contours increased, the SUV threshold percent needed to match the volume decreased. Dice coefficients showed good agreement of the PET/CT and PET/MR GTVs with an average DSC value across all volumes at 0.69. Conclusion: Gradient-based segmentation of PET volume showed good consistency in general but can vary considerably for non-uniform target shapes and intensity levels. PET/CT-derived GTV contours stemming from the gradient-based tool show good agreement with the anatomically and

  1. Preliminary Study of the Feasibility of Inverse Problem Algorithms Used for Arc Magnetic Measurement Method

    NASA Astrophysics Data System (ADS)

    Wang, Qian; Li, Xingwen; Song, Haoyong; Rong, Mingzhe

    2010-04-01

    Non-contact magnetic measurement method is an effective way to study the air arc behavior experimentally One of the crucial techniques is to solve an inverse problem for the electromagnetic field. This study is devoted to investigating different algorithms for this kind of inverse problem preliminarily, including the preconditioned conjugate gradient method, penalty function method and genetic algorithm. The feasibility of each algorithm is analyzed. It is shown that the preconditioned conjugate gradient method is valid only for few arc segments, the estimation accuracy of the penalty function method is dependent on the initial conditions, and the convergence of genetic algorithm should be studied further for more segments in an arc current.

  2. Revisiting conjugate schedules.

    PubMed

    MacAleese, Kenneth R; Ghezzi, Patrick M; Rapp, John T

    2015-07-01

    The effects of conjugate reinforcement on the responding of 13 college students were examined in three experiments. Conjugate reinforcement was provided via key presses that changed the clarity of pictures displayed on a computer monitor in a manner proportional to the rate of responding. Experiment 1, which included seven parameters of clarity change per response, revealed that responding decreased as the percentage clarity per response increased for all five participants. These results indicate that each participant's responding was sensitive to intensity change, which is a parameter of conjugate reinforcement schedules. Experiment 2 showed that responding increased during conjugate reinforcement phases and decreased during extinction phases for all four participants. Experiment 3 also showed that responding increased during conjugate reinforcement and further showed that responding decreased during a conjugate negative punishment condition for another four participants. Directions for future research with conjugate schedules are briefly discussed.

  3. Oligonucleotide conjugates for therapeutic applications

    PubMed Central

    Winkler, Johannes

    2013-01-01

    Insufficient pharmacokinetic properties and poor cellular uptake are the main hurdles for successful therapeutic development of oligonucleotide agents. The covalent attachment of various ligands designed to influence the biodistribution and cellular uptake or for targeting specific tissues is an attractive possibility to advance therapeutic applications and to expand development options. In contrast to advanced formulations, which often consist of multiple reagents and are sensitive to a variety of preparation conditions, oligonucleotide conjugates are defined molecules, enabling structure-based analytics and quality control techniques. This review gives an overview of current developments of oligonucleotide conjugates for therapeutic applications. Attached ligands comprise peptides, proteins, carbohydrates, aptamers and small molecules, including cholesterol, tocopherol and folic acid. Important linkage types and conjugation methods are summarized. The distinct ligands directly influence biochemical parameters, uptake machanisms and pharmacokinetic properties. PMID:23883124

  4. Oligonucleotide conjugates for therapeutic applications.

    PubMed

    Winkler, Johannes

    2013-07-01

    Insufficient pharmacokinetic properties and poor cellular uptake are the main hurdles for successful therapeutic development of oligonucleotide agents. The covalent attachment of various ligands designed to influence the biodistribution and cellular uptake or for targeting specific tissues is an attractive possibility to advance therapeutic applications and to expand development options. In contrast to advanced formulations, which often consist of multiple reagents and are sensitive to a variety of preparation conditions, oligonucleotide conjugates are defined molecules, enabling structure-based analytics and quality control techniques. This review gives an overview of current developments of oligonucleotide conjugates for therapeutic applications. Attached ligands comprise peptides, proteins, carbohydrates, aptamers and small molecules, including cholesterol, tocopherol and folic acid. Important linkage types and conjugation methods are summarized. The distinct ligands directly influence biochemical parameters, uptake mechanisms and pharmacokinetic properties.

  5. Gradient-index crystalline lens model: A new method for determining the paraxial properties by the axial and field rays

    NASA Astrophysics Data System (ADS)

    Rama, María. Angeles; Pérez, María. Victoria; Bao, Carmen; Flores-Arias, María. Teresa; Gómez-Reino, Carlos

    2005-05-01

    Gradient-index (GRIN) models of the human lens have received wide attention in optometry and vision sciences for considering the effect of inhomogeneity of the refractive index on the optical properties of the lens. This paper uses the continuous asymmetric bi-elliptical model to determine analytically cardinal elements, magnifications and refractive power of the lens by the axial and field rays in order to study the paraxial light propagation through the human lens from its GRIN nature.

  6. Assessment of a combined spin- and gradient-echo (SAGE) DSC-MRI method for preclinical neuroimaging.

    PubMed

    Stokes, Ashley M; Skinner, Jack T; Quarles, C Chad

    2014-12-01

    The goal of this study was to optimize and validate a combined spin- and gradient-echo (SAGE) sequence for dynamic susceptibility-contrast magnetic resonance imaging to obtain hemodynamic parameters in a preclinical setting. The SAGE EPI sequence was applied in phantoms and in vivo rat brain (normal, tumor, and stroke tissue). Partial and full Fourier encoding schemes were implemented and characterized. Maps of cerebral blood volume (CBV), cerebral blood flow (CBF), mean transit time (MTT), vessel size index (VSI), volume transfer constant (K(trans)), and volume fraction of the extravascular extracellular space (ve) were obtained. Partial Fourier encoding provided shortened echo times with acceptable signal-to-noise ratio and temporal stability, thus enabling reliable characterization of T2, T2(*) and T1 in both phantoms and rat brain. The hemodynamic parameters CBV, CBF, and MTT for gradient-echo and spin-echo contrast were determined in tumor and stroke; VSI, K(trans), and ve were also computed in tumor tissue. The SAGE EPI sequence allows the acquisition of multiple gradient- and spin-echoes, from which measures of perfusion, permeability, and vessel size can be obtained in a preclinical setting. Partial Fourier encoding can be used to minimize SAGE echo times and reliably quantify dynamic T2 and T2(*) changes. This acquisition provides a more comprehensive assessment of hemodynamic status in brain tissue with vascular and perfusion abnormalities.

  7. Applications of thermal-gradients method for the optimization of α-amylase crystallization conditions based on dynamic and static light scattering data

    NASA Astrophysics Data System (ADS)

    Delboni, L. F.; Iulek, J.; Burger, R.; da Silva, A. C. R.; Moreno, A.

    2002-02-01

    The expression, purification, crystallization, and characterization by X-ray diffraction of α-amylase are described here. Dynamic and static light scattering methods with a temperature controller was used to optimize the crystallization conditions of α-amylase from Bacillus stearothermophilus an important enzyme in many fields of industrial activity. After applying thermal gradients for growing crystals, X-ray cryo-crystallographic methods were employed for the data collection. Crystals grown by these thermal-gradients diffracted up to a maximum resolution of 3.8 Å, which allowed the determination of the unit cell constants as follows: a=61.7 Å, b=86.7 Å, c=92.2 Å and space group C222 (or C222 1).

  8. Enhanced photophysics of conjugated polymers

    DOEpatents

    Chen, Liaohai

    2007-06-12

    A particulate fluorescent conjugated polymer surfactant complex and method of making and using same. The particles are between about 15 and about 50 nm and when formed from a lipsome surfactant have a charge density similar to DNA and are strongly absorbed by cancer cells.

  9. Precise characterization method of antibody-conjugated magnetic nanoparticles for pathogen detection using stuffer-free multiplex ligation-dependent probe amplification.

    PubMed

    Chung, Boram; Shin, Gi Won; Choi, Woong; Joo, Jinmyoung; Jeon, Sangmin; Jung, Gyoo Yeol

    2014-12-01

    Antibody-conjugated magnetic nanoparticles (Ab-MNPs) have potential in pathogen detection because they allow target cells to be easily separated from complex sample matrices. However, the sensitivity and specificity of pathogen capture by Ab-MNPs generally vary according to the types of MNPs, antibodies, and sample matrices, as well as preparation methods, including immobilization. Therefore, achieving a reproducible analysis utilizing Ab-MNPs as a pathogen detection method requires accurate characterization of Ab-MNP capture ability and standardization of all handling processes. In this study, we used high-resolution CE-single strand conformational polymorphism coupled with a stuffer-free multiplex ligation-dependent probe amplification system to characterize Ab-MNPs. The capture ability of Ab-MNPs targeting Salmonella enteritidis and nine pathogens, including S. enteritidis, was analyzed in phosphate buffer and milk. The effect of storage conditions on the stability of Ab-MNPs was also assessed. The results showed that the stuffer-free multiplex ligation-dependent probe amplification system has the potential to serve as a standard characterization method for Ab-MNPs. Moreover, the precise characterization of Ab-MNPs facilitated robust pathogen detection in various applications.

  10. Optimization of the virus concentration method using polyethyleneimine-conjugated magnetic beads and its application to the detection of human hepatitis A, B and C viruses.

    PubMed

    Uchida, Eriko; Kogi, Mieko; Oshizawa, Tadashi; Furuta, Birei; Satoh, Koei; Iwata, Akiko; Murata, Mitsuhiro; Hikata, Mikio; Yamaguchi, Teruhide

    2007-07-01

    To enhance the sensitivity of virus detection by polymerase chain reaction (PCR) and reverse transcription PCR (RT-PCR), a novel virus concentration method using polyethyleneimine (PEI)-conjugated magnetic beads was developed in our previous study. However, several viruses could not be concentrated by this method. In this paper, the conditions of virus concentration were optimized to concentrate a wide range of viruses more efficiently. The PEI beads adsorbed viruses more efficiently than other cationic polymers, and the optimum virus concentration was obtained under weak acidic conditions. Mass spectrometric analysis revealed that several serum proteins, such as complement type 3, complement type 4 and immunoglobulin M (IgM), were co-adsorbed by the PEI beads, suggesting that the beads may adsorb viruses not only by direct adsorption, but also via immune complex formation. This hypothesis was confirmed by the result that poliovirus, which PEI beads could not adsorb directly, could be concentrated by the beads via immune complex formation. On the other hand, hepatitis A (HAV) and hepatitis C (HCV) viruses were adsorbed directly by PEI beads almost completely. Like poliovirus, hepatitis B virus (HBV) was concentrated efficiently by the addition of anti-HBV IgM. In conclusion, virus concentration using PEI beads is a useful method to concentrate a wide range of viruses and can be used to enhance the sensitivity of detection of HAV, HBV and HCV.

  11. Gradient vs. approximation design optimization techniques in low-dimensional convex problems

    NASA Astrophysics Data System (ADS)

    Fedorik, Filip

    2013-10-01

    Design Optimization methods' application in structural designing represents a suitable manner for efficient designs of practical problems. The optimization techniques' implementation into multi-physical softwares permits designers to utilize them in a wide range of engineering problems. These methods are usually based on modified mathematical programming techniques and/or their combinations to improve universality and robustness for various human and technical problems. The presented paper deals with the analysis of optimization methods and tools within the frame of one to three-dimensional strictly convex optimization problems, which represent a component of the Design Optimization module in the Ansys program. The First Order method, based on combination of steepest descent and conjugate gradient method, and Supbproblem Approximation method, which uses approximation of dependent variables' functions, accompanying with facilitation of Random, Sweep, Factorial and Gradient Tools, are analyzed, where in different characteristics of the methods are observed.

  12. Iterative methods for weighted least-squares

    SciTech Connect

    Bobrovnikova, E.Y.; Vavasis, S.A.

    1996-12-31

    A weighted least-squares problem with a very ill-conditioned weight matrix arises in many applications. Because of round-off errors, the standard conjugate gradient method for solving this system does not give the correct answer even after n iterations. In this paper we propose an iterative algorithm based on a new type of reorthogonalization that converges to the solution.

  13. Non-linear optical study of BODIPY-benzimidazole conjugate by solvatochromic, Z-scan and theoretical methods

    NASA Astrophysics Data System (ADS)

    Thakare, Shrikant S.; Sreenath, Mavila C.; Chitrambalam, Subramaniyan; Joe, Isaac H.; Sekar, Nagaiyan

    2017-02-01

    BODIPY chromophore flanked with the benzimidazole moiety at 2-position has been investigated for its nonlinear optical (NLO) properties. Charge transfer character developed by the unsymmetrical substitution on the molecular framework and the solvatochromic behaviour of this dye inspired us to study its NLO characteristics. NLO response has been measured using solvatochromic method as well as the Z scan technique. The values obtained for nonlinear absorption coefficient (β) and third order susceptibility χ(3) are -7.45 × 10-12 and 3.85 × 10-13 respectively. Quantum chemical calculations have also been performed to estimate the NLO properties theoretically by using DFT method with three functionals viz B3LYP, BHHLYP and CAMB3LYP with 6-311 G (d,p) basis set. The results obtained from the DFT method are in well accordance with those produced from solvatochromic method.

  14. Application and experimental validation of an integral method for simulation of gradient-induced eddy currents on conducting surfaces during magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Harris, C. T.; Haw, D. W.; Handler, W. B.; Chronik, B. A.

    2013-06-01

    The time-varying magnetic fields created by the gradient coils in magnetic resonance imaging can produce negative effects on image quality and the system itself. Additionally, they can be a limiting factor to the introduction of non-MR devices such as cardiac pacemakers, orthopedic implants, and surgical robotics. The ability to model the induced currents produced by the switching gradient fields is key to developing methods for reducing these unwanted interactions. In this work, a framework for the calculation of induced currents on conducting surface geometries is summarized. This procedure is then compared to two separate experiments: (1) the analysis of the decay of currents induced upon a conducting cylinder by an insert gradient set within a head only 7 T MR scanner; and (2) analysis of the heat deposited into a small conductor by a uniform switching magnetic field at multiple frequencies and two distinct conductor thicknesses. The method was shown to allow the accurate modeling of the induced time-varying field decay in the first case, and was able to provide accurate estimation of the rise in temperature in the second experiment to within 30% when the skin depth was greater than or equal to the thickness of the conductor.

  15. In vivo measurement of the size of oil bodies in plant seeds using a simple and robust pulsed field gradient NMR method.

    PubMed

    Gromova, Marina; Guillermo, Armel; Bayle, Pierre-Alain; Bardet, Michel

    2015-04-01

    An easy to implement and convenient method to measure the mean size of oil bodies (OBs) in plant seeds is proposed using a pulsed field gradient nuclear magnetic resonance (PFGNMR) approach. PFGNMR is a well-known technique used to study either free or restricted diffusion of molecules. As triacylglycerols (TAG) are confined in OBs, analysis of their diffusion properties is a well-suited experimental approach to determine OB sizes. In fact, at long diffusion time, TAG mean squared displacement is limited by the size of the domain where these molecules are confined. In order to access the OB size distribution, strong intensities of magnetic field gradients are generally required. In this work we demonstrate for the first time that a standard liquid-phase NMR probe equipped with a weak-intensity gradient coil can be used to determine the mean size of OBs. Average sizes were measured for several seeds, and OB diameters obtained by PFGNMR were fully consistent with previously published values obtained by microscopy techniques. Moreover, this approach provided evidence of TAG transfer through the network of interconnected OBs, which is dependent on the ability of adjacent membranes to open diffusion routes between OBs. The main advantage of the NMR method is that it does not require any sample preparation and experiments are performed with whole seeds directly introduced in a standard NMR tube.

  16. Identification of PAH conjugates in fish bile using high pressure liquid chromatography/electrospray mass spectrometry

    SciTech Connect

    Brand, D.G.; Cretney, W.J.; Ikonomou, M.

    1995-12-31

    Polycyclic aromatic hydrocarbons (PAHs) have been identified in marine sediments and water associated with many types of industrial activities and the presence of PAH metabolites in finfish bile is evidence for recent acute or chronic exposure to these contaminants. Analysis of bile for PAH metabolite conjugates, using reverse phase high pressure liquid chromatography (RP-HPLC) with fluorescence detection and quantification as benzo[a]pyrene (BaP) equivalents, revealed higher concentrations of these metabolites in English sole (pleuronectes verulus) collected from a pulp mill site (Crofton) and an aluminum smelter site (Kitimat) compared to a reference site (Bamfield). The chromatograms of bile from English sole caught at the polluted sites showed different complex mixtures of fluorescent compounds. The portion of biliary metabolite conjugates fluorescing at BaP wavelengths (380nm/430nm) that may be derived from mutagenic or carcinogenic PAHs cannot be determined quantitatively without identification of individual metabolites. Studies are being conducted to identify specific mutagenic or carcinogenic PAH precursors through their metabolite conjugates (glutathiones, glucuronides, sulfates) in bile of English sole by HPLC combined with electrospray mass spectrometry (HPLC/ES-MS). A RP-HPLC method using a Supelcosil LC-ABZ column and gradient elution has been developed that is compatible with ES ionization and still allows separation of PAH metabolite conjugates. Good separation of available glucuronide, sulfate and glutathione standards has been obtained, with the ES-MS operating in the negative ion mode, method detection limits in the pM range have been established from flow injections of individual conjugate standard solutions. HPLC/ESMS measurements of metabolite conjugates in English sole bile from coastal British Columbia sites will be presented.

  17. An efficient formulation and implementation of the analytic energy gradient method to the single and double excitation coupled-cluster wave function - Application to Cl2O2

    NASA Technical Reports Server (NTRS)

    Rendell, Alistair P.; Lee, Timothy J.

    1991-01-01

    The analytic energy gradient for the single and double excitation coupled-cluster (CCSD) wave function has been reformulated and implemented in a new set of programs. The reformulated set of gradient equations have a smaller computational cost than any previously published. The iterative solution of the linear equations and the construction of the effective density matrices are fully vectorized, being based on matrix multiplications. The new method has been used to investigate the Cl2O2 molecule, which has recently been postulated as an important intermediate in the destruction of ozone in the stratosphere. In addition to reporting computational timings, the CCSD equilibrium geometries, harmonic vibrational frequencies, infrared intensities, and relative energetics of three isomers of Cl2O2 are presented.

  18. Selected nutrient contents, fatty acid composition, including conjugated linoleic acid, and retention values in separable lean from lamb rib loins as affected by external fat and cooking method.

    PubMed

    Badiani, Anna; Montellato, Lara; Bochicchio, Davide; Anfossi, Paola; Zanardi, Emanuela; Maranesi, Magda

    2004-08-11

    Proximate composition and fatty acid profile, conjugated linoleic acid (CLA) isomers included, were determined in separable lean of raw and cooked lamb rib loins. The cooking methods compared, which were also investigated for cooking yields and true nutrient retention values, were dry heating of fat-on cuts and moist heating of fat-off cuts; the latter method was tested as a sort of dietetic approach against the more traditional former type. With significantly (P < 0.05) lower cooking losses, dry heating of fat-on rib-loins produced slightly (although only rarely significantly) higher retention values for all of the nutrients considered, including CLA isomers. On the basis of the retention values obtained, both techniques led to a minimum migration of lipids into the separable lean, which was higher (P < 0.05) in dry heating than in moist heating, and was characterized by the prevalence of saturated and monounsaturated fatty acids. On the whole, the response to cooking of the class of CLA isomers (including that of the nutritionally most important isomer cis-9,trans-11) was more similar to that of the monounsaturated than the polyunsaturated fatty acids.

  19. Research on food and nutrition characteristics of conjugated fatty acids.

    PubMed

    Tsuduki, Tsuyoshi

    2015-01-01

    In this study, the physiological effects of fatty acids with conjugated double bonds were widely examined in vitro and in vivo. Initially, a method for determination of conjugated fatty acids in food and biological samples was established. I then clarified that the oxidative stability of conjugated fatty acids was improved by the form of triacylglycerol and addition of an antioxidant, and the influence of this effect on the metabolism and pharmacokinetics of conjugated fatty acids was clarified in vivo. In addition, antitumor, anti-angiogenesis, and antiobesity effects of conjugated fatty acids were found for the first time, thus demonstrating the usefulness of conjugated fatty acids. This communication mainly outlines the data obtained for conjugated linolenic acid. In addition, this review summarizes my research on conjugated fatty acid.

  20. Nanoparticle manipulation by thermal gradient

    PubMed Central

    2012-01-01

    A method was proposed to manipulate nanoparticles through a thermal gradient. The motion of a fullerene molecule enclosed inside a (10, 10) carbon nanotube with a thermal gradient was studied by molecular dynamics simulations. We created a one-dimensional potential valley by imposing a symmetrical thermal gradient inside the nanotube. When the temperature gradient was large enough, the fullerene sank into the valley and became trapped. The escaping velocities of the fullerene were evaluated based on the relationship between thermal gradient and thermophoretic force. We then introduced a new way to manipulate the position of nanoparticles by translating the position of thermostats with desirable thermal gradients. Compared to nanomanipulation using a scanning tunneling microscope or an atomic force microscope, our method for nanomanipulation has a great advantage by not requiring a direct contact between the probe and the object. PMID:22364240

  1. AFRODITE - passive flow control for skin-friction drag reduction using the method of spanwise mean velocity gradient

    NASA Astrophysics Data System (ADS)

    Fallenius, Bengt; Sattarzadeh, Sohrab; Downs, Robert; Shahinfar, Shahab; Fransson, Jens

    2015-11-01

    Over the last decade wind tunnel experiments and numerical simulations have shown that steady spanwise mean velocity gradients are able to attenuate the growth of different types of boundary layer disturbances. Within the AFRODITE research program different techniques to setup the spanwise mean velocity variations have been studied and their stabilizing effect leading to transition delay quantified. A successful boundary-layer modulator for transition delay has turned out to be the miniature-vortex generator and has been well documented during the past years. More recent ideas of setting up spanwise mean velocity gradients will be presented here. We show that, the non-linear interaction between a pair of oblique disturbance waves creating a streaky base flow, as well as the direct surface modulation by means of applying wavy surfaces in the spanwise direction, can both successfully be utilized for transition delay and hence skin-friction drag reduction. The European Research Council is gratefully acknowledged (ERC-StG-2010- 258339).

  2. Phase-Conjugated Fluorescence

    DTIC Science & Technology

    1991-01-01

    reverse if necessary and identify by block number)FIELD GROUP SUB-GROUP PHASE-CONJUGATED FLUORESCENCE EMITTED POWER FOUR -WAVE MIXING THREE CONTRIBUTIONS...atom near a phase conjugator (PC) based on four -wave mixing is studied from first principles. The MaxwellLeisenberg equations are solved for the...Fronczak Hall State University of New York at Buffalo Buffalo, New York 14260 Fluorescent emission by an atom near a phase conjugator (PC) based on four -wave

  3. Digital optical phase conjugation of fluorescence in turbid tissue

    SciTech Connect

    Vellekoop, Ivo M.; Cui Meng; Yang Changhuei

    2012-08-20

    We demonstrate a method for phase conjugating fluorescence. Our method, called reference free digital optical phase conjugation, can conjugate extremely weak, incoherent optical signals. It was used to phase conjugate fluorescent light originating from a bead covered with 0.5 mm of light-scattering tissue. The phase conjugated beam refocuses onto the bead and causes a local increase of over two orders of magnitude in the light intensity. Potential applications are in imaging, optical trapping, and targeted photochemical activation inside turbid tissue.

  4. Combined gradient projection/single component artificial force induced reaction (GP/SC-AFIR) method for an efficient search of minimum energy conical intersection (MECI) geometries

    NASA Astrophysics Data System (ADS)

    Harabuchi, Yu; Taketsugu, Tetsuya; Maeda, Satoshi

    2017-04-01

    We report a new approach to search for structures of minimum energy conical intersection (MECIs) automatically. Gradient projection (GP) method and single component artificial force induced reaction (SC-AFIR) method were combined in the present approach. As case studies, MECIs of benzene and naphthalene between their ground and first excited singlet electronic states (S0/S1-MECIs) were explored. All S0/S1-MECIs reported previously were obtained automatically. Furthermore, the number of force calculations was reduced compared to the one required in the previous search. Improved convergence in a step in which various geometrical displacements are induced by SC-AFIR would contribute to the cost reduction.

  5. Polarisabilities of long conjugated chain molecules with density functional response methods: The role of coupled and uncoupled response

    SciTech Connect

    Heßelmann, Andreas

    2015-04-28

    The longitudinal component of the dipole-dipole polarisability of polyacetylene molecules containing 4 to 20 carbon atoms has been calculated with density-functional theory (DFT) response methods. In order to analyse the effect of the uncoupled and coupled contributions to the response matrix, a number of different sets of orbitals were combined with different approximations for the Hessian matrix. This revealed a surprising result: a qualitatively correct increase of the polarisability with the chain length can already be reproduced on the uncoupled level if the response matrix is constructed from Hartree-Fock (HF) or exact-exchange (EXX) DFT orbitals. The nonlocal HF and the local EXX exchange potentials both produce a displacement of charge from the chain ends to the centre of the polyacetylene molecule compared to DFT methods using standard exchange-correlation potentials. In this way, the reduced increase of the transition dipole moments along the molecular axis counteracts the decrease of the occupied-virtual orbital energy gaps and leads to a linear dependence of the polarisabilities (normalised by the number of carbon atoms) on the chain length. A new DFT response approach is tested which utilises unitary transformed Hartree-Fock orbitals as input and which resolves the failure of standard DFT response methods.

  6. The growth of a cubic, single phase, Cd 0.6Mn 0.4Te single crystal by the vertical gradient freeze method

    NASA Astrophysics Data System (ADS)

    Azoulay, M.; Raizman, A.; Weingarten, R.; Shacham, H.; Feldstein, H.

    1993-03-01

    The growth of CdMnTe single crystals faces some difficulties due to the phase transition in the solid state at high temperatures, just after solidification. To overcome this problem, it has been suggested to grow the crystals from a Te-rich solution by the traveling heater method at a lower temperature than that of growth from the melt, or alternatively to grow the crystal from the melt at high axial thermal gradient near the interface. In this paper, we present for the first time the growth of cubic, single phase, CdxMn1-xTe single crystals by the vertical gradient freeze technique under a very low axial thermal gradient in the melt (3°C/cm) and high manganese content (x ≈ 40%). The solidification stage is characterized by a rapid cooling of the crystal through the phase transition temperature region, followed by annealing at about 800°C. The crystal exhibits a very high crystalline perfection, as measured by the double-crystal X-ray rocking curves with a full width at half maximum of 30 arc sec and low optical losses of about 1 dB/mm between 650 and 820 nm with λ-cutoff at 630 nm. Further magneto-optical properties are currently examined for a possible application in devices.

  7. Shape optimization of radiant enclosures with specular-diffuse surfaces by means of a random search and gradient minimization

    NASA Astrophysics Data System (ADS)

    Rukolaine, Sergey A.

    2015-01-01

    A technique of the shape optimization of radiant enclosures with specular-diffuse surfaces is proposed. The shape optimization problem is formulated as an operator equation of the first kind with respect to a surface to be optimized. The operator equation is reduced to a minimization problem for a least-squares objective shape functional. The minimization problem is solved by a combination of the pure random (or blind) search (the simplest stochastic minimization method) and the conjugate gradient method. The random search is used to find a starting point for the gradient method. The latter needs the gradient of the objective functional. The shape gradient of the objective functional is derived by means of the shape sensitivity analysis and the adjoint problem method. Eventually, the shape gradient is obtained as a result of solving the direct and adjoint problems. If a surface to be optimized is given by a finite number of parameters, then the objective functional becomes a function in a finite-dimensional space and the shape gradient becomes an ordinary gradient. Numerical examples of the shape optimization of "two-dimensional" radiant enclosures with polyhedral specular or specular-diffuse surfaces are given.

  8. Method and apparatus for producing a carbon based foam article having a desired thermal-conductivity gradient

    DOEpatents

    Klett, James W [Knoxville, TN; Cameron, Christopher Stan [Sanford, NC

    2010-03-02

    A carbon based foam article is made by heating the surface of a carbon foam block to a temperature above its graphitizing temperature, which is the temperature sufficient to graphitize the carbon foam. In one embodiment, the surface is heated with infrared pulses until heat is transferred from the surface into the core of the foam article such that the graphitizing temperature penetrates into the core to a desired depth below the surface. The graphitizing temperature is maintained for a time sufficient to substantially entirely graphitize the portion of the foam article from the surface to the desired depth below the surface. Thus, the foam article is an integral monolithic material that has a desired conductivity gradient with a relatively high thermal conductivity in the portion of the core that was graphitized and a relatively low thermal conductivity in the remaining portion of the foam article.

  9. Validation of a pH gradient-based ion-exchange chromatography method for high-resolution monoclonal antibody charge variant separations.

    PubMed

    Rea, Jennifer C; Moreno, G Tony; Lou, Yun; Farnan, Dell

    2011-01-25

    Ion-exchange chromatography is widely used for profiling the charge heterogeneity of proteins, including monoclonal antibodies. Despite good resolving power and robustness, ionic strength-based ion-exchange separations are product-specific and time-consuming to develop. We have previously reported a novel pH-based separation of proteins by cation exchange chromatography that was multi-product, high-resolution, and robust against variations in sample matrix salt concentration and pH. In this study, a pH gradient-based separation method using cation exchange chromatography was evaluated in a mock validation. This method was shown to be robust for monoclonal antibodies and suitable for its intended purpose of charge heterogeneity analysis. Simple mixtures of defined buffer components were used to generate the pH gradients that separated closely related antibody species. Validation characteristics, such as precision and linearity, were evaluated. Robustness to changes in protein load, buffer pH and column oven temperature was demonstrated. The stability-indicating capability of this method was determined using thermally stressed antibody samples. In addition, intermediate precision was demonstrated using multiple instruments, multiple analysts, multiple column lots, and different column manufacturers. Finally, the precision for this method was compared to conventional ion-exchange chromatography and imaged capillary isoelectric focusing. These results demonstrate the superior precision and robustness of this multi-product method, which can be used for the high-throughput evaluation of in-process and final product samples.

  10. An ensemble average method to estimate absolute TEC using radio beacon-based differential phase measurements: Applicability to regions of large latitudinal gradients in plasma density

    NASA Astrophysics Data System (ADS)

    Thampi, Smitha V.; Bagiya, Mala S.; Chakrabarty, D.; Acharya, Y. B.; Yamamoto, M.

    2014-12-01

    A GNU Radio Beacon Receiver (GRBR) system for total electron content (TEC) measurements using 150 and 400 MHz transmissions from Low-Earth Orbiting Satellites (LEOS) is fabricated in house and made operational at Ahmedabad (23.04°N, 72.54°E geographic, dip latitude 17°N) since May 2013. This system receives the 150 and 400 MHz transmissions from high-inclination LEOS. The first few days of observations are presented in this work to bring out the efficacy of an ensemble average method to convert the relative TECs to absolute TECs. This method is a modified version of the differential Doppler-based method proposed by de Mendonca (1962) and suitable even for ionospheric regions with large spatial gradients. Comparison of TECs derived from a collocated GPS receiver shows that the absolute TECs estimated by this method are reliable estimates over regions with large spatial gradient. This method is useful even when only one receiving station is available. The differences between these observations are discussed to bring out the importance of the spatial differences between the ionospheric pierce points of these satellites. A few examples of the latitudinal variation of TEC during different local times using GRBR measurements are also presented, which demonstrates the potential of radio beacon measurements in capturing the large-scale plasma transport processes in the low-latitude ionosphere.

  11. Application of Quantum-Dot Conjugates for Detection and Subspecies Differentiation of Vibrio cholerae by Optical Methods

    NASA Astrophysics Data System (ADS)

    Erohin, P. S.; Utkin, D. V.; Kouklev, V. E.; Ossina, N. A.; Miheeva, E. A.; Alenkina, T. V.

    2016-03-01

    The application of bioconjugates of specific antibodies and CdSe quantum dots to identify two serovariants of Vibrio cholerae using fluorescence microscopy and optical spectroscopy is considered. It is found that a mixture of different bioconjugates with different emission maxima can be used without affecting the specificity of the method. Different V. cholerae serovariants are colored differently in fl uorescence microscopy (bright green and bright yellow), thereby allowing subspecies differentiation. The absorption spectrum of the bacterial suspension changed with homologous antigens in the sample and did not change with heterologous antigens. It is shown that the quantum-dot bioconjugates can serve as an alternative to the traditional fluorescence and agglutination diagnostics.

  12. Gradient forests: calculating importance gradients on physical predictors.

    PubMed

    Ellis, Nick; Smith, Stephen J; Pitcher, C Roland

    2012-01-01

    In ecological analyses of species and community distributions there is interest in the nature of their responses to environmental gradients and in identifying the most important environmental variables, which may be used for predicting patterns of biodiversity. Methods such as random forests already exist to assess predictor importance for individual species and to indicate where along gradients abundance changes. However, there is a need to extend these methods to whole assemblages, to establish where along the range of these gradients the important compositional changes occur, and to identify any important thresholds or change points. We develop such a method, called "gradient forest," which is an extension of the random forest approach. By synthesizing the cross-validated R2 and accuracy importance measures from univariate random forest analyses across multiple species, sampling devices, and surveys, gradient forest obtains a monotonic function of each predictor that represents the compositional turnover along the gradient of the predictor. When applied to a synthetic data set, the method correctly identified the important predictors and delineated where the compositional change points occurred along these gradients. Application of gradient forest to a real data set from part of the Great Barrier Reef identified mud fraction of the sediment as the most important predictor, with highest compositional turnover occurring at mud fraction values around 25%, and provided similar information for other predictors. Such refined information allows for more accurate capturing of biodiversity patterns for the purposes of bioregionalization, delineation of protected areas, or designing of biodiversity surveys.

  13. Evaluation of iodovinyl antibody conjugates: Comparison with a p-iodobenzoyl conjugate and direct radioiodination

    SciTech Connect

    Hadley, S.W.; Wilbur, D.S. )

    1990-03-01

    The preparations and conjugations of 2,3,5,6-tetrafluorophenyl 5-(125I/131I)iodo-4-pentenoate (7a) and 2,3,5,6-tetrafluorophenyl 3,3-dimethyl-5-(125I/131I)iodo-4-pentenoate (7b) to monoclonal antibodies are reported. Reagents 7a and 7b were prepared in high radiochemical yield by iododestannylation of their corresponding 5-tri-n-butylstannyl precursors. Radioiodinated antibody conjugates were prepared by reaction of 7a or 7b with the protein at basic pH. Evaluation of these conjugates by several in vitro procedures demonstrated that the radiolabel was attached to the antibody in a stable manner and that the conjugates maintained immunoreactivity. Comparative dual-isotope biodistribution studies of a monoclonal antibody Fab fragment conjugate of 7a and 7b with the same Fab fragment labeled with N-succinimidyl p-(131I)iodobenzoate (PIB, p-iodobenzoate, 2) or directly radioiodinated have been carried out in tumor-bearing nude mice. Coinjection of the Fab conjugate of 7a with the Fab conjugate of 2 demonstrated that the biodistributions were similar in most organs, except the neck tissue (thyroid-containing) and the stomach, which contained substantially increased levels of the 7a label. Coinjection of the Fab conjugate of 7a with the Fab fragment radioiodinated by using the chloramine-T method demonstrated that the biodistributions were remarkably similar, suggesting roughly equivalent in vivo deiodination of these labeled antibody fragments. Coinjection of the Fab conjugate of 7a with the Fab conjugate of 7b indicated that there was {approximately} a 2-fold reduction in the amount of in vivo deiodination of the 7b conjugate as compared to the 7a conjugate.

  14. In situ measurements of tritium evapotranspiration (³H-ET) flux over grass and soil using the gradient and eddy covariance experimental methods and the FAO-56 model.

    PubMed

    Connan, O; Maro, D; Hébert, D; Solier, L; Caldeira Ideas, P; Laguionie, P; St-Amant, N

    2015-10-01

    The behaviour of tritium in the environment is linked to the water cycle. We compare three methods of calculating the tritium evapotranspiration flux from grassland cover. The gradient and eddy covariance methods, together with a method based on the theoretical Penmann-Monteith model were tested in a study carried out in 2013 in an environment characterised by high levels of tritium activity. The results show that each of the three methods gave similar results. The various constraints applying to each method are discussed. The results show a tritium evapotranspiration flux of around 15 mBq m(-2) s(-1) in this environment. These results will be used to improve the entry parameters for the general models of tritium transfers in the environment.

  15. A Single Gradient Stability-Indicating Reversed-Phase LC Method for the Estimation of Impurities in Omeprazole and Domperidone Capsules.

    PubMed

    Seshadri, Raja Kumar; Raghavaraju, Thummala Veera; Chakravarthy, Ivon Elisha

    2013-01-01

    A gradient reversed-phase liquid chromatographic (RP-LC) method was developed for the quantitative estimation of impurities in the pharmaceutical dosage form of Omeprazole and Domperidone capsules. The developed method is a stability-indicating test method for the estimation of impurities generated during the formulation and storage of Omeprazole and Domperidone capsules. The chromatographic separation was achieved on a column packed with octadecyl silane, having a column length of 250 mm and diameter of 4.6 mm with a particle size of 5 μm, and by following a gradient program using a combination of a monobasic potassium phosphate buffer (0.05M) and acetonitrile. Since the spectral properties were similar, both compounds' individual impurities were estimated at 285 nm. Forced degradation studies were performed on Omeprazole pellets (enteric coated) and Domperidone pellets (SR coated) encapsulated in size '1' hard gelatin capsules. Omeprazole and Domperidone were degraded using acid hydrolysis (0.1 N hydrochloric acid), base (0.1 N sodium hydroxide), oxidation (50% hydrogen peroxide), heat (105 °C), and UV light (254 nm). The established method was validated and found to be linear, accurate, precise, specific, robust, and rugged.

  16. Geometry optimization of radicaloid systems using improved virtual orbital-complete active space configuration interaction (IVO-CASCI) analytical gradient method.

    PubMed

    Chattopadhyay, Sudip; Chaudhuri, Rajat K; Freed, Karl F

    2011-04-28

    The improved virtual orbital (IVO) complete active space (CAS) configuration interaction (IVO-CASCI) method is a simplified CAS self-consistent field (SCF), CASSCF, method. Unlike the CASSCF approach, the IVO-CASCI method does not require iterations beyond an initial SCF calculation, rendering the IVO-CASCI scheme computationally more tractable than the CASSCF method and devoid of the convergence problems that sometimes plague CASSCF calculations as the CAS size increases, while retaining all the essential positive benefits of the CASSCF method. Earlier applications demonstrate that the IVO-CASCI energies are at least as accurate as those from the CASSCF and provide the impetus for our recent development of the analytical derivative procedures that are necessary for a wide applicability of the IVO-CASCI approach. Here we test the ability of the analytic energy gradient IVO-CASCI approach (which can treat both closed- and open-shell molecules of arbitrary spin multiplicity) to compute the equilibrium geometries of four organic radicaloid species, namely, (i) the diradicals trimethylenemethane (TMM), 2,6-pyridyne, and the 2,6-pyridynium cation and (ii) a triradical 1,2,3-tridehydrobenzene (TDB), using various basis sets and different choices for the active space. Although these systems and related molecules have fascinated theoretical chemists for many years, their strong multireference character makes their description quite difficult with most standard many-body approaches. Thus, they provide ideal tests to assess the performance of the IVO-CASCI method. The present work demonstrates consistent agreement with far more expensive benchmark state-of-the-art ab initio calculations and thereby indicates that this new gradient method is able to describe the geometries of various radicaloids very accurately, even when small, but qualitatively correct, reference spaces are used. For example, the IVO-CASCI method leads to a monocyclic structure for the 2,6-isomers of the

  17. In Vitro Antioxidant-Activity Evaluation of Gallic-Acid-Grafted Chitosan Conjugate Synthesized by Free-Radical-Induced Grafting Method.

    PubMed

    Hu, Qiaobin; Wang, Taoran; Zhou, Mingyong; Xue, Jingyi; Luo, Yangchao

    2016-07-27

    The major objective of this work was to develop a green and facile process to prepare gallic acid-chitosan conjugate and comprehensively evaluate the physicochemical properties and biological activities of an as-prepared water-soluble chitosan derivative. A free-radical-induced grafting approach using an ascorbic acid-hydrogen peroxide redox pair was adopted. The obtained conjugate was characterized by Fourier transform infrared spectroscopy, UV-vis, X-ray diffraction, and pKa analysis. The antioxidant activities were evaluated by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis(3-ethylbenzothiazoline-6)-sulphonic acid (ABTS), reducing power, and oxygen-radical antioxidant-capacity assays. The results showed that the mass ratio of gallic acid to chitosan played a vital role in determining the grafting degree and ζ potential of the conjugates, with the ratio of 0.5:1 being the optimal ratio that resulted in the highest grafting degree. The antioxidant assays demonstrated that conjugation significantly improved the antioxidant activities, being dramatically higher than that of free chitosan. It was notable that the DPPH- and ABTS-scavenging activities of conjugate at 0.4 mg/mL reached the same level as the free gallic acid at the equivalent concentration. Our study demonstrated a green and facile synthesis approach to preparing a novel water-soluble chitosan derivative that may have promising potentials in the food industry.

  18. The Measurement of Temperature Gradients in a Soft Tissue Phantom using PVDF arrays: A Simulation Case Using the Finite Element Method (FEM)

    NASA Astrophysics Data System (ADS)

    Acevedo, Pedro; Vázquez, Mónica; Durán, Joel; Petrearce, Rodolfo

    A simulation case is presented using the Finite Element Method (FEM) to simulate the performance of PVDF arrays to measure temperature gradients through the determination of phase shifts, i.e. time shifts of the waveform of the echo due to a change in the speed of propagation of ultrasound as a result of a change in temperature, they can be interpreted as phase shifts in the frequency domain. Making it possible to determine the change in temperature from the phase shifts; in a medium of propagation previously characterized.

  19. Two-dimensional thin-layer chromatography with adsorbent gradient as a method of chromatographic fingerprinting of furanocoumarins for distinguishing selected varieties and forms of Heracleum spp.

    PubMed

    Cieśla, Lukasz; Bogucka-Kocka, Anna; Hajnos, Michał; Petruczynik, Anna; Waksmundzka-Hajnos, Monika

    2008-10-17

    There are a lot of taxonomic classifications of the genus Heracleum, and many authors indicate they need revision. Morphological identification is difficult to perform, as there are only few characteristic differences between each Heracleum species, varieties and forms. Furanocoumarins are characteristic compounds for the Apiaceae family, and they can be found in the whole genus in large quantities. Despite this fact, it is difficult to use the furanocoumarin profiles of plants, for their discrimination, as furanocoumarins are difficult to separate, due to their similar chemical structures and physicochemical properties. In this paper, a new, simple method is proposed for the discrimination of selected species, varieties and forms of the genus Heracleum. Thin-layer chromatography (TLC) with an adsorbent gradient (unmodified silica gel+octadecylsilica wettable with water) enables complete separation of the structural analogues. The proposed method gives the possibility to distinguish selected species, varieties and forms of the Heracleum genus, as they produce distinctive furanocoumarin fingerprints. The method is characterised by high specificity, precision, reproducibility and stability values. It is for the first time that graft TLC is used for constructing fingerprints of herbs. The complete separation of ten structural analogues, by combining gradient TLC with the unidimensional multiple development technique, has not been reported yet.

  20. A versatile method for the preparation of conjugates of peptides with DNA/PNA/analog by employing chemo-selective click reaction in water

    PubMed Central

    Gogoi, Khirud; Mane, Meenakshi V.; Kunte, Sunita S.; Kumar, Vaijayanti A.

    2007-01-01

    The specific 1,3 dipolar Hüisgen cycloaddition reaction known as ‘click-reaction’ between azide and alkyne groups is employed for the synthesis of peptide–oligonucleotide conjugates. The peptide nucleic acids (PNA)/DNA and peptides may be appended either by azide or alkyne groups. The cycloaddition reaction between the azide and alkyne appended substrates allows the synthesis of the desired conjugates in high purity and yields irrespective of the sequence and functional groups on either of the two substrates. The versatile approach could also be employed to generate the conjugates of peptides with thioacetamido nucleic acid (TANA) analog. The click reaction is catalyzed by Cu (I) in either water or in organic medium. In water, ∼3-fold excess of the peptide-alkyne/azide drives the reaction to completion in 2 h with no side products. PMID:17981837

  1. Parameter-exploring policy gradients.

    PubMed

    Sehnke, Frank; Osendorfer, Christian; Rückstiess, Thomas; Graves, Alex; Peters, Jan; Schmidhuber, Jürgen

    2010-05-01

    We present a model-free reinforcement learning method for partially observable Markov decision problems. Our method estimates a likelihood gradient by sampling directly in parameter space, which leads to lower variance gradient estimates than obtained by regular policy gradient methods. We show that for several complex control tasks, including robust standing with a humanoid robot, this method outperforms well-known algorithms from the fields of standard policy gradients, finite difference methods and population based heuristics. We also show that the improvement is largest when the parameter samples are drawn symmetrically. Lastly we analyse the importance of the individual components of our method by incrementally incorporating them into the other algorithms, and measuring the gain in performance after each step.

  2. Response of single benthic metrics and multi-metric methods to anthropogenic pressure gradients, in five distinct European coastal and transitional ecosystems.

    PubMed

    Borja, Angel; Barbone, Enrico; Basset, Alberto; Borgersen, Gunhild; Brkljacic, Marijana; Elliott, Michael; Garmendia, Joxe Mikel; Marques, João Carlos; Mazik, Krysia; Muxika, Iñigo; Magalhães Neto, João; Norling, Karl; Rodríguez, J Germán; Rosati, Ilaria; Rygg, Brage; Teixeira, Heliana; Trayanova, Antoaneta

    2011-03-01

    In recent times many benthic indices have been proposed to assess the ecological quality of marine waters worldwide. In this study we compared single metrics and multi-metric methods to assess coastal and transitional benthic status along human pressure gradients in five distinct environments across Europe: Varna bay and lake (Bulgaria), Lesina lagoon (Italy), Mondego estuary (Portugal), Basque coast (Spain) and Oslofjord (Norway). Hence, 13 single metrics (abundance, number of taxa, and several diversity and sensitivity indices) and eight of the most common indices used within the European Water Framework Directive (WFD) for benthic assessment were selected: index of size spectra (ISS), Benthic assessment tool (BAT), Norwegian quality index (NQI), Multivariate AMBI (M-AMBI), Benthic quality index (BQI), (Benthic ecosystem quality index (BEQI), Benthic index based on taxonomic sufficiency (BITS), and infaunal quality index (IQI). Within each system, sampling sites were ordered in an increasing pressure gradient according to a preliminary classification based on professional judgement. The different indices are largely consistent in their response to pressure gradient, except in some particular cases (i.e. BITS, in all cases, or ISS when a low number of individuals is present). Inconsistencies between indicator responses were most pronounced in transitional waters (i.e. IQI, BEQI), highlighting the difficulties of the generic application of indicators to all marine, estuarine and lagoonal environments. However, some of the single (i.e. ecological groups approach, diversity, richness) and multi-metric methods (i.e. BAT, M-AMBI, NQI) were able to detect such gradients both in transitional and coastal environments, being these multi-metric methods more consistent in the detection than single indices. This study highlights the importance of survey design and good reference conditions for some indicators. The agreement observed between different methodologies and their

  3. Fiber bundle phase conjugate mirror

    DOEpatents

    Ward, Benjamin G.

    2012-05-01

    An improved method and apparatus for passively conjugating the phases of a distorted wavefronts resulting from optical phase mismatch between elements of a fiber laser array are disclosed. A method for passively conjugating a distorted wavefront comprises the steps of: multiplexing a plurality of probe fibers and a bundle pump fiber in a fiber bundle array; passing the multiplexed output from the fiber bundle array through a collimating lens and into one portion of a non-linear medium; passing the output from a pump collection fiber through a focusing lens and into another portion of the non-linear medium so that the output from the pump collection fiber mixes with the multiplexed output from the fiber bundle; adjusting one or more degrees of freedom of one or more of the fiber bundle array, the collimating lens, the focusing lens, the non-linear medium, or the pump collection fiber to produce a standing wave in the non-linear medium.

  4. Generalized three-dimensional lattice Boltzmann color-gradient method for immiscible two-phase pore-scale imbibition and drainage in porous media

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

    This article presents a three-dimensional numerical framework for the simulation of fluid-fluid immiscible compounds in complex geometries, based on the multiple-relaxation-time lattice Boltzmann method to model the fluid dynamics and the color-gradient approach to model multicomponent flow interaction. New lattice weights for the lattices D3Q15, D3Q19, and D3Q27 that improve the Galilean invariance of the color-gradient model as well as for modeling the interfacial tension are derived and provided in the Appendix. The presented method proposes in particular an approach to model the interaction between the fluid compound and the solid, and to maintain a precise contact angle between the two-component interface and the wall. Contrarily to previous approaches proposed in the literature, this method yields accurate solutions even in complex geometries and does not suffer from numerical artifacts like nonphysical mass transfer along the solid wall, which is crucial for modeling imbibition-type problems. The article also proposes an approach to model inflow and outflow boundaries with the color-gradient method by generalizing the regularized boundary conditions. The numerical framework is first validated for three-dimensional (3D) stationary state (Jurin's law) and time-dependent (Washburn's law and capillary waves) problems. Then, the usefulness of the method for practical problems of pore-scale flow imbibition and drainage in porous media is demonstrated. Through the simulation of nonwetting displacement in two-dimensional random porous media networks, we show that the model properly reproduces three main invasion regimes (stable displacement, capillary fingering, and viscous fingering) as well as the saturating zone transition between these regimes. Finally, the ability to simulate immiscible two-component flow imbibition and drainage is validated, with excellent results, by numerical simulations in a Berea sandstone, a frequently used benchmark case used in this

  5. Mapping the Conjugate Gradient Algorithm onto High Performance Heterogeneous Computers

    DTIC Science & Technology

    2014-05-01

    2.4.1 Coordinate Format . . . . . . . . . . . . . . . . . . . . 18 2.4.2 Compressed Sparse Row . . . . . . . . . . . . . . . . . 19 2.4.3 Aligned CSR ...18 2.8 Example of COO format . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 2.9 Example of CSR format...20 2.10 Example of aligned CSR format (k = 2, knz = 5) . . . . . . . . . . . . . . . 21 2.11 SRC-7 HPHC

  6. Efficient Human Breast Cancer Xenograft Regression after a Single Treatment with a Novel Liposomal Formulation of Epirubicin Prepared Using the EDTA Ion Gradient Method

    PubMed Central

    Gubernator, Jerzy; Lipka, Dominik; Korycińska, Mariola; Kempińska, Katarzyna; Milczarek, Magdalena; Wietrzyk, Joanna; Hrynyk, Rafał; Barnert, Sabine; Süss, Regine; Kozubek, Arkadiusz

    2014-01-01

    Liposomes act as efficient drug carriers. Recently, epirubicin (EPI) formulation was developed using a novel EDTA ion gradient method for drug encapsulation. This formulation displayed very good stability and drug retention in vitro in a two-year long-term stability experiment. The cryo-TEM images show drug precipitate structures different than ones formed with ammonium sulfate method, which is usually used to encapsulate anthracyclines. Its pharmacokinetic properties and its efficacy in the human breast MDA-MB-231 cancer xenograft model were also determined. The liposomal EPI formulation is eliminated slowly with an AUC of 7.6487, while the free drug has an AUC of only 0.0097. The formulation also had a much higher overall antitumor efficacy than the free drug. PMID:24621591

  7. Fast gradient HPLC method to determine compounds binding to human serum albumin. Relationships with octanol/water and immobilized artificial membrane lipophilicity.

    PubMed

    Valko, Klara; Nunhuck, Shenaz; Bevan, Chris; Abraham, Michael H; Reynolds, Derek P

    2003-11-01

    A fast gradient HPLC method (cycle time 15 min) has been developed to determine Human Serum Albumin (HSA) binding of discovery compounds using chemically bonded protein stationary phases. The HSA binding values were derived from the gradient retention times that were converted to the logarithm of the equilibrium constants (logK HSA) using data from a calibration set of molecules. The method has been validated using literature plasma protein binding data of 68 known drug molecules. The method is fully automated, and has been used for lead optimization in more than 20 company projects. The HSA binding data obtained for more than 4000 compounds were suitable to set up global and project specific quantitative structure binding relationships that helped compound design in early drug discovery. The obtained HSA binding of known drug molecules were compared to the Immobilized Artificial Membrane binding data (CHI IAM) obtained by our previously described HPLC-based method. The solvation equation approach has been used to characterize the normal binding ability of HSA, and this relationship shows that compound lipophilicity is a significant factor. It was found that the selectivity of the "baseline" lipophilicity governing HSA binding, membrane interaction, and octanol/water partition are very similar. However, the effect of the presence of positive or negative charges have very different effects. It was found that negatively charged compounds bind more strongly to HSA than it would be expected from the lipophilicity of the ionized species at pH 7.4. Several compounds showed stronger HSA binding than can be expected from their lipophilicity alone, and comparison between predicted and experimental binding affinity allows the identification of compounds that have good complementarities with any of the known binding sites.

  8. Conjugal amyotrophic lateral sclerosis

    PubMed Central

    Dewitt, John D.; Kwon, Julia; Burton, Rebecca

    2012-01-01

    Amyotrophic lateral sclerosis (ALS) is a disease characterized by progressive degeneration of motor neurons in the motor cortex, brainstem, and spinal cord. The incidence of sporadic ALS is 1.5 to 2.7 in 100,000, and the prevalence is 5.2 to 6.0 in 100,000. Conjugal ALS is even rarer than sporadic ALS. We report a case of conjugal ALS encountered in our outpatient neurology clinic. PMID:22275781

  9. On gradient field theories: gradient magnetostatics and gradient elasticity

    NASA Astrophysics Data System (ADS)

    Lazar, Markus

    2014-09-01

    In this work, the fundamentals of gradient field theories are presented and reviewed. In particular, the theories of gradient magnetostatics and gradient elasticity are investigated and compared. For gradient magnetostatics, non-singular expressions for the magnetic vector gauge potential, the Biot-Savart law, the Lorentz force and the mutual interaction energy of two electric current loops are derived and discussed. For gradient elasticity, non-singular forms of all dislocation key formulas (Burgers equation, Mura equation, Peach-Koehler stress equation, Peach-Koehler force equation, and mutual interaction energy of two dislocation loops) are presented. In addition, similarities between an electric current loop and a dislocation loop are pointed out. The obtained fields for both gradient theories are non-singular due to a straightforward and self-consistent regularization.

  10. Full-waveform inversion in the time domain with an energy-weighted gradient

    SciTech Connect

    Zhang, Zhigang; Huang, Lianjie; Lin, Youzuo

    2011-01-01

    When applying full-waveform inversion to surface seismic reflection data, one difficulty is that the deep region of the model is usually not reconstructed as well as the shallow region. We develop an energy-weighted gradient method for the time-domain full-waveform inversion to accelerate the convergence rate and improve reconstruction of the entire model without increasing the computational cost. Three different methods can alleviate the problem of poor reconstruction in the deep region of the model: the layer stripping, depth-weighting and pseudo-Hessian schemes. The first two approaches need to subjectively choose stripping depths and weighting functions. The third one scales the gradient with only the forward propagation wavefields from sources. However, the Hessian depends on wavefields from both sources and receivers. Our new energy-weighted method makes use of the energies of both forward and backward propagated wavefields from sources and receivers as weights to compute the gradient. We compare the reconstruction of our new method with those of the conjugate gradient and pseudo-Hessian methods, and demonstrate that our new method significantly improves the reconstruction of both the shallow and deep regions of the model.

  11. Method and system for producing sputtered thin films with sub-angstrom thickness uniformity or custom thickness gradients

    DOEpatents

    Folta, James A.; Montcalm, Claude; Walton, Christopher

    2003-01-01

    A method and system for producing a thin film with highly uniform (or highly accurate custom graded) thickness on a flat or graded substrate (such as concave or convex optics), by sweeping the substrate across a vapor deposition source with controlled (and generally, time-varying) velocity. In preferred embodiments, the method includes the steps of measuring the source flux distribution (using a test piece that is held stationary while exposed to the source), calculating a set of predicted film thickness profiles, each film thickness profile assuming the measured flux distribution and a different one of a set of sweep velocity modulation recipes, and determining from the predicted film thickness profiles a sweep velocity modulation recipe which is adequate to achieve a predetermined thickness profile. Aspects of the invention include a practical method of accurately measuring source flux distribution, and a computer-implemented method employing a graphical user interface to facilitate convenient selection of an optimal or nearly optimal sweep velocity modulation recipe to achieve a desired thickness profile on a substrate. Preferably, the computer implements an algorithm in which many sweep velocity function parameters (for example, the speed at which each substrate spins about its center as it sweeps across the source) can be varied or set to zero.

  12. Gradient zone boundary control in salt gradient solar ponds

    DOEpatents

    Hull, John R.

    1984-01-01

    A method and apparatus for suppressing zone boundary migration in a salt gradient solar pond includes extending perforated membranes across the pond at the boundaries, between the convective and non-convective zones, the perforations being small enough in size to prevent individual turbulence disturbances from penetrating the hole, but being large enough to allow easy molecular diffusion of salt thereby preventing the formation of convective zones in the gradient layer. The total area of the perforations is a sizable fraction of the membrane area to allow sufficient salt diffusion while preventing turbulent entrainment into the gradient zone.

  13. Method for compression molding of thermosetting plastics utilizing a temperature gradient across the plastic to cure the article

    NASA Technical Reports Server (NTRS)

    Heier, W. C. (Inventor)

    1974-01-01

    A method is described for compression molding of thermosetting plastics composition. Heat is applied to the compressed load in a mold cavity and adjusted to hold molding temperature at the interface of the cavity surface and the compressed compound to produce a thermal front. This thermal front advances into the evacuated compound at mean right angles to the compression load and toward a thermal fence formed at the opposite surface of the compressed compound.

  14. A comparative study on pure, L-arginine and glycine doped ammonium dihydrogen orthophosphate single crystals grown by slow solvent evaporation and temperature-gradient method

    NASA Astrophysics Data System (ADS)

    Pattanaboonmee, N.; Ramasamy, P.; Yimnirun, R.; Manyum, P.

    2011-01-01

    Single crystals of pure, L-arginine and glycine doped ammonium dihydrogen orthophosphate (ADP) were grown by both the slow solvent evaporation method and the temperature-gradient method of Sankaranarayanan-Ramasamy (SR). The metastable zone width for different saturation temperatures of pure glycine and L-arginine added solutions were carried out. The grown crystals were characterized by differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), powder X-ray diffraction (XRD), optical transmission, dielectric constant, dielectric loss, and Vickers microhardness. The DSC and TG curves of the grown crystals indicated that they were stable up to 200 °C. The XRD study confirmed the structure of the grown crystal. The optical transmission analysis revealed that the pure and doped ADP crystals had very high percentage of transmission in the entire visible region. The important optical parameters such as reflectance and extinction coefficients of the grown crystals were calculated. L-arginine and glycine were used as dopants to reduce dielectric constant of ADP. The a.c. resistivity and a.c. conductivity were calculated. Dielectric loss of the doped ADP crystals grown by the SR method is lower than the doped ADP crystals grown by the conventional method. Larger hardness value for the SR method grown crystals confirmed greater crystalline perfection.

  15. A protocol for exosome isolation and characterization: evaluation of ultracentrifugation, density-gradient separation, and immunoaffinity capture methods.

    PubMed

    Greening, David W; Xu, Rong; Ji, Hong; Tauro, Bow J; Simpson, Richard J

    2015-01-01

    Exosomes are 40-150 nm extracellular vesicles that are released from a multitude of cell types, and perform diverse cellular functions including intercellular communication, antigen presentation, and transfer of tumorigenic proteins, mRNA and miRNA. Exosomes are important regulators of the cellular niche, and their altered characteristics in many diseases, such as cancer, suggest their importance for diagnostic and therapeutic applications, and as drug delivery vehicles. Exosomes have been purified from biological fluids and in vitro cell cultures using a variety of strategies and techniques. In this chapter, we reveal the protocol and key insights into the isolation, purification and characterization of exosomes, distinct from shed microvesicles and apoptotic blebs. Using the colorectal cancer cell line LIM1863 as a cell model, a comprehensive evaluation of exosome isolation methods including ultracentrifugation (UC-Exos), OptiPrep™ density-based separation (DG-Exos), and immunoaffinity capture using anti-EpCAM-coated magnetic beads (IAC-Exos) were examined. All exosome isolation methodologies contained 40-150 nm vesicles based on electron microscopy, and positive for exosome markers (Alix, TSG101, HSP70) based on immunoblotting. This protocol employed a proteomic profiling approach to characterize the protein composition of exosomes, and label-free spectral counting to evaluate the effectiveness of each method in exosome isolation. Based on the number of MS/MS spectra identified for exosome markers and proteins associated with their biogenesis, trafficking, and release, IAC-Exos was shown to be the most effective method to isolate exosomes. However, the use of density-based separation (DG-Exos) provides significant advantages for exosome isolation when the use of immunoaffinity capture is limited (due to antibody availability and suitability of exosome markers).

  16. Preconditioned minimal residual methods for Chebyshev spectral calculations

    NASA Technical Reports Server (NTRS)

    Canuto, C.; Quarteroni, A.

    1985-01-01

    The problem of preconditioning the pseudospectral Chebyshev approximation of an elliptic operator is considered. The numerical sensitiveness to variations of the coefficients of the operator are investigated for two classes of preconditioning matrices: one arising from finite differences, the other from finite elements. The preconditioned system is solved by a conjugate gradient type method, and by a Dufort-Frankel method with dynamical parameters. The methods are compared on some test problems with the Richardson method and with the minimal residual Richardson method.

  17. Thermal analysis of a functionally graded material subject to a thermal gradient using the boundary element method

    NASA Technical Reports Server (NTRS)

    Goldberg, Robert K.; Hopkins, Dale A.

    1994-01-01

    The boundary element method is utilized in this study to conduct thermal analysis of functionally graded composites, materials in which the internal microstructure or properties are explicitly tailored in order to obtain an optimal response, on the micromechanical (constituent) scale. A unique feature of the boundary element formulations used here is the use of circular shape functions to convert the two-dimensional integrations of the composite fibers to one dimensional integrations. Using the computer code BEST-CMS, the through the thickness temperature profiles are computed for a representative material with varying numbers of fibers and fiber spacing in the thickness direction. The computed temperature profiles are compared to those obtained using an alternate analytical theory which explicitly couples the heterogeneous microstructure to the global analysis. The boundary element results compared favorably to the analytical calculations, with discrepancies that are explainable based on the boundary element formulation. The results serve both to demonstrate the ability of the boundary element method to analyze these types of materials, and to verify the accuracy of the analytical theory.

  18. Implementation of Analytical Energy Gradient of Spin-Dependent General Hartree-Fock Method Based on the Infinite-Order Douglas-Kroll-Hess Relativistic Hamiltonian with Local Unitary Transformation.

    PubMed

    Nakajima, Yuya; Seino, Junji; Nakai, Hiromi

    2016-05-10

    An analytical energy gradient for the spin-dependent general Hartree-Fock method based on the infinite-order Douglas-Kroll-Hess (IODKH) method was developed. To treat realistic systems, the local unitary transformation (LUT) scheme was employed both in energy and energy gradient calculations. The present energy gradient method was numerically assessed to investigate the accuracy in several diatomic molecules containing fifth- and sixth-period elements and to examine the efficiency in one-, two-, and three-dimensional silver clusters. To arrive at a practical calculation, we also determined the geometrical parameters of fac-tris(2-phenylpyridine)iridium and investigated the efficiency. The numerical results confirmed that the present method describes a highly accurate relativistic effect with high efficiency. The present method can be a powerful scheme for determining geometries of large molecules, including heavy-element atoms.

  19. Gradient Perception of Children’s Productions of /s/ and /θ/:A Comparative Study of Rating Methods

    PubMed Central

    Schellinger, Sarah K.; Munson, Benjamin; Edwards, Jan

    2016-01-01

    Past studies have shown incontrovertible evidence for the existence of covert contrasts in children’s speech, that is, differences between target productions that are nonetheless transcribed with the same phonetic symbol. Moreover, there is evidence that these are relevant to forming prognoses and tracking progress in children with speech sound disorder. A challenge remains to find the most efficient and reliable methods for assessing covert contrasts. This study investigates how readily listeners can identify covert contrasts in children’s speech when using a continuous rating scale in the form of a visual analog scale (VAS) to denote children’s productions. Individual listeners’ VAS responses were found to correlate statistically significantly with a variety of continuous measures of children’s production accuracy, including judgments of binary accuracy pooled over a large set of listeners. These findings reinforce the growing body of evidence that VAS judgments are potentially useful clinical measures of covert contrast. PMID:27552446

  20. Design, synthesis, characterization and study of novel conjugated polymers

    SciTech Connect

    Chen, Wu

    1997-06-24

    After introducing the subject of conjugated polymers, the thesis has three sections each containing a literature survey, results and discussion, conclusions, and experimental methods on the following: synthesis, characterization of electroluminescent polymers containing conjugated aryl, olefinic, thiophene and acetylenic units and their studies for use in light-emitting diodes; synthesis, characterization and study of conjugated polymers containing silole unit in the main chain; and synthesis, characterization and study of silicon-bridged and butadiene-linked polythiophenes.

  1. An automatic differentiation-based gradient method for inversion of the shear wave equation in magnetic resonance elastography: specific application in fibrous soft tissues

    NASA Astrophysics Data System (ADS)

    Chatelin, Simon; Charpentier, Isabelle; Corbin, Nadège; Meylheuc, Laurence; Vappou, Jonathan

    2016-07-01

    Quantitative and accurate measurement of in vivo mechanical properties using dynamic elastography has been the scope of many research efforts over the past two decades. Most of the shear-wave-based inverse approaches for magnetic resonance elastography (MRE) make the assumption of isotropic viscoelasticity. In this paper, we propose a quantitative gradient method for inversion of the shear wave equation in anisotropic media derived from a full waveform description using analytical viscoelastic Green formalism and automatic differentiation. The abilities and performances of the proposed identification method are first evaluated on numerical phantoms calculated in a transversely isotropic medium, and subsequently on experimental MRE data measured on an isotropic hydrogel phantom, on an anisotropic cryogel phantom and on an ex vivo fibrous muscle. The experiments are carried out by coupling circular shear wave profiles generated by acoustic radiation force and MRE acquisition of the wave front. Shear modulus values obtained by our MRE method are compared to those obtained by rheometry in the isotropic hydrogel phantom, and are found to be in good agreement despite non-overlapping frequency ranges. Both the cryogel and the ex vivo muscle are found to be anisotropic. Stiffness values in the longitudinal direction are found to be 1.8 times and 1.9 times higher than those in the transverse direction for the cryogel and the muscle, respectively. The proposed method shows great perspectives and substantial benefits for the in vivo quantitative investigation of complex mechanical properties in fibrous soft tissues.

  2. Quantitative structure-retention relationships applied to liquid chromatography gradient elution method for the determination of carbonyl-2,4-dinitrophenylhydrazone compounds.

    PubMed

    Cirera-Domènech, Elisenda; Estrada-Tejedor, Roger; Broto-Puig, Francesc; Teixidó, Jordi; Gassiot-Matas, Miquel; Comellas, Lluís; Lliberia, Josep Lluís; Méndez, Alberto; Paz-Estivill, Susanna; Delgado-Ortiz, Maria Rosa

    2013-02-08

    A usual method for the determination of aldehydes and ketones in different matrices consists of a derivatization with 2,4-dinitrophenylhydrazine (DNPH) followed by HPLC-UV analysis. In the present work, a HPLC-UV gradient elution method has been applied to the analysis of 13 aldehydes and ketones-DNPH in automotive emission samples. In addition to these 13 compounds-DNPH, several carbonyl-DNPH compounds (linear, ramified and cyclic, saturated and unsaturated compounds) have been analyzed by HPLC-UV. Quantitative structure-retention relationships (QSRR) methods have been applied to predict the logarithm of capacity factor (logk') of carbonyl-DNPH compounds. According to its physicochemical meaning, combinations of 2 and 3 molecular descriptors have been proposed in order to achieve higher correlation with logk'. Using linear and non-linear QSRR methodologies, the resulting prediction models allowed the screening of the most probable carbonyl-DNPH derivative candidates that correspond to unknown compounds detected in automotive emission samples. This information has been useful for their identification by UPLC(®)-MS/MS. In addition, the chromatographic retention of different carbonyl-DNPH compound families was studied using two HPLC isocratic methods working with two orthogonal stationary phases (octadecylpolyethoxysilane and cyanopropyl). Differences between the retention indexes obtained for each column were used for classifying carbonyl-DNPH into compounds families.

  3. Scaling up the Single Transducer Thickness-Independent Ultrasonic Imaging Method for Accurate Characterization of Microstructural Gradients in Monolithic and Composite 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/time-of-flight imaging that uses back surface reflections to gauge 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/time-of-flight 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 time-of-flight-based ultrasonic imaging method that requires using a single transducer in combination with a reflector plate placed behind samples that eliminates the effect of thickness variation in the image. In those studies, this method was successful at isolating ultrasonic variations due to material microstructure 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/curved geometry. The experimental inspection technique and results are described as applied to (1) monolithic mullite ceramic and polymer matrix composite 'proof-of-concept' tubular structures that contain machined patches of various depths and (2) as-manufactured monolithic silicon nitride ceramic and silicon carbide/silicon carbide composite tubular structures that might be used in 'real world' applications.

  4. Comparative study of methods to calibrate the stiffness of a single-beam gradient-force optical tweezers over various laser trapping powers.

    PubMed

    Sarshar, Mohammad; Wong, Winson T; Anvari, Bahman

    2014-01-01

    Optical tweezers have become an important instrument in force measurements associated with various physical, biological, and biophysical phenomena. Quantitative use of optical tweezers relies on accurate calibration of the stiffness of the optical trap. Using the same optical tweezers platform operating at 1064 nm and beads with two different diameters, we present a comparative study of viscous drag force, equipartition theorem, Boltzmann statistics, and power spectral density (PSD) as methods in calibrating the stiffness of a single beam gradient force optical trap at trapping laser powers in the range of 0.05 to 1.38 W at the focal plane. The equipartition theorem and Boltzmann statistic methods demonstrate a linear stiffness with trapping laser powers up to 355 mW, when used in conjunction with video position sensing means. The PSD of a trapped particle's Brownian motion or measurements of the particle displacement against known viscous drag forces can be reliably used for stiffness calibration of an optical trap over a greater range of trapping laser powers. Viscous drag stiffness calibration method produces results relevant to applications where trapped particle undergoes large displacements, and at a given position sensing resolution, can be used for stiffness calibration at higher trapping laser powers than the PSD method.

  5. A new approach to mixed H2/H infinity controller synthesis using gradient-based parameter optimization methods

    NASA Technical Reports Server (NTRS)

    Ly, Uy-Loi; Schoemig, Ewald

    1993-01-01

    In the past few years, the mixed H(sub 2)/H-infinity control problem has been the object of much research interest since it allows the incorporation of robust stability into the LQG framework. The general mixed H(sub 2)/H-infinity design problem has yet to be solved analytically. Numerous schemes have considered upper bounds for the H(sub 2)-performance criterion and/or imposed restrictive constraints on the class of systems under investigation. Furthermore, many modern control applications rely on dynamic models obtained from finite-element analysis and thus involve high-order plant models. Hence the capability to design low-order (fixed-order) controllers is of great importance. In this research a new design method was developed that optimizes the exact H(sub 2)-norm of a certain subsystem subject to robust stability in terms of H-infinity constraints and a minimal number of system assumptions. The derived algorithm is based on a differentiable scalar time-domain penalty function to represent the H-infinity constraints in the overall optimization. The scheme is capable of handling multiple plant conditions and hence multiple performance criteria and H-infinity constraints and incorporates additional constraints such as fixed-order and/or fixed structure controllers. The defined penalty function is applicable to any constraint that is expressible in form of a real symmetric matrix-inequity.

  6. Gradient Index Lens Research

    DTIC Science & Technology

    1981-10-19

    Finally, an assessment of the current technologies in gradient index has been made. This includes a series of recommendations w’iich will be...17 III. Ray Tracing in Anamorphic Gradient Index Media ......... 20 IV. Fabrication of Six Gradient Index Samples ............. 27 V. Technology ...for a basic understanding of what can and cannot be done with gradient index lenses, aside from any lack of technology for making a paricular gradient

  7. The synthesis-diffusion-degradation model explains Bicoid gradient formation in unfertilized eggs

    NASA Astrophysics Data System (ADS)

    Drocco, J. A.; Wieschaus, E. F.; Tank, D. W.

    2012-10-01

    Precise formation of morphogen gradients is essential to the establishment of reproducible pattern in development. Mechanisms proposed for obtaining the requisite precision range from simple models with few parameters to more complex models involving many regulated quantities. The synthesis-diffusion-degradation (SDD) model is a relatively simple model explaining the formation of the Bicoid gradient in Drosophila melanogaster, in which the steady-state characteristic length of the gradient is determined solely by the rates of diffusion and degradation of the morphogen. In this work, we test the SDD model in unfertilized D. melanogaster eggs, which contain a single female pronucleus and lack the nuclear division cycles and other zygotic regulatory processes seen in fertilized eggs. Using two-photon live imaging as well as a novel method for quantitative imaging based on decorrelation of photoswitching waveforms, we find that the Bicoid gradient is longer and shallower in unfertilized eggs as compared to the gradient at the same time points in fertilized eggs. Using a means of measuring the Bicoid lifetime by conjugation to a photoconvertible fluorophore, we find that the lifetime is correspondingly longer in unfertilized eggs, providing qualitative and quantitative agreement with the predictions of the SDD model.

  8. Polyamine conjugates of stigmasterol.

    PubMed

    Vida, Norbert; Svobodová, Hana; Rárová, Lucie; Drašar, Pavel; Saman, David; Cvačka, Josef; Wimmer, Zdeněk

    2012-10-01

    Three new polyamine conjugates with stigmasterol [(3β,22E)-stigmasta-5,22-dien-3-ol] were synthesized and subjected to basic antimicrobial and cytotoxic tests. The conjugate derived from spermine, (3β,22E)-stigmasta-5,22-dien-3-yl 4(12-amino-4,9-diaza-dodecylamino)-4-oxobutanoate (5c), displayed considerable antimicrobial activity on Staphylococcus aureus at low concentration (50 μg mL(-1)). The cytotoxic activity was tested on cells of human T-lymfoblastic leukemia (IC(50)=35.8 ± 10.3 μM (5c) and IC(50)=35.9 ± 5.7 μM (5b)) and normal human fibroblasts (IC(50)=38.0 ± 2.8 μM (5c) and IC(50)=45.5 ± 1.9 μM (5b)). Conjugate 5a displayed no activity in both tests.

  9. Biomolecular gradients in cell culture systems

    PubMed Central

    Keenan, Thomas M.

    2013-01-01

    Biomolecule gradients have been shown to play roles in a wide range of biological processes including development, inflammation, wound healing, and cancer metastasis. Elucidation of these phenomena requires the ability to expose cells to biomolecule gradients that are quantifiable, controllable, and mimic those that are present in vivo. Here we review the major biological phenomena in which biomolecule gradients are employed, traditional in vitro gradient-generating methods developed over the past 50 years, and new microfluidic devices for generating gradients. Microfluidic gradient generators offer greater levels of precision, quantitation, and spatiotemporal gradient control than traditional methods, and may greatly enhance our understanding of many biological phenomena. For each method, we outline the salient features, capabilities, and applications. PMID:18094760

  10. Strategies and Advancement in Antibody-Drug Conjugate Optimization for Targeted Cancer Therapeutics

    PubMed Central

    Kim, Eunhee G.; Kim, Kristine M.

    2015-01-01

    Antibody-drug conjugates utilize the antibody as a delivery vehicle for highly potent cytotoxic molecules with specificity for tumor-associated antigens for cancer therapy. Critical parameters that govern successful antibody-drug conjugate development for clinical use include the selection of the tumor target antigen, the antibody against the target, the cytotoxic molecule, the linker bridging the cytotoxic molecule and the antibody, and the conjugation chemistry used for the attachment of the cytotoxic molecule to the antibody. Advancements in these core antibody-drug conjugate technology are reflected by recent approval of Adectris® (anti-CD30-drug conjugate) and Kadcyla® (anti-HER2 drug conjugate). The potential approval of an anti-CD22 conjugate and promising new clinical data for anti-CD19 and anti-CD33 conjugates are additional advancements. Enrichment of antibody-drug conjugates with newly developed potent cytotoxic molecules and linkers are also in the pipeline for various tumor targets. However, the complexity of antibody-drug conjugate components, conjugation methods, and off-target toxicities still pose challenges for the strategic design of antibody-drug conjugates to achieve their fullest therapeutic potential. This review will discuss the emergence of clinical antibody-drug conjugates, current trends in optimization strategies, and recent study results for antibody-drug conjugates that have incorporated the latest optimization strategies. Future challenges and perspectives toward making antibody-drug conjugates more amendable for broader disease indications are also discussed. PMID:26535074

  11. A low-complexity 2-point step size gradient projection method with selective function evaluations for smoothed total variation based CBCT reconstructions

    NASA Astrophysics Data System (ADS)

    Song, Bongyong; Park, Justin C.; Song, William Y.

    2014-11-01

    The Barzilai-Borwein (BB) 2-point step size gradient method is receiving attention for accelerating Total Variation (TV) based CBCT reconstructions. In order to become truly viable for clinical applications, however, its convergence property needs to be properly addressed. We propose a novel fast converging gradient projection BB method that requires ‘at most one function evaluation’ in each iterative step. This Selective Function Evaluation method, referred to as GPBB-SFE in this paper, exhibits the desired convergence property when it is combined with a ‘smoothed TV’ or any other differentiable prior. This way, the proposed GPBB-SFE algorithm offers fast and guaranteed convergence to the desired 3DCBCT image with minimal computational complexity. We first applied this algorithm to a Shepp-Logan numerical phantom. We then applied to a CatPhan 600 physical phantom (The Phantom Laboratory, Salem, NY) and a clinically-treated head-and-neck patient, both acquired from the TrueBeam™ system (Varian Medical Systems, Palo Alto, CA). Furthermore, we accelerated the reconstruction by implementing the algorithm on NVIDIA GTX 480 GPU card. We first compared GPBB-SFE with three recently proposed BB-based CBCT reconstruction methods available in the literature using Shepp-Logan numerical phantom with 40 projections. It is found that GPBB-SFE shows either faster convergence speed/time or superior convergence property compared to existing BB-based algorithms. With the CatPhan 600 physical phantom, the GPBB-SFE algorithm requires only 3 function evaluations in 30 iterations and reconstructs the standard, 364-projection FDK reconstruction quality image using only 60 projections. We then applied the algorithm to a clinically-treated head-and-neck patient. It was observed that the GPBB-SFE algorithm requires only 18 function evaluations in 30 iterations. Compared with the FDK algorithm with 364 projections, the GPBB-SFE algorithm produces visibly equivalent quality CBCT

  12. A low-complexity 2-point step size gradient projection method with selective function evaluations for smoothed total variation based CBCT reconstructions.

    PubMed

    Song, Bongyong; Park, Justin C; Song, William Y

    2014-11-07

    The Barzilai-Borwein (BB) 2-point step size gradient method is receiving attention for accelerating Total Variation (TV) based CBCT reconstructions. In order to become truly viable for clinical applications, however, its convergence property needs to be properly addressed. We propose a novel fast converging gradient projection BB method that requires 'at most one function evaluation' in each iterative step. This Selective Function Evaluation method, referred to as GPBB-SFE in this paper, exhibits the desired convergence property when it is combined with a 'smoothed TV' or any other differentiable prior. This way, the proposed GPBB-SFE algorithm offers fast and guaranteed convergence to the desired 3DCBCT image with minimal computational complexity. We first applied this algorithm to a Shepp-Logan numerical phantom. We then applied to a CatPhan 600 physical phantom (The Phantom Laboratory, Salem, NY) and a clinically-treated head-and-neck patient, both acquired from the TrueBeam™ system (Varian Medical Systems, Palo Alto, CA). Furthermore, we accelerated the reconstruction by implementing the algorithm on NVIDIA GTX 480 GPU card. We first compared GPBB-SFE with three recently proposed BB-based CBCT reconstruction methods available in the literature using Shepp-Logan numerical phantom with 40 projections. It is found that GPBB-SFE shows either faster convergence speed/time or superior convergence property compared to existing BB-based algorithms. With the CatPhan 600 physical phantom, the GPBB-SFE algorithm requires only 3 function evaluations in 30 iterations and reconstructs the standard, 364-projection FDK reconstruction quality image using only 60 projections. We then applied the algorithm to a clinically-treated head-and-neck patient. It was observed that the GPBB-SFE algorithm requires only 18 function evaluations in 30 iterations. Compared with the FDK algorithm with 364 projections, the GPBB-SFE algorithm produces visibly equivalent quality CBCT image for

  13. Validation of a simple HPLC-UV method for rifampicin determination in plasma: Application to the study of rifampicin arteriovenous concentration gradient.

    PubMed

    Goutal, Sébastien; Auvity, Sylvain; Legrand, Tiphaine; Hauquier, Fanny; Cisternino, Salvatore; Chapy, Hélène; Saba, Wadad; Tournier, Nicolas

    2016-05-10

    In clinical practice, rifampicin exposure is estimated from its concentration in venous blood samples. In this study, we hypothesized that differences in rifampicin concentration may exist between arterial and venous plasma. An HPLC-UV method for determining rifampicin concentration in plasma using rifapentine as an internal standard was validated. The method, which requires a simple protein precipitation procedure as sample preparation, was performed to compare venous and arterial plasma kinetics after a single therapeutic dose of rifampicin (8.6 mg/kg i.v, infused over 30 min) in baboons (n=3). The method was linear from 0.1 to 40 μg mL(-1) and all validation parameters fulfilled the international requirements. In baboons, rifampicin concentration in arterial plasma was higher than in venous plasma. Arterial Cmax was 2.1±0.2 fold higher than venous Cmax. The area under the curve (AUC) from 0 to 120 min was ∼80% higher in arterial plasma, indicating a significant arteriovenous concentration gradient in early rifampicin pharmacokinetics. Arterial and venous plasma concentrations obtained 6h after rifampicin injection were not different. An important arteriovenous equilibration delay for rifampicin pharmacokinetics is reported. Determination in venous plasma concentrations may considerably underestimate rifampicin exposure to organs during the distribution phase.

  14. Synthesis, characterization and biological activity of Rhein-cyclodextrin conjugate

    NASA Astrophysics Data System (ADS)

    Liu, Manshuo; Lv, Pin; Liao, Rongqiang; Zhao, Yulin; Yang, Bo

    2017-01-01

    Cyclodextrin conjugate complexation is a useful method to enhance the solubility and absorption of poorly soluble drugs. A series of new Rhein-β-cyclodextrin conjugates (Rh-CD conjugates) have been synthesized and examined. Rhein is covalently linked with the β-CD by amido linkage in a 1:1 molar ratio. The conjugates were characterized by 1H NMR, 13C NMR, HRMS, powder X-ray diffraction (powder XRD) as well as thermogravimetric analysis (TGA). The results reveal that incorporation of β-CD could improve the aqueous solubility of Rhein and the cytotoxicity against hepatocellular carcinoma (HepG2) cell line as well as antibacterial activity against three organisms. The improved biological activity and the satisfactory water solubility of the conjugates will be potentially useful for developing novel drug-cyclodextrin conjugates, such as herbal medicine.

  15. Comparison of the effect of different media on the clinical outcomes of the density-gradient centrifugation/swim-up and swim-up methods

    PubMed Central

    Kim, Eun-Kyung; Kim, Eun-Ha; Kim, Eun-Ah; Lee, Kyung-Ah; Shin, Ji-Eun

    2015-01-01

    Objective Sperm must be properly prepared in in vitro fertilization (IVF)-embryo transfer (ET) programs in order to control the fertilization rate and ensure that embryos are of high quality and have appropriate developmental abilities. The objective of this study was to determine the most optimal sperm preparation method for IVF. Methods Patients less than 40 years of age who participated in a fresh IVF-ET cycle from November 2012 to March 2013 were included in this study. Poor responders with less than three mature oocytes were excluded. Ham's F-10 medium or sperm-washing medium (SWM) was used in combination with the density-gradient centrifugation/swim-up (DGC-SUP) or SUP methods for sperm preparation. A total of 429 fresh IVF-ET cycles were grouped according to the media and methods used for sperm preparation and retrospectively analyzed (DGC-SUP/Ham's F-10, n=82; DGC-SUP/SWM, n=43; SUP/Ham's F-10, n=181; SUP/SWM, n=123). Results There were no significant differences among these four groups with respect to the mean age of the female partners, duration of infertility, number of previous IVF cycles, and retrieved oocytes. We determined that both the DGC-SUP and SUP methods for sperm preparation from whole semen, using either Ham's F-10 or SWM media, result in comparable clinical outcomes, including fertilization and pregnancy rates. Conclusion We suggest that both media and both methods for sperm preparation can be used for selecting high-quality sperm for assistive reproductive technology programs. PMID:25874170

  16. Stabilized polyacrylic saccharide protein conjugates

    DOEpatents

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

    1996-02-20

    This invention is directed to water soluble protein polymer conjugates which are stable in hostile environments. The conjugate comprises a protein which is linked to an acrylic polymer at multiple points through saccharide linker groups. 16 figs.

  17. Stabilized polyacrylic saccharide protein conjugates

    DOEpatents

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

    1996-01-01

    This invention is directed to water soluble protein polymer conjugates which are stabile in hostile environments. The conjugate comprises a protein which is linked to an acrylic polymer at multiple points through saccharide linker groups.

  18. A novel method for the quantitative determination of free and conjugated bisphenol A in human maternal and umbilical cord blood serum using a two-step solid phase extraction and gas chromatography/tandem mass spectrometry.

    PubMed

    Kosarac, Ivana; Kubwabo, Cariton; Lalonde, Kaela; Foster, Warren

    2012-06-01

    Bisphenol A is widely used as a monomer in the manufacture of polycarbonates and epoxy resins, as an antioxidant in polyvinyl chloride (PVC) plastics and as an inhibitor of end polymerisation in PVC. Several different methods have been used to quantify total BPA in biological specimens. However, quantification of both free and conjugated BPA continues to present challenges. Moreover, there is limited data concerning fetal exposure. Therefore, the objective of this study was to develop a new method for the analysis of both free and conjugated BPA in human maternal and umbilical cord blood serum. For the analysis of free BPA, the method consisted of a liquid-liquid extraction followed by a two-step solid-phase extraction sample cleanup on Florisil and Oasis HLB sorbents, derivatization of the extract using N-methyl-N-(trimethylsilyl)trifluoroacetamide (MSTFA) and analysis by gas chromatography/tandem mass spectrometry (GC/EI-MS/MS). To determine the amount of conjugated BPA in serum samples, bisphenol A-d6 β-glucuronide (4-[1-(4-hydroxyphenyl)-1-methylethyl-d6]phenyl β-D-glucopyranosiduronic acid) was added to each sample prior to enzymatic deconjugation. The MDL and LOQ for BPA were 0.026 ng/mL and 0.087 ng/mL, respectively. The observed recoveries ranged between 65% and 88%. The new method was applied to the determination of paired human maternal and umbilical cord blood serum samples. The results demonstrated that total BPA concentrations in human maternal serum at mid-pregnancy and at delivery ranged from <0.026 ng/mL to 10.425 ng/mL (median 0.548 ng/mL, n=12) and <0.026 ng/mL to 3.048 ng/mL (median 1.461 ng/mL), respectively. Results for matching umbilical cord blood serum BPA concentrations were in the range of <0.026-2.569 ng/mL (median 1.823 ng/mL). The concentrations measured in this study agreed well with BPA levels in human serum reported internationally. Only 2 mid-pregnancy serum samples out of 12 contained quantifiable amounts of conjugated BPA

  19. Covalent polymer-drug conjugates.

    PubMed

    Elvira, Carlos; Gallardo, Alberto; Roman, Julio San; Cifuentes, Alejandro

    2005-01-31

    In this work, polymer-drugs conjugates used as drug delivery systems (DDS) are revised attending to their chemical conjugation. Namely, the classification of this type of DDS is based on the conjugation sites of the reactive groups (i.e., via end groups or pendant polymer groups). Advantages and limitations of these types of DDS are discussed through representative examples of polymer-drugs and polymer-proteins conjugates recently developed.

  20. [Development of a gentamicin producer under different culture conditions studied by a method of differential centrifugation of the mycelium in a saccharose density gradient].

    PubMed

    Losev, V V; Laznikova, T N; Dmitrieva, S V

    1981-05-01

    The method of differential centrifugation in the sucrose density gradient (SDG) enabled one to trace the changes in the development of the seed and fermentation mycelium of the gentamicin-producing organism. Correlation between gentamicin distribution in the SDG and the culture productivity was found. It was shown that the culture grown under the optimal aeration and agitation conditions was characterized by formation of higher amounts of the mycelium in the 5th and 6th layers of the SDG. Such mycelium was more productive than that from the other SDG layers. The most productive 48-hour seed culture had the more significant part of the mycelium in the 3rd layer of the SDG. When such a culture had the more significant part of the mycelium in the 3rd layer of the SDG. When such a culture was used as the seed material, the activity of the fermentation broth was the highest. The method of differential centrifugation in the SDG provides determination of the culture productivity by the volumes of the fermentation mycelium in the 5th and 6th layers or the seed mycelium in the 3rd layer of the SDG.

  1. Mercury Distribution in the Deûle River (Northern France) Measured by the Diffusive Gradients in Thin Films Technique and Conventional Methods.

    PubMed

    Diviš, Pavel; Kadlecová, Milada; Ouddane, Baghdad

    2016-05-01

    The distribution of mercury in surface water and in sediment from Deûle River in Northern France was studied by application of conventional sampling methods and by diffusive gradients in thin films technique (DGT). Concentration of total dissolved mercury in surface water was 20.8 ± 0.8 ng l(-1). The particulate mercury concentration was 6.2 ± 0.6 µg g(-1). The particulate mercury was accumulated in sediment (9.9 ± 2.3 mg kg(-1)), and it was transformed by methylating bacteria to methylmercury, mainly in the first 2-cm layer of the sediment. Total dissolved concentration of mercury in sediment pore water obtained by application of centrifugation extraction was 17.6 ± 4.1 ng l(-1), and it was comparable with total dissolved pore water mercury concentration measured by DGT probe containing Duolite GT-73 resin gel (18.2 ± 4.3 ng l(-1)), taking the sediment heterogeneity and different principles of the applied methods into account. By application of two DGT probes with different resin gels specific for mercury, it was found that approximately 30% of total dissolved mercury in sediment pore water was present in labile forms easy available for biota. The resolution of mercury DGT depth profiles was 0.5 cm, which allows, unlike conventional techniques, to study the connection of the geochemical cycle of mercury with geochemical cycles of iron and manganese.

  2. Obstructive Form of Hypertrophic Cardiomyopathy-Left Ventricular Outflow Tract Gradient: Novel Methods of Provocation, Monitoring of Biomarkers, and Recent Advances in the Treatment

    PubMed Central

    Dimitrow, Pawel Petkow; Rajtar-Salwa, Renata

    2016-01-01

    Dynamic (latent or/and labile) obstruction of left ventricular outflow (LVOT) was recognized from the earliest clinical descriptions of hypertrophic cardiomyopathy (HCM) and has proved to be a complex phenomenon, as well as arguably the most audible (“visible”) pathophysiological hallmark of this heterogeneous disease. The aim of the current review is focused on two novel issues in a subgroup of obstructive HCM. Firstly, the important methodological problem in HCM is the examination of a subgroup of patients with nonobstructive hypertrophy in resting conditions and hard, but possible provoking obstruction. Recently, investigators have proposed physiological stress test (with double combined stimuli) to disclose such type of patients. The upright exercise is described in the ESC guideline on hypertrophic cardiomyopathy from 2014 and may appear as a candidate for gold standard provocation test. The second novel area of interest is associated with elevated level of signaling biomarkers: hypercoagulation, hemolysis, acquired von Willebrand 2A disease, and enhanced oxidative stress. The accelerated and turbulent flow within narrow LVOT may be responsible for these biochemical disturbances. The most recent advances in the treatment of obstructive HCM are related to nonpharmacological methods of LVOT gradient reduction. This report extensively discusses novel methods. PMID:27247935

  3. DNA-cell conjugates

    DOEpatents

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2016-05-03

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  4. Conjugate Silhouette Nets

    DTIC Science & Technology

    2000-01-01

    19) dv vEI 2 . Calling these curves the projective hodographs of p and q respectively, we can state Corollary. The Laplace transforms of a conjugate...silhouette net £ are the projective hodographs of the generating curves C1, C2 of L (considered as a projective translation surface). §3. Axial

  5. Application of conjugated heparin-albumin microparticles with laser-balloon angioplasty: a potential method for reducing adverse biologic reactivity after angioplasty

    NASA Astrophysics Data System (ADS)

    Kundu, Sourav K.; McMath, Linda P.; Zaidan, Jonathan T.; Spears, J. Richard

    1991-05-01

    Laser-balloon angioplasty (LBA) may potentially be used for local application of pharmacologically active agents which will reduce thrombogenic and proliferative responses after the angioplasty. In this study, the feasibility of applying covalently conjugated heparin- albumin microparticles onto arterial luminal surface was demonstrated. The covalent linkages were formed by reaction with 1-ethyl-3-dimethyl-aminopropyl-carbodiimide (EDC), and the resultant conjugates were used for preparation of microparticles by employing standard emulsification and heat-crosslinking techniques. The heparin release rate from the microparticles was found to be dependent upon the degree of crosslinking. When a thin coagulum of a suspension of microparticles was formed with heat on a glass surface, the treated surface demonstrated resistance to clot formation in contact with non-anticoagulated blood. A suspension of the microparticles applied during laser-balloon angioplasty onto the luminal surface of dog carotid and femoral arteries showed persistence for up to one week without thrombus formation or occlusion of the vessel. Since the rate of biodegradation is primarily dictated by the extent of crosslinking, an optimal degree of thermal denaturation will permit longer persistence of the carrier while allowing adequate release of the entrapped pharmacologic agent. A variety of antithrombotic and antiinflammatory agents are being considered as candidate bioprotective materials for local application after angioplasty.

  6. A method for allelic replacement that uses the conjugative transposon Tn916: deletion of the emm6.1 allele in Streptococcus pyogenes JRS4.

    PubMed

    Norgren, M; Caparon, M G; Scott, J R

    1989-12-01

    The emm6.1 allele of Streptococcus pyogenes JRS4 was deleted by using the conjugative transposon Tn916. The aphA-3 gene, conferring resistance to kanamycin, was cloned between the sequences flanking the structural gene for the type 6 M protein (emm6.1) and inserted into the BstXI site of Tn916 to generate the chimeric transposon Tn916-5K3. Because the BstXI site lies in a nonessential region of Tn916, the chimeric transposon could transfer by conjugation from Bacillus subtilis into JRS4. In some of the transconjugants, Tn916-5K3 replaced the emm6.1 locus of JRS4 by homologous recombination between the cloned emm6.1-flanking regions and the resident chromosome. One recombinant studied in detail, JRS75, was kanamycin resistant and tetracycline sensitive and lacked immunologically detectable M6 protein. Furthermore, by Southern blot analysis, the DNA region encompassing the emm6.1 structural gene was found to have been replaced by aphA-3.

  7. Heat shock increases conjugation efficiency in Clostridium difficile.

    PubMed

    Kirk, Joseph A; Fagan, Robert P

    2016-12-01

    Clostridium difficile infection has increased in incidence and severity over the past decade, and poses a unique threat to human health. However, genetic manipulation of C. difficile remains in its infancy and the bacterium remains relatively poorly characterised. Low-efficiency conjugation is currently the only available method for transfer of plasmid DNA into C. difficile. This is practically limiting and has slowed progress in understanding this important pathogen. Conjugation efficiency varies widely between strains, with important clinically relevant strains such as R20291 being particularly refractory to plasmid transfer. Here we present an optimised conjugation method in which the recipient C. difficile is heat treated prior to conjugation. This significantly improves conjugation efficiency in all C. difficile strains tested including R20291. Conjugation efficiency was also affected by the choice of media on which conjugations were performed, with standard BHI media giving most transconjugant recovery. Using our optimised method greatly increased the ease with which the chromosome of R20291 could be precisely manipulated by homologous recombination. Our method improves on current conjugation protocols and will help speed genetic manipulation of strains otherwise difficult to work with.

  8. Electrochemical spectroscopy of conjugated polymers

    NASA Astrophysics Data System (ADS)

    Hwang, Jungseek

    Conjugated polymers become conductors when they are doped (oxidized or reduced). The initial work was done on conducting polymers by three Nobel laureates (A. J. Heeger, H. Shirakawa, and A. G. MacDiarmid) in 1977. They discovered an increase by nearly 10 orders of magnitude in the electrical conductivity of polyacetylene when it was doped with iodine or other acceptors. Conjugated polymers have been studied intensively since that time because of their high conductivity, reversible doping and low-dimensional geometry. Doping causes electronic structure changes which have numerous potential applications. We have studied three thiophene derivative polymers: poly (3,4-ethylenedioxy-thiophene) (PEDOT), poly (3,4-propylenedioxythiophene) (PProDOT), and poly (3,4-dimethylpropylenedioxythiophene) (PProDOTMe2). Two types of samples were used for this study. The first was a thin polymer film on an indium tin oxide (ITO) coated glass slide. The polymer film was deposited on a metallic ITO surface by an electrochemical method. We measured reflectance and transmittance of the sample. The data were analyzed by modeling all layers of this multi-layer thin film structure, using the Drude-Lorentz model for each layer. We calculated the optical constants from the modeling results and obtained information on the electronic structure of the neutral and doped polymers. Conjugated polymers can be reversibly doped in an electrochemical cell. The doping causes optical absorption bands to move from one optical frequency to another frequency. To study this behavior, we prepared another type of sample. First, a thin polymer film was deposited on a gold-coated Mylar film by the same electrochemical method. Then, we built electrochromic cells with an infrared transparent window, using the polymer films on the gold/Mylar strips as electrodes. We connected the cell to an electrical supply. As we change the cell voltage (potential difference between the two electrodes), we can change the doping

  9. Physical, Chemical, and Biological Methods and Data from the Urban Land-Use-Gradient Study, Des Plaines and Fox River Basins, Illinois, 1999-2001

    USGS Publications Warehouse

    Adolphson, Debbie L.; Arnold, Terri L.; Fitzpatrick, Faith A.; Harris, Mitchell A.; Richards, Kevin D.; Scudder, Barbara C.; Stewart, Jana S.

    2001-01-01

    Physical, chemical, and biological data were collected at 46 sites in the Fox and Des Plaines River Basins as part of the upper Illinois River Basin study of the U.S. Geological Survey?s National Water-Quality Assessment Program. The data, collected from 1999 to 2001, will be used to determine the effects of urbanization on streams in the Chicago, Illinois, metropolitan area. To examine the possible effects of urbanization on stream-water quality, the sampling sites were selected to represent a gradient of land use changing from agriculture into urban. Urban land use for the selected sites ranged from less than 1 percent urban to 92 percent urban. Data-collection methods are presented in the text portion of this report. Physical characteristics of the stream that were collected include descriptive and qualitative habitat and geomorphic measures. Water samples were analyzed for nutrients (nitrogen and phosphorus), 11 major ions, 46 wastewater indicators, pH, and specific conductance. Aquatic communities were sampled to identify and quantify populations of selected algae, benthic macroinvertebrates, and fish. There were 72 unique fish species collected at all of the sites. The number of benthic macroinvertebrate taxa collected at all the sites ranged from 15 to 48. The data and the associated data documentation are presented on a CD-ROM included with this report.

  10. A simple extraction method for the simultaneous detection of tetramisole and diethylcarbamazine in milk, eggs, and porcine muscle using gradient liquid chromatography-tandem mass spectrometry.

    PubMed

    Zhang, Dan; Park, Jin-A; Kim, Dong-Soon; Kim, Seong-Kwan; Shin, Soo-Jean; Shim, Jae-Han; Shin, Sung Chul; Kim, Jin-Suk; Abd El-Aty, A M; Shin, Ho-Chul

    2016-02-01

    Analysis of residual quantities of contaminants in foods of animal origin is crucial for quality control of consumer products. This study was aimed to develop a simple and raid analytical method for detection of tetramisole and diethylcarbamazine using gradient liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS). Tetramisole, diethylcarbamazine, and guaifenesin (as an internal standard) were extracted from milk, eggs, and porcine muscle using acetonitrile followed by partitioning at -20 °C for 1h. No extract purification was deemed necessary. The analytes were separated on C18 column using ammonium formate both in water and methanol. Good linearity was achieved over the tested concentration range with R(2) ⩾ 0.974. Recovery at two fortification levels ranged between 67.47% and 97.38%. The intra- and inter-day precisions were <20%. The limit of quantification was 0.2 and 2 ng/g for tetramisole and diethylcarbamazine, respectively. An analytical survey of samples purchased from large markets showed that none of the samples contained any of the target analytes. To the best of our knowledge, this is the first report on the quantitative determination of tetramisole and diethylcarbamazine in animal food products.

  11. Gradient of molecular Hartree-Fock-Bogoliubov energy with a linear combination of atomic orbital quasiparticle wave functions

    NASA Astrophysics Data System (ADS)

    Kobayashi, Masato

    2014-02-01

    The analytical gradient for the atomic-orbital-based Hartree-Fock-Bogoliubov (HFB) energy functional, the modified form of which was proposed by Staroverov and Scuseria to account for the static electron correlation [J. Chem. Phys. 117, 11107 (2002)], is derived. Interestingly, the Pulay force for the HFB energy is expressed with the same formula as that for the Hartree-Fock method. The efficiency of the present HFB energy gradient is demonstrated in the geometry optimizations of conjugated and biradical systems. The geometries optimized by using the HFB method with the appropriate factor ζ, which controls the degree of static correlation included, are found to show good agreement with those obtained by using a complete active-space self-consistent field method, although they are significantly dependent on ζ.

  12. Gradient of molecular Hartree-Fock-Bogoliubov energy with a linear combination of atomic orbital quasiparticle wave functions.

    PubMed

    Kobayashi, Masato

    2014-02-28

    The analytical gradient for the atomic-orbital-based Hartree-Fock-Bogoliubov (HFB) energy functional, the modified form of which was proposed by Staroverov and Scuseria to account for the static electron correlation [J. Chem. Phys. 117, 11107 (2002)], is derived. Interestingly, the Pulay force for the HFB energy is expressed with the same formula as that for the Hartree-Fock method. The efficiency of the present HFB energy gradient is demonstrated in the geometry optimizations of conjugated and biradical systems. The geometries optimized by using the HFB method with the appropriate factor ζ, which controls the degree of static correlation included, are found to show good agreement with those obtained by using a complete active-space self-consistent field method, although they are significantly dependent on ζ.

  13. Gradient of molecular Hartree–Fock–Bogoliubov energy with a linear combination of atomic orbital quasiparticle wave functions

    SciTech Connect

    Kobayashi, Masato

    2014-02-28

    The analytical gradient for the atomic-orbital-based Hartree–Fock–Bogoliubov (HFB) energy functional, the modified form of which was proposed by Staroverov and Scuseria to account for the static electron correlation [J. Chem. Phys. 117, 11107 (2002)], is derived. Interestingly, the Pulay force for the HFB energy is expressed with the same formula as that for the Hartree–Fock method. The efficiency of the present HFB energy gradient is demonstrated in the geometry optimizations of conjugated and biradical systems. The geometries optimized by using the HFB method with the appropriate factor ζ, which controls the degree of static correlation included, are found to show good agreement with those obtained by using a complete active-space self-consistent field method, although they are significantly dependent on ζ.

  14. Global convergence analysis of fast multiobjective gradient-based dose optimization algorithms for high-dose-rate brachytherapy.

    PubMed

    Lahanas, M; Baltas, D; Giannouli, S

    2003-03-07

    We consider the problem of the global convergence of gradient-based optimization algorithms for interstitial high-dose-rate (HDR) brachytherapy dose optimization using variance-based objectives. Possible local minima could lead to only sub-optimal solutions. We perform a configuration space analysis using a representative set of the entire non-dominated solution space. A set of three prostate implants is used in this study. We compare the results obtained by conjugate gradient algorithms, two variable metric algorithms and fast-simulated annealing. For the variable metric algorithm BFGS from numerical recipes, large fluctuations are observed. The limited memory L-BFGS algorithm and the conjugate gradient algorithm FRPR are globally convergent. Local minima or degenerate states are not observed. We study the possibility of obtaining a representative set of non-dominated solutions using optimal solution rearrangement and a warm start mechanism. For the surface and volume dose variance and their derivatives, a method is proposed which significantly reduces the number of required operations. The optimization time, ignoring a preprocessing step, is independent of the number of sampling points in the planning target volume. Multiobjective dose optimization in HDR brachytherapy using L-BFGS and a new modified computation method for the objectives and derivatives has been accelerated, depending on the number of sampling points, by a factor in the range 10-100.

  15. [Conjugate vaccines against bacterial infections: typhoid fever].

    PubMed

    Paniagua, J; García, J A; López, C R; González, C R; Isibasi, A; Kumate, J

    1992-01-01

    Capsular polysaccharides have been studied as possible vaccines against infectious diseases. However, they are capable to induce only short-run protection because of their T-independent properties and they would not be protective against infection in high-risk populations. The alternative to face this problem is to develop methods to join covalently the polysaccharide and proteins to both increase the immunogenicity of and to confer the property of T-dependence to this antigen. In order to obtain a conjugate vaccine against typhoid fever, in our laboratory we have tried to synthesize a conjugate immunogen between the Vi antigen and porins from Salmonella typhi.

  16. Atomic Phase Conjugation From a Bose Condensate

    PubMed Central

    Goldstein, Elena V.; Plättner, Katja; Meystre, Pierre

    1996-01-01

    We discuss the possibility of observing atomic phase conjugation from Bose condensates, and using it as a diagnostic tool to access the spatial coherence properties and to measure the lifetime of the condensate. We argue that since phase conjugation results from the scattering of a partial matter wave off the spatial grating produced by two other waves, it offers a natural way to directly measure such properties, and as such provides an attractive alternative to the optical methods proposed in the past. PMID:27805111

  17. Assessment of density functional theory based Î'SCF (self-consistent field) and linear response methods for longest wavelength excited states of extended π-conjugated molecular systems

    NASA Astrophysics Data System (ADS)

    Filatov, Michael; Huix-Rotllant, Miquel

    2014-07-01

    Computational investigation of the longest wavelength excitations in a series of cyanines and linear n-acenes is undertaken with the use of standard spin-conserving linear response time-dependent density functional theory (TD-DFT) as well as its spin-flip variant and a ΔSCF method based on the ensemble DFT. The spin-conserving linear response TD-DFT fails to accurately reproduce the lowest excitation energy in these π-conjugated systems by strongly overestimating the excitation energies of cyanines and underestimating the excitation energies of n-acenes. The spin-flip TD-DFT is capable of correcting the underestimation of excitation energies of n-acenes by bringing in the non-dynamic electron correlation into the ground state; however, it does not fully correct for the overestimation of the excitation energies of cyanines, for which the non-dynamic correlation does not seem to play a role. The ensemble DFT method employed in this work is capable of correcting for the effect of missing non-dynamic correlation in the ground state of n-acenes and for the deficient description of differential correlation effects between the ground and excited states of cyanines and yields the excitation energies of both types of extended π-conjugated systems with the accuracy matching high-level ab initio multireference calculations.

  18. Assessment of density functional theory based ΔSCF (self-consistent field) and linear response methods for longest wavelength excited states of extended π-conjugated molecular systems.

    PubMed

    Filatov, Michael; Huix-Rotllant, Miquel

    2014-07-14

    Computational investigation of the longest wavelength excitations in a series of cyanines and linear n-acenes is undertaken with the use of standard spin-conserving linear response time-dependent density functional theory (TD-DFT) as well as its spin-flip variant and a ΔSCF method based on the ensemble DFT. The spin-conserving linear response TD-DFT fails to accurately reproduce the lowest excitation energy in these π-conjugated systems by strongly overestimating the excitation energies of cyanines and underestimating the excitation energies of n-acenes. The spin-flip TD-DFT is capable of correcting the underestimation of excitation energies of n-acenes by bringing in the non-dynamic electron correlation into the ground state; however, it does not fully correct for the overestimation of the excitation energies of cyanines, for which the non-dynamic correlation does not seem to play a role. The ensemble DFT method employed in this work is capable of correcting for the effect of missing non-dynamic correlation in the ground state of n-acenes and for the deficient description of differential correlation effects between the ground and excited states of cyanines and yields the excitation energies of both types of extended π-conjugated systems with the accuracy matching high-level ab initio multireference calculations.

  19. Assessment of density functional theory based ΔSCF (self-consistent field) and linear response methods for longest wavelength excited states of extended π-conjugated molecular systems

    SciTech Connect

    Filatov, Michael; Huix-Rotllant, Miquel

    2014-07-14

    Computational investigation of the longest wavelength excitations in a series of cyanines and linear n-acenes is undertaken with the use of standard spin-conserving linear response time-dependent density functional theory (TD-DFT) as well as its spin-flip variant and a ΔSCF method based on the ensemble DFT. The spin-conserving linear response TD-DFT fails to accurately reproduce the lowest excitation energy in these π-conjugated systems by strongly overestimating the excitation energies of cyanines and underestimating the excitation energies of n-acenes. The spin-flip TD-DFT is capable of correcting the underestimation of excitation energies of n-acenes by bringing in the non-dynamic electron correlation into the ground state; however, it does not fully correct for the overestimation of the excitation energies of cyanines, for which the non-dynamic correlation does not seem to play a role. The ensemble DFT method employed in this work is capable of correcting for the effect of missing non-dynamic correlation in the ground state of n-acenes and for the deficient description of differential correlation effects between the ground and excited states of cyanines and yields the excitation energies of both types of extended π-conjugated systems with the accuracy matching high-level ab initio multireference calculations.

  20. Comparison of N2O fluxes measured using flux-gradient, eddy-covariance, and chamber methods from an agricultural site

    NASA Astrophysics Data System (ADS)

    Brown, S. E.; Sargent, S.; Machado, P.; Freemantle, V.; Carvalho de Sena Rabelo, L.; Wagner-Riddle, C.

    2015-12-01

    Nitrous oxide emissions from agricultural lands occur as pulses at short intervals during various times throughout a given year, with the timing and magnitude dependent on management, soil, and climatic conditions. A thorough assessment of N2O emissions from fertilized fields requires methods capable of measuring fluxes at large temporal and spatial scales. A study investigating the effect of fertilizer treatment on the total annual N2O emissions from cornfields in Southern, Ontario, Canada provided the setting to analyze three methods for measuring N2O fluxes. Four 2-ha plots within a homogeneous 30-ha area were each subject to different nitrogen fertilizer source and timing treatments. N2O fluxes were measured using eddy-covariance (EC), multi-plot flux gradient (FG), and chamber techniques. Each method has advantages and disadvantages. Eddy-covariance is a standard method for measuring fluxes at the resolutions required to assess trace gas emissions, but the erratic nature of agricultural N2O fluxes necessitates testing of N2O analyzers, and the application of the EC method to N2O fluxes. This study acted as a field test of the Campbell Scientific TGA200A tunable diode trace gas analyzer. Testing the TGA200A against a TGA100A provided two simultaneous EC-flux measurements of N2O for one plot. Multi-plot FG measurements have the advantage of providing year-round, spatiality integrated, semi-continuous fluxes for side-by-side comparisons of N2O fluxes from separate treatments under similar climatic and soil conditions, but is a less common practice. Chambers have the advantage of being the most direct means of measuring soil fluxes; however, spatial resolution is low, and winter measurements are often impossible. Preliminary results showed that temporal patterns measured by each of the methods matched for three post-fertilizer N2O emission events of one plot. EC fluxes of N2O measured by each of the TGA analyzers correlated well (r2 = 0.90) and values were on