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Sample records for conjugate gradient methods

  1. Variable metric conjugate gradient methods

    SciTech Connect

    Barth, T.; Manteuffel, T.

    1994-07-01

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

  2. Approximate error conjugation gradient minimization methods

    DOEpatents

    Kallman, Jeffrey S

    2013-05-21

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

  3. 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.

  4. 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.

  5. Numerical experiments with a parallel conjugate gradient method

    SciTech Connect

    Oppe, T.C.; Kincaid, D.R.

    1987-04-01

    A parallel version of the conjugate gradient method introduced by Seager is implemented using various Cray multitasking tools. The parallel algorithm is used to solve a model partial differential equation on the unit square for various mesh sizes. Speed-up factors are given, and the effects of bank conflicts are noted. 8 refs., 10 figs.

  6. 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.

  7. New iterative gridding algorithm using conjugate gradient method

    NASA Astrophysics Data System (ADS)

    Jiang, Xuguang; Thedens, Daniel

    2004-05-01

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

  8. 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.

  9. On Meinardus' examples for the conjugate gradient method

    NASA Astrophysics Data System (ADS)

    Li, Ren-Cang

    2008-03-01

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

  10. 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.

  11. A stopping rule for the conjugate gradient regularization method for ill-posed problems

    NASA Astrophysics Data System (ADS)

    DeLillo, Thomas; Hrycak, Tomasz

    2002-11-01

    We present a novel parameter choice strategy for the conjugate gradient regularization algorithm which does not assume a priori information about the magnitude of the measurement error. Our approach imitates the truncated singular value decomposition within the Krylov subspaces associated with the normal equations. Conjugate gradient is implemented using the Lanczos bidiagonalization process with reorthogonalization. We compare our method with one proposed by Hanke and Raus and illustrate its performance with numerical experiments, including an inverse problem of acoustic source detection.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

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

    PubMed

    Bernal, Javier; Torres-Jimenez, Jose

    2015-01-01

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

  18. Orderings for conjugate gradient preconditionings

    NASA Technical Reports Server (NTRS)

    Ortega, James M.

    1991-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  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. Non Linear Conjugate Gradient

    2006-11-17

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

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

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

    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 percent for sufficiently large problems.

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

    NASA Astrophysics Data System (ADS)

    Michaud, Vincent; Guo, Hong

    2012-02-01

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

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

    NASA Technical Reports Server (NTRS)

    Venkatakrishnan, V.

    1990-01-01

    The compressible Navier-Stokes equations are solved for a variety of two-dimensional inviscid and viscous problems by preconditioned conjugate gradient-like algorithms. Roe's flux difference splitting technique is used to discretize the inviscid fluxes. The viscous terms are discretized by using central differences. An algebraic turbulence model is also incorporated. The system of linear equations which arises out of the linearization of a fully implicit scheme is solved iteratively by the well known methods of GMRES (Generalized Minimum Residual technique) and Chebyschev iteration. Incomplete LU factorization and block diagonal factorization are used as preconditioners. The resulting algorithm is competitive with the best current schemes, but has wide applications in parallel computing and unstructured mesh computations.

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

    PubMed

    Wang, Qi; Wang, Huaxiang

    2011-04-01

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

  8. 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.

  9. 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./.

  10. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  12. 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.

  13. 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

  14. An efficient impedance method for induced field evaluation based on a stabilized Bi-conjugate gradient algorithm

    NASA Astrophysics Data System (ADS)

    Wang, Hua; Liu, Feng; Xia, Ling; Crozier, Stuart

    2008-11-01

    This paper presents a stabilized Bi-conjugate gradient algorithm (BiCGstab) that can significantly improve the performance of the impedance method, which has been widely applied to model low-frequency field induction phenomena in voxel phantoms. The improved impedance method offers remarkable computational advantages in terms of convergence performance and memory consumption over the conventional, successive over-relaxation (SOR)-based algorithm. The scheme has been validated against other numerical/analytical solutions on a lossy, multilayered sphere phantom excited by an ideal coil loop. To demonstrate the computational performance and application capability of the developed algorithm, the induced fields inside a human phantom due to a low-frequency hyperthermia device is evaluated. The simulation results show the numerical accuracy and superior performance of the method.

  15. Detection of flaws in a two-dimensional body through measurement of surface temperatures and use of conjugate gradient method

    NASA Astrophysics Data System (ADS)

    Siavashi, Majid; Kowsary, Farshad; Abbasi-Shavazi, Ehsan

    2010-09-01

    This paper aims to obtain parameters (i.e. location and dimensions) relevant to flaws in a two-dimensional body by measuring the temperature on its boundaries. In this endeavour, a steady-state heat conduction problem is formulated, and the geometry under study is subjected to a known heat load, resulting in a specific heat distribution in the body. By using a number of heat sensors, the temperature at selected points on the boundary of the body is obtained. Inverse heat conduction methods implement these temperature data, working toward estimating the flaw parameters. The objective function is optimized using conjugate gradients method, and in solving the direct problem, an FEM code is employed. To check the effectiveness of this method, sample cases with one or more circular, elliptical cavities or cracks in the body, and a case with unknown cavity shape is solved. Finally the ensuing results analyzed.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

    Barkeshli, Kasra; Volakis, John L.

    1991-05-01

    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.

  18. Krylov-subspace recycling via the POD-augmented conjugate-gradient method

    SciTech Connect

    Carlberg, Kevin Thomas; Forstall, Virginia; Tuminaro, Raymond S.

    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.

  19. Krylov-subspace recycling via the POD-augmented conjugate-gradient method

    DOE PAGES

    Carlberg, Kevin Thomas; Forstall, Virginia; Tuminaro, Raymond S.

    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

  20. A fast, preconditioned conjugate gradient Toeplitz solver

    NASA Technical Reports Server (NTRS)

    Pan, Victor; Schrieber, Robert

    1989-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  2. Experiments with conjugate gradient algorithms for homotopy curve tracking

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1998-01-01

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

  4. 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

  5. 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.

  6. 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

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

    NASA Astrophysics Data System (ADS)

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

    1989-05-01

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

  8. 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.

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

    SciTech Connect

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

    1991-09-01

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

  10. A constrained conjugate gradient algorithm for computed tomography

    SciTech Connect

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

    1994-11-15

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

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

    SciTech Connect

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

    2008-01-01

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

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

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

    SciTech Connect

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

    1994-03-01

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

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

    PubMed

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

    2006-10-01

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

  20. 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.

  1. 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.

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

    SciTech Connect

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

    1992-09-01

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

  3. 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.

  4. 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.

  5. 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.

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

    NASA Technical Reports Server (NTRS)

    Nachtsheim, Philip R.

    1999-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  8. 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.

  9. 2D resistivity inversion using conjugate gradients for a finite element discretization

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  10. 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).

  11. 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.

  12. A Non-linear Conjugate Gradient Numerical Inverse Solution for the Problem of 3-D Global Electromagnetic Induction

    NASA Astrophysics Data System (ADS)

    Kelbert, A.; Schultz, A.; Egbert, G.

    2006-12-01

    We address the non-linear ill-posed inverse problem of reconstructing the global three-dimensional distribution of electrical conductivity in Earth's mantle. The authors have developed a numerical regularized least-squares inverse solution based on the non-linear conjugate gradients approach. We apply this methodology to the most current low-frequency global observatory data set by Fujii &Schultz (2002), that includes c- and d-responses. We obtain 4-8 layer models satisfying the data. We then describe the features common to all these models and discuss the resolution of our method.

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

    2006-11-16

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

  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. Magnetoelectrets prepared by using temperature gradient method

    NASA Astrophysics Data System (ADS)

    Ojha, Pragya; Qureshi, M. S.; Malik, M. M.

    2015-05-01

    A novel Temperature Gradient method for preparation of magnetoelectret is proposed. Non uniform magnetic field and temperature gradient are expected to be the main cause for the formation of magnetoelectrets (MEs). Being bad conductors of heat, during their formation, there is a possibility for the existence of a temperature gradient along the dielectric electrode interface. In this condition, the motion of, molecules and charge carriers are dependent on Temperature Gradient in a preferred direction. To increase this temperature gradient on both sides of the sample novel method for the preparation of MEs is developed for the first time. For this method the special sample holders are designed in our laboratory. MEs are prepared in such a way that one surface is cooled and the other is heated, during the process. With the help of XRD analysis using Type-E orientation pattern and surface charge studies on magnetoelectrets, the two main causes Non uniform magnetic field and temperature gradient for the formation of magnetoelectrets (MEs), are authenticated experimentally.

  16. 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.

  17. 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.

  18. 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.

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

    SciTech Connect

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

    2015-06-01

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

  20. 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.

  1. 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.

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

    USGS Publications Warehouse

    Naff, Richard L.; Banta, Edward R.

    2008-01-01

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

  3. A direct MP2 gradient method

    NASA Astrophysics Data System (ADS)

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

    1990-02-01

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

  4. 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. PMID:26653495

  5. Gradient-based methods for full waveform inversion

    NASA Astrophysics Data System (ADS)

    Métivier, L.; Brossier, R.; Operto, S.; Virieux, J.

    2012-12-01

    The minimization of the distance between recorded and synthetic seismograms (namely misfit function) for the reconstruction of subsurface velocity models leads to large-scale non-linear inverse problems. These problems are generally solved using gradient-based methods, such as the (preconditioned) steepest-descent method or the (preconditioned) non-linear conjugate gradient method, Gauss-Newton approach and more recently the l-BFGS quasi-Newton method. Except the Gauss-Newton approach, these methods only require the capability of computing (and storing) the gradient of the misfit function, efficiently performed through the adjoint state method, leading to the resolution of one forward problem and one adjoint problem per source. However, the inverse Hessian operator could be considered for compensating from target illumination variations coming from acquisition geometry and medium velocity variations. This operator acts as a filter in the model space when velocity is updated. For example, the l-BFGS method estimates an approximation of the inverse of the Hessian from gradients of previous iterations without no significant extra computational costs. Gauss-Newton approximation of the Hessian not only adds an extra computational cost but also neglects multi-scattering effects. Exact Newton methods will consider multi-scattering effects and may be more accurate than the l-BFGS approximation. For such investigation, we shall introduce the second-order adjoint formulation for the efficient estimation of the product of the Hessian operator and any vector in the model space. Using this product, we may update the velocity model through the resolution of the linear system associated with the computation of the Newton descent direction using a "matrix free" iterative linear solver such as the conjugate gradient method. This implementation could be performed for Newton approaches (and also the Gauss-Newton approximation) and requires an additional state and adjoint

  6. 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

  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. Conjugate heat transfer with the entropic lattice Boltzmann method.

    PubMed

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

    2016-07-01

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

  9. Conjugate heat transfer with the entropic lattice Boltzmann method

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    PubMed

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

    2016-07-01

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

  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. 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. PMID:23913152

  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. Iterative method for predistortion of MRI gradient waveforms.

    PubMed

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

    2014-08-01

    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

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

    NASA Astrophysics Data System (ADS)

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

    1988-11-01

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

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

    NASA Technical Reports Server (NTRS)

    Burrows, R. R.

    1972-01-01

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

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

    PubMed

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

    2016-05-18

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

  18. 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

  19. 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.

  20. 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…

  1. 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.

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

    PubMed

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

    2015-07-15

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

  3. Analytic energy gradient for the projected Hartree-Fock method

    NASA Astrophysics Data System (ADS)

    Schutski, Roman; Jiménez-Hoyos, Carlos A.; Scuseria, Gustavo E.

    2014-05-01

    We derive and implement the analytic energy gradient for the symmetry Projected Hartree-Fock (PHF) method avoiding the solution of coupled-perturbed HF-like equations, as in the regular unprojected method. Our formalism therefore has mean-field computational scaling and cost, despite the elaborate multi-reference character of the PHF wave function. As benchmark examples, we here apply our gradient implementation to the ortho-, meta-, and para-benzyne biradicals, and discuss their equilibrium geometries and vibrational frequencies.

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

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

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

    NASA Astrophysics Data System (ADS)

    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.

  6. 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.

  7. Methods for methotrexate determination in macromolecular conjugates drug carrier.

    PubMed

    Ciekot, Jarosław; Goszczyński, Tomasz; Boratyńskit, Janusz

    2012-01-01

    In this paper, two simple, cost-effective and fast methods for quantification of methotrexate (MTX) in the macromolecular conjugates are presented. The method for analysis of total MTX in preparations was based on absorption spectrophotometry. Validation was performed by measuring absorbance at 372 nm of the sodium bicarbonate solution. Curve describing drug concentration against absorption had a linear character in the range of 1.204-40.13 microM. The reproducibility and precision of method was 0.1558 to 3.086%. The recovery of the method was between 99.56 and 104.7%. The limit of quantitation method was 1.050 microM. The method for free MTX determination was based on size exclusion chromatography and UV-VIS detection at the wavelength of 302 nm. Superdex Peptide column (150 x 4.6 mm) and a mobile phase 0.1 M sodium bicarbonate with a flow rate of 0.4 mL/min was used. In the free drug determination method, the curve had a linear character in the range of 2.006-200.6 microM. The reproducibility and precision of method was 0.3761 to 2.452%. The recovery of the method was between 93.18 and 104.5%. The limit of quantitation method was 0.9203 microM. PMID:23285700

  8. Analytical methods for physicochemical characterization of antibody drug conjugates

    PubMed Central

    Wakankar, Aditya; Chen, Yan; Gokarn, Yatin

    2011-01-01

    Antibody-drug conjugates (ADCs), produced through the chemical linkage of a potent small molecule cytotoxin (drug) to a monoclonal antibody, have more complex and heterogeneous structures than the corresponding antibodies. This review describes the analytical methods that have been used in their physicochemical characterization. The selection of the most appropriate methods for a specific ADC is heavily dependent on the properties of the linker, the drug and the choice of attachment sites (lysines, inter-chain cysteines, Fc glycans). Improvements in analytical techniques such as protein mass spectrometry and capillary electrophoresis have significantly increased the quality of information that can be obtained for use in product and process characterization and for routine lot release and stability testing. PMID:21441786

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

    NASA Astrophysics Data System (ADS)

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

    1988-11-01

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

  10. 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.

  11. 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.

  12. 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

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

    NASA Astrophysics Data System (ADS)

    Chan, Tony; Szeto, Tedd

    1994-03-01

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

  14. Variable methods to estimate the ionospheric horizontal gradient

    NASA Astrophysics Data System (ADS)

    Nagarajoo, Karthigesu

    2016-06-01

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

  15. 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.

  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. 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).

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

    NASA Technical Reports Server (NTRS)

    Nicolaides, R. A.; Choudhury, Shenaz

    1986-01-01

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

  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. 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.

  1. 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.

  2. Polaron Localization in Conjugated Polymers by Hybrid DFT Methods

    NASA Astrophysics Data System (ADS)

    Shao, Nan; Wu, Qin; Theorey; Computation Group Team

    2013-03-01

    Reliable application of density functional theory (DFT) to study the electronic properties of polarons remains controversial. A proper description should exhibit both the formation of a charge-localized electronic state and saturation of the polaron size for increasing oligomer length. The aim of this work is to find a proper hybrid DFT method to study the chain length related electronic properties of charged conjugated polymer system. Using oligopyrrole cations as a test case, global hybrid functionals such as BHandHLYP can show charge localization, but a well-defined polaron size does not emerge when the length of the oligomer is increased; the saturation effect was not predicted correctly. By applying 100% long-range corrected hybrid functionals, LRC-PBE, the saturation of charge distribution has been achieved, implying that the LRC-PBE is a better way to describe the spatial extent of the electronic state of polypyrrole than the conventional hybrid functionals. The tuning of the range parameter and the study of other polymer polaron systems will be discussed. Supported by Brookhaven Science Associates, LLC under Contract No. DE-AC02-98CH10886 with the U.S. Department of Energy.

  3. 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.

  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. New convergence results for the scaled gradient projection method

    NASA Astrophysics Data System (ADS)

    Bonettini, S.; Prato, M.

    2015-09-01

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

  7. 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

  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. Method to create gradient index in a polymer

    SciTech Connect

    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.

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

    NASA Technical Reports Server (NTRS)

    Wieseman, C. D.

    1985-01-01

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

  11. A general method for synthesizing enzyme-polymer conjugates in reverse emulsions using Pluronic as a reactive surfactant.

    PubMed

    Wu, Xiaoling; Ge, Jun; Zhu, Jingying; Zhang, Yifei; Yong, You; Liu, Zheng

    2015-06-14

    Using aldehyde-functionalized Pluronic as the reactive surfactant, enzyme-Pluronic conjugates with sizes ranging from nanometers to micrometers were synthesized in reverse emulsions. Compared with the direct conjugation in aqueous solution, this method gave an increased conjugation efficiency and well-controlled size of the conjugates. The versatility of this method was validated using horseradish peroxidase (HRP), Candida rugosa lipase (CRL) and Candida antarctica lipase B (CALB). The resulting enzyme-Pluronic conjugates showed greatly enhanced apparent activity compared to free enzymes in organic media.

  12. 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

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

    PubMed

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

    2015-01-01

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

  14. 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.

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

    NASA Astrophysics Data System (ADS)

    Wu, R.

    2013-05-01

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

  16. 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.

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2006-11-01

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

  19. 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

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

    PubMed

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

    2016-01-01

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

  1. 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.

  2. 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.

  3. Spectral element-Fourier method for unsteady conjugate heat transfer in complex geometry flows

    NASA Astrophysics Data System (ADS)

    Amon, Cristina H.

    1995-04-01

    A spectral-element Fourier method (SEFM) is presented for the direct numerical simulation of forced convective heat transfer and conjugate conduction/convection in transitional internal flows in complex geometries. The SEFM is employed for the spatial discretization of the unsteady, incompressible, three-dimensional Navier-Stokes and energy equations. The resulting discrete equations are solved by a semi-implicit method in time treating explicitly the convection operator and implicitly the remaining pressure and viscous contributions. This methodology is illustrated by performing direct numerical simulations to investigate forced convective heat transfer in supercritical self-sustained oscillatory flows and conjugate effects in multimaterial domains. Highly unsteady flows in complex geometries are considered, including modified channels with periodic inhomogeneities such as spanwise rectangular and triangular grooves encountered in electronic equipment and compact heat exchangers.

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

    PubMed

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

    2014-12-01

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

  5. 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

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

    PubMed

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

    2001-01-01

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

  7. Design of subwavelength binary micro-optics using a gradient optimization method

    NASA Astrophysics Data System (ADS)

    Nesterenko, Dmitry V.; Kotlyar, Victor V.

    2001-12-01

    Various rigorous methods have been developed for the efficient analysis of diffractive optical elements (DOEs). We apply a gradient algorithm of synthesis to design two-dimensional DOEs, with the diffraction of the electromagnetic wave of TE polarization using a hybrid finite element - boundary element method. The hybrid method is capable of modeling inhomogeneous DOEs in unbounded free space in a computationally efficient manner. In this paper we discuss the application of the gradient optimization method to the matrix notation of the hybrid method. Such an application makes it possible to analyze DOE profiles with a large number of features. This allows one to overcome the limitations of calculation time dependent on the amount of the DOE modifications. We use the gradient method to design binary-phase lenses with subwavelength features. Although we have considered only binary-phase lenses, the gradient method presented is also suitable for designing continuous-relief DOEs.

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

    NASA Technical Reports Server (NTRS)

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

    1987-01-01

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

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

    PubMed

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

    2014-06-16

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

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

    PubMed

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

    2014-06-16

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  13. 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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    NASA Astrophysics Data System (ADS)

    He, Hexiang; Wong, Kam Sing

    2016-08-01

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

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

    PubMed

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

    2011-03-01

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

  18. Characterization and Comparison of Fumonisin B1-Protein Conjugates by Six Methods

    PubMed Central

    Wang, Ying; He, Cheng-Hua; Zheng, Hao; Zhang, Hai-Bin

    2012-01-01

    In order to generate an antibody against a small hapten molecule, the hapten is cross-linked with carrier protein to make it immunogenic. In this study, the hapten (Fumonisin B1, FB1) was coupled to ovalbumin (OVA) and bovine serum albumin (BSA), respectively by a short cross-linker reagent (glutaraldehyde, GA). To develop a technique for detecting the conjugation, the hapten-protein conjugates (FB1-OVA and FB1-BSA) were characterized thoroughly by ultraviolet (UV) spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), respectively. The molecular weights of FB1-BSA and FB1-OVA were 74,355.301 Da and 48,009.212 Da, respectively determined by the method of MALDI-TOF-MS. The molecular coupling ratios were 11 and 5 in FB1-BSA and FB1-OVA, respectively. In this experiment, MALDI-TOF-MS was selected as the most efficient method to evaluate the cross-linking effect and calculate the molecular coupling ratio. PMID:22312240

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

    NASA Astrophysics Data System (ADS)

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

    1989-10-01

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

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

    PubMed

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

    2015-01-01

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

  1. A novel Direct MIC-gradient Strip Method to screen for antibiotic-resistant faecal Enterobacteriaceae.

    PubMed

    Gammelsrud, Karianne Wiger; Knudsen, Per Kristian; Høiby, E Arne

    2016-10-01

    A novel method to detect resistant faecal Enterobacteriaceae was developed by applying MIC-gradient strips directly onto agar plates inoculated with faeces. The method provided the susceptibility pattern (MICs) of the dominant bacterial population directly on the plates and also detected smaller resistant subpopulations with a sensitivity of 1/10(5).

  2. 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.

  3. Full gradient stabilized cut finite element methods for surface partial differential equations

    NASA Astrophysics Data System (ADS)

    Burman, Erik; Hansbo, Peter; Larson, Mats G.; Massing, André; Zahedi, Sara

    2016-10-01

    We propose and analyze a new stabilized cut finite element method for the Laplace-Beltrami operator on a closed surface. The new stabilization term provides control of the full $\\mathbb{R}^3$ gradient on the active mesh consisting of the elements that intersect the surface. Compared to face stabilization, based on controlling the jumps in the normal gradient across faces between elements in the active mesh, the full gradient stabilization is easier to implement and does not significantly increase the number of nonzero elements in the mass and stiffness matrices. The full gradient stabilization term may be combined with a variational formulation of the Laplace-Beltrami operator based on tangential or full gradients and we present a simple and unified analysis that covers both cases. The full gradient stabilization term gives rise to a consistency error which, however, is of optimal order for piecewise linear elements, and we obtain optimal order a priori error estimates in the energy and $L^2$ norms as well as an optimal bound of the condition number. Finally, we present detailed numerical examples where we in particular study the sensitivity of the condition number and error on the stabilization parameter.

  4. A high-yield method for generating mass-transfer gradients in elastomer microfluidics using impermeable capillaries.

    PubMed

    Pinelis, Mike; Shamban, Leonid; Jovic, Andreja; Maharbiz, Michel M

    2008-12-01

    We demonstrated a robust, inexpensive method for fabricating high-throughput gas gradient generation devices which combined classic mass-transfer limited techniques with the versatility of elastomer microfluidics. The method allowed for dozens of replicate mass-transfer gradient experiments per day, including fabrication and assembly of devices. We demonstrated how our devices can be interfaced with microfluidics and how gradient parameters can be varied. In this work, we applied the method to characterize gradients of pH and cell viability generated in mass-transfer limited cultures of HeLa cells and observed the morphology of differentiating C2Cl2 myoblasts in an oxygen gradient.

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

    NASA Astrophysics Data System (ADS)

    Kokurin, Mihail Yu

    2006-02-01

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

  6. 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

  7. 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.

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

    PubMed

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

    2016-01-01

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

  9. 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

  10. 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.

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

    PubMed

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

    2015-06-01

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

  12. An optimized target-field method for MRI transverse biplanar gradient coil design

    NASA Astrophysics Data System (ADS)

    Zhang, Rui; Xu, Jing; Fu, Youyi; Li, Yangjing; Huang, Kefu; Zhang, Jue; Fang, Jing

    2011-12-01

    Gradient coils are essential components of magnetic resonance imaging (MRI) systems. In this paper, we present an optimized target-field method for designing a transverse biplanar gradient coil with high linearity, low inductance and small resistance, which can well satisfy the requirements of permanent-magnet MRI systems. In this new method, the current density is expressed by trigonometric basis functions with unknown coefficients in polar coordinates. Following the standard procedures, we construct an objective function with respect to the total square errors of the magnetic field at all target-field points with the penalty items associated with the stored magnetic energy and the dissipated power. By adjusting the two penalty factors and minimizing the objective function, the appropriate coefficients of the current density are determined. Applying the stream function method to the current density, the specific winding patterns on the planes can be obtained. A novel biplanar gradient coil has been designed using this method to operate in a permanent-magnet MRI system. In order to verify the validity of the proposed approach, the gradient magnetic field generated by the resulted current density has been calculated via the Biot-Savart law. The results have demonstrated the effectiveness and advantage of this proposed method.

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

    NASA Astrophysics Data System (ADS)

    Martin, Martin; Schack-Kirchner, Helmer

    2015-04-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  15. 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.

  16. Modified coherent gradient sensing method for slope measurement of reflective surfaces

    NASA Astrophysics Data System (ADS)

    Ma, Kang; Xie, Huimin

    2015-05-01

    A phase shifting method was developed for Coherent Gradient Sensing (CGS) using a three-step phase shifting method. Three different inteferograms were obtained by changing the distance between two gratings. The phase filed can be calculated accurately from the three inteferograms. The interference fringes (phase field) in reflection mode represent the gradient contours of the out-of-plane displacement of a surface. The curvatures and shape of the surface both can be calculated by numerical methods using the fringe patterns. The measurement principle and experimental setup were introduced in detail. As an application, a standard specimen with a curvature radius of 5 m was measured. From the analysis of the experimental results, we find that the relative error of the curvature using this method was about 0.78%. The method has good potentials for measuring the slopes, curvatures and shapes of thin film/substrate systems.

  17. 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%.

  18. 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.

  19. Development of Ti/Ti{sub 3}Sn functionally gradient material produced by eutectic bonding method

    SciTech Connect

    Kirihara, S.; Takeda, M.; Tsujimoto, T.

    1996-07-15

    Although many materials which have a single function have been developed, future needs are anticipated to include materials which have various functions. A functionally gradient material (FGM) which has characteristics of two different materials is a promising candidate for multi-functional material. The present methods for production of FGM, however, are very complicated and costly. In this study the authors answer the serious problem of high production cost by fabricating the FGM by a eutectic bonding method. This fabrication method includes structural control of FGM by changing the cooling process. They describe Ti/Ti{sub 3}Sn FGM obtained by the eutectic bonding method, and tell how the structure of its composition gradient part is changed by controlling the cooling process.

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

    PubMed

    Jacques, I; Dubray, G

    1991-08-01

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

  1. Inaccuracies in measurement of conjugated and unconjugated bilirubin in bile with ethyl anthranilate diazo and solvent-partition methods.

    PubMed Central

    Ostrow, J D; Boonyapisit, S T

    1978-01-01

    A criticial evaluation was made of the ethyl anthranilate diazo and two solvent-partition methods for the determination of conjugated and unconjugated bilirubin in human and rat bile. The ethyl anthranilate diazo reagent, which reacts only with conjugated bilirubin in serum, also diazotized a variable proportion of unconjugated bilirubin in bile and thus overestimated the concentration of monoconjugates. With the Weber-Schalm and modified Folsch solvent-partition methods applied to human or rat bile, 4--9% of added 14C-labelled unconjugated bilirubin partitioned with the conjugated bilirubin in the upper phase, and 4--9% of added 14C-labelled conjugated bilirubin partitioned into the lower phase. With dog bile, the spill-over of 14C-labelled bilirubin into the lower phase was 9--11%. Analysis of azopigments from the Weber-Schalm partition confirmed that over two-thirds of the bilirubin in the lower phase represents monoconjugates, principally the less-polar monoxylosides and monoglucosides. These solvent-partition methods thus overestimate the concentration of unconjugated bilirubin in bile. PMID:687371

  2. 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.

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

    NASA Astrophysics Data System (ADS)

    Yukhno, L. F.

    2007-11-01

    A modification of certain well-known methods of the conjugate direction type is proposed and examined. The modified methods are more stable with respect to the accumulation of round-off errors. Moreover, these methods are applicable for solving ill-conditioned systems of linear algebraic equations that, in particular, arise as approximations of ill-posed problems. Numerical results illustrating the advantages of the proposed modification are presented.

  4. 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.

  5. Improved convection compensating pulsed field gradient spin-echo and stimulated-echo methods.

    PubMed

    Sørland, G H; Seland, J G; Krane, J; Anthonsen, H W

    2000-02-01

    The need for convection compensating methods in NMR has been manifested through an increasing number of publications related to the subject over the past few years (J. Magn. Reson. 125, 372 (1997); 132, 13 (1998); 131, 126 (1998); 118, 50 (1996); 133, 379 (1998)). When performing measurements at elevated temperature, small convection currents may give rise to erroneous values of the diffusion coefficient. In work with high resolution NMR spectroscopy, the application of magnetic field gradients also introduces an eddy-current magnetic field which may result in errors in phase and baseline in the FFT-spectra. The eddy current field has been greatly suppressed by the application of bipolar magnetic field gradients. However, when introducing bipolar magnetic field gradients, the pulse sequence is lengthened significantly. This has recently been pointed out as a major drawback because of the loss of coherence and of NMR-signal due to transverse relaxation processes. Here we present modified convection compensating pulsed field gradient double spin echo and double stimulated echo sequences which suppress the eddy-current magnetic field without increasing the duration of the pulse sequences.

  6. A convenient solid-phase method for synthesis of 3'-conjugates of oligonucleotides.

    PubMed

    Stetsenko, D A; Gait, M J

    2001-01-01

    We present a new procedure for the preparation of 3'-conjugates of oligonucleotides through solid-phase synthesis. A suitable universal solid support was readily prepared using a series of peptide-like coupling reactions to incorporate first a spacer and then an L-homoserine branching unit. The N-alpha-position of the homoserine carries an Fmoc protecting group that is removed by treatment with piperidine to liberate an amino group suitable for attachment of the conjugate (e.g., small organic molecule, fluorescent group, cholesterol, biotin, amino acid, etc.) or for assembly of a short peptide. The side-chain hydroxyl group of the homoserine carries a trityl protecting group. After TFA deprotection, the hydroxyl group acts as the site for oligonucleotide assembly. An additional spacer, such as aminohexanoyl, may be incorporated easily between the conjugate molecule and the oligonucleotide. A number of examples of synthesis of 3'-conjugates of oligonucleotides and their analogues are described that involve standard automated oligonucleotide assembly and use of commercially available materials. The linkage between oligonucleotide and 3'-conjugate is chirally pure and is stable to conventional ammonia treatment used for oligonucleotide deprotection and release from the solid support. The homoserine-functionalized solid support system represents a simple and universal route to 3'-conjugates of oligonucleotides and their derivatives.

  7. 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.

  8. [Subunit vaccines--antigens, carriers, conjugation methods and the role of adjuvants].

    PubMed

    Jarząb, Anna; Skowicki, Michał; Witkowska, Danuta

    2013-11-27

    Vaccines are effective tools protecting against the development of infectious diseases caused by pathogenic microorganisms. Currently, we have vaccines protecting against many infections, where standard therapy is not only difficult but often impossible due to the ever-progressive increase in bacterial resistance to many available antibiotics. Among vaccines which have been used in the prevention of infection are the traditional vaccines containing live, killed or attenuated strains of microorganisms. However, it should be noted that such vaccines are not always effective, especially when the expected immune response is directed against specific antigens. Subunit vaccines belong to new generation vaccines and have gained more and more interest in recent years. These vaccines contain fragments of pathogenic microorganisms, which are highly purified and immunogenic antigens. Using these purified antigens excludes the risk of post-vaccination infection. In addition, subunit vaccines minimize side-effects associated with the use of whole bacterial cells. The paper discusses the most promising and the most tested antigens, vaccine carriers, conjugation methods and vaccine delivery systems which are being used in the design of subunit vaccines. This paper also highlights the advantages and disadvantages of adjuvants, which are substances to support the immune response in humans, and the relationship between adjuvants' efficacy and their mechanism of action.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

  11. 2D ESR image reconstruction from 1D projections using the modulated field gradient method

    NASA Astrophysics Data System (ADS)

    Páli, T.; Sass, L.; Horvat, L. I.; Ebert, B.

    A method for the reconstruction of 2D ESR images from 1 D projections which is based on the modulated field gradient method has been explored. The 2D distribution of spin-labeled stearic acid in oriented and unoriented dimyristoyl phosphatidylcholine multilayers on a flat quartz support was determined. Such samples are potentially useful for the determination of lipid lateral diffusion in oriented multilayers by monitoring the spreading of a sharp concentration profile in one or two dimensions. The limitations of the method are discussed and the improvements which are needed for dynamic measurements are outlined.

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

    NASA Astrophysics Data System (ADS)

    Wladyslawski, Mark; Nooijen, Marcel

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

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

    PubMed

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

    2005-02-01

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

  14. 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.

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

    PubMed

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

    2014-02-01

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

  16. Deterministic convergence of chaos injection-based gradient method for training feedforward neural networks.

    PubMed

    Zhang, Huisheng; Zhang, Ying; Xu, Dongpo; Liu, Xiaodong

    2015-06-01

    It has been shown that, by adding a chaotic sequence to the weight update during the training of neural networks, the chaos injection-based gradient method (CIBGM) is superior to the standard backpropagation algorithm. This paper presents the theoretical convergence analysis of CIBGM for training feedforward neural networks. We consider both the case of batch learning as well as the case of online learning. Under mild conditions, we prove the weak convergence, i.e., the training error tends to a constant and the gradient of the error function tends to zero. Moreover, the strong convergence of CIBGM is also obtained with the help of an extra condition. The theoretical results are substantiated by a simulation example.

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

    PubMed

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

    2005-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Fischer, David J.; Moore, Duncan T.

    2002-12-01

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

  19. 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.

  20. Study of random sequential adsorption by means of the gradient method

    NASA Astrophysics Data System (ADS)

    Loscar, E. S.; Guisoni, N.; Albano, E. V.

    2012-02-01

    By using the gradient method (GM) we study random sequential adsorption (RSA) processes in two dimensions under a gradient constraint that is imposed on the adsorption probability along one axis of the sample. The GM has previously been applied successfully to absorbing phase transitions (both first and second order), and also to the percolation transition. Now, we show that by using the GM the two transitions involved in RSA processes, namely percolation and jamming, can be studied simultaneously by means of the same set of simulations and by using the same theoretical background. For this purpose we theoretically derive the relevant scaling relationships for the RSA of monomers and we tested our analytical results by means of numerical simulations performed upon RSA of both monomers and dimers. We also show that two differently defined interfaces, which run in the direction perpendicular to the axis where the adsorption probability gradient is applied and separate the high-density (large-adsorption probability) and the low-density (low-adsorption probability) regimes, capture the main features of the jamming and percolation transitions, respectively. According to the GM, the scaling behaviour of those interfaces is governed by the roughness exponent α = 1/(1 + ν), where ν is the suitable correlation length exponent. Besides, we present and discuss in a brief overview some achievements of the GM as applied to different physical situations, including a comparison of the critical exponents determined in the present paper with those already published in the literature.

  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

    2016-01-01

    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

  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

    2016-01-01

    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

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

    PubMed

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

    2016-01-01

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

  6. Improved method for conjugative transfer by filter mating of Streptococcus pneumoniae

    SciTech Connect

    Smith, M.D.; Guild, W.R.

    1980-10-01

    The frequency of conjugation during filter mating of pneumococcus was increased to 10- to 100-fold when the filter was embedded in agar during incubation instead of being on the surface. The major effect was not due to protection from oxygen. The factor of increase was similar for transfer of plasmids and of chromosomal insertions of drug resistance elements.

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

    NASA Astrophysics Data System (ADS)

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

    2001-05-01

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

  8. 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

  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. 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.

  11. Remote loading of diclofenac, insulin and fluorescein isothiocyanate labeled insulin into liposomes by pH and acetate gradient methods.

    PubMed

    Hwang, S H; Maitani, Y; Qi, X R; Takayama, K; Nagai, T

    1999-03-01

    Remote loading of the model drugs diclofenac, insulin and fluorescein isothiocyanate labeled insulin (FITC-insulin) into liposomes by formation of transmembrane gradients were examined. A trapping efficiency of almost 100% was obtained for liposomal diclofenac, by the calcium acetate gradient method, whereas liposomes prepared by the conventional reverse-phase evaporation vesicle method had 1-8% trapping efficiencies. Soybean-derived sterol was a better stabilizer of the dipalmitoylphosphatidylcholine bilayer membrane than cholesterol, as shown from trapping efficiencies and drug release. The pH gradient method resulted in a 5-50% of FITC-insulin liposomal trapping efficiency, while insulin could not be loaded by this method. Liposomes released calcein in response to insulin, showing insulin interacts with the liposomal membrane in the presence of a transmembrane gradient. The present work has demonstrated a remote loading method for weak acids such as diclofenac into liposomes by the acetate gradient method. From the result of remote loading of FITC-insulin into liposomes by the pH gradient method, this method may be available for the preparation of liposomal peptides.

  12. Numerical ray tracing method for an eccentric radial gradient-index rod lens.

    PubMed

    Horiuchi, Shuma; Yoshida, Shuhei; Yamamoto, Manabu

    2014-10-01

    We propose a ray tracing method for a radial gradient-index (GRIN) rod lens with an eccentric refractive index distribution. Radial GRIN rod lenses are typically treated as being rotationally symmetric around the optical axis. However, there are several eccentricities of the refractive index distribution in the transverse section, and an eccentricity point is the position of the highest refractive index with respect to the rod axis. Some manufacturing techniques can introduce these eccentricities in the refractive index distribution, and the effect of eccentricity on the lens performance cannot be neglected in some cases. Ray tracing in an eccentric refractive index distribution is possible by extending the conventional method. This allows analysis of the imaging performance of a radial GRIN rod lens with an eccentric refractive index distribution. Since the proposed method builds on the conventional formalism for a rotationally symmetric refractive index distribution, it is simple and easy to implement.

  13. Increased ELISA sensitivity using a modified method for conjugating horseradish peroxidase to monoclonal antibodies.

    PubMed

    Madersbacher, S; Wolf, H; Gerth, R; Berger, P

    1992-07-31

    We investigated the importance of monoclonal antibody (MCA) purity and the input molar ratio of horseradish peroxidase (HRPO)/IgG used for MCA conjugation on various immunoenzymometric assay (IEMA) parameters. The sensitivity of IEMAs for human follicle stimulating hormone (hFSH), human chorionic gonadotropin (hCG) and the free alpha subunit of hCG (hCG alpha) could be increased up to 6-fold, whereas non-specific binding remained within tolerable limits (E less than 0.1), when MCAs purified by high performance liquid chromatography (HPLC) using a hydroxylapatite column (HPHT) were conjugated with an input molar HRPO/IgG ratio of four instead of the usual ratio of two.

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

    NASA Technical Reports Server (NTRS)

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

    1979-01-01

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

  15. 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.

  16. Optimization of the AC-gradient method for velocity profile measurement and application to slow flow

    NASA Astrophysics Data System (ADS)

    Kartäusch, Ralf; Helluy, Xavier; Jakob, Peter Michael; Fidler, Florian

    2014-11-01

    This work presents a spectroscopic method to measure slow flow. Within a single shot the velocity distribution is acquired. This allows distinguishing rapidly between single velocities within the sampled volume with a high sensitivity. The technique is based on signal acquisition in the presence of a periodic gradient and a train of refocussing RF pulses. The theoretical model for trapezoidal bipolar pulse shaped gradients under consideration of diffusion and the outflow effect is introduced. A phase correction technique is presented that improves the spectral accuracy. Therefore, flow phantom measurements are used to validate the new sequence and the simulation based on the theoretical model. It was demonstrated that accurate parabolic flow profiles can be acquired and flow variations below 200 μm/s can be detected. Three post-processing methods that eliminate static background signal are also presented for applications in which static background signal dominates. Finally, this technique is applied to flow measurement of a small alder tree demonstrating a typical application of in vivo plant measurements.

  17. [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.

  18. 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.

  19. 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.

  20. 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.

  1. Communication: An efficient analytic gradient theory for approximate spin projection methods

    NASA Astrophysics Data System (ADS)

    Hratchian, Hrant P.

    2013-03-01

    Spin polarized and broken symmetry density functional theory are popular approaches for treating the electronic structure of open shell systems. However, spin contamination can significantly affect the quality of predicted geometries and properties. One scheme for addressing this concern in studies involving broken-symmetry states is the approximate projection method developed by Yamaguchi and co-workers. Critical to the exploration of potential energy surfaces and the study of properties using this method will be an efficient analytic gradient theory. This communication introduces such a theory formulated, for the first time, within the framework of general post-self consistent field (SCF) derivative theory. Importantly, the approach taken here avoids the need to explicitly solve for molecular orbital derivatives of each nuclear displacement perturbation, as has been used in a recent implementation. Instead, the well-known z-vector scheme is employed and only one SCF response equation is required.

  2. The improved surface gradient method for flows simulation in variable bed topography channel using TVD-MacCormack scheme

    NASA Astrophysics Data System (ADS)

    Tseng, Ming-Hseng

    2003-09-01

    This paper reports four different approaches to discretize the source terms for the simulation of one-dimensional open-channel flows with rapidly varied bottom topography using TVD-MacCormack scheme. Compared with other high-resolution shock-capturing schemes, MacCormack-type predictor-corrector method is easy to implement and does not present any additional difficulty in dealing with the source terms. To avoid the generation of artificial numerical waves, if the bottom topography shows strong variation, special treatment of the source terms is still required to eliminate or reduce the artificial numerical error caused by adding TVD corrections to the method. The computed results demonstrated that the improved surface gradient method is more suitable for simulating open-channel flow with highly irregular bed topography by using the surface gradient instead of the depth gradient for TVD corrections and considering the balancing of the source terms and the flux gradients.

  3. 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.

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

    PubMed

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

    2011-12-21

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

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

    PubMed

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

    2016-05-01

    A new simple, rapid and precise RP-HPLC method was developed for the extraction and quantitative estimation of caffeine (C), (-)-epigallocatechin gallate (EGCG), (+)-catechin(Ct), (-)-epicatechin(EC), and (-)-epicatechin gallate (ECG) (collectively named as Tea Powder Bioactives TPBAs) extracted from tea powder using different ratios of ethanol: water. The simultaneous determination of TPBAs was performed using the UV spectrophotometric method which employs the absorbance at 205 nm (λmax of caffeine and polyphenols). This method is a gradient based HPLC method with a flow rate of 0.8 mL/min using Inertsil ODS 100 × 4.6 mm, 3 μm column with methanol and ammonium dihydrogen phosphate (pH-2.8) as mobile phase. The method was validated in terms of specificity, precision, linearity, accuracy, limit of quantification (LOQ), and limit of detection (LOD). The linearity of the proposed method was investigated for concentration ranging between 0.5-60 μg/mL with regression co-efficient, R(2) = 0.999-1.0. This method estimates all the TPBAs simultaneously with enhanced precision and linearity as per the ICH guidelines. Also, to confirm the individual TPBA, the antioxidant property of the each TPBA was analyzed which was commensurate with that of the previous reports. PMID:27407191

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

    PubMed

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

    2012-01-01

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

  7. Demonstrating the Temperature Gradient Impact on Grain Growth in UO2 Using the Phase Field Method

    SciTech Connect

    Michael R Tonks; Yongfeng Zhang; Xianming Bai; Paul C Millett

    2014-01-01

    Grain boundaries (GBs) are driven to migrate up a temperature gradient. In this work, we use a phase field (PF) model to investigate the impact of temperature gradients on normal grain growth. GB motion in 2D UO2 polycrystals is predicted under increasing temperature gradients. We find that the temperature gradient does not significantly impact the average grain growth behavior, because the curvature driving force is dominant. However, it does cause significant local migration of the individual grains. In addition, the change in the GB mobility due to the temperature gradient results in larger grains in the hot portion of the polycrystal.

  8. 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

    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 10(1) 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 10(2) 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.

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

    PubMed

    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 10(1) 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 10(2) using a high receptivity trans-kingdom conjugation strain. In addition, either increasing the amount of donor cells or pretreating the recipient cells with thiols such as dithiothreitol improved the transformation efficiency by one order of magnitude. This simple trans-kingdom conjugation-mediated transformation method could be used as a practical yeast transformation method upon enrichment of available vectors and donor E. coli strains. PMID:26849654

  10. Mitochondrial accumulation of a lipophilic cation conjugated to an ionisable group depends on membrane potential, pH gradient and pK(a): implications for the design of mitochondrial probes and therapies.

    PubMed

    Finichiu, Peter G; James, Andrew M; Larsen, Lesley; Smith, Robin A J; Murphy, Michael P

    2013-02-01

    Mitochondria play key roles in a broad range of biomedical situations, consequently there is a need to direct bioactive compounds to mitochondria as both therapies and probes. A successful approach has been to target compounds to mitochondria by conjugation to lipophilic cations, such as triphenylphosphonium (TPP), which utilize the large mitochondrial membrane potential (Δψ(m), negative inside) to drive accumulation. This has proven effective both in vitro and in vivo for a range of bioactive compounds and probes. However so far only neutral appendages have been targeted to mitochondria in this way. Many bioactive functional moieties that we would like to send to mitochondria contain ionisable groups with pK (a) in the range that creates an assortment of charged species under physiological conditions. To see if such ionisable compounds can also be taken up by mitochondria, we determined the general requirements for the accumulation within mitochondria of a TPP cation conjugated to a carboxylic acid or an amine. Both were taken up by energised mitochondria in response to the protonmotive force. A lipophilic TPP cation attached to a carboxylic acid was accumulated to a greater extent than a simple TPP cation due to the interaction of the weakly acidic group with the pH gradient (ΔpH). In contrast, a lipophilic TPP cation attached to an amine was accumulated less than the simple cation due to exclusion of the weakly basic group by the ΔpH. From these data we derived a simple equation that describes the uptake of lipophilic cations containing ionisable groups as a function of Δψ(m), ΔpH and pK(a). These findings may facilitate the rational design of additional mitochondrial targeted probes and therapies.

  11. A distributed equivalent magnetic current based FDTD method for the calculation of E-fields induced by gradient coils.

    PubMed

    Liu, Feng; Crozier, Stuart

    2004-08-01

    This paper evaluates a new, low-frequency finite-difference time-domain method applied to the problem of induced E-fields/eddy currents in the human body resulting from the pulsed magnetic field gradients in MRI. In this algorithm, a distributed equivalent magnetic current is proposed as the electromagnetic source and is obtained by quasistatic calculation of the empty coil's vector potential or measurements therein. This technique circumvents the discretization of complicated gradient coil geometries into a mesh of Yee cells, and thereby enables any type of gradient coil modelling or other complex low frequency sources. The proposed method has been verified against an example with an analytical solution. Results are presented showing the spatial distribution of gradient-induced electric fields in a multi-layered spherical phantom model and a complete body model.

  12. 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.

  13. 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.

  14. 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. PMID:27231649

  15. 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

  16. Conjugate Heat Transfer Computation for Evaluation of Single-Blow Method for Compact Fin-Tube Heat Exchangers

    NASA Astrophysics Data System (ADS)

    Song, Gil-Dal; Nishino, Koichi

    Computations have been carried out to evaluate heat transfer coefficients given by the single-blow method that is characterized by a transient and conjugate heat transfer problem between the fluid and the solid. Both heat conduction and convection equations are solved numerically to obtain the transient fluid and fin temperature distributions. Finite volume solutions indicate that the fin temperature distribution of the single-blow method varies with time and position and that the fluid temperature distribution of the single-blow method is close to that observed in the steady-state computation specified with the constant wall temperature condition. It is found that the local heat transfer coefficient resulting from the single-blow method is almost identical to that from the steady-state constant wall temperature computation and is nearly time-independent.

  17. 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

    2013-04-01

    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.

  18. 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.

  19. Density functional theory for molecular and periodic systems using density fitting and continuous fast multipole method: Analytical gradients.

    PubMed

    Łazarski, Roman; Burow, Asbjörn Manfred; Grajciar, Lukáš; Sierka, Marek

    2016-10-30

    A full implementation of analytical energy gradients for molecular and periodic systems is reported in the TURBOMOLE program package within the framework of Kohn-Sham density functional theory using Gaussian-type orbitals as basis functions. Its key component is a combination of density fitting (DF) approximation and continuous fast multipole method (CFMM) that allows for an efficient calculation of the Coulomb energy gradient. For exchange-correlation part the hierarchical numerical integration scheme (Burow and Sierka, Journal of Chemical Theory and Computation 2011, 7, 3097) is extended to energy gradients. Computational efficiency and asymptotic O(N) scaling behavior of the implementation is demonstrated for various molecular and periodic model systems, with the largest unit cell of hematite containing 640 atoms and 19,072 basis functions. The overall computational effort of energy gradient is comparable to that of the Kohn-Sham matrix formation. © 2016 Wiley Periodicals, Inc.

  20. Spike-based reinforcement learning in continuous state and action space: when policy gradient methods fail.

    PubMed

    Vasilaki, Eleni; Frémaux, Nicolas; Urbanczik, Robert; Senn, Walter; Gerstner, Wulfram

    2009-12-01

    Changes of synaptic connections between neurons are thought to be the physiological basis of learning. These changes can be gated by neuromodulators that encode the presence of reward. We study a family of reward-modulated synaptic learning rules for spiking neurons on a learning task in continuous space inspired by the Morris Water maze. The synaptic update rule modifies the release probability of synaptic transmission and depends on the timing of presynaptic spike arrival, postsynaptic action potentials, as well as the membrane potential of the postsynaptic neuron. The family of learning rules includes an optimal rule derived from policy gradient methods as well as reward modulated Hebbian learning. The synaptic update rule is implemented in a population of spiking neurons using a network architecture that combines feedforward input with lateral connections. Actions are represented by a population of hypothetical action cells with strong mexican-hat connectivity and are read out at theta frequency. We show that in this architecture, a standard policy gradient rule fails to solve the Morris watermaze task, whereas a variant with a Hebbian bias can learn the task within 20 trials, consistent with experiments. This result does not depend on implementation details such as the size of the neuronal populations. Our theoretical approach shows how learning new behaviors can be linked to reward-modulated plasticity at the level of single synapses and makes predictions about the voltage and spike-timing dependence of synaptic plasticity and the influence of neuromodulators such as dopamine. It is an important step towards connecting formal theories of reinforcement learning with neuronal and synaptic properties. PMID:19997492

  1. Spike-Based Reinforcement Learning in Continuous State and Action Space: When Policy Gradient Methods Fail

    PubMed Central

    Vasilaki, Eleni; Frémaux, Nicolas; Urbanczik, Robert; Senn, Walter; Gerstner, Wulfram

    2009-01-01

    Changes of synaptic connections between neurons are thought to be the physiological basis of learning. These changes can be gated by neuromodulators that encode the presence of reward. We study a family of reward-modulated synaptic learning rules for spiking neurons on a learning task in continuous space inspired by the Morris Water maze. The synaptic update rule modifies the release probability of synaptic transmission and depends on the timing of presynaptic spike arrival, postsynaptic action potentials, as well as the membrane potential of the postsynaptic neuron. The family of learning rules includes an optimal rule derived from policy gradient methods as well as reward modulated Hebbian learning. The synaptic update rule is implemented in a population of spiking neurons using a network architecture that combines feedforward input with lateral connections. Actions are represented by a population of hypothetical action cells with strong mexican-hat connectivity and are read out at theta frequency. We show that in this architecture, a standard policy gradient rule fails to solve the Morris watermaze task, whereas a variant with a Hebbian bias can learn the task within 20 trials, consistent with experiments. This result does not depend on implementation details such as the size of the neuronal populations. Our theoretical approach shows how learning new behaviors can be linked to reward-modulated plasticity at the level of single synapses and makes predictions about the voltage and spike-timing dependence of synaptic plasticity and the influence of neuromodulators such as dopamine. It is an important step towards connecting formal theories of reinforcement learning with neuronal and synaptic properties. PMID:19997492

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

    NASA Astrophysics Data System (ADS)

    Nakajima, Yuya; Seino, Junji; Nakai, Hiromi

    2013-12-01

    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.

  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. 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.

  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. Joint image registration and fusion method with a gradient strength regularization

    NASA Astrophysics Data System (ADS)

    Lidong, Huang; Wei, Zhao; Jun, Wang

    2015-05-01

    Image registration is an essential process for image fusion, and fusion performance can be used to evaluate registration accuracy. We propose a maximum likelihood (ML) approach to joint image registration and fusion instead of treating them as two independent processes in the conventional way. To improve the visual quality of a fused image, a gradient strength (GS) regularization is introduced in the cost function of ML. The GS of the fused image is controllable by setting the target GS value in the regularization term. This is useful because a larger target GS brings a clearer fused image and a smaller target GS makes the fused image smoother and thus restrains noise. Hence, the subjective quality of the fused image can be improved whether the source images are polluted by noise or not. We can obtain the fused image and registration parameters successively by minimizing the cost function using an iterative optimization method. Experimental results show that our method is effective with transformation, rotation, and scale parameters in the range of [-2.0, 2.0] pixel, [-1.1 deg, 1.1 deg], and [0.95, 1.05], respectively, and variances of noise smaller than 300. It also demonstrated that our method yields a more visual pleasing fused image and higher registration accuracy compared with a state-of-the-art algorithm.

  7. Crystallization of the Atg12–Atg5 conjugate bound to Atg16 by the free-interface diffusion method

    PubMed Central

    Noda, Nobuo N.; Fujioka, Yuko; Ohsumi, Yoshinori; Inagaki, Fuyuhiko

    2008-01-01

    Autophagy mediates the bulk degradation of cytoplasmic components in lysosomes/vacuoles. Five autophagy-related (Atg) proteins are involved in a ubiquitin-like protein conjugation system. Atg12 is conjugated to its sole target, Atg5, by two enzymes, Atg7 and Atg10. The Atg12–Atg5 conjugates form a multimeric complex with Atg16. Formation of the Atg12–Atg5–Atg16 ternary complex is crucial for the functions of these proteins on autophagy. Here, the expression, purification and crystallization of the Atg12–Atg5 conjugate bound to the N-terminal region of Atg16 (Atg16N) are reported. The Atg12–Atg5 conjugates were formed by co-expressing Atg5, Atg7, Atg10 and Atg12 in Eschericia coli. The Atg12–Atg5–Atg16N ternary complex was formed by mixing purified Atg12–Atg5 conjugates and Atg16N, and was further purified by gel-filtration chromatography. Crystallization screening was performed by the free-interface diffusion method. Using obtained microcrystals as seeds, large crystals for diffraction data collection were obtained by the sitting-drop vapour-diffusion method. The crystal contained one ternary complex per asymmetric unit, and diffracted to 2.6 Å resolution. PMID:18421155

  8. A neonatal pneumococcal conjugate vaccine trial in Papua New guinea: study population, methods and operational challenges.

    PubMed

    Phuanukoonnon, S; Reeder, J C; Pomat, W S; Van den Biggelaar, A H J; Holt, P G; Saleu, G; Opa, C; Michael, A; Aho, C; Yoannes, M; Francis, J; Orami, T; Namuigi, P; Siba, P M; Richmond, P C; Lehmann, D

    2010-01-01

    Infants in Papua New Guinea (PNG) are at a high risk of invasive pneumococcal disease, and a substantial burden of this falls on children less than six months old. PNG is planning to introduce a pneumococcal conjugate vaccine for infants in the near future, but to make the maximum impact neonatal immunization will have to be considered. To provide evidence on safety and immunogenicity for neonatal and early infant immunization, we undertook an open randomized controlled trial of 7-valent pneumococcal conjugate vaccine (7vPCV). 318 children received 7vPCV at ages 0, 1 and 2 months or at 1, 2 and 3 months or not at all. All children received 23-valent pneumococcal polysaccharide vaccine at age 9 months. This was a large and complex trial: village reporters visited participants weekly during the first year and fortnightly for a further 6 months and nurses monitored self-reported morbidity and collected many thousands of biological samples. The study team was remarkably successful in achieving the study aims, with 18-month follow-up completed on 77% of enrolled children and over 80% of scheduled samples collected. While the results of the trial will be reported elsewhere, this paper discusses the design of the study and dissects out some of the main reasons for its successful completion. Strong community engagement was an essential factor in success and the principles of equitable partnership and service provision led to a strong research partnership. A two-stage consent process, comprising primary assent followed by later informed consent, led to a high drop-out before initial enrolment, but an outstanding retention of those enrolled in the study. We conclude that factors such as strong community participation, reciprocity and a good relationship between the study team and participants are just as important as the technical elements of laboratory testing and data handling in ensuring the success of a vaccine trial in PNG. PMID:23163191

  9. 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.

  10. C loss of managed peatlands along a land use gradient - a comparison of three different methods

    NASA Astrophysics Data System (ADS)

    Krüger, Jan Paul; Leifeld, Jens; Glatzel, Stephan; Alewell, Christine

    2015-04-01

    Carbon (C) loss from managed organic soils is an important flux in the global carbon cycle. Different approaches exist to estimate C emissions and thus the greenhouse gas balance of soils. Here we compare two soil profile-based methods with greenhouse gas flux measurements by closed chambers to assess the net C loss from managed peatlands. We applied the different methods to the well-studied peatland complex Ahlen-Falkenberger Moor in northern Germany, which represents a land use gradient from near-natural wetland (NW) to extensively used grassland (GE) (rewetted in 2003/2004) to intensively used grassland (GI). Drainage commenced at the beginning of the 20th century, and land use was intensified in the middle of the 20th century. In November 2012, three peat cores down to approximately 100 cm were taken at each site and various biogeochemical soil parameters were analysed. The so-called combined method estimates the physical primary subsidence due to the loss of pore water and peat shrinkage, and the secondary subsidence due to the oxidative loss of organic matter. As a second method C loss was calculated using peat accumulation rates derived from 14-C age-dated samples and their C-stock in this depth. These two profile-based methods give the C loss since the onset of drainage. Compared to this, the greenhouse gas (GHG) measurements (2007-2009) represent the current C loss from the soil under given climate and management conditions. All three sites have lost C since the onset of drainage in the order NW

  11. Analysis and improvement of accuracy, sensitivity, and resolution of the coherent gradient sensing method.

    PubMed

    Dong, Xuelin; Zhang, Changxing; Feng, Xue; Duan, Zhiyin

    2016-06-10

    The coherent gradient sensing (CGS) method, one kind of shear interferometry sensitive to surface slope, has been applied to full-field curvature measuring for decades. However, its accuracy, sensitivity, and resolution have not been studied clearly. In this paper, we analyze the accuracy, sensitivity, and resolution for the CGS method based on the derivation of its working principle. The results show that the sensitivity is related to the grating pitch and distance, and the accuracy and resolution are determined by the wavelength of the laser beam and the diameter of the reflected beam. The sensitivity is proportional to the ratio of grating distance to its pitch, while the accuracy will decline as this ratio increases. In addition, we demonstrate that using phase gratings as the shearing element can improve the interferogram and enhance accuracy, sensitivity, and resolution. The curvature of a spherical reflector is measured by CGS with Ronchi gratings and phase gratings under different experimental parameters to illustrate this analysis. All of the results are quite helpful for CGS applications. PMID:27409035

  12. Three color selective stereo gradient method for fast topography recognition of metallic surfaces

    NASA Astrophysics Data System (ADS)

    Adameck, Markus; Hossfeld, Michael; Eich, Manfred

    2003-05-01

    This paper presents an enhanced vision system of the "Selective Stereo Gradient Method" (SSGM). Its purpose is the detection of topographies of highly reflective, metallic surfaces of quickly moving metallic tokens. We call this vision system the 3-Color-SSGM. It represents a decisive improvement of the serial-SSGM. The objective is to decide from comparison of the measured characteristic surface topography with topographical data stored in a database whether the token belongs to a reference class or not. In the improved SSGM a 3 sector 120° color LED-illumination setup is used for generating a single image of a moving object. Using the spectral properties of the illumination, which matches to the special spectral characteristics of the camera, three independent images can be extracted. The comparison between these images leads to a discrimination between a real object with 3D topography and a photographic image. The experimental setup and special illumination conditions are described. The raw data images are segmented and scaled. Rotation and translation invariance of the recognition and classification process are implemented. A specimen can be classified by using statistical image analysis and template matching methods. The classification statistics results will be reported.

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

    SciTech Connect

    Zou, Wenli; Filatov, Michael; Cremer, Dieter

    2015-06-07

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

  14. Analytic energy gradients for the coupled-cluster singles and doubles method with the density-fitting approximation

    NASA Astrophysics Data System (ADS)

    Bozkaya, Uǧur; Sherrill, C. David

    2016-05-01

    An efficient implementation is presented for analytic gradients of the coupled-cluster singles and doubles (CCSD) method with the density-fitting approximation, denoted DF-CCSD. Frozen core terms are also included. When applied to a set of alkanes, the DF-CCSD analytic gradients are significantly accelerated compared to conventional CCSD for larger molecules. The efficiency of our DF-CCSD algorithm arises from the acceleration of several different terms, which are designated as the "gradient terms": computation of particle density matrices (PDMs), generalized Fock-matrix (GFM), solution of the Z-vector equation, formation of the relaxed PDMs and GFM, back-transformation of PDMs and GFM to the atomic orbital (AO) basis, and evaluation of gradients in the AO basis. For the largest member of the alkane set (C10H22), the computational times for the gradient terms (with the cc-pVTZ basis set) are 2582.6 (CCSD) and 310.7 (DF-CCSD) min, respectively, a speed up of more than 8-folds. For gradient related terms, the DF approach avoids the usage of four-index electron repulsion integrals. Based on our previous study [U. Bozkaya, J. Chem. Phys. 141, 124108 (2014)], our formalism completely avoids construction or storage of the 4-index two-particle density matrix (TPDM), using instead 2- and 3-index TPDMs. The DF approach introduces negligible errors for equilibrium bond lengths and harmonic vibrational frequencies.

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

    NASA Astrophysics Data System (ADS)

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

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

  16. Method for the Compound Annotation of Conjugates in Nontargeted Metabolomics Using Accurate Mass Spectrometry, Multistage Product Ion Spectra and Compound Database Searching.

    PubMed

    Ogura, Tairo; Bamba, Takeshi; Tai, Akihiro; Fukusaki, Eiichiro

    2015-01-01

    Owing to biotransformation, xenobiotics are often found in conjugated form in biological samples such as urine and plasma. Liquid chromatography coupled with accurate mass spectrometry with multistage collision-induced dissociation provides spectral information concerning these metabolites in complex materials. Unfortunately, compound databases typically do not contain a sufficient number of records for such conjugates. We report here on the development of a novel protocol, referred to as ChemProphet, to annotate compounds, including conjugates, using compound databases such as PubChem and ChemSpider. The annotation of conjugates involves three steps: 1. Recognition of the type and number of conjugates in the sample; 2. Compound search and annotation of the deconjugated form; and 3. In silico evaluation of the candidate conjugate. ChemProphet assigns a spectrum to each candidate by automatically exploring the substructures corresponding to the observed product ion spectrum. When finished, it annotates the candidates assigning a rank for each candidate based on the calculated score that ranks its relative likelihood. We assessed our protocol by annotating a benchmark dataset by including the product ion spectra for 102 compounds, annotating the commercially available standard for quercetin 3-glucuronide, and by conducting a model experiment using urine from mice that had been administered a green tea extract. The results show that by using the ChemProphet approach, it is possible to annotate not only the deconjugated molecules but also the conjugated molecules using an automatic interpretation method based on deconjugation that involves multistage collision-induced dissociation and in silico calculated conjugation.

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

    DOE PAGES

    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 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

  18. Local CC2 response method based on the Laplace transform: analytic energy gradients for ground and excited states.

    PubMed

    Ledermüller, Katrin; Schütz, Martin

    2014-04-28

    A multistate local CC2 response method for the calculation of analytic energy gradients with respect to nuclear displacements is presented for ground and electronically excited states. The gradient enables the search for equilibrium geometries of extended molecular systems. Laplace transform is used to partition the eigenvalue problem in order to obtain an effective singles eigenvalue problem and adaptive, state-specific local approximations. This leads to an approximation in the energy Lagrangian, which however is shown (by comparison with the corresponding gradient method without Laplace transform) to be of no concern for geometry optimizations. The accuracy of the local approximation is tested and the efficiency of the new code is demonstrated by application calculations devoted to a photocatalytic decarboxylation process of present interest.

  19. 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.

  20. 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.

  1. 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.

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

    PubMed

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

    2012-12-01

    Controlled release of food ingredients and their protection from oxidation are the key functionality provided by microencapsulation. In the present study, pomegranate seed oil, rich in conjugated linolenic acid, was microencapsulated. As encapsulating agent, sodium alginate or trehalose was used. Calcium caseinate was used as the emulsifier. Performances of the two encapsulants were compared in respect of the rate of release of core material from the microcapsules and stability of microcapsules against harsh conditions. Microencapsulation was carried out by preparation of an emulsion containing calcium caseinate as the emulsion stabilizer and a water-soluble carbohydrate (either sodium alginate or trehalose) as the encapsulant. An oil-in-water emulsion was prepared with pomegranate seed oil as the inner core material. The emulsion was thereby freeze-dried and the dried product pulverized. External morphology of the microcapsules was studied under scanning electron microscope. Micrographs showed that both types of microcapsules had uneven surface morphology. Release rate of the microcapsules was studied using UV-spectrophotometer. Trehalose-based microcapsules showed higher release rate. On subjecting the microcapsules at 110 °C for specific time periods, it was observed that sodium alginate microcapsules retained their original properties. Hence, we can say that sodium alginate microcapsules are more heat resistant than trehalose microcapsules. PMID:23014855

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  4. 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.

  5. 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.

  6. Formation of microscale gradients of protein using heterobifunctional photolinkers.

    PubMed

    Hypolite, C L; McLernon, T L; Adams, D N; Chapman, K E; Herbert, C B; Huang, C C; Distefano, M D; Hu, W S

    1997-01-01

    Gradients of biological molecules on a microscale have been postulated to elicit cellular responses, such as migration. However, it has been difficult to prepare such gradients for experimental testing. A means for producing such gradients has been developed using a heterobifunctional photolinking agent with laser light activation. The photolinking agent synthesized includes an N-hydroxysuccinimide group and a photoreactive benzophenone (BP) separated by a tetraethylene glycol (TEG) spacer. The presence of the tetraethylene glycol spacer renders the photolinker hydrophilic, a desirable trait for conjugation in aqueous solutions. The linker was then conjugated to R-phycoerythrin (R-PE), a fluorescent protein. The resulting photolinker-R-phycoerythrin conjugate (BP-TEG-PE) was then immobilized onto a polystyrene surface by laser irradiation on a motorized stage. By varying exposure time of the sample to the beam, the amount of BP-TEG-PE immobilized on the surface was changed over an order of magnitude over a distance of 250 microns. This method can be applied to prepare gradients of proteins that elicit biological responses, such as extracellular matrix proteins or growth factors, and to study the biological effects of such gradients.

  7. A novel method to load topotecan into liposomes driven by a transmembrane NH₄EDTA gradient.

    PubMed

    Yang, Yuehui; Ma, Yanling; Wang, Shaoning

    2012-02-01

    Antitumor drugs not only cause cytocidal effect on cancer cells, but also damage on normal healthy tissues, resulting in side effects. Liposome encapsulation can result in reduced systematic distribution due to the enhanced permeability and retention (EPR) effect, accompanied by drug accumulation in liver, spleen, and other immune organs, which can cause damage to those organs. It has been demonstrated that EDTA, frequently used as a chelator, possesses a synergistic antitumor effect. Indeed, our previous study showed that EDTA could reduce the toxicity of anthracyclines to the heart and immune organs. In this study, we intended to encapsulate topotecan within liposome adopting transmembrane NH(4)EDTA gradient in order to increase the antitumor activity and decrease the toxicity against normal immune organs. Regarding the encapsulation efficiency of topotecan liposomes, both the pH value of the buffer and the cholesterol content showed significant effects on encapsulation and drug retention. Liposome encapsulation dramatically increased the antitumor activity of topotecan compared to free drug (p<0.05), while similar efficacy was obtained from liposomes prepared by a NH(4)EDTA gradient or a (NH(4))(2)SO(4) gradient (tumor inhibition ratios were 85.6% and 84.1%, respectively). However, a significant decrease in toxicity against the immune organs was found in liposomes prepared by a NH(4)EDTA gradient compared to those prepared by a (NH(4))(2)SO(4) gradient. These results suggest the superiority of the proposed gradient for topotecan encapsulation in decreasing its toxicity on immune systems.

  8. Mild Two-Step Method to Construct DNA-Conjugated Silicon Nanoparticles: Scaffolds for the Detection of MicroRNA-21

    PubMed Central

    2015-01-01

    We describe a novel two-step method, starting from bulk silicon wafers, to construct DNA conjugated silicon nanoparticles (SiNPs). This method first utilizes reactive high-energy ball milling (RHEBM) to obtain alkene grafted SiNPs. The alkene moieties are subsequently reacted with commercially available thiol-functionalized DNA via thiol–ene click chemistry to produce SiNP DNA conjugates wherein the DNA is attached through a covalent thioether bond. Further, to show the utility of this synthetic strategy, we illustrate how these SiNP ODN conjugates can detect cancer-associated miR-21 via a fluorescence ON strategy. Given that an array of biological molecules can be prepared with thiol termini and that SiNPs are biocompatible and biodegradable, we envision that this synthetic protocol will find utility in salient SiNP systems for potential therapeutic and diagnostic applications. PMID:25243490

  9. An approximate block Newton method for coupled iterations of nonlinear solvers: Theory and conjugate heat transfer applications

    NASA Astrophysics Data System (ADS)

    Yeckel, Andrew; Lun, Lisa; Derby, Jeffrey J.

    2009-12-01

    A new, approximate block Newton (ABN) method is derived and tested for the coupled solution of nonlinear models, each of which is treated as a modular, black box. Such an approach is motivated by a desire to maintain software flexibility without sacrificing solution efficiency or robustness. Though block Newton methods of similar type have been proposed and studied, we present a unique derivation and use it to sort out some of the more confusing points in the literature. In particular, we show that our ABN method behaves like a Newton iteration preconditioned by an inexact Newton solver derived from subproblem Jacobians. The method is demonstrated on several conjugate heat transfer problems modeled after melt crystal growth processes. These problems are represented by partitioned spatial regions, each modeled by independent heat transfer codes and linked by temperature and flux matching conditions at the boundaries common to the partitions. Whereas a typical block Gauss-Seidel iteration fails about half the time for the model problem, quadratic convergence is achieved by the ABN method under all conditions studied here. Additional performance advantages over existing methods are demonstrated and discussed.

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

    PubMed

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

    2015-08-01

    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 solvent models are examined. Enforcing a variational ground state energy 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 semiempirical model chemistry, the variational expressions are verified by numerical and analytical differentiation with respect to a static external electric field. Analytical gradients are further tested by performing microcanonical excited state molecular dynamics with p-nitroaniline. PMID:26254651

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. Method to form a fiber/growth factor dual-gradient along electrospun silk for nerve regeneration.

    PubMed

    Dinis, Tony M; Elia, Roberto; Vidal, Guillaume; Auffret, Adrien; Kaplan, David L; Egles, Christophe

    2014-10-01

    Concentration gradients of guidance molecules influence cell behavior and growth in biological tissues and are therefore of interest for the design of biomedical scaffolds for regenerative medicine. We developed an electrospining method to generate a dual-gradient of bioactive molecules and fiber density along electrospun nanofibers without any post spinning treatment. Functionalization with fluorescent molecules demonstrated the efficiency of the method to generate a discontinuous concentration gradient along the aligned fibers. As a proof of concept for tissue engineering, the silk nanofibers were functionalized with increasing concentrations of nerve growth factor (NGF) and the biological activity was assessed and quantified with rat dorsal root ganglion (DRG) neurons cultures. Protein assays showed the absence of passive release of NGF from the functionalized fibers. The results demonstrated that the NGF concentration gradient led to an oriented and increased growth of DRG neurons (417.6 ± 55.7 μm) compared to a single uniform NGF concentration (264.5 ± 37.6 μm). The easy-to-use electrospinning technique combined with the multiple molecules that can be used for fiber functionalization makes this technique versatile for a broad range of applications from biosensors to regenerative medicine.

  17. Self-generating density gradients of Percoll provide a simple and rapid method that consistently enriches natural killer cells.

    PubMed

    Ravnik, S E; Gage, S; Pollack, S B

    1988-06-13

    The separation or enrichment of natural killer (NK) cells from the heterogeneous cell populations in murine spleen or bone marrow is a vital step for the study of NK cells. We report in this study a simple and rapid method for the enrichment of NK cells from B cell-depleted spleen cells, using a self-generating density gradient of polyvinyl pyrrolidone-coated silica (Percoll). Nylon wool-passed spleen cells are suspended in Percoll that is isotonic and isosmotic with mouse blood at a density of 1.087 g/ml and ultracentrifuged at 30,000 x g for 10 min. This method consistently enriches for NK cell cytotoxic activity, in spleen cells of both unstimulated and interferon-stimulated mice, as measured in the chromium release assay. There is a concomitant enrichment for cells bearing the NK marker asialo GM-1 and depletion of L3T4 or Lyt-2-bearing T cells. In contrast to discontinuous, step-wise gradients, the self-generating Percoll gradient, which relies on the intrinsic property of Percoll to form a continuous density gradient, appears to provide the cells with a physiological environment both before and during the centrifugation step.

  18. Lateral Temperature-Gradient Method for High-Throughput Characterization of Material Processing by Millisecond Laser Annealing.

    PubMed

    Bell, Robert T; Jacobs, Alan G; Sorg, Victoria C; Jung, Byungki; Hill, Megan O; Treml, Benjamin E; Thompson, Michael O

    2016-09-12

    A high-throughput method for characterizing the temperature dependence of material properties following microsecond to millisecond thermal annealing, exploiting the temperature gradients created by a lateral gradient laser spike anneal (lgLSA), is presented. Laser scans generate spatial thermal gradients of up to 5 °C/μm with peak temperatures ranging from ambient to in excess of 1400 °C, limited only by laser power and materials thermal limits. Discrete spatial property measurements across the temperature gradient are then equivalent to independent measurements after varying temperature anneals. Accurate temperature calibrations, essential to quantitative analysis, are critical and methods for both peak temperature and spatial/temporal temperature profile characterization are presented. These include absolute temperature calibrations based on melting and thermal decomposition, and time-resolved profiles measured using platinum thermistors. A variety of spatially resolved measurement probes, ranging from point-like continuous profiling to large area sampling, are discussed. Examples from annealing of III-V semiconductors, CdSe quantum dots, low-κ dielectrics, and block copolymers are included to demonstrate the flexibility, high throughput, and precision of this technique. PMID:27385487

  19. 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. PMID:27457561

  20. 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.

  1. Method to form a fiber/growth factor dual-gradient along electrospun silk for nerve regeneration.

    PubMed

    Dinis, Tony M; Elia, Roberto; Vidal, Guillaume; Auffret, Adrien; Kaplan, David L; Egles, Christophe

    2014-10-01

    Concentration gradients of guidance molecules influence cell behavior and growth in biological tissues and are therefore of interest for the design of biomedical scaffolds for regenerative medicine. We developed an electrospining method to generate a dual-gradient of bioactive molecules and fiber density along electrospun nanofibers without any post spinning treatment. Functionalization with fluorescent molecules demonstrated the efficiency of the method to generate a discontinuous concentration gradient along the aligned fibers. As a proof of concept for tissue engineering, the silk nanofibers were functionalized with increasing concentrations of nerve growth factor (NGF) and the biological activity was assessed and quantified with rat dorsal root ganglion (DRG) neurons cultures. Protein assays showed the absence of passive release of NGF from the functionalized fibers. The results demonstrated that the NGF concentration gradient led to an oriented and increased growth of DRG neurons (417.6 ± 55.7 μm) compared to a single uniform NGF concentration (264.5 ± 37.6 μm). The easy-to-use electrospinning technique combined with the multiple molecules that can be used for fiber functionalization makes this technique versatile for a broad range of applications from biosensors to regenerative medicine. PMID:25203247

  2. A multiconfigurational time-dependent Hartree-Fock method for excited electronic states. II. Coulomb interaction effects in single conjugated polymer chains

    NASA Astrophysics Data System (ADS)

    Miranda, R. P.; Fisher, A. J.; Stella, L.; Horsfield, A. P.

    2011-06-01

    Conjugated polymers have attracted considerable attention in the last few decades due to their potential for optoelectronic applications. A key step that needs optimisation is charge carrier separation following photoexcitation. To understand better the dynamics of the exciton prior to charge separation, we have performed simulations of the formation and dynamics of localised excitations in single conjugated polymer strands. We use a nonadiabatic molecular dynamics method which allows for the coupled evolution of the nuclear degrees of freedom and of multiconfigurational electronic wavefunctions. We show the relaxation of electron-hole pairs to form excitons and oppositely charged polaron pairs and discuss the modifications to the relaxation process predicted by the inclusion of the Coulomb interaction between the carriers. The issue of charge photogeneration in conjugated polymers in dilute solution is also addressed.

  3. Velocity gradient method for calulating velocities in an axisymmetric annular duct

    NASA Technical Reports Server (NTRS)

    Katsanis, T.

    1982-01-01

    The velocity distribution along an arbitrary line between the inner and outer walls of an annular duct with axisymmetric swirling flow is calculated. The velocity gradient equation is used with an assumed variation of meridional streamline curvature. Upstream flow conditions can vary between the inner and outer walls, and an assumed total pressure distribution can be specified.

  4. 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

  5. A simple and rapid method for measuring unconjugated capsular polysaccharide (PRP) of Haemophilus influenzae type b in PRP-tetanus toxoid conjugate vaccine.

    PubMed

    Guo, Y Y; Anderson, R; McIver, J; Gupta, R K; Siber, G R

    1998-03-01

    The authors developed a simple and rapid method for quantitation of free capsular polysaccharide of Haemophilus influenzae type b (polyribosyl ribitol phosphate, PRP) in PRP-tetanus toxoid conjugate vaccine based on acid precipitation of tetanus toxoid (TT). Acid hydrolysis of PRP during the assay was not detected. The conditions used in the assay did not precipitate unconjugated PRP or adipic acid dihydrazide derivatized PRP. The method was highly reliable, reproducible and sensitive. The accuracy of the assay was confirmed by spiking known amounts of unconjugated PRP to PRP-TT conjugate preparations. A PRP-TT preparation, incubated at 37 degrees C for 6 months showing most of the PRP as unconjugated (87% determined by this method), was not immunogenic in mice for the PRP component even after two injections. In contrast, the same preparation held at 4 degrees C for 20 months, showing 17% unconjugated PRP, induced IgG antibodies to PRP which were boosted after second injection. Therefore, this method is very useful to evaluate the stability of PRP-TT conjugate vaccine. The assay may be useful for characterizing other polysaccharide-protein conjugate vaccines. PMID:9637747

  6. 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...

  7. Gradient-index lens-array method based on real-time integral photography for three-dimensional images

    NASA Astrophysics Data System (ADS)

    Arai, Jun; Okano, Fumio; Hoshino, Haruo; Yuyama, Ichiro

    1998-04-01

    Because a three-dimensional (3-D) autostereoscopic image can be seen from a desired viewpoint without the aid of special viewing glasses, integral photography (IP) is an ideal way to create 3-D autostereoscopic images. We have already proposed a real-time IP method that offers 3-D autostereoscopic images of moving objects in real time by use of a microlens array and a high-definition television camera. But there are two problems yet to be resolved: One is pseudoscopic images that show a reversed depth representation. The other is interference between the element images that constitute a 3-D autostereoscopic image. We describe a new gradient-index lense-array method based on real-time IP to overcome these two problems. Experimental results indicating the advantages of this method are shown. These results suggest the possibility of using a gradient-index lens array for real-time IP.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Validation and Application of a Method for the Determination of Buprenorphine, Norbuprenorphine, and Their Glucuronide Conjugates in Human Meconium

    PubMed Central

    Kacinko, Sherri L.; Shakleya, Diaa M.; Huestis, Marilyn A.

    2009-01-01

    A novel liquid chromatography tandem mass spectrometry method for quantification of buprenorphine, norbuprenorphine, and glucuronidated conjugates was developed and validated. Analytes were extracted from meconium using buffer, concentrated by solid-phase extraction and quantified within 13.5 min. In order to determine free and total concentrations, specimens were analyzed with and without enzyme hydrolysis. Calibration was achieved by linear regression with a 1/x weighting factor and deuterated internal standards. All analytes were linear from 20 to 2000 ng/g with a correlation of determination of >0.98. Accuracy was ≥85.7% with intra-assay and interassay imprecision ≤13.9 and 12.4%, respectively. There was no interference from 70 licit and illicit drugs and metabolites. Buffer extraction followed by SPE yielded recoveries of ≥85.0%. There was suppression of ionization by the polar matrix; however, this did not interfere with sensitivity or analyte quantification due to inclusion of deuterated internal standards. Analytes were stable on the autosampler, at room temperature, at 4 °C, and when exposed to three freeze/thaw cycles. This sensitive and specific method can be used to monitor in utero buprenorphine exposure and to evaluate correlations, if any, between buprenorphine exposure and neonatal outcomes. PMID:18044957

  13. An innovative method for quality control of conjugated Haemophilus influenzae vaccines: A short review of two-dimensional nanoparticle electrophoresis.

    PubMed

    Tietz, Dietmar

    2009-12-25

    This article provides an overview of a 2D agarose electrophoretic procedure for the characterization of semi-synthetic Haemophilus influenzae type b meningitis vaccines that were prepared for the immunization of small children. The analysis of such vaccines has been particularly challenging because the vaccine particles (i) are highly negatively charged, (ii) are as large as or even larger than intact viruses, and (iii) have a continuous (polydisperse) size distribution because of randomizing steps in the vaccine production (sonification and crosslinking). As a result of these characteristics, 1D electrophoresis of the vaccines produced smears without discernable peaks, but with a second dimension of separation a characteristic vaccine fingerprint was obtained. Whereas O'Farrell gels can accomplish a 2D separation according to size and charge for samples with protein-sized particles, nondenaturing 2D agarose electrophoresis achieves a similar result for much larger virus-sized particles. The separation principle, however, is different. Even though the 2D electrophoretic method was developed from 1983 to 1995, it remains a promising tool for vaccine quality control and for predicting vaccine effectiveness. Modern technology makes the analysis significantly more practical and affordable than it was more than 10 years ago, and the method is applicable to a variety of conjugated vaccines and complex mixtures of virus-sized particles.

  14. The optimized gradient method for full waveform inversion and its spectral implementation

    NASA Astrophysics Data System (ADS)

    Wu, Zedong; Alkhalifah, Tariq

    2016-06-01

    At the heart of the full waveform inversion (FWI) implementation is wavefield extrapolation, and specifically its accuracy and cost. To obtain accurate, dispersion free wavefields, the extrapolation for modelling is often expensive. Combining an efficient extrapolation with a novel gradient preconditioning can render an FWI implementation that efficiently converges to an accurate model. We, specifically, recast the extrapolation part of the inversion in terms of its spectral components for both data and gradient calculation. This admits dispersion free wavefields even at large extrapolation time steps, which improves the efficiency of the inversion. An alternative spectral representation of the depth axis in terms of sine functions allows us to impose a free surface boundary condition, which reflects our medium boundaries more accurately. Using a newly derived perfectly matched layer formulation for this spectral implementation, we can define a finite model with absorbing boundaries. In order to reduce the nonlinearity in FWI, we propose a multiscale conditioning of the objective function through combining the different directional components of the gradient to optimally update the velocity. Through solving a simple optimization problem, it specifically admits the smoothest approximate update while guaranteeing its ascending direction. An application to the Marmousi model demonstrates the capability of the proposed approach and justifies our assertions with respect to cost and convergence.

  15. Identification of a new potential Cd-hyperaccumulator Solanum photeinocarpum by soil seed bank-metal concentration gradient method.

    PubMed

    Zhang, Xingfeng; Xia, Hanping; Li, Zhi'an; Zhuang, Ping; Gao, Bo

    2011-05-15

    A new method, soil seed bank-metal concentration gradient method was used to screen for heavy metal hyperaccumulators, and Solanum photeinocarpum was found to be a potential Cd-hyperaccumulator. The chlorophyll content and photosynthetic rate of S. photeinocarpum were not affected by Cd pollution, while leaf stomas and transpiration rate were significantly decreased by more than 60 mg kg(-1) Cd, and leaf water use efficiency and shoot water content were significantly increased by more than 60 or 100 mg kg(-1) Cd, respectively. In the seed bank-Cd concentration gradient experiment, the shoot biomass of S. photeinocarpum showed no significant reduction with soil Cd treatment as high as 100 mg kg(-1), but the root biomass was significantly reduced by more than 60 mg kg(-1) Cd contamination. Plant tissues accumulated 544, 132 and 158 mg kg(-1) Cd in roots, stems and leaves, respectively, and extracted 157 and 195 μg Cd plant(-1) in roots and shoots at 100 mg kg(-1) Cd in soil, respectively. In the transplanting-Cd concentration gradient experiment, plant shoot biomass and root biomass were unaffected by soil Cd as high as 60 mg kg(-1). Plant tissues accumulated 473, 215 and 251 mg kg(-1) Cd in roots, stems and leaves, respectively, and extracted 176 and 787 μg Cd plant(-1) in roots and shoots at 60 mg kg(-1) soil Cd, respectively. Soil seed bank-metal concentration gradient method could be an effective method for the screening of hyperaccumulators. PMID:21397392

  16. Comparison of Fracture Gradient Methods for the FutureGen 2.0 Carbon Storage Site, Ill., USA.

    NASA Astrophysics Data System (ADS)

    Appriou, D.; Spane, F.; Wurstner White, S.; Kelley, M. E.; Sullivan, E. C.; Bonneville, A.; Gilmore, T. J.

    2014-12-01

    As part of a first-of-its-kind carbon dioxide storage project, FutureGen Industrial Alliance is planning to inject 1.1 MMt/yr of supercritical CO2 over a 20-year period within a 1240 m deep saline aquifer (Mount Simon Sandstone) located in Morgan County, Illinois, USA. Numerous aspects of the design and operational activities of the CO2 storage site are dependent on the geomechanical properties of the targeted reservoir zone, as well as of the overlying confining zone and the underlying crystalline Precambrian basement. Detailed determination of the state-of-stress within the subsurface is of paramount importance in successfully designing well drilling/completion aspects, as well as assessing the risk of induced seismicity and the potential for creating and/or reopening pre-existing fractures; all of which help ensure the safe long-term storage of injected CO2. The quantitative determination of the subsurface fracture gradient is one of the key geomechanical parameters for the site injection design and operational limits (e.g., maximum safe injection pressure). A characterization well drilled in 2011 provides subsurface geomechanical characterization information for the FutureGen 2.0 site, and includes: 1) continuous elastic properties inferred from sonic/acoustic wireline logs 2) discrete depth geomechanical laboratory core measurements and 3) results obtained from hydraulic fracturing tests of selected borehole/depth-intervals. In this paper, the precise fracture gradients derived from borehole geomechanical test results are compared with semi-empirical, fracture gradient calculation/relationships based on elastic property wireline surveys and laboratory geomechanical core test results. Implications for using various fracture-gradients obtained from the different methods are assessed using PNNL's subsurface multiphase flow and transport simulator STOMP-CO2. The implications for operational activities at the site (based on using different fracture gradients) are

  17. Critical evaluation of indirect methods for the determination of deoxynivalenol and its conjugated forms in cereals.

    PubMed

    Malachová, Alexandra; Štočková, Lenka; Wakker, Astrid; Varga, Elisabeth; Krska, Rudolf; Michlmayr, Herbert; Adam, Gerhard; Berthiller, Franz

    2015-08-01

    A critical assessment of three previously published indirect methods based on acidic hydrolysis using superacids for the determination of "free" and "total" deoxynivalenol (DON) was carried out. The modified mycotoxins DON-3-glucoside (D3G), 3-acetyl-DON (3ADON), and 15-acetyl-DON (15ADON) were chosen as model analytes. The initial experiments focused on the stability/degradation of DON under hydrolytic conditions and the ability to release DON from the modified forms. Acidic conditions that were capable of cleaving D3G, 3ADON, and 15ADON to DON were not found, raising doubts over the efficacy of previously published indirect methods for total DON determination. Validation of these indirect methods for wheat, maize, and barley using UHPLC-MS/MS was performed in order to test the accuracy of the generated results. Validation data for DON, D3G, 3ADON, and 15ADON in nonhydrolyzed and hydrolyzed matrices were obtained. Under the tested conditions, DON was not released from D3G, 3ADON, or 15ADON after hydrolysis and thus none of the published methods were able to cleave the modified forms of DON. In addition to acids, alkaline hydrolysis with KOH for an extended time and at elevated temperatures was also tested. 3ADON and 15ADON were cleaved under the alkaline pH caused by the addition of KOH or aqueous K2CO3 to "neutralize" the acidic sample extracts in the published studies. The published additional DON increase after hydrolysis may have been caused by huge differences in matrix effects and the recovery of DON in nonhydrolyzed and hydrolyzed matrices as well as by the alkaline cleavage of 3ADON or 15ADON after the neutralization of hydrolyzed extracts.

  18. A comparison of density functional theory and coupled cluster methods for the calculation of electric dipole polarizability gradients of methane

    NASA Astrophysics Data System (ADS)

    Paidarová, Ivana; Sauer, Stephan P. A.

    2012-12-01

    We have compared the performance of density functional theory (DFT) using five different exchange-correlation functionals with four coupled cluster theory based wave function methods in the calculation of geometrical derivatives of the polarizability tensor of methane. The polarizability gradients of hydrocarbons are important ingredients in the simulation of their electron energy loss spectra and reliable but cost-effective methods for obtaining the gradients need to be found. In the present work we present results of a systematic investigation on methane as a prototype molecule with special focus on DFT methods. The KT3, B3LYP, CAM-B3LYP, B97-2 and PBE0 DFT exchange-correlation functionals and the highly correlated wave function methods SOPPA(CCSD), CCSD-LR, CCSD and CCSD(T) were employed in combination with a series of eleven basis sets. Comparison of the DFT results with CCSD(T)/daug-cc-pVQZ reference values reveals that none of the investigated DFT approaches reaches the accuracy of correlated wave function based methods and that the best DFT results are obtained with the PBE0 exchange-correlation functional and Sadlej's polarized valence triple zeta basis set. The SOPPA(CCSD) method, on the other hand, produces results in close agreement with the more expensive pure coupled cluster methods.

  19. High quality Si-InP bulk crystal growth by horizontal gradient freeze method under controlled phosphorus vapor pressure

    NASA Astrophysics Data System (ADS)

    Yoshida, S.; Suzuki, J.; Nakayama, M.; Kikuta, T.

    1990-06-01

    High purity InP was grown by horizontal gradient freeze (HGF) method under controlled phosphorus vapor pressure. The ingot was free from residual In and In inclusion. The carrier concentration of undoped InP ingot was almost in the range of (1.1-4.0)×10 15 cm -3 at 77 K even though a quartz boat was used. Using this technique, Si-InP wafers with a high resistivity over 1.0×10 7 Ω cm were obtained by lower Fe doping (4.0×10 15 cm -3). The growth of single crystals using the seeding technique was also tried by direct synthesis. The strict control of the temperature gradient with the CPU system enabled the seeding to be performed reproducibly. A single crystal, 6 cm long, was obtained from the seed end of the ingot, but twin boundaries were generated from the middle of the ingot.

  20. 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.

  1. 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.

  2. 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.

  3. 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}.

  4. 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.

  5. Massively parallel conjugate heat transfer methods relying on large eddy simulation applied to an aeronautical combustor

    NASA Astrophysics Data System (ADS)

    Jaure, S.; Duchaine, F.; Staffelbach, G.; Gicquel, L. Y. M.

    2013-01-01

    Optimizing gas turbines is a complex multi-physical and multi-component problem that has long been based on expensive experiments. Today, computer simulation can reduce design process costs and is acknowledged as a promising path for optimization. However, performing such computations using high-fidelity methods such as a large eddy simulation (LES) on gas turbines is challenging. Nevertheless, such simulations become accessible for specific components of gas turbines. These stand-alone simulations face a new challenge: to improve the quality of the results, new physics must be introduced. Therefore, an efficient massively parallel coupling methodology is investigated. The flow solver modeling relies on the LES code AVBP which has already been ported on massively parallel architectures. The conduction solver is based on the same data structure and thus shares its scalability. Accurately coupling these solvers while maintaining their scalability is challenging and is the actual objective of this work. To obtain such goals, a methodology is proposed and different key issues to code the coupling are addressed: convergence, stability, parallel geometry mapping, transfers and interpolation. This methodology is then applied to a real burner configuration, hence demonstrating the possibilities and limitations of the solution.

  6. Rapid quantitative method for the detection of phenylalanine and tyrosine in human plasma using pillar array columns and gradient elution.

    PubMed

    Song, Yanting; Takatsuki, Katsuya; Sekiguchi, Tetsushi; Funatsu, Takashi; Shoji, Shuichi; Tsunoda, Makoto

    2016-07-01

    This study reports a fast and quantitative determination method for phenylalanine (Phe) and tyrosine (Tyr) in human plasma using on-chip pressure-driven liquid chromatography. A pillar array column with low-dispersion turns and a gradient elution system was used. The separation of fluorescent derivatives of Phe, Tyr, and other hydrophobic amino acids was successfully performed within 140 s. Under the optimized conditions, Phe and Tyr in human plasma were quantified. The developed method is promising for rapid diagnosis in the clinical field.

  7. 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.

  8. Emulsion droplet sizing using low-field NMR with chemical shift resolution and the block gradient pulse method

    NASA Astrophysics Data System (ADS)

    Lingwood, I. A.; Chandrasekera, T. C.; Kolz, J.; Fridjonsson, E. O.; Johns, M. L.

    2012-01-01

    Pulsed Field Gradient (PFG) measurements are commonly used to determine emulsion droplet size distributions based on restricted self-diffusion within the emulsion droplets. Such measurement capability is readily available on commercial NMR bench-top apparatus. A significant limitation is the requirement to selectively detect signal from the liquid phase within the emulsion droplets; this is currently achieved using either relaxation or self-diffusion contrast. Here we demonstrate the use of a 1.1 T bench-top NMR magnet, which when coupled with an rf micro-coil, is able to provide sufficient chemical shift resolution such that unambiguous signal selection is achieved from the dispersed droplet phase. We also improve the accuracy of the numerical inversion process required to produce the emulsion droplet size distribution, by employing the Block Gradient Pulse (bgp) method, which partially relaxes the assumptions of a Gaussian phase distribution or infinitely short gradient pulse application inherent in current application. The techniques are successfully applied to size 3 different emulsions.

  9. A new 3-D ray tracing method based on LTI using successive partitioning of cell interfaces and traveltime gradients

    NASA Astrophysics Data System (ADS)

    Zhang, Dong; Zhang, Ting-Ting; Zhang, Xiao-Lei; Yang, Yan; Hu, Ying; Qin, Qian-Qing

    2013-05-01

    We present a new method of three-dimensional (3-D) seismic ray tracing, based on an improvement to the linear traveltime interpolation (LTI) ray tracing algorithm. This new technique involves two separate steps. The first involves a forward calculation based on the LTI method and the dynamic successive partitioning scheme, which is applied to calculate traveltimes on cell boundaries and assumes a wavefront that expands from the source to all grid nodes in the computational domain. We locate several dynamic successive partition points on a cell's surface, the traveltimes of which can be calculated by linear interpolation between the vertices of the cell's boundary. The second is a backward step that uses Fermat's principle and the fact that the ray path is always perpendicular to the wavefront and follows the negative traveltime gradient. In this process, the first-arriving ray path can be traced from the receiver to the source along the negative traveltime gradient, which can be calculated by reconstructing the continuous traveltime field with cubic B-spline interpolation. This new 3-D ray tracing method is compared with the LTI method and the shortest path method (SPM) through a number of numerical experiments. These comparisons show obvious improvements to computed traveltimes and ray paths, both in precision and computational efficiency.

  10. Method To Determine Protein Concentration in the Protein-Nanoparticle Conjugates Aqueous Solution Using Circular Dichroism Spectroscopy.

    PubMed

    Li, Shanghao; Peng, Zhili; Leblanc, Roger M

    2015-07-01

    Considerable efforts have been made to synthesize and characterize protein-nanoparticle conjugates (protein-NPs) for their promising applications in bionanotechnology. However, protein concentration determination in the protein-NPs has so far not been reported. In this Letter, we present a simple and nondestructive approach to quantify the protein concentration in the protein-NPs aqueous solution using circular dichroism (CD) spectroscopy. Carbon dots (∼4 nm), gold nanoparticles (∼10 nm), and polyethylene glycol (PEG, molecular weight ∼3000) were either physically mixed or covalently conjugated (not in the case of gold nanoparticles) with proteins (human transferrin, human serum albumin, and ovalbumin). We were able to quantify the protein concentration in the protein-nanoparticle conjugates using a calibration curve from the CD spectra. PMID:26070096

  11. Experiment, monitoring, and gradient methods used to infer climate change effects on plant communities yield consistent patterns.

    PubMed

    Elmendorf, Sarah C; Henry, Gregory H R; Hollister, Robert D; Fosaa, Anna Maria; Gould, William A; Hermanutz, Luise; Hofgaard, Annika; Jónsdóttir, Ingibjörg S; Jónsdóttir, Ingibjörg I; Jorgenson, Janet C; Lévesque, Esther; Magnusson, Borgþór; Molau, Ulf; Myers-Smith, Isla H; Oberbauer, Steven F; Rixen, Christian; Tweedie, Craig E; Walker, Marilyn D; Walker, Marilyn

    2015-01-13

    Inference about future climate change impacts typically relies on one of three approaches: manipulative experiments, historical comparisons (broadly defined to include monitoring the response to ambient climate fluctuations using repeat sampling of plots, dendroecology, and paleoecology techniques), and space-for-time substitutions derived from sampling along environmental gradients. Potential limitations of all three approaches are recognized. Here we address the congruence among these three main approaches by comparing the degree to which tundra plant community composition changes (i) in response to in situ experimental warming, (ii) with interannual variability in summer temperature within sites, and (iii) over spatial gradients in summer temperature. We analyzed changes in plant community composition from repeat sampling (85 plant communities in 28 regions) and experimental warming studies (28 experiments in 14 regions) throughout arctic and alpine North America and Europe. Increases in the relative abundance of species with a warmer thermal niche were observed in response to warmer summer temperatures using all three methods; however, effect sizes were greater over broad-scale spatial gradients relative to either temporal variability in summer temperature within a site or summer temperature increases induced by experimental warming. The effect sizes for change over time within a site and with experimental warming were nearly identical. These results support the view that inferences based on space-for-time substitution overestimate the magnitude of responses to contemporary climate warming, because spatial gradients reflect long-term processes. In contrast, in situ experimental warming and monitoring approaches yield consistent estimates of the magnitude of response of plant communities to climate warming.

  12. Experiment, monitoring, and gradient methods used to infer climate change effects on plant communities yield consistent patterns.

    PubMed

    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. PMID:25548195

  13. 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…

  14. 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.

  15. 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

  16. 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. PMID:24081815

  17. 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.

  18. Distributed detection of temperature gradients with single-wavelength phase-sensitive OTDR and speckle analysis methods

    NASA Astrophysics Data System (ADS)

    Garcia-Ruiz, Andres; Pastor-Graells, Juan; Martins, Hugo F.; Martin-Lopez, Sonia; Gonzalez-Herraez, Miguel

    2016-05-01

    A method to evaluate distributed temperature gradients along an optical fiber using phase-sensitive optical time domain reflectometry (ΦOTDR) with direct detection is proposed and experimentally validated. The measurement principle derives from the perturbation response of a single-wavelength ΦOTDR signal, which is analyzed as a unidimensional speckle pattern. Our method can be implemented in real-time, relies solely on a low-cost post-processing of the standard ΦOTDR traces and requires no scanning of the laser frequency. This post-processing method can be implemented over a conventional ΦOTDR system used for distributed intrusion detection, without affecting its operation or requiring any additional hardware.

  19. Stochastic gradient method for training of a class of recurrent neural nets

    SciTech Connect

    Gaivoronski, A.; Cazzol, A.

    1994-12-31

    A recurrent neural net is defined by set I of nodes, set of input nodes J {contained_in} I, set of output nodes, K {improper_subset} I, set of oriented arcs A {improper_subset} I {times} I. Each node i {element_of} I is characterized by state z{sub i} and function f{sup i} x, z{sub i+} where x is the vector of the network parameters and z{sub i+} is the vector of states of input nodes to node i, i.e. such nodes from which start arcs which point to node i. At the beginning values z{sub i}{sup 0} are assigned to states of all inputs nodes i {element_of} J and the net starts to function in discrete time s = 0, 1, ..., by changing the states as follows: z{sub i}{sup 8+1} = f{sup i}(x, z{sub i+}{sup s}). To each output node j {element_of} K the reference values y{sub j} are assigned. The objective is to train the network, i.e. to select the values x of the network measures the difference between reference values and states of the output nodes is minimized: min{sub x}F(x, z) = {sub j{element_of}K}{sup {Sigma}} {phi}(y{sub j} - z{sub j}). The principle difficulty compared with simple feedforward networks is the presence of cycles which lead to a nontrivial transient behavior of the net. In this talk we use stochastic gradient ideas in order to construct analogue of backpropagation techniques which permits to train the network in real time, i.e. changing the vector x each moment of discrete time without waiting that the net reaches the steady state. We prove the convergence of proposed techniques.

  20. The effects of size and synthesis methods of gold nanoparticle-conjugated MαHIgG4 for use in an immunochromatographic strip test to detect brugian filariasis

    NASA Astrophysics Data System (ADS)

    Rabizah Makhsin, Siti; Razak, Khairunisak Abdul; Noordin, Rahmah; Dyana Zakaria, Nor; Chun, Tan Soo

    2012-12-01

    This study describes the properties of colloidal gold nanoparticles (AuNPs) with sizes of 20, 30 and 40 nm, which were synthesized using citrate reduction or seeding-growth methods. Likewise, the conjugation of these AuNPs to mouse anti-human IgG4 (MαHIgG4) was evaluated for an immunochromatographic (ICG) strip test to detect brugian filariasis. The morphology of the AuNPs was studied based on the degree of ellipticity (G) of the transmission electron microscopy images. The AuNPs produced using the seeding-growth method showed lower ellipticity (G ≤ 1.11) as compared with the AuNPs synthesized using the citrate reduction method (G ≤ 1.18). Zetasizer analysis showed that the AuNPs that were synthesized using the seeding-growth method were almost monodispersed with a lower polydispersity index (PDI; PDI≤0.079), as compared with the AuNPs synthesized using the citrate reduction method (PDI≤0.177). UV-visible spectroscopic analysis showed a red-shift of the absorbance spectra after the reaction with MαHIgG4, which indicated that the AuNPs were successfully conjugated. The optimum concentration of the BmR1 recombinant antigen that was immobilized on the surface of the ICG strip on the test line was 1.0 mg ml-1. When used with the ICG test strip assay and brugian filariasis serum samples, the conjugated AuNPs-MαHIgG4 synthesized using the seeding-growth method had faster detection times, as compared with the AuNPs synthesized using the citrate reduction method. The 30 nm AuNPs-MαHIgG4, with an optical density of 4 from the seeding-growth method, demonstrated the best performance for labelling ICG strips because it displayed the best sensitivity and the highest specificity when tested with serum samples from brugian filariasis patients and controls.

  1. 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.

  2. Creating stiffness gradient polyvinyl alcohol hydrogel using a simple gradual freezing-thawing method to investigate stem cell differentiation behaviors.

    PubMed

    Kim, Tae Ho; An, Dan Bi; Oh, Se Heang; Kang, Min Kwan; Song, Hyun Hoon; Lee, Jin Ho

    2015-02-01

    Polyvinyl alcohol (PVA) cylindrical hydrogel with a stiffness gradient was prepared using a simple liquid nitrogen (LN2)-contacting gradual freezing and thawing method in order to investigate the effects of substrate stiffness on stem cell differentiation into specific cell types. The prepared cylindrical PVA hydrogel showed a gradually increasing stiffness along the longitudinal direction from the top at approximately 1 kPa to the bottom (LN2 contacted side) at approximately 24 kPa. From the in vitro culture of bone marrow stem cells, it was observed that each soft (∼1 kPa) and stiff (∼24 kPa) hydrogel section promotes effective neurogenesis and osteogenesis of the cells, respectively, with the tendency to gradually decrease toward the opposing characteristic's side. The stiffness gradient cylindrical PVA hydrogel fabricated using this simple gradual freezing and thawing method can be a useful tool for basic studies, including the determination of optimum stiffness ranges for a variety of stem cell differentiations, as well as the investigation of cell migration in terms of substrate stiffness.

  3. 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.

  4. Quantitative structure-retention relationships applied to development of liquid chromatography gradient-elution method for the separation of sartans.

    PubMed

    Golubović, Jelena; Protić, Ana; Otašević, Biljana; Zečević, Mira

    2016-04-01

    QSRR are mathematically derived relationships between the chromatographic parameters determined for a representative series of analytes in given separation systems and the molecular descriptors accounting for the structural differences among the investigated analytes. Artificial neural network is a technique of data analysis, which sets out to emulate the human brain's way of working. The aim of the present work was to optimize separation of six angiotensin receptor antagonists, so-called sartans: losartan, valsartan, irbesartan, telmisartan, candesartan cilexetil and eprosartan in a gradient-elution HPLC method. For this purpose, ANN as a mathematical tool was used for establishing a QSRR model based on molecular descriptors of sartans and varied instrumental conditions. The optimized model can be further used for prediction of an external congener of sartans and analysis of the influence of the analyte structure, represented through molecular descriptors, on retention behaviour. Molecular descriptors included in modelling were electrostatic, geometrical and quantum-chemical descriptors: connolly solvent excluded volume non-1,4 van der Waals energy, octanol/water distribution coefficient, polarizability, number of proton-donor sites and number of proton-acceptor sites. Varied instrumental conditions were gradient time, buffer pH and buffer molarity. High prediction ability of the optimized network enabled complete separation of the analytes within the run time of 15.5 min under following conditions: gradient time of 12.5 min, buffer pH of 3.95 and buffer molarity of 25 mM. Applied methodology showed the potential to predict retention behaviour of an external analyte with the properties within the training space. Connolly solvent excluded volume, polarizability and number of proton-acceptor sites appeared to be most influential paramateres on retention behaviour of the sartans.

  5. Charge Transport and Light Absorption in Conjugated Systems from Extended HÜCKEL Method and Marcus Theory

    NASA Astrophysics Data System (ADS)

    To, Tran Thinh; Adams, Stefan

    2012-06-01

    A simple first principle model was developed based on extended Hückel-type orbital calculation, Marcus electron transport theory and two-dimensional-electron-gas model for the treatment of charge transport in conjugated polymers. Though simple and easy to compute, the effect of the applied electric-field is factored in. Based on this, a complete one-dimensional device model with a single layer of conjugated polymer sandwiched between two electrodes was developed with poly(3-hexylthiophene) (P3HT) as a case study. Simulated J-V curves show that π-π charge transport is much more pronounced than intra-chain transport, hence agree with previous findings. Using the same framework, we also calculated the absorption spectra of P3HT by considering the electronic energy barrier for electronic transitions that would satisfy Franck-Condon principle. Absorption spectra closely harmonize to experimental UV-Vis result. The model also reveals intra-chain electronic transitions to be the dominant absorption mechanism. All parameters of the model are obtained from either ab-initio Density Functional Theory (DFT) or Molecular Dynamics (MD) calculations, so that this model is capable of predicting charge transport and light absorption properties of new conjugated polymers without introducing fit parameters.

  6. Method of carrier-free delivery of therapeutic RNA importable into human mitochondria: Lipophilic conjugates with cleavable bonds.

    PubMed

    Dovydenko, Ilya; Tarassov, Ivan; Venyaminova, Alya; Entelis, Nina

    2016-01-01

    Defects in mitochondrial DNA often cause neuromuscular pathologies, for which no efficient therapy has yet been developed. MtDNA targeting nucleic acids might therefore be promising therapeutic candidates. Nevertheless, mitochondrial gene therapy has never been achieved because DNA molecules can not penetrate inside mitochondria in vivo. In contrast, some small non-coding RNAs are imported into mitochondrial matrix, and we recently designed mitochondrial RNA vectors that can be used to address therapeutic oligoribonucleotides into human mitochondria. Here we describe an approach of carrier-free targeting of the mitochondrially importable RNA into living human cells. For this purpose, we developed the protocol of chemical synthesis of oligoribonucleotides conjugated with cholesterol residue through cleavable covalent bonds. Conjugates containing pH-triggered hydrazone bond were stable during the cell transfection procedure and rapidly cleaved in acidic endosomal cellular compartments. RNAs conjugated to cholesterol through a hydrazone bond were characterized by efficient carrier-free cellular uptake and partial co-localization with mitochondrial network. Moreover, the imported oligoribonucleotide designed to target a pathogenic point mutation in mitochondrial DNA was able to induce a decrease in the proportion of mutant mitochondrial genomes. This newly developed approach can be useful for a carrier-free delivery of therapeutic RNA into mitochondria of living human cells.

  7. 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.

  8. What Is the Best Way to Contour Lung Tumors on PET Scans? Multiobserver Validation of a Gradient-Based Method Using a NSCLC Digital PET Phantom

    SciTech Connect

    Werner-Wasik, Maria; Nelson, Arden D.; Choi, Walter; Arai, Yoshio; Faulhaber, Peter F.; Kang, Patrick; Almeida, Fabio D.; Xiao, Ying; Ohri, Nitin; Brockway, Kristin D.; Piper, Jonathan W.; Nelson, Aaron S.

    2012-03-01

    Purpose: To evaluate the accuracy and consistency of a gradient-based positron emission tomography (PET) segmentation method, GRADIENT, compared with manual (MANUAL) and constant threshold (THRESHOLD) methods. Methods and Materials: Contouring accuracy was evaluated with sphere phantoms and clinically realistic Monte Carlo PET phantoms of the thorax. The sphere phantoms were 10-37 mm in diameter and were acquired at five institutions emulating clinical conditions. One institution also acquired a sphere phantom with multiple source-to-background ratios of 2:1, 5:1, 10:1, 20:1, and 70:1. One observer segmented (contoured) each sphere with GRADIENT and THRESHOLD from 25% to 50% at 5% increments. Subsequently, seven physicians segmented 31 lesions (7-264 mL) from 25 digital thorax phantoms using GRADIENT, THRESHOLD, and MANUAL. Results: For spheres <20 mm in diameter, GRADIENT was the most accurate with a mean absolute % error in diameter of 8.15% (10.2% SD) compared with 49.2% (51.1% SD) for 45% THRESHOLD (p < 0.005). For larger spheres, the methods were statistically equivalent. For varying source-to-background ratios, GRADIENT was the most accurate for spheres >20 mm (p < 0.065) and <20 mm (p < 0.015). For digital thorax phantoms, GRADIENT was the most accurate (p < 0.01), with a mean absolute % error in volume of 10.99% (11.9% SD), followed by 25% THRESHOLD at 17.5% (29.4% SD), and MANUAL at 19.5% (17.2% SD). GRADIENT had the least systematic bias, with a mean % error in volume of -0.05% (16.2% SD) compared with 25% THRESHOLD at -2.1% (34.2% SD) and MANUAL at -16.3% (20.2% SD; p value <0.01). Interobserver variability was reduced using GRADIENT compared with both 25% THRESHOLD and MANUAL (p value <0.01, Levene's test). Conclusion: GRADIENT was the most accurate and consistent technique for target volume contouring. GRADIENT was also the most robust for varying imaging conditions. GRADIENT has the potential to play an important role for tumor delineation in

  9. 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. PMID

  10. An equivalent distributed magnetic current based FDTD method for the calculation of E-fields induced by gradient coils in MRI.

    PubMed

    Crozier, S; Liu, F; Wei, Q

    2004-01-01

    This paper evaluates a low-frequency FDTD method applied to the problem of induced E-fields/eddy currents in the human body resulting from the pulsed magnetic field gradients in MRI. In this algorithm, a distributed equivalent magnetic current (DEMC) is proposed as the electromagnetic source and is obtained by quasistatic calculation of the empty coil's vector potential or measurements therein. This technique circumvents the discretizing of complicated gradient coil geometries into a mesh of Yee cells, and thereby enables any type of gradient coil modeling or other complex low frequency sources. The proposed method has been verified against an example with an analytical solution. Results are presented showing the spatial distribution of gradient-induced electric fields in a multilayered spherical phantom model and a complete body model.

  11. 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.

  12. The spectrophotometric method of determining the transmission of solar energy in salt gradient solar ponds

    NASA Astrophysics Data System (ADS)

    Giulianelli, J.

    1984-09-01

    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.

  13. 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.

  14. Solving the structural inverse gravity problem by the modified gradient methods

    NASA Astrophysics Data System (ADS)

    Martyshko, P. S.; Akimova, E. N.; Misilov, V. E.

    2016-09-01

    New methods for solving the three-dimensional inverse gravity problem in the class of contact surfaces are described. Based on the approach previously suggested by the authors, new algorithms are developed. Application of these algorithms significantly reduces the number of the iterations and computing time compared to the previous ones. The algorithms have been numerically implemented on the multicore processor. The example of solving the structural inverse gravity problem for a model of four-layer medium (with the use of gravity field measurements) is constructed.

  15. Analytical method of free and conjugated neutral aroma components in tobacco by solvent extraction coupled with comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry.

    PubMed

    Ding, Yu; Zhu, Lijun; Liu, Shaomin; Yu, Hanqing; Dai, Ya

    2013-03-01

    A reliable and simple method for quantitative analysis of free and conjugated neutral aroma components (including aldehydes, ketones, alcohols, esters and alkenes) in tobacco using comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) is described. Simple solvent extraction using methyl tert-butyl ether (MTBE) ensured extraction of the neutral aroma components in their free form. The components present as conjugates were isolated using MTBE extraction following acid-catalysed hydrolysis. The GC × GC-TOFMS analysis was performed to comprehensively identify different forms of neutral aroma components in tobacco. Compared with the conventional methods, our method not only simplified the process but also saved time and solvent. It also exhibited higher selectivity and sensitivity and demonstrated the following results: the limit of detection of the neutral aroma components varied from 0.006 μg/g for 2-acetylfuran to 0.133 μg/g for 5-(hydroxymethyl)-2-furfural, the relative standard deviations were from 0.5% to 6.8% and the recovery ranged from 82.4% to 118.2%. The optimized method was successfully employed to analyse real tobacco samples. Eighty-three neutral aroma components of interest were identified. PMID:23357748

  16. Analytical method of free and conjugated neutral aroma components in tobacco by solvent extraction coupled with comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry.

    PubMed

    Ding, Yu; Zhu, Lijun; Liu, Shaomin; Yu, Hanqing; Dai, Ya

    2013-03-01

    A reliable and simple method for quantitative analysis of free and conjugated neutral aroma components (including aldehydes, ketones, alcohols, esters and alkenes) in tobacco using comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) is described. Simple solvent extraction using methyl tert-butyl ether (MTBE) ensured extraction of the neutral aroma components in their free form. The components present as conjugates were isolated using MTBE extraction following acid-catalysed hydrolysis. The GC × GC-TOFMS analysis was performed to comprehensively identify different forms of neutral aroma components in tobacco. Compared with the conventional methods, our method not only simplified the process but also saved time and solvent. It also exhibited higher selectivity and sensitivity and demonstrated the following results: the limit of detection of the neutral aroma components varied from 0.006 μg/g for 2-acetylfuran to 0.133 μg/g for 5-(hydroxymethyl)-2-furfural, the relative standard deviations were from 0.5% to 6.8% and the recovery ranged from 82.4% to 118.2%. The optimized method was successfully employed to analyse real tobacco samples. Eighty-three neutral aroma components of interest were identified.

  17. 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.

  18. Bulk Crystal Growth of Nonlinear Optical Organic Materials Using Inverted Vertical Gradient Freeze Method

    NASA Technical Reports Server (NTRS)

    Choi, J.; Cruz, Magda; Metzl, R.; Wang, W. S.; Aggarwal, M. D.; Penn, Benjamin G.; Frazier, Donald O.

    1998-01-01

    A new process for producing large bulk single crystals of benzil (C6H5COCOC6H5) is reported in this paper. Good quality crystals have been successfully grown using this approach to crystal growth. This method seems to be very promising for other thermally stable NLO organic materials also. The entire contents vycor crucible 1.5 inch in diameter and 2 inch deep was converted to single crystal. Purity of the starting growth material is also an important factor in the final quality of the grown crystals. The entire crystal can be very easily taken out of the crucible by simple maneuvering. Initial characterization of the grown crystals indicated that the crystals are as good as other crystals grown by conventional Bridgman Stockbarger technique.

  19. A practical method of Ludox density gradient centrifugation combined with protargol staining for extracting and estimating ciliates in marine sediments.

    PubMed

    Xu, Kuidong; Du, Yongfen; Lei, Yanli; Dai, Renhai

    2010-11-01

    Methodological impediments have long been the main problem in estimating the ecological role of marine benthic ciliates. Percoll density centrifugation is currently the most efficient technique for extracting ciliates from fine-grained sediments, while the high cost and low density of Percoll limit its wide application. We developed a protocol of density gradient centrifugation using the cheap sol Ludox HS 40 in combination with the quantitative protargol stain (QPS) to enumerate and identify marine benthic ciliates. The combined Ludox-QPS method involves sample collection and salt reduction, extraction with Ludox centrifugation, and preparation with the QPS technique. The recovery efficiency of Ludox was first tested with azoic sandy and muddy sediments. A 94-100% recovery rate of ciliates was reached. The method was further tested with natural sandy, muddy-sand and muddy sediments. Excellent extraction efficiencies were consistently obtained: an average of 97.6% for ciliates in sand, and 96.9-97.8% for nematodes in the three types of sediments. The high efficiencies indicate that the method allows for simultaneous enumeration of micro- and meiobenthos. Advantages of the new method include: (i) reliable and cost-efficient operation; (ii) appropriate centrifugation for both micro- and meiobenthos; and (iii) applicability to large samples and routine ecological surveys. PMID:20843673

  20. Electronic properties of water in liquid environment. A sequential QM/MM study using the free energy gradient method.

    PubMed

    Georg, Herbert C; Canuto, Sylvio

    2012-09-13

    There is a continuous search for theoretical methods that are able to describe the effects of the liquid environment on molecular systems. Different methods emphasize different aspects, and the treatment of both the local and bulk properties is still a great challenge. In this work, the electronic properties of a water molecule in liquid environment is studied by performing a relaxation of the geometry and electronic distribution using the free energy gradient method. This is made using a series of steps in each of which we run a purely molecular mechanical (MM) Monte Carlo Metropolis simulation of liquid water and subsequently perform a quantum mechanical/molecular mechanical (QM/MM) calculation of the ensemble averages of the charge distribution, atomic forces, and second derivatives. The MP2/aug-cc-pV5Z level is used to describe the electronic properties of the QM water. B3LYP with specially designed basis functions are used for the magnetic properties. Very good agreement is found for the local properties of water, such as geometry, vibrational frequencies, dipole moment, dipole polarizability, chemical shift, and spin-spin coupling constants. The very good performance of the free energy method combined with a QM/MM approach along with the possible limitations are briefly discussed.

  1. 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

  2. Mixed-norm estimates for the M/EEG inverse problem using accelerated gradient methods

    PubMed Central

    Gramfort, Alexandre; Kowalski, Matthieu; Hämäläinen, Matti

    2012-01-01

    Magneto- and electroencephalography (M/EEG) measure the electromagnetic fields produced by the neural electrical currents. Given a conductor model for the head, and the distribution of source currents in the brain, Maxwell’s equations allow one to compute the ensuing M/EEG signals. Given the actual M/EEG measurements and the solution of this forward problem, one can localize, in space and in time, the brain regions than have produced the recorded data. However, due to the physics of the problem, the limited number of sensors compared to the number of possible source locations, and measurement noise, this inverse problem is ill-posed. Consequently, additional constraints are needed. Classical inverse solvers, often called Minimum Norm Estimates (MNE), promote source estimates with a small ℓ2 norm. Here, we consider a more general class of priors based on mixed-norms. Such norms have the ability to structure the prior in order to incorporate some additional assumptions about the sources. We refer to such solvers as Mixed-Norm Estimates (MxNE). In the context of M/EEG, MxNE can promote spatially focal sources with smooth temporal estimates with a two-level ℓ1/ℓ2 mixed-norm, while a three-level mixed-norm can be used to promote spatially non-overlapping sources between different experimental conditions. In order to efficiently solve the optimization problems of MxNE, we introduce fast first-order iterative schemes that for the ℓ1/ℓ2 norm give solutions in a few seconds making such a prior as convenient as the simple MNE. Furhermore, thanks to the convexity of the optimization problem, we can provide optimality conditions that guarantee global convergence. The utility of the methods is demonstrated both with simulations and experimental MEG data. PMID:22421459

  3. Mixed-norm estimates for the M/EEG inverse problem using accelerated gradient methods

    NASA Astrophysics Data System (ADS)

    Gramfort, Alexandre; Kowalski, Matthieu; Hämäläinen, Matti

    2012-04-01

    Magneto- and electroencephalography (M/EEG) measure the electromagnetic fields produced by the neural electrical currents. Given a conductor model for the head, and the distribution of source currents in the brain, Maxwell's equations allow one to compute the ensuing M/EEG signals. Given the actual M/EEG measurements and the solution of this forward problem, one can localize, in space and in time, the brain regions that have produced the recorded data. However, due to the physics of the problem, the limited number of sensors compared to the number of possible source locations, and measurement noise, this inverse problem is ill-posed. Consequently, additional constraints are needed. Classical inverse solvers, often called minimum norm estimates (MNE), promote source estimates with a small ℓ2 norm. Here, we consider a more general class of priors based on mixed norms. Such norms have the ability to structure the prior in order to incorporate some additional assumptions about the sources. We refer to such solvers as mixed-norm estimates (MxNE). In the context of M/EEG, MxNE can promote spatially focal sources with smooth temporal estimates with a two-level ℓ1/ℓ2 mixed-norm, while a three-level mixed-norm can be used to promote spatially non-overlapping sources between different experimental conditions. In order to efficiently solve the optimization problems of MxNE, we introduce fast first-order iterative schemes that for the ℓ1/ℓ2 norm give solutions in a few seconds making such a prior as convenient as the simple MNE. Furthermore, thanks to the convexity of the optimization problem, we can provide optimality conditions that guarantee global convergence. The utility of the methods is demonstrated both with simulations and experimental MEG data.

  4. Sucrose density gradient centrifugation and cross-flow filtration methods for the production of arbovirus antigens inactivated by binary ethylenimine

    PubMed Central

    Pyke, Alyssa T; Phillips, Debra A; Chuan, Teck F; Smith, Greg A

    2004-01-01

    Background Sucrose density gradient centrifugation and cross-flow filtration methods have been developed and standardised for the safe and reproducible production of inactivated arbovirus antigens which are appropriate for use in diagnostic serological applications. Methods To optimise the maximum titre of growth during the propagation of arboviruses, the multiplicity of infection and choice of cell line were investigated using stocks of Ross River virus and Barmah Forest virus grown in both mosquito and mammalian cell lines. To standardise and improve the efficacy of the inactivation of arboviral suspensions, stocks of Ross River virus, Barmah Forest virus, Japanese encephalitis virus, Murray Valley encephalitis virus and Alfuy virus were chemically inactivated using binary ethylenimine at a final concentration of 3 mM. Aliquots were then taken at hourly intervals and crude inactivation rates were determined for each virus using a plaque assay. To ensure complete inactivation, the same aliquots were each passaged 3 times in Aedes albopictus C6/36 cells and the presence of viral growth was detected using an immunofluorescent assay. For larger quantities of viral suspensions, centrifugation on an isopycnic sucrose density gradient or cross-flow filtration was used to produce concentrated, pure antigens or partially concentrated, semi-purified antigens respectively. Results The results of the propagation experiments suggested that the maximum viral titres obtained for both Ross River virus and Barmah Forest virus were affected by the incubation period and choice of cell line, rather than the use of different multiplicity of infection values. Results of the binary ethylenimine inactivation trial suggested that standardised periods of 5 or 8 hours would be suitable to ensure effective and complete inactivation for a number of different arboviral antigens. Conclusion Two methods used to prepare inactivated arbovirus antigens have been standardised to minimise production

  5. 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.

  6. Estimation of Free, Conjugated, and Diffusible Indole-3-acetic Acid in Etiolated Maize Shoots by the Indolo-α-pyrone Fluorescence Method

    PubMed Central

    Iino, Moritoshi; Carr, Denis J.

    1982-01-01

    Procedures for estimating free indoleacetic acid (IAA extracted from tissue homogenates by aqueous acetone), conjugated IAA (extracted by aqueous acetone and hydrolyzed by 1 n KOH), and diffusible IAA (diffused from the excised tissue into water), in shoots of etiolated 3-day-old maize (Zea mays L. cv. GH 390) seedlings are described, the indolo-α-pyrone fluorescence method being used to assay IAA. The reliability of the procedure is shown by comparative IAA determinations of the extracts using the gas chromatography-mass spectrometry method in which the methyl ester, heptafluorobutyryl derivative of IAA is assayed using the selected-ion-monitoring technique with deuterated IAA as an internal standard. A 3-millimeter-long coleoptile tip, a coleoptile with its included leaves and nodal region (whole coleoptile), and a mesocotyl each contains 0.2, 1.7, and 1.5 nanograms of free IAA, respectively. The whole coleoptile and the mesocotyl contain slightly less conjugated IAA than their content of free IAA. IAA diffuses from the coleoptile tip at the rate of 1.0 nanograms per tip per hour; from the base of the whole coleoptile and a set of leaves excised from a coleoptile, IAA diffuses at the rate of 0.62 and 0.17 nanogram per plant part per hour, respectively. The data obtained support the classical assumption that the coleoptile tip produces IAA. It is also suggested that some IAA is decomposed during its downward transport in the coleoptile. PMID:16662325

  7. 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.

  8. Effect of cooking methods on fatty acids, conjugated isomers of linoleic acid and nutritional quality of beef intramuscular fat.

    PubMed

    Alfaia, Cristina M M; Alves, Susana P; Lopes, Anabela F; Fernandes, Maria J E; Costa, Ana S H; Fontes, Carlos M G A; Castro, Matilde L F; Bessa, Rui J B; Prates, José A M

    2010-04-01

    The effect of boiling, microwaving and grilling on the composition and nutritional quality of beef intramuscular fat from cattle fed with two diets was investigated. Longissimus lumborum muscle from 15 Alentejano young bulls fed on concentrate or pasture was analyzed. Cooking losses and, consequently, total lipids, increased directly with the cooking time and internal temperature reached by meat (microwaving>boiling>grilling). The major changes in fatty acid composition, which implicated 16 out of 34 fatty acids, resulted in higher percentages in cooked beef of SFA and MUFA and lower proportions of PUFA, relative to raw meat, while conjugated linoleic acid (CLA) isomers revealed a great stability to thermal processes. Heating decreased the PUFA/SFA ratio of meat but did not change its n-6/n-3 index. Thermal procedures induced only slight oxidative changes in meat immediately after treatment but hardly affected the true retention values of its individual fatty acids (72-168%), including CLA isomers (81-128%).

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

    DOEpatents

    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.

  10. 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.

  11. Increases in water potential gradient reduce xylem conductivity in whole plants. Evidence from a low-pressure conductivity method.

    PubMed

    Brodribb, T J; Hill, R S

    2000-07-01

    A new method using hydrostatic suctions (less than 0.02 MPa) was used to measure whole-root conductivity (K(r)) in saplings of two angiosperm pioneer trees (Eucalyptus regnans and Toona australis) and two rainforest conifers (Dacrycarpus dacrydioides and Nageia fleurii). The resultant K(r) was combined with measurements of stem and leaf hydraulic conductivity to calculate whole-plant conductivity and to predict leaf water potential (Psi(l)) during transpiration. At normal soil temperatures there was good agreement between measured and predicted Psi(l) 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 Psi(l) corresponded to those expected by the effect of increased water viscosity on K(r). In one species, however, root chilling produced severe plant wilting and a decline in Psi(l) significantly below the predicted value. In this species Psi(l) decreased to a value close to, or below, the Psi(l) 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.

  12. 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.

  13. 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).

  14. Ultimately accurate SRAF replacement for practical phases using an adaptive search algorithm based on the optimal gradient method

    NASA Astrophysics Data System (ADS)

    Maeda, Shimon; Nosato, Hirokazu; Matsunawa, Tetsuaki; Miyairi, Masahiro; Nojima, Shigeki; Tanaka, Satoshi; Sakanashi, Hidenori; Murakawa, Masahiro; Saito, Tamaki; Higuchi, Tetsuya; Inoue, Soichi

    2010-04-01

    SRAF (Sub Resolution Assist Feature) technique has been widely used for DOF enhancement. Below 40nm design node, even in the case of using the SRAF technique, the resolution limit is approached due to the use of hyper NA imaging or low k1 lithography conditions especially for the contact layer. As a result, complex layout patterns or random patterns like logic data or intermediate pitch patterns become increasingly sensitive to photo-resist pattern fidelity. This means that the need for more accurate resolution technique is increasing in order to cope with lithographic patterning fidelity issues in low k1 lithography conditions. To face with these issues, new SRAF technique like model based SRAF using an interference map or inverse lithography technique has been proposed. But these approaches don't have enough assurance for accuracy or performance, because the ideal mask generated by these techniques is lost when switching to a manufacturable mask with Manhattan structures. As a result it might be very hard to put these things into practice and production flow. In this paper, we propose the novel method for extremely accurate SRAF placement using an adaptive search algorithm. In this method, the initial position of SRAF is generated by the traditional SRAF placement such as rule based SRAF, and it is adjusted by adaptive algorithm using the evaluation of lithography simulation. This method has three advantages which are preciseness, efficiency and industrial applicability. That is, firstly, the lithography simulation uses actual computational model considering process window, thus our proposed method can precisely adjust the SRAF positions, and consequently we can acquire the best SRAF positions. Secondly, because our adaptive algorithm is based on optimal gradient method, which is very simple algorithm and rectilinear search, the SRAF positions can be adjusted with high efficiency. Thirdly, our proposed method, which utilizes the traditional SRAF placement, is

  15. 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.

  16. 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.

  17. 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

  18. 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).

  19. Studies on m-benzyne and phenol via improved virtual orbital-complete active space configuration interaction (IVO-CASCI) analytical gradient method

    NASA Astrophysics Data System (ADS)

    Chattopadhyay, Sudip; Chaudhuri, Rajat K.; Mahapatra, Uttam Sinha

    2010-05-01

    Improved virtual orbital-complete active space configuration interaction (IVO-CASCI) analytical gradient theory has been used to investigate geometrical parameters, vibrational frequencies and excitation energies of m-benzyne and phenol using different reference spaces and basis sets. Compared to the results obtained via CASSCF treatments, it has been found that the IVO-CASCI gradient method provides very satisfactory results with low computational cost. IVO-CASCI values compare reasonably well with the earlier established theoretical results and experimental values whenever available.

  20. 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.

  1. Red clover Trifolium pratense L. phytoestrogens: UV-B radiation increases isoflavone yield, and postharvest drying methods change the glucoside conjugate profiles.

    PubMed

    Swinny, Ewald E; Ryan, Ken G

    2005-10-19

    Isoflavone extracts of red clover Trifolium pratense L. (cv. Pawera) with dissimilar glucoside conjugate profiles were obtained by employing different postharvest drying methods. The most prominent isoflavones found were formononetin and biochanin A and their corresponding glucosides and malonyl glucoside esters. Postharvest freeze drying inhibited the conversion of the glycosides to the aglycones, while vacuum drying allowed for maximum conversion of the glycosides to their corresponding aglycones. Air drying produced a low level of the aglycones formononetin and biochanin A, and oven drying promoted decarboxylation of the malonyl glucosides to the acetyl glucosides. Exposure to enhanced UV-B radiation resulted in an increase in total formononetin and biochanin A isoflavone levels, indicating that harvest during a period of high ambient UV-B radiation may be appropriate for maximum yield. The levels of caffeic acid and flavonols also increased by about 40 and 250%, respectively, on exposure to enhanced UV-B radiation.

  2. 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.

  3. 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. PMID:20740333

  4. 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.

  5. 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.

  6. Analytical gradients of the state-average complete active space self-consistent field method with density fitting

    SciTech Connect

    Delcey, Mickaël G.; Pedersen, Thomas Bondo; Aquilante, Francesco; Lindh, Roland

    2015-07-28

    An efficient implementation of the state-averaged complete active space self-consistent field (SA-CASSCF) gradients employing density fitting (DF) is presented. The DF allows a reduction both in scaling and prefactors of the different steps involved. The performance of the algorithm is demonstrated on a set of molecules ranging up to an iron-Heme b complex which with its 79 atoms and 811 basis functions is to our knowledge the largest SA-CASSCF gradient computed. For smaller systems where the conventional code could still be used as a reference, both the linear response calculation and the gradient formation showed a clear timing reduction and the overall cost of a geometry optimization is typically reduced by more than one order of magnitude while the accuracy loss is negligible.

  7. Analytical gradients of the state-average complete active space self-consistent field method with density fitting

    NASA Astrophysics Data System (ADS)

    Delcey, Mickaël G.; Pedersen, Thomas Bondo; Aquilante, Francesco; Lindh, Roland

    2015-07-01

    An efficient implementation of the state-averaged complete active space self-consistent field (SA-CASSCF) gradients employing density fitting (DF) is presented. The DF allows a reduction both in scaling and prefactors of the different steps involved. The performance of the algorithm is demonstrated on a set of molecules ranging up to an iron-Heme b complex which with its 79 atoms and 811 basis functions is to our knowledge the largest SA-CASSCF gradient computed. For smaller systems where the conventional code could still be used as a reference, both the linear response calculation and the gradient formation showed a clear timing reduction and the overall cost of a geometry optimization is typically reduced by more than one order of magnitude while the accuracy loss is negligible.

  8. New Langevin and gradient thermostats for rigid body dynamics

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    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.

  9. 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. PMID:25877569

  10. 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.

  11. Method of propulsion of a ferromagnetic core in the cardiovascular system through magnetic gradients generated by an MRI system.

    PubMed

    Mathieu, Jean-Baptiste; Beaudoin, Gilles; Martel, Sylvain

    2006-02-01

    This paper reports the use of a magnetic resonance imaging (MRI) system to propel a ferromagnetic core. The concept was studied for future development of microdevices designed to perform minimally invasive interventions in remote sites accessible through the human cardiovascular system. A mathematical model is described taking into account various parameters such as the size of blood vessels, the velocities and viscous properties of blood, the magnetic properties of the materials, the characteristics of MRI gradient coils, as well as the ratio between the diameter of a spherical core and the diameter of the blood vessels. The concept of magnetic propulsion by MRI is validated experimentally by measuring the flow velocities that magnetized spheres (carbon steel 1010/1020) can withstand inside cylindrical tubes under the different magnetic forces created with a Siemens Magnetom Vision 1.5 T MRI system. The differences between the velocities predicted by the theoretical model and the experiments are approximately 10%. The results indicate that with the technology available today for gradient coils used in clinical MRI systems, it is possible to generate sufficient gradients to propel a ferromagnetic sphere in the larger sections of the arterial system. In other words, the results show that in the larger blood vessels where the diameter of the microdevices could be as large as a couple a millimeters, the few tens of mT/m of gradients required for displacement against the relatively high blood flow rate is well within the limits of clinical MRI systems. On the other hand, although propulsion of a ferromagnetic core with diameter of approximately 600 microm may be possible with existing clinical MRI systems, gradient amplitudes of several T/m would be required to propel a much smaller ferromagnetic core in small vessels such as capillaries and additional gradient coils would be required to upgrade existing MRI systems for operations at such a scale.

  12. Analysis and calculation by integral methods of laminar compressible boundary-layer with heat transfer and with and without pressure gradient

    NASA Technical Reports Server (NTRS)

    Morduchow, Morris

    1955-01-01

    A survey of integral methods in laminar-boundary-layer analysis is first given. A simple and sufficiently accurate method for practical purposes of calculating the properties (including stability) of the laminar compressible boundary layer in an axial pressure gradient with heat transfer at the wall is presented. For flow over a flat plate, the method is applicable for an arbitrarily prescribed distribution of temperature along the surface and for any given constant Prandtl number close to unity. For flow in a pressure gradient, the method is based on a Prandtl number of unity and a uniform wall temperature. A simple and accurate method of determining the separation point in a compressible flow with an adverse pressure gradient over a surface at a given uniform wall temperature is developed. The analysis is based on an extension of the Karman-Pohlhausen method to the momentum and the thermal energy equations in conjunction with fourth- and especially higher degree velocity and stagnation-enthalpy profiles.

  13. The Exact Formula for an Energy Band Spectrum Gradient within the New Completely Orthogonalized Plane Wave Method

    NASA Astrophysics Data System (ADS)

    Syrotyuk, S. V.; Kynash, Yu. E.; Sobchuk, I. S.

    1997-03-01

    The formula for calculating the spectrum gradient gk = gradk E(k) at an arbitrary point k in the Brillouin zone has been derived on the basis of the new completely orthogonalized plane wave formalism (COPW). This important physical quantity has been obtained within the COPW basis for the first time. It displays a true plane wave basis limit.

  14. Method development for the separation of monoclonal antibody charge variants in cation exchange chromatography, Part I: salt gradient approach.

    PubMed

    Fekete, Szabolcs; Beck, Alain; Fekete, Jenő; Guillarme, Davy

    2015-01-01

    Ion exchange chromatography (IEX) is a historical technique widely used for the detailed characterization of therapeutic proteins and can be considered as a reference and powerful technique for the qualitative and quantitative evaluation of charge variants. When applying salt gradient IEX approach for monoclonal antibodies (mAbs) characterization, this approach is described as time-consuming to develop and product-specific. The goal of this study was to tackle these two bottle-necks. By modeling the retention of several commercial mAbs and their variants in IEX, we proved that the mobile phase temperature was not relevant for tuning selectivity, while optimal salt gradient program can be easily found based on only two initial gradients of different slopes. Last but not least, the dependence of retention vs. pH being polynomial, three initial runs at different pH were required to optimize mobile phase pH. Finally, only 9h of initial experiments were necessary to simultaneously optimize salt gradient profile and pH in IEX. The data can then be treated with commercial modeling software to find out the optimal conditions to be used, and accuracy of retention times prediction was excellent (less than 1% variation between predicted and experimental values). Second, we also proved that generic IEX conditions can be applied for the characterization of mAbs possessing a wide range of pI, from 6.7 to 9.1. For this purpose, a strong cation exchange column has to be employed at a pH below 6 and using a proportion of NaCl up to 0.2M. Under these conditions, all the mAbs were properly eluted from the column. Therefore, salt gradient CEX can be considered as a generic multi-product approach. PMID:25240157

  15. 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. PMID:26150349

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. Localization of the cortical motor area by functional magnetic resonance imaging with gradient echo and echo-planar methods, using clinical 1.5 Tesla MR imaging systems.

    PubMed

    Nakayama, K

    1997-06-01

    Functional magnetic resonance imaging (MRI) with gradient echo and echo-planar sequences was applied to healthy volunteers and neurological patients to evaluate the feasibility of detecting and localizing the motor cortex. Time course of the change in signal intensity by an alternate repetition of motor task (squeezing hand) and rest periods was also examined. The motor cortex was localized as the area of signal increase in 88.9% of 45 healthy volunteers by gradient echo method, which mainly reflected the cortical vein, and 83.3% of 30 healthy volunteers by echo-planar method, which mainly reflected the cerebral gyrus. Among 21 volunteers who participated in the both studies, success rate in the localization for the motor cortex was 90.5% (21 volunteers) by gradient echo method and 81% (17 volunteers) by echo-planar method. It was also shown from the time course of the change in signal intensity that signal increase in the most significantly activated area generally corresponded with the periods of the motor task, and the latency between the onset of signal increase and the onset of motor task was usually about 4 seconds. In four of 6 patients with brain tumor, the motor cortex was localized, although activated areas were displaced or distorted. The results indicate that fMRI, either with gradient echo or echo-planar sequence, is a useful method for localizing the primary motor area activated during the motor task and clinically available for noninvasive evaluation of the anatomical relation between brain tumors and the motor area before surgical therapy.

  1. 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.

  2. 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.

  3. A method for introduction of magnetic nanoparticles into tissues by means of magnetic field gradient: an experimental study.

    PubMed

    Dobretsov, K G; Afon'kin, V Yu; Kirichenko, A K; Ladygina, V P; Stolyar, S V; Bayukov, O A; Sipkin, A V

    2009-06-01

    Targeted effects of magnetic nanoparticles were studied. Solution with iron-containing nanosubstance was applied to resected nasal bone and cartilage tissues. Magnetic field was generated by a Polus-101 device for low-frequency magnetotherapy, which provided permanent work of one inductor (10.14+/-19.56 mT). The results indicate that magnetic nanoparticles placed into magnetic field gradient penetrate into the thickness of the cartilage and bone tissues. PMID:19902074

  4. 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).

  5. 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.

  6. Enhancing the volume and the optical quality of hen egg-white lysozyme crystals by coupling the salt concentration gradient crystallization method with a magnetic field

    PubMed Central

    Magay, Elena; Cho, Sang Jin; Kim, Shin Ae

    2012-01-01

    The effect of coupling the salt concentration gradient crystallization method with the use of the paramagnetic salt MnCl2 and a magnetic field is reported. The use of a simple magnetic device is proposed to have a significant effect on hen egg-white lysozyme crystal growth. Large single crystals greater than 10 mm3 in volume with optical perfection were consistently obtained in this study. PMID:22997475

  7. 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.

  8. A strategy for the systematic development of a liquid chromatographic mass spectrometric screening method for polymer electrolyte membrane degradation products using isocratic and gradient phase optimized liquid chromatography.

    PubMed

    Zedda, M; Tuerk, J; Teutenberg, T; Peil, S; Schmidt, T C

    2009-12-18

    Within the scope of research for target and non-target LC-MS/MS analysis of membrane degradation products of polymer electrolyte membrane fuel cells, a systematic method development for the separation of structurally similar compounds was performed by phase optimized liquid chromatography. Five different stationary phases with different selectivities were used. Isocratic separation for 4-hydroxybenzoic acid, isophthalic acid, terephthalic acid, 4-hydroxybenzaldehyde and 4-formylbenzoic acid was achieved on a C18 and a Phenyl phase. Using the PRISMA model the separation efficiency was optimized. This was achieved on a serially connected mixed stationary phase composed of 30 mm C18, 150 mm Phenyl and 60 mm C30. For the LC-MS screening of unknown degradation products from polymer electrolyte membranes in the product water of a fuel cell, a solvent gradient is mandatory for less polar or later eluting compounds. By means of 4-mercaptobenzoic acid it could be shown that a solvent gradient can be applied in order to elute later eluting compounds in a short time. The adaptability of this method for the qualitative analysis by target and non-target LC-MS/MS screening has been shown by means of 4-hydroxybenzoic acid. The combination of solvent gradient and isocratic conditions makes this approach attractive for the purpose of a screening method for known and unknown analytes in a water sample.

  9. 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.

  10. Determination of catecholamine in human serum by a fluorescent quenching method based on a water-soluble fluorescent conjugated polymer-enzyme hybrid system.

    PubMed

    Huang, Hui; Gao, Yuan; Shi, Fanping; Wang, Guannan; Shah, Syed Mazhar; Su, Xingguang

    2012-03-21

    In this paper, a sensitive water-soluble fluorescent conjugated polymer biosensor for catecholamine (dopamine DA, adrenaline AD and norepinephrine NE) was developed. In the presence of horse radish peroxidase (HRP) and H(2)O(2), catecholamine could be oxidized and the oxidation product of catecholamine could quench the photoluminescence (PL) intensity of poly(2,5-bis(3-sulfonatopropoxy)-1,4-phenylethynylenealt-1,4-poly(phenylene ethynylene)) (PPESO(3)). The quenching PL intensity of PPESO(3) (I(0)/I) was proportional to the concentration of DA, AD and NE in the concentration ranges of 5.0 × 10(-7) to 1.4 × 10(-4), 5.0 × 10(-6) to 5.0 × 10(-4), and 5.0 × 10(-6) to 5.0 × 10(-4) mol L(-1), respectively. The detection limit for DA, AD and NE was 1.4 × 10(-7) mol L(-1), 1.0 × 10(-6) and 1.0 × 10(-6) mol L(-1), respectively. The PPESO(3)-enzyme hybrid system based on the fluorescence quenching method was successfully applied for the determination of catecholamine in human serum samples with good accuracy and satisfactory recovery. The results were in good agreement with those provided by the HPLC-MS method. PMID:22314795

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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).

  16. 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.

  17. Analysis of linear and cyclic oligomers in polyamide-6 without sample preparation by liquid chromatography using the sandwich injection method. III. Separation mechanism and gradient optimization.

    PubMed

    Mengerink, Y; Peters, R; van der Wal, Sj; Claessens, H A; Cramers, C A

    2002-03-01

    The first six linear and cyclic oligomers of polyamide-6 can be quantitatively determined in the polymer using HPLC with the sandwich injection method and an aqueous acetonitrile gradient. In this final part of the triptych concerning the determination of the oligomers in polyamide-6, the irregular elution behavior of the cyclic monomer compared to the cyclic oligomers was investigated. We also optimized the separation of the involved polyamide oligomers, with respect to gradient steepness, stationary phase, column temperature and mobile phase pH. The irregular elution behavior of the cyclic monomer could be caused by its relatively large exposed/accessible hydrophobic surface, which permits relatively easy penetration into the hydrophobic stationary phase giving extra retention. The dipole moment of the different oligomers was used as a measure for this exposed/accessible hydrophobic area to correlate the retention factors using quantitative structure-retention relationships. We also studied the retention behavior of the polyamide, which is injected each run directly onto the column and modifies the stationary phase. Using a 250-microl post gradient injection zone of formic acid on a 250x3 mm Zorbax SB-C18 column, the polyamide could be effectively removed from the stationary phase after each separation. The linear solvent strength (LSS) model was used to optimize the separation of the first six linear and cyclic oligomers. As the LSS model assumes a linear correlation between the modifier concentration and the logarithm of the retention factor and the cyclic monomer and dimer show extreme curvation of this relation in the eluting region, we investigated different models to predict gradient elution from isocratic data. A direct translation of the isocratic data to gradient retention times did not yield adequate retention times using the LSS model. It was found that the LSS model worked acceptably if gradient retention times were used as input data. Even for fast

  18. 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.

  19. 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.

  20. 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.

  1. Iterative and multigrid methods in the finite element solution of incompressible and turbulent fluid flow

    NASA Astrophysics Data System (ADS)

    Lavery, N.; Taylor, C.

    1999-07-01

    Multigrid and iterative methods are used to reduce the solution time of the matrix equations which arise from the finite element (FE) discretisation of the time-independent equations of motion of the incompressible fluid in turbulent motion. Incompressible flow is solved by using the method of reduce interpolation for the pressure to satisfy the Brezzi-Babuska condition. The k-l model is used to complete the turbulence closure problem. The non-symmetric iterative matrix methods examined are the methods of least squares conjugate gradient (LSCG), biconjugate gradient (BCG), conjugate gradient squared (CGS), and the biconjugate gradient squared stabilised (BCGSTAB). The multigrid algorithm applied is based on the FAS algorithm of Brandt, and uses two and three levels of grids with a V-cycling schedule. These methods are all compared to the non-symmetric frontal solver. Copyright

  2. Gradient boosting machines, a tutorial

    PubMed Central

    Natekin, Alexey; Knoll, Alois

    2013-01-01

    Gradient boosting machines are a family of powerful machine-learning techniques that have shown considerable success in a wide range of practical applications. They are highly customizable to the particular needs of the application, like being learned with respect to different loss functions. This article gives a tutorial introduction into the methodology of gradient boosting methods with a strong focus on machine learning aspects of modeling. A theoretical information is complemented with descriptive examples and illustrations which cover all the stages of the gradient boosting model design. Considerations on handling the model complexity are discussed. Three practical examples of gradient boosting applications are presented and comprehensively analyzed. PMID:24409142

  3. 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.

  4. Statistical and optimization methods to expedite neural network training for transient identification

    SciTech Connect

    Reifman, J. . Reactor Analysis Div.); Vitela, E.J. . Inst. de Ciencias Nucleares); Lee, J.C. . Dept. of Nuclear Engineering)

    1993-01-01

    Two complementary methods, statistical feature selection and nonlinear optimization through conjugate gradients, are used to expedite feedforward neural network training. Statistical feature selection techniques in the form of linear correlation coefficients and information-theoretic entropy are used to eliminate redundant and non-informative plant parameters to reduce the size of the network. The method of conjugate gradients is used to accelerate the network training convergence and to systematically calculate the Teaming and momentum constants at each iteration. The proposed techniques are compared with the backpropagation algorithm using the entire set of plant parameters in the training of neural networks to identify transients simulated with the Midland Nuclear Power Plant Unit 2 simulator. By using 25% of the plant parameters and the conjugate gradients, a 30-fold reduction in CPU time was obtained without degrading the diagnostic ability of the network.

  5. Statistical and optimization methods to expedite neural network training for transient identification

    SciTech Connect

    Reifman, J.; Vitela, E.J.; Lee, J.C.

    1993-03-01

    Two complementary methods, statistical feature selection and nonlinear optimization through conjugate gradients, are used to expedite feedforward neural network training. Statistical feature selection techniques in the form of linear correlation coefficients and information-theoretic entropy are used to eliminate redundant and non-informative plant parameters to reduce the size of the network. The method of conjugate gradients is used to accelerate the network training convergence and to systematically calculate the Teaming and momentum constants at each iteration. The proposed techniques are compared with the backpropagation algorithm using the entire set of plant parameters in the training of neural networks to identify transients simulated with the Midland Nuclear Power Plant Unit 2 simulator. By using 25% of the plant parameters and the conjugate gradients, a 30-fold reduction in CPU time was obtained without degrading the diagnostic ability of the network.

  6. Development of a Gradient HPLC Method for the Simultaneous Determination of Sotalol and Sorbate in Oral Liquid Preparations Using Solid Core Stationary Phase

    PubMed Central

    2015-01-01

    A selective and sensitive gradient HPLC-UV method for quantification of sotalol hydrochloride and potassium sorbate in five types of oral liquid preparations was developed and fully validated. The separation of an active substance sotalol hydrochloride, potassium sorbate (antimicrobial agent), and other substances (for taste and smell correction, etc.) was performed using an Ascentis Express C18 (100 × 4.6 mm, particles 2.7 μm) solid core HPLC column. Linear gradient elution mode with a flow rate of 1.3 mL min−1 was used, and the injection volume was 5 µL. The UV/Vis absorbance detector was set to a wavelength of 237 nm, and the column oven was conditioned at 25°C. A sodium dihydrogen phosphate dihydrate solution (pH 2.5; 17.7 mM) was used as the mobile phase buffer. The total analysis time was 4.5 min (+2.5 min for reequilibration). The method was successfully employed in a stability evaluation of the developed formulations, which are now already being used in the therapy of arrhythmias in pediatric patients; the method is also suitable for general quality control, that is, not only just for extemporaneous preparations containing the mentioned substances. PMID:25878920

  7. Development of a gradient HPLC method for the simultaneous determination of sotalol and sorbate in oral liquid preparations using solid core stationary phase.

    PubMed

    Matysova, Ludmila; Zahalkova, Oxana; Klovrzova, Sylva; Sklubalova, Zdenka; Solich, Petr; Zahalka, Lukas

    2015-01-01

    A selective and sensitive gradient HPLC-UV method for quantification of sotalol hydrochloride and potassium sorbate in five types of oral liquid preparations was developed and fully validated. The separation of an active substance sotalol hydrochloride, potassium sorbate (antimicrobial agent), and other substances (for taste and smell correction, etc.) was performed using an Ascentis Express C18 (100 × 4.6 mm, particles 2.7 μm) solid core HPLC column. Linear gradient elution mode with a flow rate of 1.3 mL min(-1) was used, and the injection volume was 5 µL. The UV/Vis absorbance detector was set to a wavelength of 237 nm, and the column oven was conditioned at 25°C. A sodium dihydrogen phosphate dihydrate solution (pH 2.5; 17.7 mM) was used as the mobile phase buffer. The total analysis time was 4.5 min (+2.5 min for reequilibration). The method was successfully employed in a stability evaluation of the developed formulations, which are now already being used in the therapy of arrhythmias in pediatric patients; the method is also suitable for general quality control, that is, not only just for extemporaneous preparations containing the mentioned substances. PMID:25878920

  8. The ISG15 conjugation system.

    PubMed

    Durfee, Larissa A; Huibregtse, Jon M

    2012-01-01

    ISG15 is a ubiquitin-like modifier that is expressed in response to type 1 interferon signaling (IFN-α/β) and plays a role in antiviral responses. The core E1, E2, and E3 enzymes for ISG15 are Ube1L, UbcH8, and Herc5, respectively, and these are all also induced at the transcriptional level by IFN-α/β. We recently showed that Herc5 associates with polysomes and modifies target proteins in a cotranslational manner. Here, we describe the expression of the core conjugating enzymes in human cells, the detection of ISG15 conjugates, and the methods for fractionation of Herc5 with polysomes. PMID:22350882

  9. 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

  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. 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.

  12. Towards Reduced Parameter Uncertainty in Groundwater Model Calibration: Comparison of Local Gradient and Global Evolutionary Search Methods

    NASA Astrophysics Data System (ADS)

    Zyvoloski, G. A.; Vrugt, J. A.; Wolfsberg, A.; Stauffer, P.; Doherty, J.

    2006-12-01

    The calibration of very large and complex groundwater models is becoming common as a means to help address issues of reliability and uncertainty. Models with many parameters might require thousands of model runs to achieve an acceptable calibration. In addition, larger basin scale models often take hours to run. Obviously, the efficiency of the calibration method can be crucial to practical calibration of these large models. Model-independent estimation packages such as PEST (Doherty, 2005) that are based on the Gauss-Newton- Levenberg-Marquardt (GNLM) method provide inverse modeling capabilities with considerable flexibility in choosing parameters and observations. However, when dealing with highly nonlinear problems, they may converge to a local, rather than global optimum. Recently, Vrugt and Robinson (2006) presented a new concept of genetically adaptive multi-method search that has shown to significantly improve the efficiency of global search, approaching a factor of ten improvement for the more complex, higher dimensional problems. This new optimization method is called AMALGAM. In this study, we compare the GNLM and AMALGAM methods on several different synthetic groundwater models ranging from a layered basin model to a complex unconfined model. Algorithms are compared on a basis of computational efficiency and robustness of the solution.

  13. Conjugated microporous polymers: design, synthesis and application.

    PubMed

    Xu, Yanhong; Jin, Shangbin; Xu, Hong; Nagai, Atsushi; Jiang, Donglin

    2013-10-21

    Conjugated microporous polymers (CMPs) are a class of organic porous polymers that combine π-conjugated skeletons with permanent nanopores, in sharp contrast to other porous materials that are not π-conjugated and with conventional conjugated polymers that are nonporous. As an emerging material platform, CMPs offer a high flexibility for the molecular design of conjugated skeletons and nanopores. Various chemical reactions, building blocks and synthetic methods have been developed and a broad variety of CMPs with different structures and specific properties have been synthesized, driving the rapid growth of the field. CMPs are unique in that they allow the complementary utilization of π-conjugated skeletons and nanopores for functional exploration; they have shown great potential for challenging energy and environmental issues, as exemplified by their excellent performance in gas adsorption, heterogeneous catalysis, light emitting, light harvesting and electrical energy storage. This review describes the molecular design principles of CMPs, advancements in synthetic and structural studies and the frontiers of functional exploration and potential applications.

  14. 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.

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

    SciTech Connect

    Chen, W.

    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.

  16. 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.

  17. 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

  18. 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.

  19. Governing equations for electro-conjugate fluid flow

    NASA Astrophysics Data System (ADS)

    Hosoda, K.; Takemura, K.; Fukagata, K.; Yokota, S.; Edamura, K.

    2013-12-01

    An electro-conjugation fluid (ECF) is a kind of dielectric liquid, which generates a powerful flow when high DC voltage is applied with tiny electrodes. This study deals with the derivation of the governing equations for electro-conjugate fluid flow based on the Korteweg-Helmholtz (KH) equation which represents the force in dielectric liquid subjected to high DC voltage. The governing equations consist of the Gauss's law, charge conservation with charge recombination, the KH equation, the continuity equation and the incompressible Navier-Stokes equations. The KH equation consists of coulomb force, dielectric constant gradient force and electrostriction force. The governing equation gives the distribution of electric field, charge density and flow velocity. In this study, direct numerical simulation (DNS) is used in order to get these distribution at arbitrary time. Successive over-relaxation (SOR) method is used in analyzing Gauss's law and constrained interpolation pseudo-particle (CIP) method is used in analyzing charge conservation with charge recombination. The third order Runge-Kutta method and conservative second-order-accurate finite difference method is used in analyzing the Navier-Stokes equations with the KH equation. This study also deals with the measurement of ECF ow generated with a symmetrical pole electrodes pair which are made of 0.3 mm diameter piano wire. Working fluid is FF-1EHA2 which is an ECF family. The flow is observed from the both electrodes, i.e., the flow collides in between the electrodes. The governing equation successfully calculates mean flow velocity in between the collector pole electrode and the colliding region by the numerical simulation.

  20. 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.

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

    PubMed

    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.

  3. 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.

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

    PubMed Central

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

    2014-01-01

    Abstract. 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. PMID:25375348

  5. 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

    2013-02-01

    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. PMID:23298845

  6. Control of conformational and interpolymer effects in conjugated polymers

    NASA Astrophysics Data System (ADS)

    Kim, J.; Swager, T. M.

    2001-06-01

    The role of conjugated polymers in emerging electronic, sensor and display technologies is rapidly expanding. In spite of extensive investigations, the intrinsic spectroscopic properties of conjugated polymers in precise conformational and spatial arrangements have remained elusive. The difficulties of obtaining such information are endemic to polymers, which often resist assembly into single crystals or organized structures owing to entropic and polydispersity considerations. Here we show that the conformation of individual polymers and interpolymer interactions in conjugated polymers can be controlled through the use of designed surfactant poly(p-phenylene-ethynylene) Langmuir films. We show that by mechanically inducing reversible conformational changes of these Langmuir monolayers, we can obtain the precise interrelationship of the intrinsic optical properties of a conjugated polymer and a single chain's conformation and/or interpolymer interactions. This method for controlling the structure of conjugated polymers and establishing their intrinsic spectroscopic properties should permit a more comprehensive understanding of fluorescent conjugated materials.

  7. Control of conformational and interpolymer effects in conjugated polymers.

    PubMed

    Kim, J; Swager, T M

    2001-06-28

    The role of conjugated polymers in emerging electronic, sensor and display technologies is rapidly expanding. In spite of extensive investigations, the intrinsic spectroscopic properties of conjugated polymers in precise conformational and spatial arrangements have remained elusive. The difficulties of obtaining such information are endemic to polymers, which often resist assembly into single crystals or organized structures owing to entropic and polydispersity considerations. Here we show that the conformation of individual polymers and interpolymer interactions in conjugated polymers can be controlled through the use of designed surfactant poly(p-phenylene-ethynylene) Langmuir films. We show that by mechanically inducing reversible conformational changes of these Langmuir monolayers, we can obtain the precise interrelationship of the intrinsic optical properties of a conjugated polymer and a single chain's conformation and/or interpolymer interactions. This method for controlling the structure of conjugated polymers and establishing their intrinsic spectroscopic properties should permit a more comprehensive understanding of fluorescent conjugated materials.

  8. 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.

  9. 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.

  10. Preparation and in vitro evaluation of liposomal chloroquine diphosphate loaded by a transmembrane pH-gradient method.

    PubMed

    Qiu, Liyan; Jing, Na; Jin, Yi

    2008-09-01

    This study developed an active loading method for encapsulating chloroquine diphosphate (CQ) into liposomes. The effects of different formulation factors on the encapsulation efficiency (EE) and the size of CQ liposomes were investigated. These factors included the internal phase of liposomes, the external phase of liposomes, the ratio of drug to soybean phosphatidylcholine (drug/SPC), the ratio of cholesterol to soybean phosphatidylcholine (Chol/SPC), and the incubation temperature and time. The EE (93%) was obtained when using drug/SPC (1:50 mass ratio), SPC/Chol (1:5 mass ratio) at 0.10 M citrate-sodium citrate buffer (pH 3.6). As 5 mol% methoxypoly(ethylene glycol)(2,000) cholesteryl succinate (CHS-PEG(2000)) or distearoyl phosphatidylethanolamine-poly (ethylene glycol)(2,000) (DSPE-PEG(2000)) was added, the size of particle was reduced and the EE was improved. Freeze-drying with 5% trehalose as a cryoprotectant was carried out to achieve long-term stability. The drug release studies were performed in vitro simulating the desired application conditions, such as physiological fluids (pH 7.4), tumor tissues (pH 6.5) and endosomal compartments (pH 5.5). The release of CQ from the liposomes prepared via remote loading showed the significant pH-sensitivity and retention properties, which favored the application of liposomal CQ at tumor tissues and endosomal compartments.

  11. Novel, cyclic heat dissipation method for the correction of natural temperature gradients in sap flow measurements. Part 1. Theory and application.

    PubMed

    Lubczynski, Maciek W; Chavarro-Rincon, Diana; Roy, Jean

    2012-07-01

    Natural temperature gradient (NTG) can be a significant problem in thermal sap flow measurements, particularly in dry environments with sparse vegetation. To resolve this problem, we propose a novel correction method called cyclic heat dissipation (CHD) in its thermal dissipation probe (TDP) application. The CHD method is based on cyclic, switching ON/OFF power schema measurements and a three-exponential model, extrapolating measured signal to steady state thermal equilibrium. The extrapolated signal OFF represents NTG, whereas the extrapolated signal ON represents standard TDP signal, biased by NTG. Therefore, subtraction of the OFF signal from the ON signal allows defining the unbiased TDP signal, finally processed according to standard Granier calibration. The in vivo Kalahari measurements were carried out in three steps on four different tree species, first as NTG, then as standard TDP and finally in CHD mode, each step for ∼1-2 days. Afterwards, each tree was separated from its stem following modified Roberts' (1977) procedure, and CHD verification was applied. The typical NTG varying from ∼0.5 °C during night-time to -1 °C during day-time, after CHD correction, resulted in significant reduction of sap flux densities (J(p)) as compared with the standard TDP, particularly distinct for low J(p). The verification of the CHD method indicated ∼20% agreement with the reference method, largely dependent on the sapwood area estimate. The proposed CHD method offers the following advantages: (i) in contrast to any other NTG correction method, it removes NTG bias from the measured signal by using in situ, extrapolated to thermal equilibrium signal; (ii) it does not need any specific calibration making use of the standard Granier calibration; (iii) it provides a physical background to the proposed NTG correction; (iv) it allows for power savings; (v) it is not tied to TDP, and so can be adapted to other thermal methods. In its current state, the CHD data

  12. 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.

  13. 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.

  14. 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

  15. 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. PMID:26907700

  16. 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.

  17. 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

  18. Fast Gradient Elution Reversed-Phase Liquid Chromatography with Diode-Array Detection as a High-throughput Screening Method for Drugs of Abuse II. Data Analysis

    PubMed Central

    Porter, Sarah E. G.; Stoll, Dwight R.; Paek, Changyub; Rutan, Sarah C.; Carr, Peter W.

    2009-01-01

    In Part I of this work, we developed a method for the detection of drugs of abuse in biological samples based on fast gradient elution liquid-chromatography coupled with diode array spectroscopic detection (LC-DAD). In this part of the work, we apply the chemometric method of target factor analysis (TFA) to the chromatograms. This algorithm identifies the target compounds present in chromatograms based on a spectral library, resolves nearly co-eluting components, and differentiates between drugs with similar spectra. The ability to resolve highly overlapped peaks using the spectral data afforded by the DAD is what distinguishes the present method from conventional library searching methods. Our library has a mean list length of 1.255 and a discriminating power of 0.997 when both retention index and spectral factors are considered. The algorithm compares a library of 47 different compounds of toxicological relevance to unknown samples and identifies which compounds are present based on spectral and retention index matching. The application of a corrected retention index for identification rather than raw retention times compensates for long-term and column-to-column retention time shifts and allows for the use of a single library of spectral and retention data. Training data sets were used to establish the search and identification parameters of the method. A validation data set of 70 chromatograms was used to calculate the sensitivity (correct identification of positives) and specificity (correct identification of negatives) of the method, which were found to be 92 % and 94% respectively. PMID:17070534

  19. Implementation of iterative methods for large sparse nonsymmetric linear systems on a parallel vector machine

    SciTech Connect

    Ma, S.; Chronopoulos, A.T. )

    1990-01-01

    This paper reports on the restructure of three outstanding iterative methods for large space nonsymmetric linear systems. These methods are CGS (conjugate gradient squared), CRS (conjugate residual squared), and Orthomin(k). The restructured methods are more suitable for vector and parallel processing. The authors implemented these methods on a parallel vector system. The linear systems for the numerical tests are obtained from discretizing four two- dimensional elliptic partial differential equations by finite difference and finite element methods. A vectorizable and parallelizable version of incomplete LU preconditioning is used. The authors restructured the subroutines to enhance the data locality in vector machines with storage hierarchy. Speedup was measured for multitasking by four processors.

  20. Determining trace amounts and the origin of formaldehyde impurity in Neisseria meningitidis A/C/Y/W-135-DT conjugate vaccine formulated in isotonic aqueous 1× PBS by improved C18-UPLC method.

    PubMed

    Gudlavalleti, Seshu K; Crawford, Erika N; Tran, Nhi N; Orten, Dana J; Harder, Jeffery D; Reddy, Jeeri R

    2015-03-25

    The ability to accurately measure and report trace amounts of residual formaldehyde impurity in a vaccine product is not only critical in the product release but also a regulatory requirement. In many bacterial or viral vaccine manufacturing procedures, formaldehyde is used either at a live culture inactivation step or at a protein de-toxification step or at both. Reported here is a validated and improved C18-UPLC method (developed based on previously published C-8 HPLC method) to determine the traces of formaldehyde process impurity in a liquid form Neisseria meningitidis A/C/Y/W-135-DT conjugate vaccine formulated in isotonic aqueous 1× PBS. UPLC C-18 column and the conditions described distinctly resolved the 2,4-DNPH-HCHO adduct from the un-reacted 2,4-DNPH as detected by TUV detector at 360 nm. This method was shown to be compatible with PBS formulation and extremely sensitive (with a quantitation limit of 0.05 ppm) and aided to determine formaldehyde contamination sources by evaluating the in-process materials as a track-down analysis. Final nanogram levels of formaldehyde in the formulated single dose vialed vaccine mainly originated from the diphtheria toxoid carrier protein used in the production of the conjugate vaccine, whereas relative contribution from polysaccharide API was minimal.

  1. Gradient equivalent crystal theory.

    PubMed

    Zypman, F R; Ferrante, J

    2006-07-01

    This paper presents an extension of the formalism of equivalent crystal theory (ECT) by introducing an electron density gradient term so that the total model density becomes a more accurate representation of the real local density. Specifically, we allow for the electron density around a lattice site to have directionality, in addition to an average value, as assumed in ECT. We propose that an atom senses its neighbouring density as a weighted sum-the weights given by the its own electronic probability. As a benchmark, the method is used to compute vacancy migration energy curves of iron. These energies are in good agreement with previously published results. PMID:21690822

  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. The retrieval of a buried cylindrical obstacle by a constrained modified gradient method in the H-polarization case and for Maxwellian materials

    NASA Astrophysics Data System (ADS)

    Lambert, M.; Lesselier, D.; Kooij, B. J.

    1998-10-01

    The retrieval of an unknown, possibly inhomogeneous, penetrable cylindrical obstacle buried entirely in a known homogeneous half-space - the constitutive material parameters of the obstacle and of its embedding obey a Maxwell model - is considered from single- or multiple-frequency aspect-limited data collected by ideal sensors located in air above the embedding half-space, when a small number of time-harmonic transverse electric (TE)-polarized line sources - the magnetic field H is directed along the axis of the cylinder - is also placed in air. The wavefield is modelled from a rigorous H-field domain integral-differential formulation which involves the dot product of the gradients of the single component of H and of the Green function of the stratified environment times a scalar-valued contrast function which contains the obstacle parameters (the frequency-independent, position-dependent relative permittivity and conductivity). A modified gradient method is developed in order to reconstruct the maps of such parameters within a prescribed search domain from the iterative minimization of a cost functional which incorporates both the error in reproducing the data and the error on the field built inside this domain. Non-physical values are excluded and convergence reached by incorporating in the solution algorithm, from a proper choice of unknowns, the condition that the relative permittivity be larger than or equal to 1, and the conductivity be non-negative. The efficiency of the constrained method is illustrated from noiseless and noisy synthetic data acquired independently. The importance of the choice of the initial values of the sought quantities, the need for a periodic refreshment of the constitutive parameters to avoid the algorithm providing inconsistent results, and the interest of a frequency-hopping strategy to obtain finer and finer features of the obstacle when the frequency is raised, are underlined. It is also shown that though either the permittivity

  4. Comparison of conjugates composed of lipopolysaccharide from Shigella flexneri type 2a detoxified by two methods and bound to tetanus toxoid.

    PubMed Central

    Polotsky, V Y; Robbins, J B; Bryla, D; Schneerson, R

    1994-01-01

    Shigella flexneri type 2a lipopolysaccharide (LPS) was detoxified with acetic acid (O-SP) or with hydrazine (DeALPS). DeALPS, but not O-SP, retained part of its lipid A. Both gave an identical line of precipitation with typing antiserum by double immunodiffusion, and both had low levels of LPS activity by the Limulus amoebocyte lysate assay. O-SP had an M(r) of approximately 17,000. DeALPS had two components of M(r)s approximately 30,00 (major and approximately 10,000 (minor). Adipic acid hydrazide derivatives of O-SP and DeALPS were conjugated to tetanus toxoid (TT), purified by gel filtration through CL-6B Sepharose, and designated O-SP-TT and DeALPS-TT, respectively. Saccharide (2.5 micrograms) as O-SP, DeALPS, or their conjugates was injected subcutaneously into 5-week-old mice three times 2 weeks apart. The mice were bled before the second injection and 7 days after the second and third. O-SP alone did not elicit immunoglobulin M (IgM) or IgG LPS antibodies. DeALPS elicited low levels of IgM LPS antibodies after the third injection only. Two of three lots of O-SP-TT induced significant levels of IgM LPS antibodies after the third injection. One O-SP-TT lot elicited IgG LPS antibodies after the second injection, and all three lots elicited significant levels of IgG after the third. DeALPS-TT induced low levels of anti-LPS IgM and IgG only after the third injection. The geometric mean antibody titers of both immunoglobulin classes induced by O-SP-TT were higher than those induced by DeALPS-TT. By these criteria, O-SP provided a more immunogenic saccharide than DeALPS for S. flexneri type 2a conjugates. Images PMID:8262629

  5. Dynamics of photogenerated polarons in conjugated polymers.

    PubMed

    An, Z; Wu, C Q; Sun, X

    2004-11-19

    Within a tight-binding electron-phonon interacting model, we investigate the dynamics of photoexcitations to address the generation mechanism of charged polarons in conjugated polymers by using a nonadiabatic evolution method. Besides the neutral polaron exciton which is well known, we identify a novel product of lattice dynamic relaxation from the photoexcited states in a few hundreds of femtoseconds, which is a mixed state composed of both charged polarons and neutral excitons. Our results show that the charged polarons are generated directly with a yield of about 25%, which is independent of the excitation energies, in good agreement with results from experiments. Effects of the conjugation length are also discussed.

  6. Dynamics of Photogenerated Polarons in Conjugated Polymers

    NASA Astrophysics Data System (ADS)

    An, Z.; Wu, C. Q.; Sun, X.

    2004-11-01

    Within a tight-binding electron-phonon interacting model, we investigate the dynamics of photoexcitations to address the generation mechanism of charged polarons in conjugated polymers by using a nonadiabatic evolution method. Besides the neutral polaron exciton which is well known, we identify a novel product of lattice dynamic relaxation from the photoexcited states in a few hundreds of femtoseconds, which is a mixed state composed of both charged polarons and neutral excitons. Our results show that the charged polarons are generated directly with a yield of about 25%, which is independent of the excitation energies, in good agreement with results from experiments. Effects of the conjugation length are also discussed.

  7. Combining Step Gradients and Linear Gradients in Density.

    PubMed

    Kumar, Ashok A; Walz, Jenna A; Gonidec, Mathieu; Mace, Charles R; Whitesides, George M

    2015-06-16

    Combining aqueous multiphase systems (AMPS) and magnetic levitation (MagLev) provides a method to produce hybrid gradients in apparent density. AMPS—solutions of different polymers, salts, or surfactants that spontaneously separate into immiscible but predominantly aqueous phases—offer thermodynamically stable steps in density that can be tuned by the concentration of solutes. MagLev—the levitation of diamagnetic objects in a paramagnetic fluid within a magnetic field gradient—can be arranged to provide a near-linear gradient in effective density where the height of a levitating object above the surface of the magnet corresponds to its density; the strength of the gradient in effective density can be tuned by the choice of paramagnetic salt and its concentrations and by the strength and gradient in the magnetic field. Including paramagnetic salts (e.g., MnSO4 or MnCl2) in AMPS, and placing them in a magnetic field gradient, enables their use as media for MagLev. The potential to create large steps in density with AMPS allows separations of objects across a range of densities. The gradients produced by MagLev provide resolution over a continuous range of densities. By combining these approaches, mixtures of objects with large differences in density can be separated and analyzed simultaneously. Using MagLev to add an effective gradient in density also enables tuning the range of densities captured at an interface of an AMPS by simply changing the position of the container in the magnetic field. Further, by creating AMPS in which phases have different concentrations of paramagnetic ions, the phases can provide different resolutions in density. These results suggest that combining steps in density with gradients in density can enable new classes of separations based on density. PMID:25978093

  8. Computational methods to obtain time optimal jet engine control

    NASA Technical Reports Server (NTRS)

    Basso, R. J.; Leake, R. J.

    1976-01-01

    Dynamic Programming and the Fletcher-Reeves Conjugate Gradient Method are two existing methods which can be applied to solve a general class of unconstrained fixed time, free right end optimal control problems. New techniques are developed to adapt these methods to solve a time optimal control problem with state variable and control constraints. Specifically, they are applied to compute a time optimal control for a jet engine control problem.

  9. Conjugated polymer nanoparticles

    NASA Astrophysics Data System (ADS)

    Tuncel, Dönüs; Demir, Hilmi Volkan

    2010-04-01

    Conjugated polymer nanoparticles are highly versatile nano-structured materials that can potentially find applications in various areas such as optoelectronics, photonics, bio-imaging, bio-sensing and nanomedicine. Their straightforward synthesis in desired sizes and properties, biocompatibility and non-toxicity make these materials highly attractive for the aforementioned applications. This feature article reviews the recent developments in the synthesis, characterization, properties and application of these exciting nanostructured materials.

  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. PMID:26304351

  11. 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.

  12. Anti- (conjugate) linearity

    NASA Astrophysics Data System (ADS)

    Uhlmann, Armin

    2016-03-01

    This is an introduction to antilinear operators. In following Wigner the terminus antilinear is used as it is standard in Physics. Mathematicians prefer to say conjugate linear. By restricting to finite-dimensional complex-linear spaces, the exposition becomes elementary in the functional analytic sense. Nevertheless it shows the amazing differences to the linear case. Basics of antilinearity is explained in sects. 2, 3, 4, 7 and in sect. 1.2: Spectrum, canonical Hermitian form, antilinear rank one and two operators, the Hermitian adjoint, classification of antilinear normal operators, (skew) conjugations, involutions, and acq-lines, the antilinear counterparts of 1-parameter operator groups. Applications include the representation of the Lagrangian Grassmannian by conjugations, its covering by acq-lines. As well as results on equivalence relations. After remembering elementary Tomita-Takesaki theory, antilinear maps, associated to a vector of a two-partite quantum system, are defined. By allowing to write modular objects as twisted products of pairs of them, they open some new ways to express EPR and teleportation tasks. The appendix presents a look onto the rich structure of antilinear operator spaces.

  13. Conjugate flow action functionals

    SciTech Connect

    Venturi, Daniele

    2013-11-15

    We present a new general framework to construct an action functional for a non-potential field theory. The key idea relies on representing the governing equations relative to a diffeomorphic flow of curvilinear coordinates which is assumed to be functionally dependent on the solution field. Such flow, which will be called the conjugate flow, evolves in space and time similarly to a physical fluid flow of classical mechanics and it can be selected in order to symmetrize the Gâteaux derivative of the field equations with respect to suitable local bilinear forms. This is equivalent to requiring that the governing equations of the field theory can be derived from a principle of stationary action on a Lie group manifold. By using a general operator framework, we obtain the determining equations of such manifold and the corresponding conjugate flow action functional. In particular, we study scalar and vector field theories governed by second-order nonlinear partial differential equations. The identification of transformation groups leaving the conjugate flow action functional invariant could lead to the discovery of new conservation laws in fluid dynamics and other disciplines.

  14. Gradient echo MRI

    PubMed Central

    Copenhaver, B R.; Shin, J; Warach, S; Butman, J A.; Saver, J L.; Kidwell, C S.

    2009-01-01

    Background: Recent studies have demonstrated that gradient echo (GRE) MRI sequences are as accurate as CT for the detection of intracerebral hemorrhage (ICH) in the context of acute stroke. However, many physicians who currently read acute stroke imaging studies may be unfamiliar with interpretation of GRE images. Methods: An NIH Web-based training program was developed including a pretest, tutorial, and posttest. Physicians involved in the care of acute stroke patients were encouraged to participate. The tutorial covered acute, chronic, and mimic hemorrhages as they appear on CT, diffusion-weighted imaging, and GRE sequences. Ability of users to identify ICH presence, type, and age on GRE was compared from the pretest to posttest timepoint. Results: A total of 104 users completed the tutorial. Specialties represented included general radiology (42%), general neurology (16%), neuroradiology (15%), stroke neurology (14%), emergency medicine (1%), and other (12%). Median overall score improved pretest to posttest from 66.7% to 83.3%, p < 0.001. Improvement by category was as follows: acute ICH, 66.7%–100%, p < 0.001; chronic ICH, 33.3%–66.7%, p < 0.001; ICH negatives/mimics, 100%–100%, p = 0.787. Sensitivity for identification of acute hemorrhage improved from 68.2% to 96.4%. Conclusions: Physicians involved in acute stroke care achieved significant improvement in gradient echo (GRE) hemorrhage interpretation after completing the NIH GRE MRI tutorial. This indicates that a Web-based tutorial may be a viable option for the widespread education of physicians to achieve an acceptable level of diagnostic accuracy at reading GRE MRI, thus enabling confident acute stroke treatment decisions. GLOSSARY AHA/ASA = American Heart Association/American Stroke Association; CME = continuing medical education; DWI = diffusion-weighted imaging; GRE = gradient echo; ICH = intracerebral hemorrhage; tPA = tissue plasminogen activator. PMID:19414724

  15. Comparative assessment of next-generation sequencing, denaturing gradient gel electrophoresis, clonal restriction fragment length polymorphism and cloning-sequencing as methods for characterizing commercial microbial consortia.

    PubMed

    Samarajeewa, A D; Hammad, A; Masson, L; Khan, I U H; Scroggins, R; Beaudette, L A

    2015-01-01

    Characterization of commercial microbial consortia products for human and environmental health risk assessment is a major challenge for regulatory agencies. As a means to develop an approach to assess the potential environmental risk of these products, research was conducted to compare four genomics methods for characterizing bacterial communities; (i) Denaturing Gradient Gel Electrophoresis (DGGE), (ii) Clonal-Restriction Fragment Length Polymorphism (C/RFLP), (iii) partial 16S rDNA amplification, cloning followed by Sanger sequencing (PRACS) and (iv) Next-Generation Sequencing (NGS) based on Ion Torrent technology. A commercially available microbial consortium, marketed as a remediation agent for degrading petroleum hydrocarbon contamination in soil and water, was assessed. The bacterial composition of the commercial microbial product was characterized using the above four methods. PCR amplification of 16S rDNA was performed targeting the variable region V6 for DGGE, C/RFLP and PRACS and V5 for Ion Torrent sequencing. Ion Torrent technology was shown to be a promising tool for initial screening by detecting the majority of bacteria in the consortium that were also detected by DGGE, C/RFLP and PRACS. Additionally, Ion Torrent sequencing detected some of the bacteria that were claimed to be in the product, while three other methods failed to detect these specific bacteria. However, the relative proportions of the microbial composition detected by Ion Torrent were found to be different from DGGE, C/RFLP and PRACS, which gave comparable results across these three methods. The discrepancy of the Ion Torrent results may be due to the short read length generated by this technique and the targeting of different variable regions on the 16S rRNA gene used in this study. Arcobacter spp. a potential pathogenic bacteria was detected in the product by all methods, which was further confirmed using genus and species-specific PCR, RFLP and DNA-based sequence analyses. However

  16. Iterative methods for the solution of very large complex symmetric linear systems of equations in electrodynamics

    SciTech Connect

    Clemens, M.; Weiland, T.

    1996-12-31

    In the field of computational electrodynamics the discretization of Maxwell`s equations using the Finite Integration Theory (FIT) yields very large, sparse, complex symmetric linear systems of equations. For this class of complex non-Hermitian systems a number of conjugate gradient-type algorithms is considered. The complex version of the biconjugate gradient (BiCG) method by Jacobs can be extended to a whole class of methods for complex-symmetric algorithms SCBiCG(T, n), which only require one matrix vector multiplication per iteration step. In this class the well-known conjugate orthogonal conjugate gradient (COCG) method for complex-symmetric systems corresponds to the case n = 0. The case n = 1 yields the BiCGCR method which corresponds to the conjugate residual algorithm for the real-valued case. These methods in combination with a minimal residual smoothing process are applied separately to practical 3D electro-quasistatical and eddy-current problems in electrodynamics. The practical performance of the SCBiCG methods is compared with other methods such as QMR and TFQMR.

  17. Product development studies of amino acid conjugate of Aceclofenac.

    PubMed

    Singh, Ajay Pal; Ramadan, Wafa Mossa; Dahiya, Rajiv; Sarpal, A S; Pathak, Kamla

    2009-04-01

    The prodrugs designed by classical approach increase lipophilicity of the drug, which decreases the water solubility thus decreasing the concentration gradient, which controls drug absorption. To overcome the limitations of traditional prodrug approach, water soluble prodrugs can be designed by adding selected amino acid to the drug moiety that are the substrates for the enzyme located at the intestinal brush border thus overcoming pharmaceutical problem without compromising bioavailability. ACaa (Amino acid conjugate of Aceclofenac) was synthesized by conjugation with l-phenylalanine by conventional coupling method using N, N-dicyclohexylcarbodiimide and ACaa was characterized by melting point, TLC, photomicrograph, UV, FT-IR, FT-NMR, MS-FAB, XRD and DSC. As a part of product development study ACaa was subjected to studies like In-vivo in albino rats and in-vitro like ACaa reversion to AC (Aceclofenac) in aqueous buffers of pH 1.21, 2.38. 3.10, 6.22 and 7.41, at a constant concentration (0.05M), ionic strength (micro = 0.5) and at a temperature of 37 degrees C +/- 0.5 degrees C, ACaa showed negligible reversion (2.15 %) up to 24 hrs study at acidic pH thus suggesting stability in acidic environment of stomach, the rate of reversion increased as pH of medium increased. pH- partition profile, pH- solubility profile and micromeritic studies were also carried out in comparison to pure drug. The solubility and lipophilicity of ACaa exhibited higher values at all pH range when compared to AC. The micromeritic properties also evaluated in terms of particle shape and size, IQCS and kurtosis. Resulting IQCS value approached zero thus suggesting reducing in the degree of skewness.

  18. A fast method for video deblurring based on a combination of gradient methods and denoising algorithms in Matlab and C environments

    NASA Astrophysics Data System (ADS)

    Mirzadeh, Zeynab; Mehri, Razieh; Rabbani, Hossein

    2010-01-01

    In this paper the degraded video with blur and noise is enhanced by using an algorithm based on an iterative procedure. In this algorithm at first we estimate the clean data and blur function using Newton optimization method and then the estimation procedure is improved using appropriate denoising methods. These noise reduction techniques are based on local statistics of clean data and blur function. For estimated blur function we use LPA-ICI (local polynomial approximation - intersection of confidence intervals) method that use an anisotropic window around each point and obtain the enhanced data employing Wiener filter in this local window. Similarly, to improvement the quality of estimated clean video, at first we transform the data to wavelet transform domain and then improve our estimation using maximum a posterior (MAP) estimator and local Laplace prior. This procedure (initial estimation and improvement of estimation by denoising) is iterated and finally the clean video is obtained. The implementation of this algorithm is slow in MATLAB1 environment and so it is not suitable for online applications. However, MATLAB has the capability of running functions written in C. The files which hold the source for these functions are called MEX-Files. The MEX functions allow system-specific APIs to be called to extend MATLAB's abilities. So, in this paper to speed up our algorithm, the written code in MATLAB is sectioned and the elapsed time for each section is measured and slow sections (that use 60% of complete running time) are selected. Then these slow sections are translated to C++ and linked to MATLAB. In fact, the high loads of information in images and processed data in the "for" loops of relevant code, makes MATLAB an unsuitable candidate for writing such programs. The written code for our video deblurring algorithm in MATLAB contains eight "for" loops. These eighth "for" utilize 60% of the total execution time of the entire program and so the runtime should be

  19. Predicting tree species presence and basal area in Utah: A comparison of stochastic gradient boosting, generalized additive models, and tree-based methods

    USGS Publications Warehouse

    Moisen, G.G.; Freeman, E.A.; Blackard, J.A.; Frescino, T.S.; Zimmermann, N.E.; Edwards, T.C.

    2006-01-01

    Many efforts are underway to produce broad-scale forest attribute maps by modelling forest class and structure variables collected in forest inventories as functions of satellite-based and biophysical information. Typically, variants of classification and regression trees implemented in Rulequest's?? See5 and Cubist (for binary and continuous responses, respectively) are the tools of choice in many of these applications. These tools are widely used in large remote sensing applications, but are not easily interpretable, do not have ties with survey estimation methods, and use proprietary unpublished algorithms. Consequently, three alternative modelling techniques were compared for mapping presence and basal area of 13 species located in the mountain ranges of Utah, USA. The modelling techniques compared included the widely used See5/Cubist, generalized additive models (GAMs), and stochastic gradient boosting (SGB). Model performance was evaluated using independent test data sets. Evaluation criteria for mapping species presence included specificity, sensitivity, Kappa, and area under the curve (AUC). Evaluation criteria for the continuous basal area variables included correlation and relative mean squared error. For predicting species presence (setting thresholds to maximize Kappa), SGB had higher values for the majority of the species for specificity and Kappa, while GAMs had higher values for the majority of the species for sensitivity. In evaluating resultant AUC values, GAM and/or SGB models had significantly better results than the See5 models where significant differences could be detected between models. For nine out of 13 species, basal area prediction results for all modelling techniques were poor (correlations less than 0.5 and relative mean squared errors greater than 0.8), but SGB provided the most stable predictions in these instances. SGB and Cubist performed equally well for modelling basal area for three species with moderate prediction success

  20. Effect of drying methods on the free and conjugated bufadienolide content in toad venom determined by ultra-performance liquid chromatography-triple quadrupole mass spectrometry coupled with a pattern recognition approach.

    PubMed

    Zhou, Jing; Gong, Yan; Ma, Hongyue; Wang, Honglan; Qian, Dawei; Wen, Hongmei; Liu, Rui; Duan, Jinao; Wu, Qinan

    2015-10-10

    Drying is a useful technique for extending the shelf-life of biological products and enabling long-term storage; however, improper drying can reduce the chemical quality of the products. In this study, we used ultra-performance liquid chromatography-triple quadrupole/mass spectrometry (LC-MS/MS) and multivariate statistical analysis to investigate the effects of four drying methods (V: vacuum-drying at 60°C, F: freeze-drying, H: air-drying at 60°C and R: air-drying at room temperature) on the levels of 36 bufadienolides in toad venom. Vacuum-drying at 60°C produced the highest quality dried toad venom in terms of total bufadienolide content, whereas traditional air-drying at room temperature (RT) to dehydrate the toad venom led to a dramatic loss in free and conjugated bufadienolides, reaching up to 60% and 70%, respectively. Assaying for free bufadienolides ranked the drying methods as V≈F>H>R, whereas assaying for conjugated bufadienolides slightly changed the order to V>F≈H>R. Furthermore, we identified 21 bufadienolides as biomarkers responsible for the decline in the quality of dried toad venom, whose loss varied from 1.5-fold to 100-fold. Of these biomarkers, group I bufadienolides that contain 16-OAc (e.g., cinobufagin and its hydroxyl or arginine ester derivatives) were characteristic components and were reduced to trace levels (loss of more than 10-fold) following traditional air-drying at RT. This might be attributed to the fact that most enzyme-sensitive bufadienolides were biotransformed or degraded at room temperature but were retained using other drying methods.

  1. Recent Advances in Site Specific Conjugations of Antibody Drug Conjugates (ADCs).

    PubMed

    Gao, Wenlong; Zhang, Jingxin; Xiang, Jun; Zhang, Lei; Wu, Chengbin; Dhal, Pradeep K; Chen, Bo

    2016-01-01

    Antibody-drug conjugates (ADCs) take the advantage of antigen specificity of monoclonal antibodies to deliver highly potent cytotoxic drugs selectively to antigen-expressing tumor cells. The recent approval of Adcetris™ and Kadcyla™ as well as emerging data from numerous ongoing clinical trials underscore the role of ADCs as a new therapeutic option for cancer patients. However, conventional conjugation methods generally result in a heterogeneous mixture of ADCs, which can result in significant therapeutic liabilities and can lead to complicated manufacturing processes. The increased understanding from the clinical investigation of current ADCs and site-specific bioconjugation technologies has enabled scientists to accelerate the discovery and development of the next generation ADCs with defined and homogeneous composition. The present manuscript reviews the recent advances and trends in the research and development of novel ADCs obtained by site-specific conjugation method. PMID:27174056

  2. Optimization of the diffusive gradients in thin films (DGT) method for simultaneous assay of potassium and plant-available phosphorus in soils.

    PubMed

    Zhang, Yulin; Mason, Sean; McNeill, Ann; McLaughlin, Michael J

    2013-09-15

    Potassium (K) and phosphorus (P) are two important macronutrients for crops, and are usually applied to soils as granular fertilizer before seeding. Therefore, accurate soil tests prior to planting to predict crop response to fertilizers are important in optimizing crop yields. Traditional methods used for testing both available K and P in soils, which are based on chemical extraction procedures, are to be soil-type dependent, and the predictive relationships across a broad range of soils are generally poor. The diffusive gradients in thin films (DGT) technique, based on diffusion theory, is extensively used to measure the diffusive supply of trace elements, metals and some nutrients in soils and water. When DGT is used to assess plant-available P in soils, a good relationship is found between crop response to P fertilizer and concentrations of P in soil measured by DGT, and therefore the DGT method provides a more precise recommendation of P fertilizer requirements. Adaptation of the DGT method to measure plant-available K in soils has already been attempted [1], but limitations were reported due to the non-uniform size of the resin gel, decreased K binding rate of the gel at long deployment times and a limited ability to measure a wide range of K concentrations. To eliminate these problems, a new resin gel has been developed by combining Amberlite and ferrihydrite. This mixed Amberlite and ferrihydrite (MAF) gel has improved properties in terms of handling and even distribution of Amberlite in the gel. The elution efficiencies of the MAF gel for K and P were 90% and 96%, respectively. The diffusion coefficient of K through the diffusive gel was 1.30 × 10(-5)cm(2)s(-1) at 22 ± 1°C and was stable through time. Since ferrihydrite is already used in DGT P testing, the ability of the MAF gel to assess available P simultaneously was also assessed. The MAF gel performed the same as the traditional ferrihydrite gel for available P assessment in a wide variety of

  3. Conjugated Polymer Surfaces and Interfaces

    NASA Astrophysics Data System (ADS)

    Salaneck, W. R.; Stafstrom, S.; Brédas, J. L.

    2003-10-01

    The authors illustrate the basic physics and materials science of conjugated polymers and their interfaces, particularly, but not exclusively, as they are applied to polymer-based light emitting diodes. The approach is to describe the basic physical and associated chemical principles that apply to these materials, which in many instances are different from those that apply to their inorganic counterparts. The main aim of the authors is to highlight specific issues and properties of polymer surfaces and interfaces that are relevant in the context of the emerging field of polymer-based electronics in general, and polymer-based light emitting diodes in particular. Both theoretical and experimental methods used in the study of these systems are discussed. This book will be of interest to graduate students and research workers in departments of physics, chemistry, electrical engineering and materials sciences studying polymer surfaces and interfaces and their application in polymer-based electronics.

  4. Impact of conjugation chemistry on the immunogenicity of S. Typhimurium conjugate vaccines.

    PubMed

    Stefanetti, G; Rondini, S; Lanzilao, L; Saul, A; MacLennan, C A; Micoli, F

    2014-10-21

    Salmonella Typhimurium is major cause of invasive nontyphoidal Salmonella disease in Africa. Conjugation of S. Typhimurium O-antigen to an appropriate carrier protein constitutes a possible strategy for the development of a vaccine against this disease, for which no vaccines are currently available. The conjugation chemistry used is one of the parameters that can affect the immunogenicity of glycoconjugate vaccines. Herein different glycoconjugates were synthesized to investigate the impact of this variable on the immunogenicity of S. Typhimurium conjugate vaccines in mice, all with CRM₁₉₇ as carrier protein. Random derivatization along the O-antigen chain was compared with site-directed activation of the terminal KDO sugar residue of the core oligosaccharide. In particular, two different random approaches were used, based on the oxidation of the polysaccharide, which differently impact the structure and conformation of the O-antigen chain. For the selective conjugation methods, linkers of two different lengths were compared. When tested in mice, all conjugates induced anti-O-antigen IgG antibodies with serum bactericidal activity. Similar anti-O-antigen antibody levels were elicited independent of the chemistry used and a higher degree of saccharide derivatization did not impact negatively on the anti-O-antigen IgG response. Bactericidal activity of serum antibodies induced by selective conjugates was similar independent of the length of the spacer used. Random conjugates elicited antibodies with greater bactericidal activity than selective ones, and an inverse correlation was found between degree of O-antigen modification and antibody functional activity.

  5. Impact of conjugation chemistry on the immunogenicity of S. Typhimurium conjugate vaccines.

    PubMed

    Stefanetti, G; Rondini, S; Lanzilao, L; Saul, A; MacLennan, C A; Micoli, F

    2014-10-21

    Salmonella Typhimurium is major cause of invasive nontyphoidal Salmonella disease in Africa. Conjugation of S. Typhimurium O-antigen to an appropriate carrier protein constitutes a possible strategy for the development of a vaccine against this disease, for which no vaccines are currently available. The conjugation chemistry used is one of the parameters that can affect the immunogenicity of glycoconjugate vaccines. Herein different glycoconjugates were synthesized to investigate the impact of this variable on the immunogenicity of S. Typhimurium conjugate vaccines in mice, all with CRM₁₉₇ as carrier protein. Random derivatization along the O-antigen chain was compared with site-directed activation of the terminal KDO sugar residue of the core oligosaccharide. In particular, two different random approaches were used, based on the oxidation of the polysaccharide, which differently impact the structure and conformation of the O-antigen chain. For the selective conjugation methods, linkers of two different lengths were compared. When tested in mice, all conjugates induced anti-O-antigen IgG antibodies with serum bactericidal activity. Similar anti-O-antigen antibody levels were elicited independent of the chemistry used and a higher degree of saccharide derivatization did not impact negatively on the anti-O-antigen IgG response. Bactericidal activity of serum antibodies induced by selective conjugates was similar independent of the length of the spacer used. Random conjugates elicited antibodies with greater bactericidal activity than selective ones, and an inverse correlation was found between degree of O-antigen modification and antibody functional activity. PMID:25192974

  6. Templating Surfaces with Gradient Assemblies

    SciTech Connect

    Genzer,J.

    2005-01-01

    One of the most versatile and widely used methods of forming surfaces with position-dependent wettability is that conceived by Chaudhury and Whitesides more than a decade ago. In this paper we review several projects that utilize this gradient-forming methodology for: controlled of deposition of self-assembled monolayers on surfaces, generating arrays of nanoparticles with number density gradients, probing the mushroom-to-brush transition in surface-anchored polymers, and controlling the speed of moving liquid droplets on surfaces.

  7. Rapid Gradient-Echo Imaging

    PubMed Central

    Hargreaves, Brian

    2012-01-01

    Gradient echo sequences are widely used in magnetic resonance imaging (MRI) for numerous applications ranging from angiography to perfusion to functional MRI. Compared with spin-echo techniques, the very short repetition times of gradient-echo methods enable very rapid 2D and 3D imaging, but also lead to complicated “steady states.” Signal and contrast behavior can be described graphically and mathematically, and depends strongly on the type of spoiling: fully balanced (no spoiling), gradient spoiling, or RF-spoiling. These spoiling options trade off between high signal and pure T1 contrast while the flip angle also affects image contrast in all cases, both of which can be demonstrated theoretically and in image examples. As with spin-echo sequences, magnetization preparation can be added to gradient-echo sequences to alter image contrast. Gradient echo sequences are widely used for numerous applications such as 3D perfusion imaging, functional MRI, cardiac imaging and MR angiography. PMID:23097185

  8. Novel speciation method based on Diffusive Gradients in Thin Films for in situ measurement of uranium in the vicinity of the former uranium mining sites.

    PubMed

    Drozdzak, Jagoda; Leermakers, Martine; Gao, Yue; Phrommavanh, Vannapha; Descostes, Michael

    2016-07-01

    The Diffusive Gradients in Thin Films (DGT) technique using PIWBA resin (The Dow Chemical Company) was developed and validated for the measurement of uranium (U) concentration in natural and uranium mining influenced waters. The U uptake on the PIWBA resin gel was 97.3 ± 0.4% (batch method; Vsol = 5 mL; [U] = 20 μg L(-1); 0.01 M NaNO3; pH = 7.0 ± 0.2). The optimal eluent was found to be HNO3conc/70 °C with an elution efficiency of 88.9 ± 1.4%. The laboratory DGT investigation demonstrated that the PIWBA resin gel exhibits a very good performance across a wide range of pH (3-9) and ionic strength (0.001-0.7 M NaNO3) at different time intervals. Neither effect of PO4(3-) (up to 1.72 × 10(-4) M), nor of HCO3(-) (up to 8.20 × 10(-3) M) on the quantitative measurement of uranium by DGT-PIWBA method were observed. Only at very high Ca(2+) (2.66 × 10(-4) M), and SO4(2-) (5.55 × 10(-4) M) concentration, the U uptake on DGT-PIWBA was appreciably lessened. In-situ DGT field evaluation was carried out in the vicinity of three former uranium mining sites in France (Loire-Atlantique and Herault departments), which employ different water treatment technologies and have different natural geochemical characteristics. There was a similar or inferior U uptake on DGT-Chelex(®)-100 in comparison with the U accumulation on a DGT-PIWBA sampler. Most likely, the performance of Chelex(®)-100 was negatively affected by a highly complex matrix of mining waters. The high concentration and identity of co-accumulating analytes, typical for the mining environment, did not have a substantial impact on the quantitative uptake of labile U species on DGT- PIWBA. The use of the polyphenol impregnated anion exchange resin leads to a significant advancement in the application and development of the DGT technique for determination of U in the vicinity of the former uranium mining sites. PMID:27070846

  9. Novel speciation method based on Diffusive Gradients in Thin Films for in situ measurement of uranium in the vicinity of the former uranium mining sites.

    PubMed

    Drozdzak, Jagoda; Leermakers, Martine; Gao, Yue; Phrommavanh, Vannapha; Descostes, Michael

    2016-07-01

    The Diffusive Gradients in Thin Films (DGT) technique using PIWBA resin (The Dow Chemical Company) was developed and validated for the measurement of uranium (U) concentration in natural and uranium mining influenced waters. The U uptake on the PIWBA resin gel was 97.3 ± 0.4% (batch method; Vsol = 5 mL; [U] = 20 μg L(-1); 0.01 M NaNO3; pH = 7.0 ± 0.2). The optimal eluent was found to be HNO3conc/70 °C with an elution efficiency of 88.9 ± 1.4%. The laboratory DGT investigation demonstrated that the PIWBA resin gel exhibits a very good performance across a wide range of pH (3-9) and ionic strength (0.001-0.7 M NaNO3) at different time intervals. Neither effect of PO4(3-) (up to 1.72 × 10(-4) M), nor of HCO3(-) (up to 8.20 × 10(-3) M) on the quantitative measurement of uranium by DGT-PIWBA method were observed. Only at very high Ca(2+) (2.66 × 10(-4) M), and SO4(2-) (5.55 × 10(-4) M) concentration, the U uptake on DGT-PIWBA was appreciably lessened. In-situ DGT field evaluation was carried out in the vicinity of three former uranium mining sites in France (Loire-Atlantique and Herault departments), which employ different water treatment technologies and have different natural geochemical characteristics. There was a similar or inferior U uptake on DGT-Chelex(®)-100 in comparison with the U accumulation on a DGT-PIWBA sampler. Most likely, the performance of Chelex(®)-100 was negatively affected by a highly complex matrix of mining waters. The high concentration and identity of co-accumulating analytes, typical for the mining environment, did not have a substantial impact on the quantitative uptake of labile U species on DGT- PIWBA. The use of the polyphenol impregnated anion exchange resin leads to a significant advancement in the application and development of the DGT technique for determination of U in the vicinity of the former uranium mining sites.

  10. Predicting the optical gap of conjugated systems

    NASA Astrophysics Data System (ADS)

    Botelho, Andre Leitao

    The adapted Su-Schrieffer-Heeger model is developed in this work as a tool for in silico prediction of the optical gap of pi-conjugated systems for photovoltaic applications. Full transferability of the model ensures reliable predictive power - excellent agreement with 180 independent experimental data points covering virtually all existing conjugated system types with an accuracy exceeding the time-dependent density functional theory, one of the most accurate first-principles methods. Insights on the structure-property relation of conjugated systems obtained from the model lead to guiding rules for optical gap design: 1) fusing aromatic rings parallel to the conjugated path does not significantly lower the optical gap, 2) fusing rings perpendicularly lowers the optical gap of the monomer, but has a reduced benefit from polymerization, and 3) copolymers take advantage of the lower optical gap of perpendicular fused rings and benefit from further optical gap reduction through added parallel fused rings as electronic communicators. A copolymer of parallel and perpendicular benzodithiophenes, differing only in sulfur atom locations, is proposed as a candidate to achieve the optimal 1.2 eV donor optical gap for organic photovoltaics. For small-molecule organic photovoltaics, substituting the end pairs of carbon atoms on pentacene with sulfur atoms is predicted to lower the optical gap from 1.8 eV to 1.1 eV. Furthermore, the model offers an improvement of orders of magnitude in the computational efficiency over commonly used first-principles tools.

  11. Combinational concentration gradient confinement through stagnation flow.

    PubMed

    Alicia, Toh G G; Yang, Chun; Wang, Zhiping; Nguyen, Nam-Trung

    2016-01-21

    Concentration gradient generation in microfluidics is typically constrained by two conflicting mass transport requirements: short characteristic times (τ) for precise temporal control of concentration gradients but at the expense of high flow rates and hence, high flow shear stresses (σ). To decouple the limitations from these parameters, here we propose the use of stagnation flows to confine concentration gradients within large velocity gradients that surround the stagnation point. We developed a modified cross-slot (MCS) device capable of feeding binary and combinational concentration sources in stagnation flows. We show that across the velocity well, source-sink pairs can form permanent concentration gradients. As source-sink concentration pairs are continuously supplied to the MCS, a permanently stable concentration gradient can be generated. Tuning the flow rates directly controls the velocity gradients, and hence the stagnation point location, allowing the confined concentration gradient to be focused. In addition, the flow rate ratio within the MCS rapidly controls (τ ∼ 50 ms) the location of the stagnation point and the confined combinational concentration gradients at low flow shear (0.2 Pa < σ < 2.9 Pa). The MCS device described in this study establishes the method for using stagnation flows to rapidly generate and position low shear combinational concentration gradients for shear sensitive biological assays. PMID:26671507

  12. Combinational concentration gradient confinement through stagnation flow.

    PubMed

    Alicia, Toh G G; Yang, Chun; Wang, Zhiping; Nguyen, Nam-Trung

    2016-01-21

    Concentration gradient generation in microfluidics is typically constrained by two conflicting mass transport requirements: short characteristic times (τ) for precise temporal control of concentration gradients but at the expense of high flow rates and hence, high flow shear stresses (σ). To decouple the limitations from these parameters, here we propose the use of stagnation flows to confine concentration gradients within large velocity gradients that surround the stagnation point. We developed a modified cross-slot (MCS) device capable of feeding binary and combinational concentration sources in stagnation flows. We show that across the velocity well, source-sink pairs can form permanent concentration gradients. As source-sink concentration pairs are continuously supplied to the MCS, a permanently stable concentration gradient can be generated. Tuning the flow rates directly controls the velocity gradients, and hence the stagnation point location, allowing the confined concentration gradient to be focused. In addition, the flow rate ratio within the MCS rapidly controls (τ ∼ 50 ms) the location of the stagnation point and the confined combinational concentration gradients at low flow shear (0.2 Pa < σ < 2.9 Pa). The MCS device described in this study establishes the method for using stagnation flows to rapidly generate and position low shear combinational concentration gradients for shear sensitive biological assays.

  13. Performance of Neural Networks Methods In Intrusion Detection

    SciTech Connect

    Dao, V N; Vemuri, R

    2001-07-09

    By accurately profiling the users via their unique attributes, it is possible to view the intrusion detection problem as a classification of authorized users and intruders. This paper demonstrates that artificial neural network (ANN) techniques can be used to solve this classification problem. Furthermore, the paper compares the performance of three neural networks methods in classifying authorized users and intruders using synthetically generated data. The three methods are the gradient descent back propagation (BP) with momentum, the conjugate gradient BP, and the quasi-Newton BP.

  14. Continuous spray forming of functionally gradient materials

    SciTech Connect

    McKechnie, T.N.; Richardson, E.H.; Watson, R.D.

    1995-12-31

    Researchers at Plasma Processes Inc. have produced a Functional Gradient Material (FGM) through advanced vacuum plasma spray processing for high heat flux applications. Outlined in this paper are the manufacturing methods used to develop a four component functional gradient material of copper, tungsten, boron, and boron nitride. The FGM was formed with continuous gradients and integral cooling channels eliminating bondlines and providing direct heat transfer from the high temperature exposed surface to a cooling medium. Metallurgical and X-ray diffraction analyses of the materials formed through innovative VPS processing are also presented. Applications for this functional gradient structural material range from fusion reactor plasma facing components to missile nose cones to boilers.

  15. Improved parameterization of dust emission (PM10) fluxes by the gradient method using the Naiman tower data at the Horqin desert in China.

    PubMed

    Park, Moon-Soo; Park, Soon-Ung; Chun, Youngsin

    2011-12-15

    Dust emission/deposition flux has been estimated using the gradient method with the two-level (3 and 15m high) measured PM(10) concentrations and the sonic anemometer measured momentum and kinematic heat fluxes at 8m high from a 20-m monitoring tower located at Naiman (Horqin desert) in the Asian dust source region in China for the winter of November 2007 to March 2008. The time series of measured PM(10) concentration at 3m high is used to identify the dust event and the non-dust event periods. It is found that the dust emission/deposition flux (F(C)) shows a significant diurnal variation with the maximum emission flux of 5.8 kg km(-2)h(-1) at noon and the minimum of -1.6 kg km(-2)h(-1) in the afternoon for the non-dust event cases. Whereas for the dust event cases, the dust emission flux is found to occur when the prevailing winds are westerlies to northerlies with the maximum flux of 1275 kg km(-2)d(-1), while the maximum dust deposition flux of 148 kg km(-2)d(-1) occurs with the prevailing winds of southerlies to easterlies without any diurnal variation. The optimal regression equation between F(C) and the friction velocity (u(*)) for the dust emission cases is found to be F(C)=9.55 u(*)(3.13) with the R(2) value of 0.73. However, this regression equation can be improved by taking into account the convective velocity (w(*)). The resulting optimal regression equation is found to be F(C)=9.3(u(*)-0.1w(*))(3.19) for the stable stratification (w(*)<0) with the R(2) value of 0.77 and F(C)=10.5(u(*)+0.34w(*))(4.11) for the unstable stratification (w(*)>0) with the R(2) value of 0.78, suggesting the importance of the convective velocity on the dust emission flux.

  16. Derivatized gold clusters and antibody-gold cluster conjugates

    DOEpatents

    Hainfeld, J.F.; Furuya, F.R.

    1994-11-01

    Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab')[sub 2] fragments are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy. 7 figs.

  17. Derivatized gold clusters and antibody-gold cluster conjugates

    DOEpatents

    Hainfeld, James F.; Furuya, Frederic R.

    1994-11-01

    Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab').sub.2 fragments thereof are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy.

  18. Lipid-peptide-polymer conjugates and nanoparticles thereof

    SciTech Connect

    Xu, Ting; Dong, He; Shu, Jessica

    2015-06-02

    The present invention provides a conjugate having a peptide with from about 10 to about 100 amino acids, wherein the peptide adopts a helical structure. The conjugate also includes a first polymer covalently linked to the peptide, and a hydrophobic moiety covalently linked to the N-terminus of the peptide, wherein the hydrophobic moiety comprises a second polymer or a lipid moiety. The present invention also provides helix bundles form by self-assembling the conjugates, and particles formed by self-assembling the helix bundles. Methods of preparing the helix bundles and particles are also provided.

  19. Structural characterization of antibody drug conjugate by a combination of intact, middle-up and bottom-up techniques using sheathless capillary electrophoresis - Tandem mass spectrometry as nanoESI infusion platform and separation method.

    PubMed

    Said, Nassur; Gahoual, Rabah; Kuhn, Lauriane; Beck, Alain; François, Yannis-Nicolas; Leize-Wagner, Emmanuelle

    2016-04-28

    Antibody-drug conjugates (ADCs) represent a fast growing class of biotherapeutic products. Their production leads to a distribution of species exhibiting different number of conjugated drugs overlaying the inherent complexity resulting from the monoclonal antibody format, such as glycoforms. ADCs require an additional level of characterization compared to first generation of biotherapeutics obtained through multiple analytical techniques for complete structure assessment. We report the development of complementary approaches implementing sheathless capillary electrophoresis-mass spectrometry (sheathless CE-MS) to characterize the different aspects defining the structure of brentuximab vedotin. Native MS using sheathless CE-MS instrument as a nanoESI infusion platform enabled accurate mass measurements and estimation of the average drug to antibody ratio alongside to drug load distribution. Middle-up analysis performed after limited IdeS proteolysis allowed to study independently the light chain, Fab and F(ab')2 subunits incorporating 1, 0 to 4 and 0 to 8 payloads respectively. Finally, a CZE-ESI-MS/MS methodology was developed in order to be compatible with hydrophobic drug composing ADCs. From a single injection, complete sequence coverage could be achieved. Using the same dataset, glycosylation and drug-loaded peptides could be simultaneously identified revealing robust information regarding their respective localization and abundance. Drug-loaded peptide fragmentation mass spectra study demonstrated drug specific fragments reinforcing identification confidence, undescribed so far. Results reveal the method ability to characterize ADCs primary structure in a comprehensive manner while reducing tremendously the number of experiments required. Data generated showed that sheathless CZE-ESI-MS/MS characteristics position the methodology developed as a relevant alternative for comprehensive multilevel characterization of these complex biomolecules. PMID:27046210

  20. On the design of parallel numerical methods in message passing and shared memory environments

    SciTech Connect

    Saad, Y.

    1987-02-01

    This paper presents a comparative view of the methodologies used in parallel methods for scientific computing. Our goal is to put in contrast the approaches taken when developing scientific software for two broad classes of parallel machines namely shared memory machines and distributed memory machines. We will illustrate our discussion with two specific algorithms namely the Alternating Directions Implicit method and the Preconditioned Conjugate Gradient method.

  1. Nanostructured conjugated polymers in chemical sensors: synthesis, properties and applications.

    PubMed

    Correa, D S; Medeiros, E S; Oliveira, J E; Paterno, L G; Mattoso, Luiz C

    2014-09-01

    Conjugated polymers are organic materials endowed with a π-electron conjugation along the polymer backbone that present appealing electrical and optical properties for technological applications. By using conjugated polymeric materials in the nanoscale, such properties can be further enhanced. In addition, the use of nanostructured materials makes possible miniaturize devices at the micro/nano scale. The applications of conjugated nanostructured polymers include sensors, actuators, flexible displays, discrete electronic devices, and smart fabric, to name a few. In particular, the use of conjugated polymers in chemical and biological sensors is made feasible owning to their sensitivity to the physicochemical conditions of its surrounding environment, such as chemical composition, pH, dielectric constant, humidity or even temperature. Subtle changes in these conditions bring about variations on the electrical (resistivity and capacitance), optical (absorptivity, luminescence, etc.), and mechanical properties of the conjugated polymer, which can be precisely measured by different experimental methods and ultimately associated with a specific analyte and its concentration. The present review article highlights the main features of conjugated polymers that make them suitable for chemical sensors. An especial emphasis is given to nanostructured sensors systems, which present high sensitivity and selectivity, and find application in beverage and food quality control, pharmaceutical industries, medical diagnosis, environmental monitoring, and homeland security, and other applications as discussed throughout this review.

  2. Coherent scattering of phase conjugate ultrasound waves in bubbly media.

    PubMed

    Shirkovskiy, Pavel; Preobrazhensky, Vladimir L; Pernod, Philippe

    2015-04-01

    Wave phase conjugation of ultrasound scattered by clouds of micro-bubbles in water has been studied experimentally and expounded theoretically. The clouds of microbubbles with variable concentration and sizes have been generated here using electrolytic method. The wave front of the ultrasound beam of frequency 10 MHz was reversed by a parametric phase conjugator. The signal of phase conjugate wave (PCW) detected by an acoustic transceiver was compared with the signal of the wave scattered toward the phase conjugator. The scattered wave (SW) signal was detected by the transducer substituting the phase conjugator. It is shown that, in contrast with stochastic SW signal, wave phase conjugation forms regular PCW signal on the transceiver in spite of random distribution of the scatterers. The PCW signal is found to be much more sensitive to variations of bubbles concentration comparing with the mean value of the SW amplitude. Moreover, the relative error of measurements of PCW signals is much smaller than that of the SW signal. The revealed properties of phase conjugate waves are applicable for testing of concentration of scatterers in dispersive systems.

  3. Nanostructured conjugated polymers in chemical sensors: synthesis, properties and applications.

    PubMed

    Correa, D S; Medeiros, E S; Oliveira, J E; Paterno, L G; Mattoso, Luiz C

    2014-09-01

    Conjugated polymers are organic materials endowed with a π-electron conjugation along the polymer backbone that present appealing electrical and optical properties for technological applications. By using conjugated polymeric materials in the nanoscale, such properties can be further enhanced. In addition, the use of nanostructured materials makes possible miniaturize devices at the micro/nano scale. The applications of conjugated nanostructured polymers include sensors, actuators, flexible displays, discrete electronic devices, and smart fabric, to name a few. In particular, the use of conjugated polymers in chemical and biological sensors is made feasible owning to their sensitivity to the physicochemical conditions of its surrounding environment, such as chemical composition, pH, dielectric constant, humidity or even temperature. Subtle changes in these conditions bring about variations on the electrical (resistivity and capacitance), optical (absorptivity, luminescence, etc.), and mechanical properties of the conjugated polymer, which can be precisely measured by different experimental methods and ultimately associated with a specific analyte and its concentration. The present review article highlights the main features of conjugated polymers that make them suitable for chemical sensors. An especial emphasis is given to nanostructured sensors systems, which present high sensitivity and selectivity, and find application in beverage and food quality control, pharmaceutical industries, medical diagnosis, environmental monitoring, and homeland security, and other applications as discussed throughout this review. PMID:25924296

  4. Nanofiber Scaffold Gradients for Interfacial Tissue Engineering

    PubMed Central

    Ramalingam, Murugan; Young, Marian F.; Thomas, Vinoy; Sun, Limin; Chow, Laurence C.; Tison, Christopher K.; Chatterjee, Kaushik; Miles, William C.; Simon, Carl G.

    2012-01-01

    We have designed a 2-spinnerette device that can directly electrospin nanofiber scaffolds containing a gradient in composition that can be used to engineer interfacial tissues such as ligament and tendon. Two types of nanofibers are simultaneously electrospun in an overlapping pattern to create a nonwoven mat of nanofibers containing a composition gradient. The approach is an advance over previous methods due to its versatility - gradients can be formed from any materials that can be electrospun. A dye was used to characterize the 2-spinnerette approach and applicability to tissue engineering was demonstrated by fabricating nanofibers with gradients in amorphous calcium phosphate nanoparticles (nACP). Adhesion and proliferation of osteogenic cells (MC3T3-E1 murine pre-osteoblasts) on gradients was enhanced on the regions of the gradients that contained higher nACP content yielding a graded osteoblast response. Since increases in soluble calcium and phosphate ions stimulate osteoblast function, we measured their release and observed significant release from nanofibers containing nACP. The nanofiber-nACP gradients fabricated herein can be applied to generate tissues with osteoblast gradients such as ligaments or tendons. In conclusion, these results introduce a versatile approach for fabricating nanofiber gradients that can have application for engineering graded tissues. PMID:22286209

  5. Salinity gradient power: utilizing vapor pressure differences.

    PubMed

    Olsson, M; Wick, G L; Isaacs, J D

    1979-10-26

    By utilizing the vapor pressure difference between high-salinity and lowsalinity wvater, one can obtain power from the gradients of salinity. This scheme eliminates the major problems associated with conversion methods in which membranes are used. The method we tested gave higher conversion efficiencies than membrane methods. Furthermore, hardware and techniques being developed for ocean thermal energy conversion may be applied to this approach to salinity gradient energy conversion. PMID:17809370

  6. An automated dual-gradient liquid chromatography-MS/MS method for the simultaneous determination of ferulic acid, ligustrazine and ligustilide in rat plasma and its application to a pharmacokinetic study.

    PubMed

    Zeng, Mingfei; Zhang, Jing; Yang, Yifang; Jin, Yan; Xiao, Wei; Wang, Zhenzhong; Ding, Gang; Yan, Renjie

    2014-01-01

    An automated on-line SPE and innovative fast polarity switch bioanalysis method employing dual-gradient liquid chromatography (DGLC) coupled with mass spectrometry (DGLC-MS/MS) was established and validated for the simultaneous determination of ferulic acid, ligustrazine and ligustilide in rat plasma after administration of Rhizoma Chuanxiong, Angelica sinensis extract or monomer. The proteins in plasma samples were precipitated using acetonitrile: methanol (1:1, v/v). Sulfamethoxazole was used as an internal standard. The DGLC system contains two high-pressure pumps. The first pump was used for on-line solid phase extraction with a Cyclone™ SPE column. Chromatographic separations were performed with the other pump on a Syncronis C18 rapid analytical column. The analytical column was eluted by a gradient program that featured an acetonitrile/methanol/water gradient (flow-rate, 0.4ml/min). DGLC afforded greater convenience for bioanalysis. All analytes were simultaneously monitored in positive- and negative-ion mode by SRM (selective reaction monitoring) using the fast polarity switch speed of TSQ Vantage™. Method validation of the assay was implemented. No significant matrix effect was observed. The LLOQ of all analytes were <1.0ng/ml. The precision, recovery and linearity of the analysis met the pre-established requirements. The method was applied to the pharmacokinetics of ferulic acid, ligustrazine and ligustilide in Rhizoma Chuanxiong or Angelica sinensis extracts or monomers. PMID:24140450

  7. Targeting cancer using cholesterol conjugates

    PubMed Central

    Radwan, Awwad A.; Alanazi, Fares K.

    2013-01-01

    Conjugation of cholesterol moiety to active compounds for either cancer treatment or diagnosis is an attractive approach. Cholesterol derivatives are widely studied as cancer diagnostic agents and as anticancer derivatives either in vitro or in vivo using animal models. In largely growing studies, anticancer agents have been chemically conjugated to cholesterol molecules, to enhance their pharmacokinetic behavior, cellular uptake, target specificity, and safety. To efficiently deliver anticancer agents to the target cells and tissues, many different cholesterol–anticancer conjugates were synthesized and characterized, and their anticancer efficiencies were tested in vitro and in vivo. PMID:24493968

  8. Ordering effects of conjugate thermal fields in simulations of molecular liquids: Carbon dioxide and water

    NASA Astrophysics Data System (ADS)

    Dittmar, Harro R.; Kusalik, Peter G.

    2016-10-01

    As shown previously, it is possible to apply configurational and kinetic thermostats simultaneously in order to induce a steady thermal flux in molecular dynamics simulations of many-particle systems. This flux appears to promote motion along potential gradients and can be utilized to enhance the sampling of ordered arrangements, i.e., it can facilitate the formation of a critical nucleus. Here we demonstrate that the same approach can be applied to molecular systems, and report a significant enhancement of the homogeneous crystal nucleation of a carbon dioxide (EPM2 model) system. Quantitative ordering effects and reduction of the particle mobilities were observed in water (TIP4P-2005 model) and carbon dioxide systems. The enhancement of the crystal nucleation of carbon dioxide was achieved with relatively small conjugate thermal fields. The effect is many orders of magnitude bigger at milder supercooling, where the forward flux sampling method was employed, than at a lower temperature that enabled brute force simulations of nucleation events. The behaviour exhibited implies that the effective free energy barrier of nucleation must have been reduced by the conjugate thermal field in line with our interpretation of previous results for atomic systems.

  9. Measuring the acoustic absorption coefficient in biological tissue specimens using ultrasonic phase conjugation

    NASA Astrophysics Data System (ADS)

    Smagin, N. V.; Krutyansky, L. M.; Zelenova, Z. V.; Brysev, A. P.

    2014-03-01

    Acoustic absorption has been measured in a series of biological tissue specimens—porcine muscle, renal and fat tissues—by the standard insert-substitution method, as well as by ultrasonic phase conjugation. Comparison of the experimental results and revealed differences confirm the promise of using phase conjugate waves to measure acoustic losses in biological objects. It is demonstrated that in inhomogeneous tissues, the phase conjugation method makes it possible to obtain a more reliable estimate of dissipative losses.

  10. A Rapid Method for Determination of the Main Conjugated Linoleic Acid Precursors (C18:2 n-6 and C18:3 n-3) in Forage by Capillary Zone Electrophoresis with Ultraviolet Detection Using Gas Chromatography with Flame Ionization Detection as a Comparative Method.

    PubMed

    de Jesus Coelho Castro, Renata; Sobrinho, Fausto Souza; Sundfeld da Gama, Marco Antônio; Takabayashi Sato, Renata; Lavorato Lima, Larissa; Leal de Oliveira, Marcone Augusto

    2015-01-01

    A rapid method has been proposed for determination of the main conjugated linoleic acid precursors such as linoleic (C18:2 n-6) and linolenic (C18:3 n-3) acids in forages by capillary zone electrophoresis (CZE) with direct UV detection at 200 nm. Among the fatty acids found in forages, C18:2 n-6 and C18:3 n-3 have received particular attention due to their roles as precursors for the synthesis of conjugated linoleic acid, a class of health-enhancing compounds that is predominantly found in dairy products. The electrolyte background consisted of 12.0 mmol/L tetraborate buffer (pH 9.2) added to 12.0 mmol/L Brij 35®, 17% acetonitrile, and 33% methanol. Under the optimized conditions, the baseline separation of C18:2 n-6 and C18:3 n-3 was achieved within 4 min. The CZE-UV method was compared to GC with a flame ionization detector, which is the American Oil Chemists' Society (AOCS 996.06) official method for fatty acid analysis. The methods did not show any evidence of significant differences within 95% confidence interval (P>0.05). The CZE-UV method was successfully applied to the analysis of 80 genotypes of Brachiaria ruzizienses clones submitted to a genetic improvement program in agricultural research. PMID:26651572

  11. Metallocene-containing conjugated polymers.

    PubMed

    Vorotyntsev, Mikhail A; Vasilyeva, Svetlana V

    2008-06-22

    The paper gives a review of publications on polymers with conjugated matrices (PPy, PTh, PAni, hydrocarbon or mixed chains...) which incorporate metallocene complexes (Fe, Ru, Co; Ni, Ti, Zr, Ta) with two cyclopentadienyl ligands (Cp) and their derivatives, in particular with methylated cyclopentadienyl rings (Cp*), as well as hemi-metallocene complexes (Fe, Ru, Co, Mn), as pendant groups or inside the principal chain (part B). The information on related short-chain systems, monomers and oligomers, is also included. In part A, a brief overview of various conjugated polymer materials is presented, with their classification in accordance with the conductivity mechanism (ionic, electronic or mixed conductors) or with the structural type (linear-chain organic or mixed polymers, derivatization, metallopolymers, multi-dimensional structures, alternating and block copolymers with organic or mixed units, hybrid materials with a mixture of conjugated and inert polymers, polymers inside a solid matrix, conjugated polymers with incorporated nanoelements of transition metals, carbon, semiconductors etc.

  12. A broad-spectrum equine urine screening method for free and enzyme-hydrolysed conjugated drugs with ultra performance liquid chromatography/tandem mass spectrometry.

    PubMed

    Wong, Colton H F; Tang, Francis P W; Wan, Terence S M

    2011-07-01

    The authors' laboratory at one time employed four liquid chromatography/mass spectrometric (LC/MS) methods for the detection of a large variety of drugs in equine urine. Drug classes covered by these methods included anti-diabetics, anti-ulcers, cyclooxygenase-2 (COX-2) inhibitors, sedatives, corticosteroids, anabolic steroids, sulfur diuretics, xanthines, etc. With the objective to reduce labour and instrumental workload, a new ultra performance liquid chromatography/tandem mass spectrometric (UPLC/MS/MS) method has been developed, which encompasses all target analytes detected by the original four LC/MS methods. The new method has better detection limits than the superseded methods. In addition, it covers new target analytes that could not be adequately detected by the four LC/MS methods. The new method involves solid-phase extraction (SPE) of two aliquots of equine urine using two Abs Elut Nexus cartridges. One aliquot of the urine sample is treated with β-glucuronidase before subjecting to SPE. A second aliquot of the same urine sample is processed directly using another SPE cartridge, so that drugs that are prone to decomposition during enzyme hydrolysis can be preserved. The combined eluate is analysed by UPLC/MS/MS using alternating positive and negative electrospray ionisation in the selected-reaction-monitoring mode. Exceptional chromatographic separation is achieved using an UPLC system equipped with a UPLC(®) BEH C18 column (10 cm L×2.1 mm ID with 1.7 μm particles). With this newly developed UPLC/MS/MS method, the simultaneous detection of 140 drugs at ppb to sub-ppb levels in equine urine can be achieved in less than 13 min inclusive of post-run equilibration. Matrix interference for the selected transitions at the expected retention times is minimised by the excellent UPLC chromatographic separation. The method has been validated for recovery and precision, and is being used regularly in the authors' laboratory as an important component of the

  13. Brazilian meningococcal C conjugate vaccine: Scaling up studies.

    PubMed

    Bastos, Renata Chagas; de Souza, Iaralice Medeiros; da Silva, Milton Neto; Silva, Flavia de Paiva; Figueira, Elza Scott; Leal, Maria de Lurdes; Jessouroun, Ellen; da Silva, José Godinho; Medronho, Ricardo de Andrade; da Silveira, Ivna Alana Freitas Brasileiro

    2015-08-20

    Several outbreaks caused by Neisseria meningitidis group C have been occurred in different regions of Brazil. A conjugate vaccine for Neisseria meningitidis was produced by chemical linkage between periodate-oxidized meningococcal C polysaccharide and hydrazide-activated monomeric tetanus toxoid via a modified reductive amination conjugation method. Vaccine safety and immunogenicity tested in Phase I and II trials showed satisfactory results. Before starting Phase III trials, vaccine production was scaled up to obtain industrial lots under Good Manufacture Practices (GMP). Comparative analysis between data obtained from industrial and pilot scales of the meningococcal C conjugate bulk showed similar execution times in the scaling up production process without significant losses or alterations in the quality attributes of purified compounds. In conclusion, scale up was considered satisfactory and the Brazilian meningococcal conjugate vaccine production aiming to perform Phase III trials is feasible.

  14. Laser textured surface gradients

    NASA Astrophysics Data System (ADS)

    Ta, Van Duong; Dunn, Andrew; Wasley, Thomas J.; Li, Ji; Kay, Robert W.; Stringer, Jonathan; Smith, Patrick J.; Esenturk, Emre; Connaughton, Colm; Shephard, Jonathan D.

    2016-05-01

    This work demonstrates a novel technique for fabricating surfaces with roughness and wettability gradients and their subsequent applications for chemical sensors. Surface roughness gradients on brass sheets are obtained directly by nanosecond laser texturing. When these structured surfaces are exposed to air, their wettability decreases with time (up to 20 days) achieving both spatial and temporal wettability gradients. The surfaces are responsive to organic solvents. Contact angles of a series of dilute isopropanol solutions decay exponentially with concentration. In particular, a fall of 132° in contact angle is observed on a surface gradient, one order of magnitude higher than the 14° observed for the unprocessed surface, when the isopropanol concentration increased from 0 to 15.6 wt%. As the wettability changes gradually over the surface, contact angle also changes correspondingly. This effect offers multi-sensitivity at different zones on the surface and is useful for accurate measurement of chemical concentration.

  15. A consistent direct discretization scheme on Cartesian grids for convective and conjugate heat transfer

    NASA Astrophysics Data System (ADS)

    Sato, Norikazu; Takeuchi, Shintaro; Kajishima, Takeo; Inagaki, Masahide; Horinouchi, Nariaki

    2016-09-01

    A new discretization scheme on Cartesian grids, namely, a "consistent direct discretization scheme", is proposed for solving incompressible flows with convective and conjugate heat transfer around a solid object. The Navier-Stokes and the pressure Poisson equations are discretized directly even in the immediate vicinity of a solid boundary with the aid of the consistency between the face-velocity and the pressure gradient. From verifications in fundamental flow problems, the present method is found to significantly improve the accuracy of the velocity and the wall shear stress. It is also confirmed that the numerical results are less sensitive to the Courant number owing to the consistency between the velocity and pressure fields. The concept of the consistent direct discretization scheme is also explored for the thermal field; the energy equations for the fluid and solid phases are discretized directly while satisfying the thermal relations that should be valid at their interface. It takes different forms depending on the thermal boundary conditions: Dirichlet (isothermal) and Neumann (adiabatic/iso-heat-flux) boundary conditions for convective heat transfer and a fluid-solid thermal interaction for conjugate heat transfer. The validity of these discretizations is assessed by comparing the simulated results with analytical solutions for the respective thermal boundary conditions, and it is confirmed that the present schemes also show high accuracy for the thermal field. A significant improvement for the conjugate heat transfer problems is that the second-order spatial accuracy and numerical stability are maintained even under severe conditions of near-practical physical properties for the fluid and solid phases.

  16. New flow cytometric method for detection of minimally expressed multidrug resistance P-glycoprotein on normal and acute leukemia cells using biotinylated MRK16 and streptavidin-RED670 conjugate.

    PubMed

    Takeshita, A; Shinjo, K; Ohnishi, K; Ohno, R

    1995-06-01

    To evaluate the expression of multidrug resistance (MDR) on normal and leukemia cells, we examined P-glycoprotein (P-gp) by a newly devised flow cytometric method, utilizing a biotinylated monoclonal antibody (mAb) against P-gp (MRK16), a streptavidin-RED670 conjugate (SA-RED670) and appropriate emission filters. The combination of biotinylated MRK16 (b-MRK16) and SA-RED670 resulted in higher sensitivity as compared with standard methods such as the use of streptavidin-phycoerythrin (SA-PE) conjugate. The sensitivity was examined in K562, K562/ADR, NOMO-1, NOMO-1/ADR and HL60 cells, and compared with the data obtained from reverse transcription polymerase chain reaction (RT-PCR) of mdr-1 gene. P-gp positivity on flow cytometry was 10.4%, 99.9%, 1.4%, 90.4% and 0%, respectively. Mdr-1 mRNA was well expressed in K562/ADR and NOMO-1/ADR cells, but not in NOMO-1 and HL60 cells. In K562 cells, mdr-1 was found after 40 cycles of PCR, but not 25 cycles. These data are well correlated with those from the flow cytometry. We then studied the P-gp expression on normal peripheral blood cells and acute leukemia cells. P-gp was little expressed on peripheral lymphocytes, monocytes and granulocytes. It was also little expressed on blast cells from 5 patients with acute promyelocytic leukemia (AML) and 5 acute lymphocytic leukemia (ALL) expressed P-gp at diagnosis, ranging from 8.5% to 34.5% (16.9 +/- 11.8%) and from 2.3% to 45.6% (24.0 +/- 17.8%), respectively. All 9 relapsed or refractory cases expressed P-gp, ranging from 21.1% to 99.8% (52.2 +/- 29.9%). Significant differences were found in APL, CD34-positive and relapse and refractory cases (P = 0.0006, 0.0007 and 0.0088, respectively). These results indicate that this flow cytometric analysis is useful for the evaluation of clinical MDR status and can identify a group of patients with resistant leukemia. PMID:7622426

  17. Polymeric conjugates for drug delivery

    PubMed Central

    Larson, Nate; Ghandehari, Hamidreza

    2012-01-01

    The field of polymer therapeutics has evolved over the past decade and has resulted in the development of polymer-drug conjugates with a wide variety of architectures and chemical properties. Whereas traditional non-degradable polymeric carriers such as poly(ethylene glycol) (PEG) and N-(2-hydroxypropyl methacrylamide) (HPMA) copolymers have been translated to use in the clinic, functionalized polymer-drug conjugates are increasingly being utilized to obtain biodegradable, stimuli-sensitive, and targeted systems in an attempt to further enhance localized drug delivery and ease of elimination. In addition, the study of conjugates bearing both therapeutic and diagnostic agents has resulted in multifunctional carriers with the potential to both “see and treat” patients. In this paper, the rational design of polymer-drug conjugates will be discussed followed by a review of different classes of conjugates currently under investigation. The design and chemistry used for the synthesis of various conjugates will be presented with additional comments on their potential applications and current developmental status. PMID:22707853

  18. Protein carriers of conjugate vaccines

    PubMed Central

    Pichichero, Michael E

    2013-01-01

    The immunogenicity of polysaccharides as human vaccines was enhanced by coupling to protein carriers. Conjugation transformed the T cell-independent polysaccharide vaccines of the past to T cell-dependent antigenic vaccines that were much more immunogenic and launched a renaissance in vaccinology. This review discusses the conjugate vaccines for prevention of infections caused by Hemophilus influenzae type b, Streptococcus pneumoniae, and Neisseria meningitidis. Specifically, the characteristics of the proteins used in the construction of the vaccines including CRM, tetanus toxoid, diphtheria toxoid, Neisseria meningitidis outer membrane complex, and Hemophilus influenzae protein D are discussed. The studies that established differences among and key features of conjugate vaccines including immunologic memory induction, reduction of nasopharyngeal colonization and herd immunity, and antibody avidity and avidity maturation are presented. Studies of dose, schedule, response to boosters, of single protein carriers with single and multiple polysaccharides, of multiple protein carriers with multiple polysaccharides and conjugate vaccines administered concurrently with other vaccines are discussed along with undesirable consequences of conjugate vaccines. The clear benefits of conjugate vaccines in improving the protective responses of the immature immune systems of young infants and the senescent immune systems of the elderly have been made clear and opened the way to development of additional vaccines using this technology for future vaccine products. PMID:23955057

  19. Explosives conjugation products in remediation matrices: Interim report. Final report

    SciTech Connect

    Pennington, J.C.; Honeycutt, M.E.; Jarvis, A.S.; McFarland, V.A.; Gunnison, D.

    1997-08-01

    During investigations of potential treatment technologies for explosives-contaminated soils, 2,4,6-trinitrotoluene (TNT) has been observed to interact with some component of the matrix in such a way as to preclude extraction with organic solvents. Mass balance studies using radiolabeled TNT reveal that as much as 80 percent of the radioactivity added to tests is still present in the matrix. The objectives of this study were to characterize the conjugates, develop analytical methods for their identification, and determine their potential long-term stability and environmental safety. The approach includes development of hydrolytic methods for releasing identifiable explosives-related products from conjugated matrices, formation of conjugates by covalent linkage with humic acid functional groups using nuclear magnetic resonance, dialysis partitioning of explosives and transformation products with humic acid, surface plasmon resonance as a tool for assessing the interaction with humic acid, microbial degradability of conjugated products, and toxicology of explosives transformation and conjugated products. Results to date indicate that conjugates result from several processes occurring in the matrix. Some of these processes are potentially reversible, while others are more stable.

  20. Dual fuel gradients in uranium silicide plates

    SciTech Connect

    Pace, B.W.

    1997-08-01

    Babcock & Wilcox has been able to achieve dual gradient plates with good repeatability in small lots of U{sub 3}Si{sub 2} plates. Improvements in homogeneity and other processing parameters and techniques have allowed the development of contoured fuel within the cladding. The most difficult obstacles to overcome have been the ability to evaluate the bidirectional fuel loadings in comparison to the perfect loading model and the different methods of instilling the gradients in the early compact stage. The overriding conclusion is that to control the contour of the fuel, a known relationship between the compact, the frames and final core gradient must exist. Therefore, further development in the creation and control of dual gradients in fuel plates will involve arriving at a plausible gradient requirement and building the correct model between the compact configuration and the final contoured loading requirements.