Variable metric conjugate gradient methods
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.
Approximate error conjugation gradient minimization methods
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.
A new nonlinear conjugate gradient method
NASA Astrophysics Data System (ADS)
Abdelrahman, Awad; Mamat, Mustafa; Mohd, Ismail bin; Rivaie, Mohd; Omer, Osman
2015-02-01
Conjugate gradient (CG) methods are essential for solving large-scale unconstrained optimization problems. Many of studies and modifications have been practiced to improve this method. In this paper, a new class of conjugate gradient coefficients (βk) with a new parameter m = ‖g/k‖ ‖dk-1‖ that possess global convergence properties is presented. The global convergence and sufficient decent property result is established using inexact line searches to determine the step size of CG, denoted as ∝k. Numerical result shows that the new formula is superior and more efficient when compared to other CG coefficients.
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.
The multigrid preconditioned conjugate gradient method
NASA Technical Reports Server (NTRS)
Tatebe, Osamu
1993-01-01
A multigrid preconditioned conjugate gradient method (MGCG method), which uses the multigrid method as a preconditioner of the PCG method, is proposed. The multigrid method has inherent high parallelism and improves convergence of long wavelength components, which is important in iterative methods. By using this method as a preconditioner of the PCG method, an efficient method with high parallelism and fast convergence is obtained. First, it is considered a necessary condition of the multigrid preconditioner in order to satisfy requirements of a preconditioner of the PCG method. Next numerical experiments show a behavior of the MGCG method and that the MGCG method is superior to both the ICCG method and the multigrid method in point of fast convergence and high parallelism. This fast convergence is understood in terms of the eigenvalue analysis of the preconditioned matrix. From this observation of the multigrid preconditioner, it is realized that the MGCG method converges in very few iterations and the multigrid preconditioner is a desirable preconditioner of the conjugate gradient method.
Polynomial preconditioning for conjugate gradient methods
Ashby, S.F.
1987-12-01
The solution of a linear system of equations, Ax = b, arises in many scientific applications. If A is large and sparse, an iterative method is required. When A is hermitian positive definite (hpd), the conjugate gradient method of Hestenes and Stiefel is popular. When A is hermitian indefinite (hid), the conjugate residual method may be used. If A is ill-conditioned, these methods may converge slowly, in which case a preconditioner is needed. In this thesis we examine the use of polynomial preconditioning in CG methods for both hermitian positive definite and indefinite matrices. Such preconditioners are easy to employ and well-suited to vector and/or parallel architectures. We first show that any CG method is characterized by three matrices: an hpd inner product matrix B, a preconditioning matrix C, and the hermitian matrix A. The resulting method, CG(B,C,A), minimizes the B-norm of the error over a Krylov subspace. We next exploit the versatility of polynomial preconditioners to design several new CG methods. To obtain an optimum preconditioner, we solve a constrained minimax approximation problem. The preconditioning polynomial, C(lambda), is optimum in that it minimizes a bound on the condition number of the preconditioned matrix, p/sub m/(A). An adaptive procedure for dynamically determining the optimum preconditioner is also discussed. Finally, in a variety of numerical experiments, conducted on a Cray X-MP/48, we demonstrate the effectiveness of polynomial preconditioning. 66 ref., 19 figs., 39 tabs.
A taxonomy for conjugate gradient methods
Ashby, S.F.; Manteuffel, T.A.; Saylor, P.E.
1988-03-01
The conjugate method of Hestenes and Stiefel is an effective method to solve large, sparse hermitian positive definite (hpd) systems of linear equations, Ax = b. Generalizations to non-hpd matrices have long been sought. The recent theory of Faber and Manteuffle gives necessary and sufficient conditions for the existence of CG method. This paper uses these conditions to develop and organize such methods. We show that any CG method for Ax = b is characterized by and hpd inner product matrix B and a left preconditioning matrix C. At each step the method minimizes the B-norm of the error over a Krylov space. This characterization is then used to classify known and new methods. Finally, it is shown how eigenvalue estimates may be obtained from the iteration parameters, generalizing the well known connection between CG and Lanczos. Such estimates allow implementation of a stopping criterion based more nearly on the true error. 29 refs., 4 tabs.
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.
Application of Conjugate Gradient methods to tidal simulation
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.
Two modified Dai-Yuan nonlinear conjugate gradient methods
NASA Astrophysics Data System (ADS)
Zhang, Li
2009-01-01
In this paper, we propose two modified versions of the Dai-Yuan (DY) nonlinear conjugate gradient method. One is based on the MBFGS method (Li and Fukushima, J Comput Appl Math 129:15-35, 2001) and inherits all nice properties of the DY method. Moreover, this method converges globally for nonconvex functions even if the standard Armijo line search is used. The other is based on the ideas of Wei et al. (Appl Math Comput 183:1341-1350, 2006), Zhang et al. (Numer Math 104:561-572, 2006) and possesses good performance of the Hestenes-Stiefel method. Numerical results are also reported.
Shang, Shang; Bai, Jing; Song, Xiaolei; Wang, Hongkai; Lau, Jaclyn
2007-01-01
Conjugate gradient method is verified to be efficient for nonlinear optimization problems of large-dimension data. In this paper, a penalized linear and nonlinear combined conjugate gradient method for the reconstruction of fluorescence molecular tomography (FMT) is presented. The algorithm combines the linear conjugate gradient method and the nonlinear conjugate gradient method together based on a restart strategy, in order to take advantage of the two kinds of conjugate gradient methods and compensate for the disadvantages. A quadratic penalty method is adopted to gain a nonnegative constraint and reduce the illposedness of the problem. Simulation studies show that the presented algorithm is accurate, stable, and fast. It has a better performance than the conventional conjugate gradient-based reconstruction algorithms. It offers an effective approach to reconstruct fluorochrome information for FMT. PMID:18354740
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.
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.
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
Preconditioned Conjugate Gradient methods for low speed flow calculations
NASA Technical Reports Server (NTRS)
Ajmani, Kumud; Ng, Wing-Fai; Liou, Meng-Sing
1993-01-01
An investigation is conducted into the viability of using a generalized Conjugate Gradient-like method as an iterative solver to obtain steady-state solutions of very low-speed fluid flow problems. Low-speed flow at Mach 0.1 over a backward-facing step is chosen as a representative test problem. The unsteady form of the two dimensional, compressible Navier-Stokes equations are integrated in time using discrete time-steps. The Navier-Stokes equations are cast in an implicit, upwind finite-volume, flux split formulation. The new iterative solver is used to solve a linear system of equations at each step of the time-integration. Preconditioning techniques are used with the new solver to enhance the stability and the convergence rate of the solver and are found to be critical to the overall success of the solver. A study of various preconditioners reveals that a preconditioner based on the lower-upper (L-U)-successive symmetric over-relaxation iterative scheme is more efficient than a preconditioner based on incomplete L-U factorizations of the iteration matrix. The performance of the new preconditioned solver is compared with a conventional line Gauss-Seidel relaxation (LGSR) solver. Overall speed-up factors of 28 (in terms of global time-steps required to converge to a steady-state solution) and 20 (in terms of total CPU time on one processor of a CRAY-YMP) are found in favor of the new preconditioned solver, when compared with the LGSR solver.
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.
Blockwise conjugate gradient methods for image reconstruction in volumetric CT.
Qiu, W; Titley-Peloquin, D; Soleimani, M
2012-11-01
Cone beam computed tomography (CBCT) enables volumetric image reconstruction from 2D projection data and plays an important role in image guided radiation therapy (IGRT). Filtered back projection is still the most frequently used algorithm in applications. The algorithm discretizes the scanning process (forward projection) into a system of linear equations, which must then be solved to recover images from measured projection data. The conjugate gradients (CG) algorithm and its variants can be used to solve (possibly regularized) linear systems of equations Ax=b and linear least squares problems minx∥b-Ax∥2, especially when the matrix A is very large and sparse. Their applications can be found in a general CT context, but in tomography problems (e.g. CBCT reconstruction) they have not widely been used. Hence, CBCT reconstruction using the CG-type algorithm LSQR was implemented and studied in this paper. In CBCT reconstruction, the main computational challenge is that the matrix A usually is very large, and storing it in full requires an amount of memory well beyond the reach of commodity computers. Because of these memory capacity constraints, only a small fraction of the weighting matrix A is typically used, leading to a poor reconstruction. In this paper, to overcome this difficulty, the matrix A is partitioned and stored blockwise, and blockwise matrix-vector multiplications are implemented within LSQR. This implementation allows us to use the full weighting matrix A for CBCT reconstruction without further enhancing computer standards. Tikhonov regularization can also be implemented in this fashion, and can produce significant improvement in the reconstructed images. PMID:22325240
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.
Generalized conjugate gradient squared
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.
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.
A new type of descent conjugate gradient method with exact line search
NASA Astrophysics Data System (ADS)
Hajar, Nurul; Mamat, Mustafa; Rivaie, Mohd.; Jusoh, Ibrahim
2016-06-01
Nowadays, conjugate gradient (CG) methods are impressive for solving nonlinear unconstrained optimization problems. In this paper, a new CG method is proposed and analyzed. This new CG method satisfies descent condition and its global convergence is established using exact line search. Numerical results show that this new CG method substantially outperforms the previous CG methods. This new CG method is considered robust, efficient and provided faster and stable convergence.
NASA Astrophysics Data System (ADS)
Zhao, Li-Ming; Yue, Gui-Kuan; Zhou, Yun-Song; Wang, Fu-He
2015-04-01
A new method, namely the nonlinear conjugate-gradient (NCG) method, is proposed to design nonlinear domains with a disordered distribution, in which an efficient broadband second harmonic generation can be achieved simultaneously with high conversion efficiency. It is demonstrated by numerical simulation that the NCG method has obvious advantages in realizing the optimal quasi-phase-matching, in comparison with the traditional simulated annealing method.
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.
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
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
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.
Preconditioned conjugate gradient methods for the Navier-Stokes equations
Ajmani, K.; Ng, Wing Fai ); Liou, Meng Sing )
1994-01-01
A preconditioned Krylov subspace method (GMRES) is used to solve the linear systems of equations formed at each time-integration step of the unsteady, two-dimensional, compressible Navier-Stokes equations of fluid flow. The Navier-Stokes equations are cast in an implicit, upwind finite-volume, flux-split formulations. Several preconditioning techniques are investigated to enhance the efficiency and convergence rate of the implicit solver based on the GMRES algorithm. The superiority of the new solver is established by comparisons with a (LGSR). Computational test results for low-speed (incompressible flow over a backward-facing step at Mach 0.1), transonic flow (trailing edge flow in a transonic turbine cascade), and hypersonic flow (shock-on-shock interactions on a cylindrical leading edge at Mach 6.0) are presented. For the Mach 0.1 case, overall speedup factors of up to 17 (in terms of time-steps) and 15 (in terms of CPU times on a CRAY-YMP/8) are found in favor of the preconditioned GMRES solver, when compared with the LGSR solver. The corresponding speedup factors for the transonic flow cases are 17 and 23, respectively. The hypersonic flow case shows slightly lower speedup factors of 9 and 13, respectively. The study of preconditioners conducted in this research reveals that a new LUSGS-type preconditioner is much more efficient than a conventional incomplete LU-type preconditioner. 34 refs., 15 figs.
Preconditioned conjugate gradient methods for the Navier-Stokes equations
NASA Technical Reports Server (NTRS)
Ajmani, Kumud; Ng, Wing-Fai; Liou, Meng-Sing
1994-01-01
A preconditioned Krylov subspace method (GMRES) is used to solve the linear systems of equations formed at each time-integration step of the unsteady, two-dimensional, compressible Navier-Stokes equations of fluid flow. The Navier-Stokes equations are cast in an implicit, upwind finite-volume, flux-split formulation. Several preconditioning techniques are investigated to enhance the efficiency and convergence rate of the implicit solver based on the GMRES algorithm. The superiority of the new solver is established by comparisons with a conventional implicit solver, namely line Gauss-Seidel relaxation (LGSR). Computational test results for low-speed (incompressible flow over a backward-facing step at Mach 0.1), transonic flow (trailing edge flow in a transonic turbine cascade), and hypersonic flow (shock-on-shock interactions on a cylindrical leading edge at Mach 6.0) are presented. For the Mach 0.1 case, overall speedup factors of up to 17 (in terms of time-steps) and 15 (in terms of CPU time on a CRAY-YMP/8) are found in favor of the preconditioned GMRES solver, when compared with the LGSR solver. The corresponding speedup factors for the transonic flow case are 17 and 23, respectively. The hypersonic flow case shows slightly lower speedup factors of 9 and 13, respectively. The study of preconditioners conducted in this research reveals that a new LUSGS-type preconditioner is much more efficient than a conventional incomplete LU-type preconditioner.
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.
A spectral KRMI conjugate gradient method under the strong-Wolfe line search
NASA Astrophysics Data System (ADS)
Khadijah, Wan; Rivaie, Mohd.; Mamat, Mustafa; Jusoh, Ibrahim
2016-06-01
In this paper, a modification of spectral conjugate gradient (CG) method is proposed which combines the advantages of the spectral CG method and the RMIL method namely as spectral Khadijah-Rivaie-Mustafa-Ibrahim (SKRMI) to solve unconstrained optimization problems. Based on inexact line searches, the objective function generates a sufficient descent direction and the global convergence property for the proposed method has been proved. Moreover, the method reduces to the standard RMIL method if exact line search is applied. Numerical results are also presented to examine the efficiency of the proposed method.
A new Liu-Storey type nonlinear conjugate gradient method for unconstrained optimization problems
NASA Astrophysics Data System (ADS)
Zhang, Li
2009-03-01
Although the Liu-Storey (LS) nonlinear conjugate gradient method has a similar structure as the well-known Polak-Ribière-Polyak (PRP) and Hestenes-Stiefel (HS) methods, research about this method is very rare. In this paper, based on the memoryless BFGS quasi-Newton method, we propose a new LS type method, which converges globally for general functions with the Grippo-Lucidi line search. Moreover, we modify this new LS method such that the modified scheme is globally convergent for nonconvex minimization if the strong Wolfe line search is used. Numerical results are also reported.
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.
The conjugate gradient method for linear ill-posed problems with operator perturbations
NASA Astrophysics Data System (ADS)
Plato, Robert
1999-03-01
We consider an ill-posed problem Ta = f* in Hilbert spaces and suppose that the linear bounded operator T is approximately available, with a known estimate for the operator perturbation at the solution. As a numerical scheme the CGNR-method is considered, that is, the classical method of conjugate gradients by Hestenes and Stiefel applied to the associated normal equations. Two a posteriori stopping rules are introduced, and convergence results are provided for the corresponding approximations, respectively. As a specific application, a parameter estimation problem is considered.
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.
Energy Science and Technology Software Center (ESTSC)
2006-11-17
Software that simulates and inverts electromagnetic field data for subsurface electrical properties (electrical conductivity) of geological media. The software treats data produced by a time harmonic source field excitation arising from the following antenna geometery: loops and grounded bipoles, as well as point electric and magnetic dioples. The inversion process is carried out using a non-linear conjugate gradient optimization scheme, which minimizes the misfit between field data and model data using a least squares criteria.more » The software is an upgrade from the code NLCGCS_MP ver 1.0. The upgrade includes the following components: Incorporation of new 1 D field sourcing routines to more accurately simulate the 3D electromagnetic field for arbitrary geologic& media, treatment for generalized finite length transmitting antenna geometry (antennas with vertical and horizontal component directions). In addition, the software has been upgraded to treat transverse anisotropy in electrical conductivity.« less
NASA Astrophysics Data System (ADS)
Andrei, Petru; Oniciuc, Liviu; Stancu, Alexandru; Stoleriu, Laurentiu
2007-09-01
An identification technique for the parameters of phenomenological models of hysteresis is presented. The basic idea of our technique is to set up a system of equations for the parameters of the model as a function of known quantities on the major or minor hysteresis loops (e.g. coercive force, susceptibilities at various points, remanence), or other magnetization curves. This system of equations can be either over or underspecified and is solved by using the conjugate gradient method. Numerical results related to the identification of parameters in the Energetic, Jiles-Atherton, and Preisach models are presented.
NASA Astrophysics Data System (ADS)
Jönsthövel, T. B.; van Gijzen, M. B.; MacLachlan, S.; Vuik, C.; Scarpas, A.
2012-09-01
Many applications in computational science and engineering concern composite materials, which are characterized by large discontinuities in the material properties. Such applications require fine-scale finite-element meshes, which lead to large linear systems that are challenging to solve with current direct and iterative solutions algorithms. In this paper, we consider the simulation of asphalt concrete, which is a mixture of components with large differences in material stiffness. The discontinuities in material stiffness give rise to many small eigenvalues that negatively affect the convergence of iterative solution algorithms such as the preconditioned conjugate gradient (PCG) method. This paper considers the deflated preconditioned conjugate gradient (DPCG) method in which the rigid body modes of sets of elements with homogeneous material properties are used as deflation vectors. As preconditioner we consider several variants of the algebraic multigrid smoothed aggregation method. We evaluate the performance of the DPCG method on a parallel computer using up to 64 processors. Our test problems are derived from real asphalt core samples, obtained using CT scans. We show that the DPCG method is an efficient and robust technique for solving these challenging linear systems.
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.
A conjugate gradient method for solving the non-LTE line radiation transfer problem
NASA Astrophysics Data System (ADS)
Paletou, F.; Anterrieu, E.
2009-12-01
This study concerns the fast and accurate solution of the line radiation transfer problem, under non-LTE conditions. We propose and evaluate an alternative iterative scheme to the classical ALI-Jacobi method, and to the more recently proposed Gauss-Seidel and successive over-relaxation (GS/SOR) schemes. Our study is indeed based on applying a preconditioned bi-conjugate gradient method (BiCG-P). Standard tests, in 1D plane parallel geometry and in the frame of the two-level atom model with monochromatic scattering are discussed. Rates of convergence between the previously mentioned iterative schemes are compared, as are their respective timing properties. The smoothing capability of the BiCG-P method is also demonstrated.
NASA Astrophysics Data System (ADS)
Kapitza, H.; Eppel, D.
1987-02-01
A conjugate gradient method for solving a 3-D Poisson equation in Cartesian unequally spaced coordinates is tested in concurrence to standard iterative methods. It is found that the tested algorithm is far superior to Red-Black-SOR with optimal parameter. In the conjugate gradient method no relaxation parameter is needed, and there are no restrictions on the number of gridpoints in the three directions. The iteration routine is vectorizable to a large extent by the compiler of a CYBER 205 without any special preparations. Utilizing some special features of vector computers it is completely vectorizable with only minor changes in the code.
A modified conjugate gradient method based on the Tikhonov system for computerized tomography (CT).
Wang, Qi; Wang, Huaxiang
2011-04-01
During the past few decades, computerized tomography (CT) was widely used for non-destructive testing (NDT) and non-destructive examination (NDE) in the industrial area because of its characteristics of non-invasiveness and visibility. Recently, CT technology has been applied to multi-phase flow measurement. Using the principle of radiation attenuation measurements along different directions through the investigated object with a special reconstruction algorithm, cross-sectional information of the scanned object can be worked out. It is a typical inverse problem and has always been a challenge for its nonlinearity and ill-conditions. The Tikhonov regulation method is widely used for similar ill-posed problems. However, the conventional Tikhonov method does not provide reconstructions with qualities good enough, the relative errors between the reconstructed images and the real distribution should be further reduced. In this paper, a modified conjugate gradient (CG) method is applied to a Tikhonov system (MCGT method) for reconstructing CT images. The computational load is dominated by the number of independent measurements m, and a preconditioner is imported to lower the condition number of the Tikhonov system. Both simulation and experiment results indicate that the proposed method can reduce the computational time and improve the quality of image reconstruction. PMID:21129739
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./.
Conjugate gradient algorithms using multiple recursions
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.
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.
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.
NASA Astrophysics Data System (ADS)
Arioli, M.; Gratton, S.
2012-11-01
Minimum-variance unbiased estimates for linear regression models can be obtained by solving least-squares problems. The conjugate gradient method can be successfully used in solving the symmetric and positive definite normal equations obtained from these least-squares problems. Taking into account the results of Golub and Meurant (1997, 2009) [10,11], Hestenes and Stiefel (1952) [17], and Strakoš and Tichý (2002) [16], which make it possible to approximate the energy norm of the error during the conjugate gradient iterative process, we adapt the stopping criterion introduced by Arioli (2005) [18] to the normal equations taking into account the statistical properties of the underpinning linear regression problem. Moreover, we show how the energy norm of the error is linked to the χ2-distribution and to the Fisher-Snedecor distribution. Finally, we present the results of several numerical tests that experimentally validate the effectiveness of our stopping criteria.
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.
NASA Astrophysics Data System (ADS)
Xu, Zhengwei
Modeling of induced polarization (IP) phenomena is important for developing effective methods for remote sensing of subsurface geology and is widely used in mineral exploration. However, the quantitative interpretation of IP data in a complex 3D environment is still a challenging problem of applied geophysics. In this dissertation I use the regularized conjugate gradient method to determine the 3D distribution of the four parameters of the Cole-Cole model based on surface induced polarization (IP) data. This method takes into account the nonlinear nature of both electromagnetic induction (EMI) and IP phenomena. The solution of the 3D IP inverse problem is based on the regularized smooth inversion only. The method was tested on synthetic models with DC conductivity, intrinsic chargeability, time constant, and relaxation parameters, and it was also applied to the practical 3D IP survey data. I demonstrate that the four parameters of the Cole-Cole model, DC electrical resistivity, rho 0 , chargeability, eta time constant, tau and the relaxation parameter, C, can be recovered from the observed IP data simultaneously. There are four Cole-Cole parameters involved in the inversion, in other words, within each cell, there are DC conductivity (sigma0 ), chargeability (eta), time parameters (tau), and relaxation parameters (C) compared to conductivity only, used in EM only inversion. In addition to more inversion parameters used in IP survey, dipole-dipole configuration which requires more sources and receivers. One the other hand, calculating Green tensor and Frechet matrix time consuming and storing them requires a lot of memory. So, I develop parallel computation using MATLAB parallel tool to speed up the calculation.
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.
A modified conjugate gradient solver for very large systems
NASA Astrophysics Data System (ADS)
Barkai, D.; Moriarty, K. J. M.; Rebbi, C.
1985-03-01
A modified conjugate gradient method is derived which requires only one pass through the coefficients and the temporary vectors. The method is applicable to problems which may be complex and non-symmetric. The method is implemented on a vector processor (the CDC CYBER 205) and applied to a high-energy physics lattice gauge theory problem, though the implementation methodology is quite general.
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.
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.
Conjugate-Gradient Algorithms For Dynamics Of Manipulators
NASA Technical Reports Server (NTRS)
Fijany, Amir; Scheid, Robert E.
1993-01-01
Algorithms for serial and parallel computation of forward dynamics of multiple-link robotic manipulators by conjugate-gradient method developed. Parallel algorithms have potential for speedup of computations on multiple linked, specialized processors implemented in very-large-scale integrated circuits. Such processors used to stimulate dynamics, possibly faster than in real time, for purposes of planning and control.
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.
Two New PRP Conjugate Gradient Algorithms for Minimization Optimization Models
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
Minimizing inner product data dependencies in conjugate gradient iteration
NASA Technical Reports Server (NTRS)
Vanrosendale, J.
1983-01-01
The amount of concurrency available in conjugate gradient iteration is limited by the summations required in the inner product computations. The inner product of two vectors of length N requires time c log(N), if N or more processors are available. This paper describes an algebraic restructuring of the conjugate gradient algorithm which minimizes data dependencies due to inner product calculations. After an initial start up, the new algorithm can perform a conjugate gradient iteration in time c*log(log(N)).
A matrix analysis of conjugate gradient algorithms
Ashby, S.F.; Gutknecht, M.H.
1993-04-01
This paper explores the relationships between the conjugate gradient algorithms Orthodir, Orthomin, and Orthores. To facilitate this exploration, a matrix formulation for each algorithm is given. It is shown that Orthodir directly computes a Hessenberg matrix H{sub k} at step k. Orthores also computes a Hessenberg matrix, G{sub k}, which is similar to a Hessenberg matrix obtained from H{sub k} by perturbing its last column. (This perturbation vanishes at convergence.) Orthomin, on the other hand, computes a UL and LU factorization of the perturbed H{sub k} and G{sub k}, respectively. The breakdown of Orthomin and Orthores are interpreted in terms of these underlying matrix factorizations. A connection with Lanczos algorithms is also examined, as is the special case of B-normal(1) matrices (for which efficient three-term CG algorithms exist).
NASA Astrophysics Data System (ADS)
Canning, Andrew; Raczkowski, David; Leung, Mary Ann; Wang, Lin-Wang; An, Joonhee; van Hove, Michel A.
2003-03-01
We will present the Grassman-metal conjugate gradient (GMCG) method for iterative diagonalization for the solution of the Kohn-Sham equations with a plane wave basis set. This is an all-bands method with variable occupancy for iterative diagonalization at fixed charge density. We will then present some results for sandwiches of Co, Cu and Ni systems which exhibit quantum well states. In particular we will show the effect of a single Ni layer at different positions on Quantum well states in a Co/Cu system. We have found that these systems are extremely difficult to converge without the use of the Grassman-metal approach. (This work was supported by the Director, Office of Advanced Scientific Computing Research, Division of Mathematical, Information and Computational Sciences of the U.S. Department of Energy and the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under contract number DE-AC03-76SF00098)
Conjugate gradient coupled with multigrid for an indefinite problem
NASA Technical Reports Server (NTRS)
Gozani, J.; Nachshon, A.; Turkel, E.
1984-01-01
An iterative algorithm for the Helmholtz equation is presented. This scheme was based on the preconditioned conjugate gradient method for the normal equations. The preconditioning is one cycle of a multigrid method for the discrete Laplacian. The smoothing algorithm is red-black Gauss-Seidel and is constructed so it is a symmetric operator. The total number of iterations needed by the algorithm is independent of h. By varying the number of grids, the number of iterations depends only weakly on k when k(3)h(2) is constant. Comparisons with a SSOR preconditioner are presented.
3D Electromagnetic inversion using conjugate gradients
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.
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
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.
Another hybrid conjugate gradient algorithm for unconstrained optimization
NASA Astrophysics Data System (ADS)
Andrei, Neculai
2008-02-01
Another hybrid conjugate gradient algorithm is subject to analysis. The parameter ? k is computed as a convex combination of beta ^{{HS}}_{k} (Hestenes-Stiefel) and beta ^{{DY}}_{k} (Dai-Yuan) algorithms, i.eE beta ^{C}_{k} = {left( {1 - theta _{k} } right)}beta ^{{HS}}_{k} + theta _{k} beta ^{{DY}}_{k} . The parameter ? k in the convex combination is computed in such a way so that the direction corresponding to the conjugate gradient algorithm to be the Newton direction and the pair (s k , y k ) to satisfy the quasi-Newton equation nabla ^{2} f{left( {x_{{k + 1}} } right)}s_{k} = y_{k} , where s_{k} = x_{{k + 1}} - x_{k} and y_{k} = g_{{k + 1}} - g_{k} . The algorithm uses the standard Wolfe line search conditions. Numerical comparisons with conjugate gradient algorithms show that this hybrid computational scheme outperforms the Hestenes-Stiefel and the Dai-Yuan conjugate gradient algorithms as well as the hybrid conjugate gradient algorithms of Dai and Yuan. A set of 750 unconstrained optimization problems are used, some of them from the CUTE library.
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.
Preconditioned conjugate gradient algorithms and software for solving large sparse linear systems
Young, D.M.; Jea, K.C.; Mai, Tsun-Zee
1987-03-01
The classical form of the conjugate gradient method (CG method), developed by Hestenes and Stiefel, for solving the linear system Au = b is applicable when the coefficient matrix A is symmetric and positive definite (SPD). In this paper we consider various alternative forms of the CG method as well as generalizations to cases where A is not necessarily SPD. This analysis includes the ''preconditioned conjugate gradient method'' which is equivalent to conjugate gradient acceleration of a basic iterative method corresponding to a preconditioned system. Both the symmetrizable case and the nonsymmetrizable case are considered. For the nonsymmetrizable case there are very few useful theoretical results available. A package of programs, known as ITPACK, has been developed as a tool for carrying out experimental studies on various algorithms. Preliminary conclusions based on experimental results are given. 42 refs.
Parallel conjugate gradient algorithms for manipulator dynamic simulation
NASA Technical Reports Server (NTRS)
Fijany, Amir; Scheld, Robert E.
1989-01-01
Parallel conjugate gradient algorithms for the computation of multibody dynamics are developed for the specialized case of a robot manipulator. For an n-dimensional positive-definite linear system, the Classical Conjugate Gradient (CCG) algorithms are guaranteed to converge in n iterations, each with a computation cost of O(n); this leads to a total computational cost of O(n sq) on a serial processor. A conjugate gradient algorithms is presented that provide greater efficiency using a preconditioner, which reduces the number of iterations required, and by exploiting parallelism, which reduces the cost of each iteration. Two Preconditioned Conjugate Gradient (PCG) algorithms are proposed which respectively use a diagonal and a tridiagonal matrix, composed of the diagonal and tridiagonal elements of the mass matrix, as preconditioners. Parallel algorithms are developed to compute the preconditioners and their inversions in O(log sub 2 n) steps using n processors. A parallel algorithm is also presented which, on the same architecture, achieves the computational time of O(log sub 2 n) for each iteration. Simulation results for a seven degree-of-freedom manipulator are presented. Variants of the proposed algorithms are also developed which can be efficiently implemented on the Robot Mathematics Processor (RMP).
Ship wake-detection procedure using conjugate gradient trained artificial neural networks
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.
Partial least squares, conjugate gradient and the fisher discriminant
Faber, V.
1996-12-31
The theory of multivariate regression has been extensively studied and is commonly used in many diverse scientific areas. A wide variety of techniques are currently available for solving the problem of multivariate calibration. The volume of literature on this subject is so extensive that understanding which technique to apply can often be very confusing. A common class of techniques for solving linear systems, and consequently applications of linear systems to multivariate analysis, are iterative methods. While common linear system solvers typically involve the factorization of the coefficient matrix A in solving the system Ax = b, this method can be impractical if A is large and sparse. Iterative methods such as Gauss-Seidel, SOR, Chebyshev semi-iterative, and related methods also often depend upon parameters that require calibration and which are sometimes hard to choose properly. An iterative method which surmounts many of these difficulties is the method of conjugate gradient. Algorithms of this type find solutions iteratively, by optimally calculating the next approximation from the residuals.
Syntheses of Gradient pi-Conjugated Copolymers of Thiophene
Locke, Jonas R.; McNeil, Anne J.
2010-11-09
we prepared the first gradient π-conjugated copolymers via Ni-catalyzed chain-growth copolymerization of 3-hexylthiophene and 3-((hexyloxy)methyl)thiophene. Because rate studies indicated little difference in monomer reactivities, one monomer was gradually added to the polymerization over time to form gradient copolymers. Now that controlled sequence π-conjugated copolymers can be synthesized, the next goal is to identify their unique properties, including phase-compatibilizing abilities in homopolymer blends. Preliminary data reported herein suggest that the solid-state optical and physical properties are influenced by the copolymer sequence. Finally, although the Ni-catalyzed copolymerizations are chain growth under the conditions reported herein, our preliminary attempts to expand the substrate scope by examining the copolymerization of monomers with varying steric and electronic properties has highlighted a need for developing improved catalysts.
A constrained conjugate gradient algorithm for computed tomography
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.
A complete implementation of the conjugate gradient algorithm on a reconfigurable supercomputer
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.
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.
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.
Two grid iteration with a conjugate gradient fine grid smoother applied to a groundwater flow model
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.
Efficient conjugate gradient algorithms for computation of the manipulator forward dynamics
NASA Technical Reports Server (NTRS)
Fijany, Amir; Scheid, Robert E.
1989-01-01
The applicability of conjugate gradient algorithms for computation of the manipulator forward dynamics is investigated. The redundancies in the previously proposed conjugate gradient algorithm are analyzed. A new version is developed which, by avoiding these redundancies, achieves a significantly greater efficiency. A preconditioned conjugate gradient algorithm is also presented. A diagonal matrix whose elements are the diagonal elements of the inertia matrix is proposed as the preconditioner. In order to increase the computational efficiency, an algorithm is developed which exploits the synergism between the computation of the diagonal elements of the inertia matrix and that required by the conjugate gradient algorithm.
Conjugate and method for forming aminomethyl phosphorus conjugates
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.
Solving large test-day models by iteration on data and preconditioned conjugate gradient.
Lidauer, M; Strandén, I; Mäntysaari, E A; Pösö, J; Kettunen, A
1999-12-01
A preconditioned conjugate gradient method was implemented into an iteration on a program for data estimation of breeding values, and its convergence characteristics were studied. An algorithm was used as a reference in which one fixed effect was solved by Gauss-Seidel method, and other effects were solved by a second-order Jacobi method. Implementation of the preconditioned conjugate gradient required storing four vectors (size equal to number of unknowns in the mixed model equations) in random access memory and reading the data at each round of iteration. The preconditioner comprised diagonal blocks of the coefficient matrix. Comparison of algorithms was based on solutions of mixed model equations obtained by a single-trait animal model and a single-trait, random regression test-day model. Data sets for both models used milk yield records of primiparous Finnish dairy cows. Animal model data comprised 665,629 lactation milk yields and random regression test-day model data of 6,732,765 test-day milk yields. Both models included pedigree information of 1,099,622 animals. The animal model ¿random regression test-day model¿ required 122 ¿305¿ rounds of iteration to converge with the reference algorithm, but only 88 ¿149¿ were required with the preconditioned conjugate gradient. To solve the random regression test-day model with the preconditioned conjugate gradient required 237 megabytes of random access memory and took 14% of the computation time needed by the reference algorithm. PMID:10629827
T2CG1, a package of preconditioned conjugate gradient solvers for TOUGH2
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.
NASA Technical Reports Server (NTRS)
Benediktsson, J. A.; Swain, P. H.; Ersoy, O. K.
1993-01-01
Application of neural networks to classification of remote sensing data is discussed. Conventional two-layer backpropagation is found to give good results in classification of remote sensing data but is not efficient in training. A more efficient variant, based on conjugate-gradient optimization, is used for classification of multisource remote sensing and geographic data and very-high-dimensional data. The conjugate-gradient neural networks give excellent performance in classification of multisource data, but do not compare as well with statistical methods in classification of very-high-dimentional data.
A preliminary investigation of 3D preconditioned conjugate gradient reconstruction for cone-beam CT
NASA Astrophysics Data System (ADS)
Fu, Lin; De Man, Bruno; Zeng, Kai; Benson, Thomas M.; Yu, Zhou; Cao, Guangzhi; Thibault, Jean-Baptiste
2012-03-01
Model-based iterative reconstruction (MBIR) methods based on maximum a posteriori (MAP) estimation have been recently introduced to multi-slice CT scanners. The model-based approach has shown promising image quality improvement with reduced radiation dose compared to conventional FBP methods, but the associated high computation cost limits its widespread use in clinical environments. Among the various choices of numerical algorithms to optimize the MAP cost function, simultaneous update methods such as the conjugate gradient (CG) method have a relatively high level of parallelism to take full advantage of a new generation of many-core computing hardware. With proper preconditioning techniques, fast convergence speeds of CG algorithms have been demonstrated in 3D emission and 2D transmission reconstruction. However, 3D transmission reconstruction using preconditioned conjugate gradient (PCG) has not been reported. Additional challenges in applying PCG in 3D CT reconstruction include the large size of clinical CT data, shift-variant and incomplete sampling, and complex regularization schemes to meet the diagnostic standard of image quality. In this paper, we present a ramp-filter based PCG algorithm for 3D CT MBIR. Convergence speeds of algorithms with and without using the preconditioner are compared.
Non-preconditioned conjugate gradient on cell and FPCA-based hybrid supercomputer nodes
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.
Non-preconditioned conjugate gradient on cell and FPGA based hybrid supercomputer nodes
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.
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.
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.
The conjugate gradient NAS parallel benchmark on the IBM SP1
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.
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.
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
Tsuruta, S; Misztal, I; Strandén, I
2001-05-01
Utility of the preconditioned conjugate gradient algorithm with a diagonal preconditioner for solving mixed-model equations in animal breeding applications was evaluated with 16 test problems. The problems included single- and multiple-trait analyses, with data on beef, dairy, and swine ranging from small examples to national data sets. Multiple-trait models considered low and high genetic correlations. Convergence was based on relative differences between left- and right-hand sides. The ordering of equations was fixed effects followed by random effects, with no special ordering within random effects. The preconditioned conjugate gradient program implemented with double precision converged for all models. However, when implemented in single precision, the preconditioned conjugate gradient algorithm did not converge for seven large models. The preconditioned conjugate gradient and successive overrelaxation algorithms were subsequently compared for 13 of the test problems. The preconditioned conjugate gradient algorithm was easy to implement with the iteration on data for general models. However, successive overrelaxation requires specific programming for each set of models. On average, the preconditioned conjugate gradient algorithm converged in three times fewer rounds of iteration than successive overrelaxation. With straightforward implementations, programs using the preconditioned conjugate gradient algorithm may be two or more times faster than those using successive overrelaxation. However, programs using the preconditioned conjugate gradient algorithm would use more memory than would comparable implementations using successive overrelaxation. Extensive optimization of either algorithm can influence rankings. The preconditioned conjugate gradient implemented with iteration on data, a diagonal preconditioner, and in double precision may be the algorithm of choice for solving mixed-model equations when sufficient memory is available and ease of implementation is
Ghosh, A
1988-08-01
Lanczos and conjugate gradient algorithms are important in computational linear algebra. In this paper, a parallel pipelined realization of these algorithms on a ring of optical linear algebra processors is described. The flow of data is designed to minimize the idle times of the optical multiprocessor and the redundancy of computations. The effects of optical round-off errors on the solutions obtained by the optical Lanczos and conjugate gradient algorithms are analyzed, and it is shown that optical preconditioning can improve the accuracy of these algorithms substantially. Algorithms for optical preconditioning and results of numerical experiments on solving linear systems of equations arising from partial differential equations are discussed. Since the Lanczos algorithm is used mostly with sparse matrices, a folded storage scheme to represent sparse matrices on spatial light modulators is also described. PMID:20531907
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 Ã 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.
A nonrecursive order N preconditioned conjugate gradient: Range space formulation of MDOF dynamics
NASA Technical Reports Server (NTRS)
Kurdila, Andrew J.
1990-01-01
While excellent progress has been made in deriving algorithms that are efficient for certain combinations of system topologies and concurrent multiprocessing hardware, several issues must be resolved to incorporate transient simulation in the control design process for large space structures. Specifically, strategies must be developed that are applicable to systems with numerous degrees of freedom. In addition, the algorithms must have a growth potential in that they must also be amenable to implementation on forthcoming parallel system architectures. For mechanical system simulation, this fact implies that algorithms are required that induce parallelism on a fine scale, suitable for the emerging class of highly parallel processors; and transient simulation methods must be automatically load balancing for a wider collection of system topologies and hardware configurations. These problems are addressed by employing a combination range space/preconditioned conjugate gradient formulation of multi-degree-of-freedom dynamics. The method described has several advantages. In a sequential computing environment, the method has the features that: by employing regular ordering of the system connectivity graph, an extremely efficient preconditioner can be derived from the 'range space metric', as opposed to the system coefficient matrix; because of the effectiveness of the preconditioner, preliminary studies indicate that the method can achieve performance rates that depend linearly upon the number of substructures, hence the title 'Order N'; and the method is non-assembling. Furthermore, the approach is promising as a potential parallel processing algorithm in that the method exhibits a fine parallel granularity suitable for a wide collection of combinations of physical system topologies/computer architectures; and the method is easily load balanced among processors, and does not rely upon system topology to induce parallelism.
NASA Astrophysics Data System (ADS)
Perez, L.; Autrique, L.; Gillet, M.
2008-11-01
The aim of this paper is to investigate the thermal diffusivity identification of a multilayered material dedicated to fire protection. In a military framework, fire protection needs to meet specific requirements, and operational protective systems must be constantly improved in order to keep up with the development of new weapons. In the specific domain of passive fire protections, intumescent coatings can be an effective solution on the battlefield. Intumescent materials have the ability to swell up when they are heated, building a thick multi-layered coating which provides efficient thermal insulation to the underlying material. Due to the heat aggressions (fire or explosion) leading to the intumescent phenomena, high temperatures are considered and prevent from linearization of the mathematical model describing the system state evolution. Previous sensitivity analysis has shown that the thermal diffusivity of the multilayered intumescent coating is a key parameter in order to validate the predictive numerical tool and therefore for thermal protection optimisation. A conjugate gradient method is implemented in order to minimise the quadratic cost function related to the error between predicted temperature and measured temperature. This regularisation algorithm is well adapted for a large number of unknown parameters.
NASA Astrophysics Data System (ADS)
Singh, A.; Sharma, S. P.
2015-12-01
We describe the implementation of a new fast imaging technique to invert very low frequency (VLF) data measured on profiles into corresponding apparent current density systems over the 2D earth. First, a formulation has been derived to compute the vertical component of the magnetic field for a given 2D current density distribution in the Earth's subsurface. Since the vertical component of the magnetic field is proportional to the real anomaly of VLF electromagnetic measurement, the derived formulation has been used for imaging subsurface structures. The 2D inversion code incorporating the preconditioned conjugate gradient approach was developed for imaging of the subsurface conductors using the real VLF anomaly in terms of apparent current density distribution in the subsurface. The preconditioner determined by the distances between the cells and the observation points greatly improved the quality of the very low frequency imaging. Finally, we tested our method using synthetic and real data and all tests returned favorable results. The presented formulation were also compared with other imaging techniques in terms of apparent current density and resistivity distribution using a standard numerical forward modeling and inversion technique. The presented imaging technique shows improvement with respect to the filtering approaches in depicting subsurface conductors. Further, results obtained using the presented approach is closer to the results of rigorous resistivity inversion.
Embedding SAS approach into conjugate gradient algorithms for asymmetric 3D elasticity problems
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).
Rakvongthai, Yothin; Ouyang, Jinsong; Guerin, Bastien; Li, Quanzheng; Alpert, Nathaniel M.; El Fakhri, Georges
2013-01-01
Purpose: Our research goal is to develop an algorithm to reconstruct cardiac positron emission tomography (PET) kinetic parametric images directly from sinograms and compare its performance with the conventional indirect approach. Methods: Time activity curves of a NCAT phantom were computed according to a one-tissue compartmental kinetic model with realistic kinetic parameters. The sinograms at each time frame were simulated using the activity distribution for the time frame. The authors reconstructed the parametric images directly from the sinograms by optimizing a cost function, which included the Poisson log-likelihood and a spatial regularization terms, using the preconditioned conjugate gradient (PCG) algorithm with the proposed preconditioner. The proposed preconditioner is a diagonal matrix whose diagonal entries are the ratio of the parameter and the sensitivity of the radioactivity associated with parameter. The authors compared the reconstructed parametric images using the direct approach with those reconstructed using the conventional indirect approach. Results: At the same bias, the direct approach yielded significant relative reduction in standard deviation by 12%–29% and 32%–70% for 50 × 106 and 10 × 106 detected coincidences counts, respectively. Also, the PCG method effectively reached a constant value after only 10 iterations (with numerical convergence achieved after 40–50 iterations), while more than 500 iterations were needed for CG. Conclusions: The authors have developed a novel approach based on the PCG algorithm to directly reconstruct cardiac PET parametric images from sinograms, and yield better estimation of kinetic parameters than the conventional indirect approach, i.e., curve fitting of reconstructed images. The PCG method increases the convergence rate of reconstruction significantly as compared to the conventional CG method. PMID:24089922
Preconditioned conjugate gradient wave-front reconstructors for multiconjugate adaptive optics
NASA Astrophysics Data System (ADS)
Gilles, Luc; Ellerbroek, Brent L.; Vogel, Curtis R.
2003-09-01
Multiconjugate adaptive optics (MCAO) systems with 104-105 degrees of freedom have been proposed for future giant telescopes. Using standard matrix methods to compute, optimize, and implement wave-front control algorithms for these systems is impractical, since the number of calculations required to compute and apply the reconstruction matrix scales respectively with the cube and the square of the number of adaptive optics degrees of freedom. We develop scalable open-loop iterative sparse matrix implementations of minimum variance wave-front reconstruction for telescope diameters up to 32 m with more than 104 actuators. The basic approach is the preconditioned conjugate gradient method with an efficient preconditioner, whose block structure is defined by the atmospheric turbulent layers very much like the layer-oriented MCAO algorithms of current interest. Two cost-effective preconditioners are investigated: a multigrid solver and a simpler block symmetric Gauss-Seidel (BSGS) sweep. Both options require off-line sparse Cholesky factorizations of the diagonal blocks of the matrix system. The cost to precompute these factors scales approximately as the three-halves power of the number of estimated phase grid points per atmospheric layer, and their average update rate is typically of the order of 10-2 Hz, i.e., 4-5 orders of magnitude lower than the typical 103 Hz temporal sampling rate. All other computations scale almost linearly with the total number of estimated phase grid points. We present numerical simulation results to illustrate algorithm convergence. Convergence rates of both preconditioners are similar, regardless of measurement noise level, indicating that the layer-oriented BSGS sweep is as effective as the more elaborated multiresolution preconditioner.
Preconditioned conjugate gradient wave-front reconstructors for multiconjugate adaptive optics.
Gilles, Luc; Ellerbroek, Brent L; Vogel, Curtis R
2003-09-10
Multiconjugate adaptive optics (MCAO) systems with 10(4)-10(5) degrees of freedom have been proposed for future giant telescopes. Using standard matrix methods to compute, optimize, and implement wavefront control algorithms for these systems is impractical, since the number of calculations required to compute and apply the reconstruction matrix scales respectively with the cube and the square of the number of adaptive optics degrees of freedom. We develop scalable open-loop iterative sparse matrix implementations of minimum variance wave-front reconstruction for telescope diameters up to 32 m with more than 10(4) actuators. The basic approach is the preconditioned conjugate gradient method with an efficient preconditioner, whose block structure is defined by the atmospheric turbulent layers very much like the layer-oriented MCAO algorithms of current interest. Two cost-effective preconditioners are investigated: a multigrid solver and a simpler block symmetric Gauss-Seidel (BSGS) sweep. Both options require off-line sparse Cholesky factorizations of the diagonal blocks of the matrix system. The cost to precompute these factors scales approximately as the three-halves power of the number of estimated phase grid points per atmospheric layer, and their average update rate is typically of the order of 10(-2) Hz, i.e., 4-5 orders of magnitude lower than the typical 10(3) Hz temporal sampling rate. All other computations scale almost linearly with the total number of estimated phase grid points. We present numerical simulation results to illustrate algorithm convergence. Convergence rates of both preconditioners are similar, regardless of measurement noise level, indicating that the layer-oriented BSGS sweep is as effective as the more elaborated multiresolution preconditioner. PMID:14503692
Non-linear Conjugate Gradient Time-Domain Controlled Inversion Source
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.
Non-linear Conjugate Gradient Time-Domain Controlled Inversion Source
Energy Science and Technology Software Center (ESTSC)
2006-11-16
Software that simulates and inverts time-domain electromagnetic field data for subsurface electrical properties (electrical conductivity) of geological media. The software treats data produced by a step-wise source signal from either galvanic (grounded wires) or inductive (magnetic loops) sources. The inversion process is carried inductive (magnetic loops) sources. The inversion process is carried out using a non-linear conjugate gradient optimization scheme, which minimizes the misfit between field data and model data using a least squares criteria.more » The software is an upgrade from the code TEM3D ver. 2.0. The upgrade includes the following components: (1) Improved (faster)memory access during gradient computation. (2) Data parellelization scheme: Multiple transmitters (sources) can be distributed accross several banks of processors (daa-planes). Similarly, the receivers of each source are also distributed accross the corresponding data-plane. (3) Improved data-IO.« less
Method for synthesizing peptides with saccharide linked enzyme polymer conjugates
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.
Method for synthesizing peptides with saccharide linked enzyme polymer conjugates
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.
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.
Preconditioned conjugate gradient technique for the analysis of symmetric anisotropic structures
NASA Technical Reports Server (NTRS)
Noor, Ahmed K.; Peters, Jeanne M.
1987-01-01
An efficient preconditioned conjugate gradient (PCG) technique and a computational procedure are presented for the analysis of symmetric anisotropic structures. The technique is based on selecting the preconditioning matrix as the orthotropic part of the global stiffness matrix of the structure, with all the nonorthotropic terms set equal to zero. This particular choice of the preconditioning matrix results in reducing the size of the analysis model of the anisotropic structure to that of the corresponding orthotropic structure. The similarities between the proposed PCG technique and a reduction technique previously presented by the authors are identified and exploited to generate from the PCG technique direct measures for the sensitivity of the different response quantities to the nonorthotropic (anisotropic) material coefficients of the structure. The effectiveness of the PCG technique is demonstrated by means of a numerical example of an anisotropic cylindrical panel.
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.
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.
A conjugate gradient algorithm for the astrometric core solution of Gaia
NASA Astrophysics Data System (ADS)
Bombrun, A.; Lindegren, L.; Hobbs, D.; Holl, B.; Lammers, U.; Bastian, U.
2012-02-01
Context. The ESA space astrometry mission Gaia, planned to be launched in 2013, has been designed to make angular measurements on a global scale with micro-arcsecond accuracy. A key component of the data processing for Gaia is the astrometric core solution, which must implement an efficient and accurate numerical algorithm to solve the resulting, extremely large least-squares problem. The Astrometric Global Iterative Solution (AGIS) is a framework that allows to implement a range of different iterative solution schemes suitable for a scanning astrometric satellite. Aims: Our aim is to find a computationally efficient and numerically accurate iteration scheme for the astrometric solution, compatible with the AGIS framework, and a convergence criterion for deciding when to stop the iterations. Methods: We study an adaptation of the classical conjugate gradient (CG) algorithm, and compare it to the so-called simple iteration (SI) scheme that was previously known to converge for this problem, although very slowly. The different schemes are implemented within a software test bed for AGIS known as AGISLab. This allows to define, simulate and study scaled astrometric core solutions with a much smaller number of unknowns than in AGIS, and therefore to perform a large number of numerical experiments in a reasonable time. After successful testing in AGISLab, the CG scheme has been implemented also in AGIS. Results: The two algorithms CG and SI eventually converge to identical solutions, to within the numerical noise (of the order of 0.00001 micro-arcsec). These solutions are moreover independent of the starting values (initial star catalogue), and we conclude that they are equivalent to a rigorous least-squares estimation of the astrometric parameters. The CG scheme converges up to a factor four faster than SI in the tested cases, and in particular spatially correlated truncation errors are much more efficiently damped out with the CG scheme. While it appears to be difficult
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.
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.
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.
Methods to Design and Synthesize Antibody-Drug Conjugates (ADCs)
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
The application of projected conjugate gradient solvers on graphical processing units
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.
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.
Conjugate heat transfer with the entropic lattice Boltzmann method.
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
NASA Astrophysics Data System (ADS)
Yeole, Sachin D.; Gadre, Shridhar R.
2010-03-01
For the accurate ab initio treatment of large molecular systems, linear scaling methods (LSMs) have been devised and successfully applied to covalently bonded systems as well as to those involving weak intra/intermolecular bonds. Very few attempts to apply LSM to highly conjugated molecules, especially to two-dimensional systems, have so far been reported in the literature. The present article examines the applicability of a LSM, viz., molecular tailoring approach (MTA), to π-conjugated systems within density functional theory. A few test cases within second order Møller-Plesset framework are also reported. MTA is applied to some one-dimensional π-conjugated molecules, for which the difference between MTA energy and actual energy is found out to be less than 1 mhartree and also reduced computation time as well as hardware requirements. The method is also extended to some small/medium-sized two-dimensional π-conjugated molecules by developing a systematic algorithm for tailoring such systems. However, for such systems, although the energies are in error by a few millihartrees, gradients are found to match reasonably well their actual counterparts. Hence, geometry optimization of these systems within MTA framework is attempted. The geometries thus generated are found to be in good agreement with their actual counterparts, with the actual single point energies matching within 1 mhartree, along with reduced computational effort. These results point toward the potential applicability of MTA to large two- and three-dimensional π-conjugated systems.
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.
NASA Astrophysics Data System (ADS)
Vollebregt, E. A. H.
2014-01-01
This paper presents our new solver BCCG+FAI for solving elastic normal contact problems. This is a comprehensible approach that is based on the Conjugate Gradients (CG) algorithm and that uses FFTs. A first novel aspect is the definition of the “FFT-based Approximate Inverse” preconditioner. The underlying idea is that the inverse matrix can be approximated well using a Toeplitz or block-Toeplitz form, which can be computed using the FFT of the original matrix elements. This preconditioner makes the total number of CG iterations effectively constant in 2D and very slowly increasing in 3D problems. A second novelty is how we deal with a prescribed total force. This uses a deflation technique in such a way that CGs convergence and finite termination properties are maintained. Numerical results show that this solver is more effective than existing CG-based strategies, such that it can compete with Multi-Grid strategies over a much larger problem range. In our opinion it could be the new method of choice because of its simple structure and elegant theory, and because robust performance is achieved independently of any problem specific parameters.
A method for easily customizable gradient gel electrophoresis.
Miller, Andrew J; Roman, Brandon; Norstrom, Eric
2016-09-15
Gradient polyacrylamide gel electrophoresis is a powerful tool for the resolution of polypeptides by relative mobility. Here, we present a simplified method for generating polyacrylamide gradient gels for routine analysis without the need for specialized mixing equipment. The method allows for easily customizable gradients which can be optimized for specific polypeptide resolution requirements. Moreover, the method eliminates the possibility of buffer cross contamination in mixing equipment, and the time and resources saved with this method in place of traditional gradient mixing, or the purchase of pre-cast gels, are noteworthy given the frequency with which many labs use gradient gel SDS-PAGE. PMID:27393767
A nonrecursive 'Order N' preconditioned conjugate gradient/range space formulation of MDOF dynamics
NASA Technical Reports Server (NTRS)
Kurdila, A. J.; Menon, R.; Sunkel, John
1991-01-01
This paper addresses the requirements of present-day mechanical system simulations of algorithms that induce parallelism on a fine scale and of transient simulation methods which must be automatically load balancing for a wide collection of system topologies and hardware configurations. To this end, a combination range space/preconditioned conjugage gradient formulation of multidegree-of-freedon dynamics is developed, which, by employing regular ordering of the system connectivity graph, makes it possible to derive an extremely efficient preconditioner from the range space metric (as opposed to the system coefficient matrix). Because of the effectiveness of the preconditioner, the method can achieve performance rates that depend linearly on the number of substructures. The method, termed 'Order N' does not require the assembly of system mass or stiffness matrices, and is therefore amenable to implementation on work stations. Using this method, a 13-substructure model of the Space Station was constructed.
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.
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.
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
Multi-gradient drilling method and system
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.
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
Gradient porous hydroxyapatite ceramics fabricated by freeze casting method
NASA Astrophysics Data System (ADS)
Zuo, Kai-hui; zhang, Yuan; Jiang, Dongliang; Zeng, Yu-Ping
2011-04-01
By controlling the cooling rates and the composition of slurries, the gradient porous hydroxyapatite ceramics are fabricated by the freeze casting method. According to the different cooling rate, the pores of HAP ceramics fabricated by gradient freeze casting are divided into three parts: one is lamellar pores, another is column pore and the last one is fine round pores. The laminated freeze casting is in favour of obtaining the gradient porous ceramics composed of different materials and the ceramics have unclear interfaces.
Methods for calculating conjugate problems of heat transfer
NASA Astrophysics Data System (ADS)
Kalinin, E. K.; Dreitser, G. A.; Kostiuk, V. V.; Berlin, I. I.
Methods are examined for calculating various conjugate problems of heat transfer in channels and closed vessels in cases of single-phase and two-phase flow in steady and unsteady conditions. The single-phase-flow studies involve the investigation of gaseous and liquid heat-carriers in pipes, annular and plane channels, and pipe bundles in cases of cooling and heating. General relationships are presented for heat transfer in cases of film, transition, and nucleate boiling, as well as for boiling crises. Attention is given to methods for analyzing the filling and cooling of conduits and tanks by cryogenic liquids; and ways to intensify heat transfer in these conditions are examined.
Liu, Guhuan; Hu, Jinming; Zhang, Guoying; Liu, Shiyong
2015-07-15
Spatiotemporal switching of respective phototherapy modes at the cellular level with minimum side effects and high therapeutic efficacy is a major challenge for cancer phototherapy. Herein we demonstrate how to address this issue by employing photosensitizer-conjugated pH-responsive block copolymers in combination with intracellular endocytic pH gradients. At neutral pH corresponding to extracellular and cytosol milieu, the copolymers self-assemble into micelles with prominently quenched fluorescence emission and low (1)O2 generation capability, favoring a highly efficient photothermal module. Under mildly acidic pH associated with endolysosomes, protonation-triggered micelle-to-unimer transition results in recovered emission and enhanced photodynamic (1)O2 efficiency, which synergistically actuates release of encapsulated drugs, endosomal escape, and photochemical internalization processes. PMID:25514473
Efficient algorithms for the recognition of topologically conjugate gradient-like diffeomorhisms
NASA Astrophysics Data System (ADS)
Grines, Vyacheslav Z.; Malyshev, Dmitry S.; Pochinka, Olga V.; Zinina, Svetlana Kh.
2016-03-01
It is well known that the topological classification of structurally stable flows on surfaces as well as the topological classification of some multidimensional gradient-like systems can be reduced to a combinatorial problem of distinguishing graphs up to isomorphism. The isomorphism problem of general graphs obviously can be solved by a standard enumeration algorithm. However, an efficient algorithm (i. e., polynomial in the number of vertices) has not yet been developed for it, and the problem has not been proved to be intractable (i. e., NPcomplete). We give polynomial-time algorithms for recognition of the corresponding graphs for two gradient-like systems. Moreover, we present efficient algorithms for determining the orientability and the genus of the ambient surface. This result, in particular, sheds light on the classification of configurations that arise from simple, point-source potential-field models in efforts to determine the nature of the quiet-Sun magnetic field.
Adaptive method of realizing natural gradient learning for multilayer perceptrons.
Amari, S; Park, H; Fukumizu, K
2000-06-01
The natural gradient learning method is known to have ideal performances for on-line training of multilayer perceptrons. It avoids plateaus, which give rise to slow convergence of the backpropagation method. It is Fisher efficient, whereas the conventional method is not. However, for implementing the method, it is necessary to calculate the Fisher information matrix and its inverse, which is practically very difficult. This article proposes an adaptive method of directly obtaining the inverse of the Fisher information matrix. It generalizes the adaptive Gauss-Newton algorithms and provides a solid theoretical justification of them. Simulations show that the proposed adaptive method works very well for realizing natural gradient learning. PMID:10935719
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.
Counter-extrapolation method for conjugate interfaces in computational heat and mass transfer.
Le, Guigao; Oulaid, Othmane; Zhang, Junfeng
2015-03-01
In this paper a conjugate interface method is developed by performing extrapolations along the normal direction. Compared to other existing conjugate models, our method has several technical advantages, including the simple and straightforward algorithm, accurate representation of the interface geometry, applicability to any interface-lattice relative orientation, and availability of the normal gradient. The model is validated by simulating the steady and unsteady convection-diffusion system with a flat interface and the steady diffusion system with a circular interface, and good agreement is observed when comparing the lattice Boltzmann results with respective analytical solutions. A more general system with unsteady convection-diffusion process and a curved interface, i.e., the cooling process of a hot cylinder in a cold flow, is also simulated as an example to illustrate the practical usefulness of our model, and the effects of the cylinder heat capacity and thermal diffusivity on the cooling process are examined. Results show that the cylinder with a larger heat capacity can release more heat energy into the fluid and the cylinder temperature cools down slower, while the enhanced heat conduction inside the cylinder can facilitate the cooling process of the system. Although these findings appear obvious from physical principles, the confirming results demonstrates the application potential of our method in more complex systems. In addition, the basic idea and algorithm of the counter-extrapolation procedure presented here can be readily extended to other lattice Boltzmann models and even other computational technologies for heat and mass transfer systems. PMID:25871245
DFT methods for conjugated materials: From benchmarks to functionals
NASA Astrophysics Data System (ADS)
Sears, John; Bredas, Jean-Luc
2012-02-01
From a theoretical standpoint, many of the problems of interest in the study of pi-conjugated materials for organic electronics applications pose a particular challenge for many modern density functional theory methods. Systematic errors have been observed, for instance, in the description of charge-transfer excitations at donor/acceptor interfaces, in linear and non-linear polarizabilites, as well as in the geometric and electronic properties of conjugated polymers [1,2]. We will discuss recent results in our lab aimed at: (i) understanding the sources of error for some of these problems; (ii) addressing these errors using tuned long-range corrected functionals; and (iii) using these results to guide the development of state-of-the-art methodologies in a new open-source DFT code. [4pt] [1] J. S. Sears, T. Korzdorfer, C. R. Zhang, and J. L. Bredas, J. Chem. Phys. 135 151103 (2011)[0pt] [2] T. Korzdorfer, J. S. Sears, C. Sutton, and J. L. Bredas, J. Chem. Phys., accepted.
NASA Astrophysics Data System (ADS)
Prasuhn, Duane E.; Blanco-Canosa, Juan B.; Vora, Gary J.; Mattoussi, Hedi M.; Dawson, Philip E.; Medintz, Igor L.
2009-02-01
One of the most prominent research areas in nanotechnology is the development of nanoparticle systems for biomedical applications. This is founded upon the expectation that such species could ultimately be imbued with multiple simultaneous functions, such as the presentation of a therapeutic payload or diagnostic sensor for in vivo trafficking to desired cell types. In recent years, semiconductor quantum dots (QDs) have been actively explored as novel display systems, because of their unique photophysical properties. Using an aniline-mediated hydrazone coupling, a polyhisitidine-appended peptide was derivatized with a DNA strand and successfully self-assembled to QDs, yielding nanoparticles displaying up to approximately 15 peptide/DNA conjugates. This ligation method is a viable chemistry for displaying biomolecules, because of the orthogonality of the ketone and hydrazine moieties to most biological functionality and the reaction can be performed under mild conditions in aqueous media. The modified QDs were further characterized by gel electrophoresis, and microarray studies; showing the self-assembly was successful and the DNA strands were still available for hybridization with a complement sequence.
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.
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.
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.
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.
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.
A new simple method to estimate fracture pressure gradient
Rocha, L.A.; Bourgoyne, A.T.
1994-12-31
Projecting safer and more economic wells calls for estimating correctly the fracture pressure gradient. On the other hand, a poor prediction of the fracture pressure gradient may lead to serious accidents such as lost circulation followed by a kick. Although these kinds of accidents can occur in any phase of the well, drilling shallow formations can offer additional dangerous due to shallow gas kicks, because they have the potential of becoming a shallow gas blowout leading sometimes to the formation of craters. Often, one of the main problems when estimating the fracture pressure gradient is the lack of data. In fact, drilling engineers generally face situations where only leak off test data (frequently having questionable results) are available. This problem is normally the case when drilling shallow formations where very few information is collected. This paper presents a new method to estimate fracture pressure gradient. The proposed method has the advantage of (a) using only the knowledge of leak off test data and (b) being independent of the pore pressure. The method is based on a new concept called pseudo-overburden pressure, defined as the overburden pressure a formation would exhibit if it were plastic. The method was applied in several areas of the world such as US Gulf Coast (Mississippi Canyon and Green Canyon) with very good results.
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.
Discontinuous Galerkin finite element methods for gradient plasticity.
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.
Material point method enhanced by modified gradient of shape function
NASA Astrophysics Data System (ADS)
Zhang, Duan Z.; Ma, Xia; Giguere, Paul T.
2011-07-01
A numerical scheme of computing quantities involving gradients of shape functions is introduced for the material point method (MPM), so that the quantities are continuous as material points move across cell boundaries. The noise and instability caused by cell crossing of the material points are then eliminated. In this scheme, the formulas used to compute these quantities can be expressed in the same forms as in the original material point method, but with the gradient of the shape function modified. For one-dimensional cases, the gradient of the shape function used in the generalized interpolation material point (GIMP) method is a special case of the modified gradient if the characteristic function of a material point is introduced. The characteristic function of a material point is not otherwise needed in this scheme, therefore difficulties in tracking its evolution are avoided. Although the support of the modified gradient of a shape function is enlarged from the cell containing the material point to also include the immediate neighbor cells, all the non-local effects of a material point can be accounted for by two consecutive local operations. Therefore this scheme can be used in calculations with unstructured grids. This scheme is proved to satisfy mass and momentum conservations exactly. The error in energy conservation is shown to be second order on both spatial and temporal discretizations. Although the error in energy conservation is the same order as that in the original material point method, numerical examples show that this scheme has significantly better energy conservation properties than those of the original material point method.
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.
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.
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.
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.
Gilles, Luc; Massioni, Paolo; Kulcsár, Caroline; Raynaud, Henri-François; Ellerbroek, Brent
2013-05-01
This paper discusses the performance and cost of two computationally efficient Fourier-based tomographic wavefront reconstruction algorithms for wide-field laser guide star (LGS) adaptive optics (AO). The first algorithm is the iterative Fourier domain preconditioned conjugate gradient (FDPCG) algorithm developed by Yang et al. [Appl. Opt.45, 5281 (2006)], combined with pseudo-open-loop control (POLC). FDPCG's computational cost is proportional to N log(N), where N denotes the dimensionality of the tomography problem. The second algorithm is the distributed Kalman filter (DKF) developed by Massioni et al. [J. Opt. Soc. Am. A28, 2298 (2011)], which is a noniterative spatially invariant controller. When implemented in the Fourier domain, DKF's cost is also proportional to N log(N). Both algorithms are capable of estimating spatial frequency components of the residual phase beyond the wavefront sensor (WFS) cutoff frequency thanks to regularization, thereby reducing WFS spatial aliasing at the expense of more computations. We present performance and cost analyses for the LGS multiconjugate AO system under design for the Thirty Meter Telescope, as well as DKF's sensitivity to uncertainties in wind profile prior information. We found that, provided the wind profile is known to better than 10% wind speed accuracy and 20 deg wind direction accuracy, DKF, despite its spatial invariance assumptions, delivers a significantly reduced wavefront error compared to the static FDPCG minimum variance estimator combined with POLC. Due to its nonsequential nature and high degree of parallelism, DKF is particularly well suited for real-time implementation on inexpensive off-the-shelf graphics processing units. PMID:23695321
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.
A new simple method to estimate fracture pressure gradient
Rocha, L.A.; Bourgoyne, A.T.
1996-09-01
Projecting safety and more economic wells calls for estimating correctly the fracture pressure gradient. On the other hand, a poor prediction of the fracture pressure gradient may lead to serious accidents, such as lost circulation followed by a kick. Although these kind of accidents can occur in any phase of the well, drilling shallow formations can offer additional dangers caused by shallow gas kicks because they have the potential of becoming a shallow gas blowout leading sometimes to the formation of craters. This paper presents a new method to estimate fracture pressure gradient. The proposed method has the advantage of (1) using only the knowledge of leakoff test data and (2) being independent of the pore pressure. The method is based on a new concept called pseudo-overburden pressure, defined as the overburden pressure a formation would exhibit if it were plastic. The method was applied in several areas of the world, such as the US Gulf Coast (Mississippi Canyon and Green Canyon), with very good results.
Gradient-based image recovery methods from incomplete Fourier measurements.
Patel, Vishal M; Maleh, Ray; Gilbert, Anna C; Chellappa, Rama
2012-01-01
A major problem in imaging applications such as magnetic resonance imaging and synthetic aperture radar is the task of trying to reconstruct an image with the smallest possible set of Fourier samples, every single one of which has a potential time and/or power cost. The theory of compressive sensing (CS) points to ways of exploiting inherent sparsity in such images in order to achieve accurate recovery using sub-Nyquist sampling schemes. Traditional CS approaches to this problem consist of solving total-variation (TV) minimization programs with Fourier measurement constraints or other variations thereof. This paper takes a different approach. Since the horizontal and vertical differences of a medical image are each more sparse or compressible than the corresponding TV image, CS methods will be more successful in recovering these differences individually. We develop an algorithm called GradientRec that uses a CS algorithm to recover the horizontal and vertical gradients and then estimates the original image from these gradients. We present two methods of solving the latter inverse problem, i.e., one based on least-square optimization and the other based on a generalized Poisson solver. After a thorough derivation of our complete algorithm, we present the results of various experiments that compare the effectiveness of the proposed method against other leading methods. PMID:21690011
Conjugation behaviours of CdTe quantum dots and antibody by a novel immunochromatographic method.
Wang, Y; Bai, Y; Wei, X
2011-03-01
Three water-soluble CdTe quantum dots (QDs) (green-emitting, yellow-emitting and red-emitting) were synthesised for different refluxing time with 3-mercaptopropionic acid (MPA) as stabiliser. Then the red-emitting CdTe QDs and mouse immunoglobulin G (IgG) were taken as the representative to study the conjugation behaviour of QDs and antibody by a novel immunochromatographic method. After comparing with several methods, that is, direct conjugation, 1-ethyl-3(3-dimethylaminopropyl) carbodiimides hydrochloride (EDC)-mediated conjugation, N-hydroxysuccinimide (NHS)-mediated conjugation, EDC/NHS-mediated conjugation by immunochromatographic strips, EDC and NHS were selected together as coupling agents to conjugate QDs with antibody efficiently. Finally, the K562 leukaemia cells were incubated with the EDC/NHS-mediated conjugates to evaluate the performance in practical application, and the result from fluorescence images showed that it was successfully applied to label cells. The immunochromatographic strip was a superior method to study the conjugation of the fluorophore and antibody. PMID:21241157
Method to conjugate polysaccharide antigens to surfaces for the detection of antibodies.
Boas, Ulrik; Lind, Peter; Riber, Ulla
2014-11-15
A new generic method for the conjugation of lipopolysaccharide (LPS)-derived polysaccharide antigens from gram-negative bacteria has been developed using Salmonella as a model. After removal of lipid A from the LPS by mild acidolysis, the polysaccharide antigen was conjugated to polystyrene microbeads modified with N-alkyl hydroxylamine and N-alkyl-O-methyl hydroxylamine surface groups by incubation of antigen and beads for 16 h at 40 °C without the need for coupling agents. The efficiency of the new method was evaluated by flow cytometry in model samples and serum samples containing antibodies against Salmonella typhimurium and Salmonella dublin. The presented method was compared with a similar method for conjugation of Salmonella polysaccharide antigens to surfaces. Here, the new method showed higher antigen coupling efficiency by detecting low concentrations of antibodies. Furthermore, the polysaccharide-conjugated beads showed preserved bioactivity after 1 year of use. PMID:25076184
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.
Multispectral face liveness detection method based on gradient features
NASA Astrophysics Data System (ADS)
Hou, Ya-Li; Hao, Xiaoli; Wang, Yueyang; Guo, Changqing
2013-11-01
Face liveness detection aims to distinguish genuine faces from disguised faces. Most previous works under visible light focus on classification of genuine faces and planar photos or videos. To handle the three-dimensional (3-D) disguised faces, liveness detection based on multispectral images has been shown to be an effective choice. In this paper, a gradient-based multispectral method has been proposed for face liveness detection. Three feature vectors are developed to reduce the influence of varying illuminations. The reflectance-based feature achieves the best performance, which has a true positive rate of 98.3% and a true negative rate of 98.7%. The developed methods are also tested on individual bands to provide a clue for band selection in the imaging system. Preliminary results on different face orientations are also shown. The contributions of this paper are threefold. First, a gradient-based multispectral method has been proposed for liveness detection, which considers the reflectance properties of all the distinctive regions in a face. Second, three illumination-robust features are studied based on a dataset with two-dimensional planar photos, 3-D mannequins, and masks. Finally, the performance of the method on different spectral bands and face orientations is also shown in the evaluations.
Conjugate heat and mass transfer in the lattice Boltzmann equation method
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
EVALUATION OF A METHOD TO MEASURE CONJUGAL TRANSFER OF RECOMBINANT DNA IN SOIL SLURRIES
Release of recombinant microbes into the environment necessitates an evaluation of their ability to transfer genetic material. he present report evaluates a method to detect conjugal DNA plasmid transfer in soil slurries under various environmental conditions. onor Pseudomonas ce...
Streptavidin conjugation and quantification-a method evaluation for nanoparticles.
Quevedo, Pablo Darío; Behnke, Thomas; Resch-Genger, Ute
2016-06-01
Aiming at the development of validated protocols for protein conjugation of nanomaterials and the determination of protein labeling densities, we systematically assessed the conjugation of the model protein streptavidin (SAv) to 100-, 500-, and 1000-nm-sized polystyrene and silica nanoparticles and dye-encoded polymer particles with two established conjugation chemistries, based upon achievable coupling efficiencies and labeling densities. Bioconjugation reactions compared included EDC/sulfo NHS ester chemistry for direct binding of the SAv to carboxyl groups at the particle surface and maleimide-thiol chemistry in conjunction with heterobifunctional PEG linkers and aminated nanoparticles (NPs). Quantification of the total and functional amounts of SAv on these nanomaterials and unreacted SAv in solution was performed with the BCA assay and the biotin-FITC (BF) titration, relying on different signal generation principles, which are thus prone to different interferences. Our results revealed a clear influence of the conjugation chemistry on the amount of NP crosslinking, yet under optimized reaction conditions, EDC/sulfo NHS ester chemistry and the attachment via heterobifunctional PEG linkers led to comparably efficient SAv coupling and good labeling densities. Particle size can obviously affect protein labeling densities and particularly protein functionality, especially for larger particles. For unstained nanoparticles, direct bioconjugation seems to be the most efficient strategy, whereas for dye-encoded nanoparticles, PEG linkers are to be favored for the prevention of dye-protein interactions which can affect protein functionality specifically in the case of direct SAv binding. Moreover, an influence of particle size on achievable protein labeling densities and protein functionality could be demonstrated. PMID:27038055
Testing Method for Heat Resistance Under Temperature Gradient
NASA Astrophysics Data System (ADS)
Takagi, K.; Kawasaki, A.; Itoh, Y.; Harada, Y.; Ono, F.
2007-12-01
“Testing Method for Heat Resistance under Temperature Gradient” is a Japanese Industrial Standard (JIS) newly established by the Minister of Economy, Trade and Industry, after deliberations by the Japanese Industrial Standards Committee, in accordance with the Industrial Standardization Law. This standard specified the testing method for heat resistance under temperature gradient of materials and coated members of equipment exposed to high temperature, such as aircraft engines, gas turbines, and so on. This paper introduces the principle and overview of the established standard. In addition, taking the heat cycle test using the burner rig for instance, we specifically illustrate the acquirable data and their analysis in the standard. Monitoring of the effective thermal conductivity and acoustic emission particularly enables to the non-destructive evaluation of failure cycle.
Method to create gradient index in a polymer
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.
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.
[Spectral discrimination method information divergence combined with gradient angle].
Zhang, Xiu-bao; Yuan, Yan; Jing, Juan-juan; Sun, Cheng-ming; Wang, Qian
2011-03-01
The present paper proposes a spectral discrimination method combining spectral information divergence with spectral gradient angle (SID x tan(SGA(pi/2)) which overcomes the shortages of the existing methods which can not take the whole spectral shape and local characteristics into account simultaneously. Using the simulation spectra as input data, according to the interferogram acquirement principle and spectrum recovery algorithm of the temporally and spatially modulated Fourier transform imaging spectrometer (TSMFTIS), we simulated the distortion spectra recovery process of the TMSFTIS in different maximum mix ratio and distinguished the difference between the recovered spectra and the true spectrum by different spectral discrimination methods. The experiment results show that the SID x tan(SGA(pi/2)) can not only identify the similarity of the whole spectral shapes, but also distinguish local differences of the spectral characteristics. A comparative study was conducted among the different discrimination methods. The results have validated that the SID x tan(SGA(pi/2)) has a significant improvement in the discriminatory ability. PMID:21595255
Absolute measurement of optical flat surface shape based on the conjugate differential method.
Huang, Ya; Ma, Jun; Zhu, Rihong; Yuan, Caojin; Chen, Lei; Cai, Huijuan; Sun, Weiyuan
2015-11-16
In this paper the conjugate differential method is proposed to measure the absolute surface shape of the flat mirror using a phase-shifting interferometer. The conjugate differential method is derived from the differential method, which extracts absolute phase differences by introducing the slight transverse shifts of the optic. It employs the measurement schemes making transverse shifts on the orthogonally bilateral symmetry positions. So the measurement procedures have been changed into four-step tests to get the phase difference map instead of three-step tests for the differential method. The precision of the slope approximation is enhanced by reducing couplings between multi-step tests, and the reliability of the measurements can be improved. Several differential wavefront reconstruction methods, such as Fourier transform, Zernike polynomial fitting and Hudgin model method, can be applied to reconstruct the absolute surface shape from the differencing phase maps in four different simulation environment. They were also used to reconstruct the absolute surface shape with the conjugate differential method in the experiment. Our method accords with the classical three-flat test better than the traditional differential method, where the deviation of RMS value between the conjugate differential method and the three-flat test is less than 0.3 nm. PMID:26698450
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
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.
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.
Birdsall, Robert E; Shion, Henry; Kotch, Frank W; Xu, April; Porter, Thomas J; Chen, Weibin
2015-01-01
Cysteine-conjugated antibody-drug conjugates (ADCs) are manufactured using controlled partial reduction and conjugation chemistry with drug payloads that typically occur in intervals of 0, 2, 4, 6, and 8. Control of heterogeneity is of particular importance to the quality of ADC product because drug loading and distribution can affect the safety and efficacy of the ADC. Liquid chromatography ultra-violet (LC-UV)-based methods can be used to acquire the drug distribution profiles of cysteine-conjugated ADCs when analyzed using hydrophobic interaction chromatography (HIC). However, alternative analysis techniques are often required for structural identification when conjugated drugs do not possess discrete ultra-violet absorbance properties for precise assessment of the drug-to-antibody ratio (DAR). In this study, multidimensional chromatography was used as an efficient method for combining non-compatible techniques, such as HIC, with analysis by mass spectrometry (LC/LC/QTOF-MS) for rapid on-line structural elucidation of species observed in HIC distribution profiles of cysteine-conjugated ADCs. The methodology was tested using an IgG1 mAb modified by cysteine conjugation with a non-toxic drug mimic. Structural elucidation of peaks observed in the HIC analysis (1st dimension) were successfully identified based on their unique sub-unit masses via mass spectrometry techniques once dissociation occurred under denaturing reversed phase conditions (2nd dimension). Upon identification, the DAR values were determined to be 2.83, 4.44, and 5.97 for 3 drug load levels (low-, medium-, and high-loaded ADC batches), respectively, based on relative abundance from the LC-UV data. This work demonstrates that multidimensional chromatography coupled with MS, provides an efficient approach for on-line biotherapeutic characterization to ensure ADC product quality. PMID:26305867
Birdsall, Robert E; Shion, Henry; Kotch, Frank W; Xu, April; Porter, Thomas J; Chen, Weibin
2015-01-01
Cysteine-conjugated antibody-drug conjugates (ADCs) are manufactured using controlled partial reduction and conjugation chemistry with drug payloads that typically occur in intervals of 0, 2, 4, 6, and 8. Control of heterogeneity is of particular importance to the quality of ADC product because drug loading and distribution can affect the safety and efficacy of the ADC. Liquid chromatography ultra-violet (LC-UV)-based methods can be used to acquire the drug distribution profiles of cysteine-conjugated ADCs when analyzed using hydrophobic interaction chromatography (HIC). However, alternative analysis techniques are often required for structural identification when conjugated drugs do not possess discrete ultra-violet absorbance properties for precise assessment of the drug-to-antibody ratio (DAR). In this study, multidimensional chromatography was used as an efficient method for combining non-compatible techniques, such as HIC, with analysis by mass spectrometry (LC/LC/QTOF-MS) for rapid on-line structural elucidation of species observed in HIC distribution profiles of cysteine-conjugated ADCs. The methodology was tested using an IgG1 mAb modified by cysteine conjugation with a non-toxic drug mimic. Structural elucidation of peaks observed in the HIC analysis (1(st) dimension) were successfully identified based on their unique sub-unit masses via mass spectrometry techniques once dissociation occurred under denaturing reversed phase conditions (2(nd) dimension). Upon identification, the DAR values were determined to be 2.83, 4.44, and 5.97 for 3 drug load levels (low-, medium-, and high-loaded ADC batches), respectively, based on relative abundance from the LC-UV data. This work demonstrates that multidimensional chromatography coupled with MS, provides an efficient approach for on-line biotherapeutic characterization to ensure ADC product quality. PMID:26305867
Optimization of the conjugation method for a serogroup B/C meningococcal vaccine.
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
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
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
Gradient index liquid crystal devices and method of fabrication thereof
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.
Gradient index liquid crystal devices and method of fabrication thereof
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.
Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method.
Brorsen, Kurt R; Zahariev, Federico; Nakata, Hiroya; Fedorov, Dmitri G; Gordon, Mark S
2014-12-01
The equations for the response terms for the fragment molecular orbital (FMO) method interfaced with the density functional theory (DFT) gradient are derived and implemented. Compared to the previous FMO-DFT gradient, which lacks response terms, the FMO-DFT analytic gradient has improved accuracy for a variety of functionals, when compared to numerical gradients. The FMO-DFT gradient agrees with the fully ab initio DFT gradient in which no fragmentation is performed, while reducing the nonlinear scaling associated with standard DFT. Solving for the response terms requires the solution of the coupled perturbed Kohn-Sham (CPKS) equations, where the CPKS equations are solved through a decoupled Z-vector procedure called the self-consistent Z-vector method. FMO-DFT is a nonvariational method and the FMO-DFT gradient is unique compared to standard DFT gradients in that the FMO-DFT gradient requires terms from both DFT and time-dependent density functional theory (TDDFT) theories. PMID:26583213
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
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
An improved method for covalently conjugating morpholino oligomers to antitumor antibodies.
He, Jiang; Liu, Guozheng; Dou, Shuping; Gupta, Suresh; Rusckowski, Mary; Hnatowich, Donald
2007-01-01
Whether for conventional pretargeting, amplification pretargeting, or affinity enhancement pretargeting, it will be necessary to conjugate an antitumor antibody as the first injectate. This laboratory is investigating phosphorodiamidate morpholinos (MORFs) for pretargeting, and accordingly we are examining methods of attaching MORFs to antitumor antibodies that provide at least one group per molecule (gpm) without adversely influencing antibody properties. The aim of this investigation was to evaluate the commercial Hydralink for the conjugation of the anti-CEA MN14 antibody with an 18 mer amine-derivatized MORF. The conjugation was approached in both directions by first reacting MN14 with the NHS derivatives of 4-hydrozinonicotinate acetone hydrazone (SANH) or 4-formylbenzoate (SFB) and then combining with MORF that was previously reacted with SFB or SANH to yield MN14(SANH)-MORF and MN14(SFB)-MORF respectively. The storage stability, immunoreactive fraction, and the biodistribution in normal mice were compared for both conjugates. Thereafter, MN14(SANH)-MORF was used in a pretargeting study in tumored nude mice, and the results were compared to that obtained historically with MN14-MORF prepared by carbodiimide (EDC) coupling. Both new methods of conjugation provided between 1 and 2 gpm compared to 0.2 achieved previously by EDC. Furthermore, by repeat SE HPLC with and without CEA, both showed an unimpaired immunoreactive fraction. MN14(SANH)-MORF tolerated long-term storage best. More importantly, when labeled by hybridization with 99mTc-labeled complementary MORF (99mTc-cMORF), the biodistribution of MN14(SANH)-MORF was more favorable than that of MN14(SFB)-MORF in normal mice with lower liver (5.7 vs 9.4 %ID/g at 18 h) and spleen (3.5 vs 8.4 %ID/g) accumulations and higher blood levels (4.8 vs 3.4 %ID/g). Accordingly, only MN14(SANH)-MORF was used in a pretargeting study in tumored mice. When targeted with 99mTc-cMORF and at 2 days postinjection of antibody
Gradient-free MCMC methods for dynamic causal modelling
Sengupta, Biswa; Friston, Karl J.; Penny, Will D.
2015-01-01
In this technical note we compare the performance of four gradient-free MCMC samplers (random walk Metropolis sampling, slice-sampling, adaptive MCMC sampling and population-based MCMC sampling with tempering) in terms of the number of independent samples they can produce per unit computational time. For the Bayesian inversion of a single-node neural mass model, both adaptive and population-based samplers are more efficient compared with random walk Metropolis sampler or slice-sampling; yet adaptive MCMC sampling is more promising in terms of compute time. Slice-sampling yields the highest number of independent samples from the target density — albeit at almost 1000% increase in computational time, in comparison to the most efficient algorithm (i.e., the adaptive MCMC sampler). PMID:25776212
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.
Comparison between pressure gradient method and MAC method on high Re calculation
NASA Technical Reports Server (NTRS)
Tan, C.-H.; Duh, J. C.
1989-01-01
A cavity flow driven by shear and buoyancy forces is used as a test problem in the application of a nonstaggered pressure gradient (PG) method in solving the two-dimensional incompressible Navier-Stokes equations. Twelve finite differencing schemes are used to solve the cavity flow problem. The schemes consist of various combinations of grid arrangements, upwinding treatments, and conservativeness of convection terms. An artificial source term is introduced, and the solutions are compared with those obtained by the conventional marker-and-cell (MAC) method. The comparisons favor the PG method. Numerical results obtained by the twelve schemes are compared with exact solutions in order to assess the stability and accuracy of each scheme.
Li, Guofei; Cai, Cuifang; Ren, Tianyang; Tang, Xing
2014-01-01
With the purpose to carry out the pharmacokinetic studies of 10-hydroxy camptothecin (10-HCPT) and hydroxyethyl starch (10-HCPT-HES) conjugate, an ultraperformance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) method has been developed and validated. The analytes, 10-HCPT and the internal standard, Diphenhydramine hydrochloride were extracted with ethyl acetate-isopropanol (95:5, v/v) and separated on an ACQUITY UPLC™ BEH C18 column using a mobile phase composed of acetonitrile and water (containing 0.1% formic acid) with a linear gradient program. With positive ion electrospray ionization (ESI), the analytes were monitored on a triple quadrupole mass spectrometer in the multiple reaction monitoring (MRM) mode. Linear calibration curves were obtained over the concentration ranges of 0.5-2500ng/mL. The intra- and inter-day precisions were less than 9.8% and 10.8%, respectively. The accuracy was within 12.1%. The mean recoveries of 10-HCPT at three concentrations of 2.5, 100, 2000ng/mL were higher than 87.2%. Commercial 10-HCPT injection and 10-HCPT-HES conjugate were administered intravenously at an equal dose of 10-HCPT at 0.5mg/kg. The biological half-life of conjugate was increased significantly from 10min to 3.15h and the bioavailability was 40 times higher than 10-HCPT injection. Consequently, the proposed UPLC-ESI-MS/MS method was proved to be sensitive, specific and reliable to analyze 10-HCPT in biological samples; 10-HCPT and HES conjugate is a promising strategy for delivery of 10-HCPT with prolonged half time and improved bioavailability. PMID:24140449
NASA Astrophysics Data System (ADS)
Wu, Z. Y.; Zhang, L.; Wang, X. M.; Munger, J. W.
2015-07-01
Small pollutant concentration gradients between levels above a plant canopy result in large uncertainties in estimated air-surface exchange fluxes when using existing micrometeorological gradient methods, including the aerodynamic gradient method (AGM) and the modified Bowen ratio method (MBR). A modified micrometeorological gradient method (MGM) is proposed in this study for estimating O3 dry deposition fluxes over a forest canopy using concentration gradients between a level above and a level below the canopy top, taking advantage of relatively large gradients between these levels due to significant pollutant uptake in the top layers of the canopy. The new method is compared with the AGM and MBR methods and is also evaluated using eddy-covariance (EC) flux measurements collected at the Harvard Forest Environmental Measurement Site, Massachusetts, during 1993-2000. All three gradient methods (AGM, MBR, and MGM) produced similar diurnal cycles of O3 dry deposition velocity (Vd(O3)) to the EC measurements, with the MGM method being the closest in magnitude to the EC measurements. The multi-year average Vd(O3) differed significantly between these methods, with the AGM, MBR, and MGM method being 2.28, 1.45, and 1.18 times that of the EC, respectively. Sensitivity experiments identified several input parameters for the MGM method as first-order parameters that affect the estimated Vd(O3). A 10% uncertainty in the wind speed attenuation coefficient or canopy displacement height can cause about 10% uncertainty in the estimated Vd(O3). An unrealistic leaf area density vertical profile can cause an uncertainty of a factor of 2.0 in the estimated Vd(O3). Other input parameters or formulas for stability functions only caused an uncertainly of a few percent. The new method provides an alternative approach to monitoring/estimating long-term deposition fluxes of similar pollutants over tall canopies.
A modified micrometeorological gradient method for estimating O3 dry deposition over a forest canopy
NASA Astrophysics Data System (ADS)
Wu, Z. Y.; Zhang, L.; Wang, X. M.; Munger, J. W.
2015-01-01
Small pollutant concentration gradients between levels above a plant canopy result in large uncertainties in estimated air-surface exchange fluxes when using existing micrometeorological gradient methods, including the aerodynamic gradient method (AGM) and the modified Bowen-Ratio method (MBR). A modified micrometeorological gradient method (MGM) is proposed in this study for estimating O3 dry deposition fluxes over a forest canopy using concentration gradients between a level above and a level below the canopy top, taking advantage of relatively large gradients between these levels due to significant pollutant uptake at top layers of the canopy. The new method is compared with the AGM and MBR methods and is also evaluated using eddy-covariance (EC) flux measurements collected at the Harvard Forest Environmental Measurement Site, Massachusetts during 1993-2000. All the three gradient methods (AGM, MBR and MGM) produced similar diurnal cycles of O3 dry deposition velocity (Vd(O3)) to the EC measurements, with the MGM method being the closest in magnitude to the EC measurements. The multi-year average Vd(O3) differed significantly between these methods, with the AGM, MBR and MGM method being 2.28, 1.45 and 1.18 times of that of the EC. Sensitivity experiments identified several input parameters for the MGM method as first-order parameters that affect the estimated Vd(O3). A 10% uncertainty in the wind speed attenuation coefficient or canopy displacement height can cause about 10% uncertainty in the estimated Vd(O3). An unrealistic leaf area density vertical profile can cause an uncertainty of a factor of 2.0 in the estimated Vd(O3). Other input parameters or formulas for stability functions only caused an uncertainly of a few percent. The new method provides an alternative approach in monitoring/estimating long-term deposition fluxes of similar pollutants over tall canopies.
Method for auto-alignment of digital optical phase conjugation systems based on digital propagation
Jang, Mooseok; Ruan, Haowen; Zhou, Haojiang; Judkewitz, Benjamin; Yang, Changhuei
2014-01-01
Optical phase conjugation (OPC) has enabled many optical applications such as aberration correction and image transmission through fiber. In recent years, implementation of digital optical phase conjugation (DOPC) has opened up the possibility of its use in biomedical optics (e.g. deep-tissue optical focusing) due to its ability to provide greater-than-unity OPC reflectivity (the power ratio of the phase conjugated beam and input beam to the OPC system) and its flexibility to accommodate additional wavefront manipulations. However, the requirement for precise (pixel-to-pixel matching) alignment of the wavefront sensor and the spatial light modulator (SLM) limits the practical usability of DOPC systems. Here, we report a method for auto-alignment of a DOPC system by which the misalignment between the sensor and the SLM is auto-corrected through digital light propagation. With this method, we were able to accomplish OPC playback with a DOPC system with gross sensor-SLM misalignment by an axial displacement of up to~1.5 cm, rotation and tip/tilt of ~5∘, and in-plane displacement of ~5 mm (dependent on the physical size of the sensor and the SLM). Our auto-alignment method robustly achieved a DOPC playback peak-to-background ratio (PBR) corresponding to more than ~30 % of the theoretical maximum. As an additional advantage, the auto-alignment procedure can be easily performed at will and, as such, allows us to correct for small mechanical drifts within the DOPC systems, thus overcoming a previously major DOPC system vulnerability. We believe that this reported method for implementing robust DOPC systems will broaden the practical utility of DOPC systems. PMID:24977504
Method for auto-alignment of digital optical phase conjugation systems based on digital propagation.
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
An analysis method for evaluating gradient-index fibers based on Monte Carlo method
NASA Astrophysics Data System (ADS)
Yoshida, S.; Horiuchi, S.; Ushiyama, Z.; Yamamoto, M.
2011-05-01
We propose a numerical analysis method for evaluating gradient-index (GRIN) optical fiber using the Monte Carlo method. GRIN optical fibers are widely used in optical information processing and communication applications, such as an image scanner, fax machine, optical sensor, and so on. An important factor which decides the performance of GRIN optical fiber is modulation transfer function (MTF). The MTF of a fiber is swayed by condition of manufacturing process such as temperature. Actual measurements of the MTF of a GRIN optical fiber using this method closely match those made by conventional methods. Experimentally, the MTF is measured using a square wave chart, and is then calculated based on the distribution of output strength on the chart. In contrast, the general method using computers evaluates the MTF based on a spot diagram made by an incident point light source. But the results differ greatly from those by experiment. In this paper, we explain the manufacturing process which affects the performance of GRIN optical fibers and a new evaluation method similar to the experimental system based on the Monte Carlo method. We verified that it more closely matches the experimental results than the conventional method.
A new gradient shimming method based on undistorted field map of B0 inhomogeneity.
Bao, Qingjia; Chen, Fang; Chen, Li; Song, Kan; Liu, Zao; Liu, Chaoyang
2016-04-01
Most existing gradient shimming methods for NMR spectrometers estimate field maps that resolve B0 inhomogeneity spatially from dual gradient-echo (GRE) images acquired at different echo times. However, the distortions induced by B0 inhomogeneity that always exists in the GRE images can result in estimated field maps that are distorted in both geometry and intensity, leading to inaccurate shimming. This work proposes a new gradient shimming method based on undistorted field map of B0 inhomogeneity obtained by a more accurate field map estimation technique. Compared to the traditional field map estimation method, this new method exploits both the positive and negative polarities of the frequency encoded gradients to eliminate the distortions caused by B0 inhomogeneity in the field map. Next, the corresponding automatic post-data procedure is introduced to obtain undistorted B0 field map based on knowledge of the invariant characteristics of the B0 inhomogeneity and the variant polarity of the encoded gradient. The experimental results on both simulated and real gradient shimming tests demonstrate the high performance of this new method. PMID:26851711
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.
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.
Zhou, Wang; Yoo, H M; Prabhu-Gaunkar, S; Tiemann, L; Reichl, C; Wegscheider, W; Grayson, M
2015-10-30
A longitudinal magnetoresistance asymmetry (LMA) between a positive and negative magnetic field is known to occur in both the extreme quantum limit and the classical Drude limit in samples with a nonuniform doping density. By analyzing the current stream function in van der Pauw measurement geometry, it is shown that the electron density gradient can be quantitatively deduced from this LMA in the Drude regime. Results agree with gradients interpolated from local densities calibrated across an entire wafer, establishing a generalization of the van der Pauw method to quantify density gradients. PMID:26565488
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.
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.
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.
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.
A comparison of gradient estimation methods for volume rendering on unstructured meshes.
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
Sotnikov, Dmitriy V.; Zherdev, Anatoly V.; Dzantiev, Boris B.
2014-01-01
A method was developed for determining the composition of the conjugates between gold nanoparticles and proteins based on the intrinsic fluorescence of unbound protein molecules. The fluorescence was evaluated after separation of the conjugates from the reaction mixture by centrifugation. Gold nanoparticles obtained using the citrate technique (average diameter 24 nm) were conjugated at pH 5.4 with the following four proteins: human immunoglobulin G (IgG), bovine serum albumin (BSA), recombinant streptococcal protein G (protein G), and Kunitz-type soybean trypsin inhibitor (STI). The compositions of these conjugates were determined using the developed method. The conjugate compositions were dependent on the concentration of the added protein, and in all cases reached saturation. The equilibrium dissociation constants of the gold nanoparticle conjugates with IgG, BSA, protein G, STI in the initial section of the concentration dependence curve were 4, 6, 10, and 15 nM, respectively. Close to saturation, the corresponding values were 25, 76, 175, and 100 nM, respectively. The maximal binding capacities of a single gold nanoparticle for IgG, BSA, Protein G, and STI were 52, 90, 500, and 550, respectively, which agrees well with the hypothesis of monolayer immobilization. PMID:25561238
HNO 3 fluxes to a deciduous forest derived using gradient and REA methods
NASA Astrophysics Data System (ADS)
Pryor, S. C.; Barthelmie, R. J.; Jensen, B.; Jensen, N. O.; Sørensen, L. L.
Summertime nitric acid concentrations over a deciduous forest in the midwestern United States are reported, which range between 0.36 and 3.3 μg m -3. Fluxes to the forest are computed using the relaxed eddy accumulation technique and gradient methods. In accord with previous studies, the results indicate substantial uncertainties in the gradient-based calculations. The relaxed eddy accumulation (REA) derived fluxes are physically reasonable and are shown to be of similar magnitude to dry deposition estimates from gradient sampling. The REA derived mean deposition velocity is approximately 3 cm s -1, which is also comparable to growing season estimates derived by Meyers et al. for a similar deciduous forest. Occasional inverted concentration gradients and fluxes are observed but most are not statistically significant. Data are also presented that indicate substantial through canopy penetration of nitric acid.
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.
A simple method for MR elastography: a gradient-echo type multi-echo sequence.
Numano, Tomokazu; Mizuhara, Kazuyuki; Hata, Junichi; Washio, Toshikatsu; Homma, Kazuhiro
2015-01-01
To demonstrate the feasibility of a novel MR elastography (MRE) technique based on a conventional gradient-echo type multi-echo MR sequence which does not need additional bipolar magnetic field gradients (motion encoding gradient: MEG), yet is sensitive to vibration. In a gradient-echo type multi-echo MR sequence, several images are produced from each echo of the train with different echo times (TEs). If these echoes are synchronized with the vibration, each readout's gradient lobes achieve a MEG-like effect, and the later generated echo causes a greater MEG-like effect. The sequence was tested for the tissue-mimicking agarose gel phantoms and the psoas major muscles of healthy volunteers. It was confirmed that the readout gradient lobes caused an MEG-like effect and the later TE images had higher sensitivity to vibrations. The magnitude image of later generated echo suffered the T2 decay and the susceptibility artifacts, but the wave image and elastogram of later generated echo were unaffected by these effects. In in vivo experiments, this method was able to measure the mean shear modulus of the psoas major muscle. From the results of phantom experiments and volunteer studies, it was shown that this method has clinical application potential. PMID:25311570
Basic theory and experimental techniques of the strain-gradient method
Hecker, F.W.; Pindera, J.T.
1987-09-01
The theories of presently used experimental methods of stress and deformation analysis which employ radiant energy as a detector are based on the assumption that light propagates rectilinearly within both undeformed and deformed bodies which are initially homogeneous and isotropic when diffraction phenomena are negligible. This assumption is not correct: light propagation within deformed bodies is nonrectilinear in a general case. Although this has already been observed and applied practically by some researchers in photoelasticity, it has not so far been generally acknowledged and accepted in experimental mechanics. On the basis of empirical data produced in the period 1948-1983, theories and foundations are presented for a new experimental method which is based on the relations between stress/strain gradients and curvatures of light beams. This method is called the strain-gradient method or, less rigorously, gradient photoelasticity. 39 references.
Sokolov, Viktor I; Panchenko, Vladislav Ya; Seminogov, V N
2012-08-31
A method is proposed for measuring the refractive index gradient n(z) in nonuniformly thick dielectric films. The method is based on the excitation of waveguide modes in a film using the prism coupling technique and on the calculation of n(z) and film thickness H{sub f} with the help of the angular positions of the TE or TM modes. The method can be used for an arbitrary shape of the index modulation over the film thickness in the limit of a small gradient [{Delta} n(z)/n(z) || 1]. (laser applications and other topics in quantum electronics)
[Head and Neck Tumor Segmentation Based on Augmented Gradient Level Set Method].
Zhang, Qiongmin; Zhang, Jing; Wang, Mintang; He, Ling; Men, Yi; Wei, Jun; Haung, Hua
2015-08-01
To realize the accurate positioning and quantitative volume measurement of tumor in head and neck tumor CT images, we proposed a level set method based on augmented gradient. With the introduction of gradient information in the edge indicator function, our proposed level set model is adaptive to different intensity variation, and achieves accurate tumor segmentation. The segmentation result has been used to calculate tumor volume. In large volume tumor segmentation, the proposed level set method can reduce manual intervention and enhance the segmentation accuracy. Tumor volume calculation results are close to the gold standard. From the experiment results, the augmented gradient based level set method has achieved accurate head and neck tumor segmentation. It can provide useful information to computer aided diagnosis. PMID:26710464
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.
Mahmoudian, Jafar; Jeddi-Tehrani, Mahmood; Rabbani, Hodjattallah; Mahmoudi, Ahmad Reza; Akhondi, Mohammad Mehdi; Zarnani, Amir Hassan; Goli, Leila Balaei; Babaei, Mahdokht; Ghods, Roya
2010-04-01
R-Phycoerythrin (R-PE), a fluorescent protein from phycobiliprotein family, is isolated from red algae. Conjugation of antibodies to R-PE facilitates multiple fluorescent staining methods. In the present study polyclonal antibodies and polyclonal F(ab')2 fragment antibodies were conjugated to R-PE by two different methods. The efficiency of the methods was evaluated using Immunocytochemistry (ICC) and Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE). In the first conjugation method, PE was attached to SMCC linker followed by conjugation of antibody to PE-SMCC. In the second method, SH groups were added onto R-PE molecule, while the antibody was attached to SPDP linker. Then, the antibody-SPDP molecule was conjugated to R-PE. Our results showed that the two conjugation methods did not have any abrogative effects on the antibody binding activity. PMID:23407609
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.
A new robust gradient-based method for detection of symmetry axis
NASA Astrophysics Data System (ADS)
Hu, Jing; Wan, Qinqi; Hu, Yongli
2015-12-01
Symmetry axis extraction is an important part of the image feature detection. So far, various classical symmetry axes extraction algorithms have been proposed, such as the minimum-inertia-axis-based method, the SIFT-based method. If the input image is blurry, or it's difficult to extract feature points or corner points from input images, however, the above algorithms are difficult to obtain satisfied results. This paper presents a gradient-based method that can robustly extract symmetry axis from visual pattern. The key points of our methods are gradient calculation, symmetric weight calculation, and Hough Transform. Our method was evaluated on several datasets, including both blurred and smooth-edged cases. Experimental results demonstrated that our method achieves a more robust performance than previous methods.
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
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.
NASA Astrophysics Data System (ADS)
Grayson, M.; Zhou, Wang; Yoo, Heun-Mo; Prabhu-Gaunkar, S.; Tiemann, L.; Reichl, C.; Wegscheider, W.
A longitudinal magnetoresistance asymmetry (LMA) between a positive and negative magnetic field is known to occur in both the extreme quantum limit and the classical Drude limit in samples with a nonuniform doping density. By analyzing the current stream function in van der Pauw measurement geometry, it is shown that the electron density gradient can be quantitatively deduced from this LMA in the Drude regime. Results agree with gradients interpolated from local densities calibrated across an entire wafer, establishing a generalization of the van der Pauw method to quantify density gradients. Results will be shown of various semoconductor systems where this method is applied, from bulk doped semiconductors, to exfoliated 2D materials. McCormick Catalyst Award from Northwestern University, EECS Bridge Funding, and AFOSR FA9550-15-1-0247.
A method for controlling the synthesis of stable twisted two-dimensional conjugated molecules.
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
A method for controlling the synthesis of stable twisted two-dimensional conjugated molecules
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
Microreactor and method for preparing a radiolabeled complex or a biomolecule conjugate
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.
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
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...
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.
Beck, Alain; Terral, Guillaume; Debaene, François; Wagner-Rousset, Elsa; Marcoux, Julien; Janin-Bussat, Marie-Claire; Colas, Olivier; Dorsselaer, Alain Van; Cianférani, Sarah
2016-02-01
Antibody drug conjugates (ADCs) are highly cytotoxic drugs covalently attached via conditionally stable linkers to monoclonal antibodies (mAbs) and are among the most promising next-generation empowered biologics for cancer treatment. ADCs are more complex than naked mAbs, as the heterogeneity of the conjugates adds to the inherent microvariability of the biomolecules. The development and optimization of ADCs rely on improving their analytical and bioanalytical characterization by assessing several critical quality attributes, namely the distribution and position of the drug, the amount of naked antibody, the average drug to antibody ratio, and the residual drug-linker and related product proportions. Here brentuximab vedotin (Adcetris®) and trastuzumab emtansine (Kadcyla®), the first and gold-standard hinge-cysteine and lysine drug conjugates, respectively, were chosen to develop new mass spectrometry (MS) methods and to improve multiple-level structural assessment protocols. PMID:26653789
A projection gradient method for computing ground state of spin-2 Bose–Einstein condensates
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.
Technology Transfer Automated Retrieval System (TEKTRAN)
There is an increasing demand for a sensitive screening method for ractopamine because of the zero tolerance policy in many countries. Most of the commercially available ractopamine ELISA kits require concentrated conjugate to be diluted prior to use. We have observed that the highly diluted racto...
Gong, Haibiao; Holcomb, Ilona; Ooi, Aik; Wang, Xiaohui; Majonis, Daniel; Unger, Marc A; Ramakrishnan, Ramesh
2016-01-20
The diversity of nucleic acid sequences enables genomics studies in a highly multiplexed format. Since multiplex protein detection is still a challenge, it would be useful to use genomics tools for this purpose. This can be accomplished by conjugating specific oligonucleotides to antibodies. Upon binding of the oligonucleotide-conjugated antibodies to their targets, the protein levels can be converted to oligonucleotide levels. In this report we describe a simple method for preparing oligonucleotide-conjugated antibodies and discuss this method's application in oligonucleotide extension reaction (OER) for multiplex protein detection. Conjugation is based on strain-promoted alkyne-azide cycloaddition (the Cu-free click reaction), in which the antibody is activated with a dibenzocyclooctyne (DBCO) moiety and subsequently linked covalently with an azide-modified oligonucleotide. In the functional test, the reaction conditions and purification processes were optimized to achieve maximum yield and best performance. The OER assay employs a pair of antibody binders (two antibodies, each conjugated with its own oligonucleotide) developed for each protein target. The two oligonucleotides contain unique six-base complementary regions at their 3' prime ends to allow annealing and extension by DNA synthesis enzymes to form a DNA template. Following preamplification, the DNA template is detected by qPCR. Distinct oligonucleotide sequences are assigned to different antibody binders to enable multiplex protein detection. When tested using recombinant proteins, some antibody binders, such as those specific to CSTB, MET, EpCAM, and CASP3, had dynamic ranges of 5-6 logs. The antibody binders were also used in a multiplexed format in OER assays, and the binders successfully detected their protein targets in cell lysates, and in single cells in combination with the C1 system. This click reaction-based antibody conjugation procedure is cost-effective, needs minimal hands-on time, and
Interpretation of Gravity Anomalies with the Normalized Full Gradient (NFG) Method and an Example
NASA Astrophysics Data System (ADS)
Aydin, Ali
2007-12-01
The Normalized Full Gradient (NFG) method which was put forward about 50 years ago has been used for downward continuation of gravity potential data, especially in the former Union of Soviet Socialist Republics. This method nullifies perturbations due to the passage of mass depth during downward continuation. The method depends on the downwards analytical continuation of normalized full gradient values of gravity data. Analytical continuation discriminates certain structural anomalies which cannot be distinguished in the observed gravity field. This method has been used in various petroleum and tectonic studies. The Trapeze method was used for the determination of Fourier coefficients during the application of this method. No other techniques for calculating these coefficients have been used. However, the Filon method was used for the determination of Fourier coefficients during the application of the NFG method in this work. This method, rather than the Trapeze method, should be preferred for indicating abnormal mass resources at the lower harmonics. In this study, the NFG method using the Filon method has been applied the first time to theoretical models of gravity profiles as example field at the Hasankale-Horasan petroleum exploration province where successful results were achieved. Hydrocarbon presence was shown on the NFG sections by the application of NFG downward continuation operations on theoretical models. Important signs of hydrocarbon structure on the NFG section for field and model data at low harmonics are obtained more effectively using this method.
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
Dynamics of the adaptive natural gradient descent method for soft committee machines
NASA Astrophysics Data System (ADS)
Inoue, Masato; Park, Hyeyoung; Okada, Masato
2004-05-01
Adaptive natural gradient descent (ANGD) method realizes natural gradient descent (NGD) without needing to know the input distribution of learning data and reduces the calculation cost from a cubic order to a square order. However, no performance analysis of ANGD has been done. We have developed a statistical-mechanical theory of the simplified version of ANGD dynamics for soft committee machines in on-line learning; this method provides deterministic learning dynamics expressed through a few order parameters, even though ANGD intrinsically holds a large approximated Fisher information matrix. Numerical results obtained using this theory were consistent with those of a simulation, with respect not only to the learning curve but also to the learning failure. Utilizing this method, we numerically evaluated ANGD efficiency and found that ANGD generally performs as well as NGD. We also revealed the key condition affecting the learning plateau in ANGD.
Biconjugate gradient stabilized method in image deconvolution of a wavefront coding system
NASA Astrophysics Data System (ADS)
Liu, Peng; Liu, Qin-xiao; Zhao, Ting-yu; Chen, Yan-ping; Yu, Fei-hong
2013-04-01
The point spread function (PSF) is a non-rotational symmetric for the wavefront coding (WFC) system with a cubic phase mask (CPM). Antireflective boundary conditions (BCs) are used to eliminate the ringing effect on the border and vibration on the edge of the image. The Kronecker product approximation is used to reduce the computation consumption. The image-formation process of the WFC system is transformed into a matrix equation. In order to save storage space, biconjugate gradient (Bi-CG) and biconjugate gradient stabilized (Bi-CGSTAB) methods are used to solve the asymmetric matrix equation, which is a typical iteration algorithm of the Krylov subspace using the two-side Lanczos process. Simulation and experimental results illustrate the efficiency of the proposed algorithm for the image deconvolution. The result based on the Bi-CGSTAB method is smoother than the classic Wiener filter, while preserving more details than the Truncated Singular Value Decomposition (TSVD) method.
Evaluating angular deflections from the digital gradient sensing method with rigid-motion deleted
NASA Astrophysics Data System (ADS)
Zhang, Rui
2016-06-01
The digital gradient sensing method is used for measuring small angular deflections of light rays due to local stresses in transparent planar solids. The method is based on two-dimensional (2D) digital image correlation (DIC) to measure the angular deflection of light rays; however, when a specimen is subjected to loading, deformation measurement from DIC is not perfect because of the existence of small in-plane and out-of-plane motions of the test sample surface that occurred after loading. These disadvantages will lead to errors in the measured angular deflections. The influence of unavoidable in-plane and out-of-plane motions was discussed, and a method to eliminate the influence to show the pure stress gradient of polymethy methacrylate is demonstrated.
Torres, Oscar B; Jalah, Rashmi; Rice, Kenner C; Li, Fuying; Antoline, Joshua F G; Iyer, Malliga R; Jacobson, Arthur E; Boutaghou, Mohamed Nazim; Alving, Carl R; Matyas, Gary R
2014-09-01
A potential new treatment for drug addiction is immunization with vaccines that induce antibodies that can abrogate the addictive effects of the drug of abuse. One of the challenges in the development of a vaccine against drugs of abuse is the availability of an optimum procedure that gives reproducible and high yielding hapten-protein conjugates. In this study, a heroin/morphine surrogate hapten (MorHap) was coupled to bovine serum albumin (BSA) using maleimide-thiol chemistry. MorHap-BSA conjugates with 3, 5, 10, 15, 22, 28, and 34 haptens were obtained using different linker and hapten ratios. Using this optimized procedure, MorHap-BSA conjugates were synthesized with highly reproducible results and in high yields. The number of haptens attached to BSA was compared by 2,4,6-trinitrobenzenesulfonic acid (TNBS) assay, modified Ellman's test and matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Among the three methods, MALDI-TOF MS discriminated subtle differences in hapten density. The effect of hapten density on enzyme-linked immunosorbent assay (ELISA) performance was evaluated with seven MorHap-BSA conjugates of varying hapten densities, which were used as coating antigens. The highest antibody binding was obtained with MorHap-BSA conjugates containing 3-5 haptens. This is the first report that rigorously analyzes, optimizes and characterizes the conjugation of haptens to proteins that can be used for vaccines against drugs of abuse. The effect of hapten density on the ELISA detection of antibodies against haptens demonstrates the importance of careful characterization of the hapten density by the analytical techniques described. PMID:25084736
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.
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.
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.
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
NASA Astrophysics Data System (ADS)
Cao, Jingjie; Wang, Yanfei; Wang, Benfeng
2015-08-01
Seismic interpolation, as an efficient strategy of providing reliable wavefields, belongs to large-scale computing problems. The rapid increase of data volume in high dimensional interpolation requires highly efficient methods to relieve computational burden. Most methods adopt the L1 norm as a sparsity constraint of solutions in some transformed domain; however, the L1 norm is non-differentiable and gradient-type methods cannot be applied directly. On the other hand, methods for unconstrained L1 norm optimisation always depend on the regularisation parameter which needs to be chosen carefully. In this paper, a fast gradient projection method for the smooth L1 problem is proposed based on the tight frame property of the curvelet transform that can overcome these shortcomings. Some smooth L1 norm functions are discussed and their properties are analysed, then the Huber function is chosen to replace the L1 norm. The novelty of the proposed method is that the tight frame property of the curvelet transform is utilised to improve the computational efficiency. Numerical experiments on synthetic and real data demonstrate the validity of the proposed method which can be used in large-scale computing.
NASA Astrophysics Data System (ADS)
Nie, Zhi-Feng; Zhou, Shen-Jie; Han, Ru-Jun; Xiao, Lin-Jing; Wang, Kai
2012-02-01
C 1 natural element method ( C 1 NEM) is applied to strain gradient linear elasticity, and size effects on microstructures are analyzed. The shape functions in C 1 NEM are built upon the natural neighbor interpolation (NNI), with interpolation realized to nodal function and nodal gradient values, so that the essential boundary conditions (EBCs) can be imposed directly in a Galerkin scheme for partial differential equations (PDEs). In the present paper, C 1 NEM for strain gradient linear elasticity is constructed, and several typical examples which have analytical solutions are presented to illustrate the effectiveness of the constructed method. In its application to microstructures, the size effects of bending stiffness and stress concentration factor (SCF) are studied for microspeciem and microgripper, respectively. It is observed that the size effects become rather strong when the width of spring for microgripper, the radius of circular perforation and the long axis of elliptical perforation for microspeciem come close to the material characteristic length scales. For the U-shaped notch, the size effects decline obviously with increasing notch radius, and decline mildly with increasing length of notch.
Fixed and pulsed gradient diffusion methods in low-field core analysis.
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
Wu, Wei; Fan, Qinwei; Zurada, Jacek M; Wang, Jian; Yang, Dakun; Liu, Yan
2014-02-01
The aim of this paper is to develop a novel method to prune feedforward neural networks by introducing an L1/2 regularization term into the error function. This procedure forces weights to become smaller during the training and can eventually removed after the training. The usual L1/2 regularization term involves absolute values and is not differentiable at the origin, which typically causes oscillation of the gradient of the error function during the training. A key point of this paper is to modify the usual L1/2 regularization term by smoothing it at the origin. This approach offers the following three advantages: First, it removes the oscillation of the gradient value. Secondly, it gives better pruning, namely the final weights to be removed are smaller than those produced through the usual L1/2 regularization. Thirdly, it makes it possible to prove the convergence of the training. Supporting numerical examples are also provided. PMID:24291693
A novel model-based hearing compensation design using a gradient-free optimization method.
Chen, Zhe; Becker, Suzanna; Bondy, Jeff; Bruce, Ian C; Haykin, Simon
2005-12-01
We propose a novel model-based hearing compensation strategy and gradient-free optimization procedure for a learning-based hearing aid design. Motivated by physiological data and normal and impaired auditory nerve models, a hearing compensation strategy is cast as a neural coding problem, and a Neurocompensator is designed to compensate for the hearing loss and enhance the speech. With the goal of learning the Neurocompensator parameters, we use a gradient-free optimization procedure, an improved version of the ALOPEX that we have developed, to learn the unknown parameters of the Neurocompensator. We present our methodology, learning procedure, and experimental results in detail; discussion is also given regarding the unsupervised learning and optimization methods. PMID:16212766
A gradient-free adaptation method for nonlinear active noise control
NASA Astrophysics Data System (ADS)
Spiriti, Emanuele; Morici, Simone; Piroddi, Luigi
2014-01-01
Active Noise Control (ANC) problems are often affected by nonlinear effects, such as saturation and distortion of microphones and loudspeakers. Nonlinear models and specific adaptation algorithms must be employed to properly account for these effects. The nonlinear structure of the problem complicates the application of gradient-based Least Mean Squares (LMS) algorithms, due to the fact that exact gradient calculation requires executing nonlinear recursive filtering operations, which pose computational and stability issues. One favored solution to this problem consists in neglecting recursive terms in the gradient calculation, an approximation which is not always without consequences on the convergence performance. Besides, an efficient application of nonlinear models cannot avoid some form of model structure selection, to avoid the well-known effects of overparametrization and to reduce the computational load on-line. Unfortunately, the standard ANC setting configures an indirect identification problem, due to the presence of the secondary path in the control loop. In the nonlinear case, this destroys the linear regression structure of the problem even if the control filter is linear-in-the-parameters, thereby making it impossible to apply the many existing model selection methods for linear regression problems. A simple and computationally wise low demanding approach is here proposed for parameter estimation and model structure selection that provides an answer to the mentioned issues. The proposed method avoids altogether the use of the error gradient and relies on direct cost function evaluations. A virtualization scheme is used to assess the accuracy improvements when the model is subject to parametric or structural modifications, without directly affecting the control performance. Several simulation examples are discussed to show the effectiveness of the proposed algorithms.
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.
Fattebert, J.-L.
2010-01-20
An Accelerated Block Preconditioned Gradient (ABPG) method is proposed to solve electronic structure problems in Density Functional Theory. This iterative algorithm is designed to solve directly the non-linear Kohn-Sham equations for accurate discretization schemes involving a large number of degrees of freedom. It makes use of an acceleration scheme similar to what is known as RMM-DIIS in the electronic structure community. The method is illustrated with examples of convergence for large scale applications using a finite difference discretization and multigrid preconditioning.
ABCD matrix of the human lens gradient-index profile: applicability of the calculation methods.
Díaz, José Antonio
2008-01-10
The applicability of different approximate methods proposed to determine the paraxial properties of the gradient-index (GRIN) distribution resembling that of the human lens, by means of the system ABCD matrix, is tested. Thus, the parabolic-ray-path approximation has been extended to provide the ABCD matrix of a slab lens comprised of a rotationally GRIN medium. The results show that this method has good numerical stability, and it is also the easiest one in determining the Gaussian constants of the human lens GRIN profile. PMID:18188201
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.
Gradients for the partitioned equation-of-motion coupled-cluster method
Gwaltney, S.R.; Bartlett, R.J.
1996-12-31
The Equation-of-Motion Coupled-Cluster method restricted to singles and doubles (EOM-CCSD) is a highly accurate method for calculating excited states of molecules. Errors of 0.1 to 0.3 eV are typical for excitation energies. But a major drawback is that EOM-CCSD is an iterative n{sup 6} method, and for large cases the cost can be prohibitive. For a partitioned EOM-CCSD calculation, the doubles-doubles block of the H matrix is replaced with Ho. Combined with truncating the H matrix at second order (i.e. basing the excited state calculation on a MBPT(2) ground state), the partitioning technique creates an iterative n{sup 5} method for excited states, the P-EOM-MBPT(2) method. In this poster we will present the theory and examples of P-EOM-MBPT(2) gradient calculations. The gradients provide an inexpensive way to look at potential energy surfaces of excited states of molecules.
A comparison of the Monte Carlo and the flux gradient method for atmospheric diffusion
Lange, R.
1990-05-01
In order to model the dispersal of atmospheric pollutants in the planetary boundary layer, various methods of parameterizing turbulent diffusion have been employed. The purpose of this paper is to use a three-dimensional particle-in-cell transport and diffusion model to compare the Markov chain (Monte Carlo) method of statistical particle diffusion with the deterministic flux gradient (K-theory) method. The two methods are heavily used in the study of atmospheric diffusion under complex conditions, with the Monte Carlo method gaining in popularity partly because of its more direct application of turbulence parameters. The basis of comparison is a data set from night-time drainage flow tracer experiments performed by the US Department of Energy Atmospheric Studies in Complex Terrain (ASCOT) program at the Geysers geothermal region in northern California. The Atmospheric Diffusion Particle-In-Cell (ADPIC) model used is the main model in the Lawrence Livermore National Laboratory emergency response program: Atmospheric Release Advisory Capability (ARAC). As a particle model, it can simulate diffusion in both the flux gradient and Monte Carlo modes. 9 refs., 6 figs.
A Sea-Sky Line Detection Method for Unmanned Surface Vehicles Based on Gradient Saliency.
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
A Sea-Sky Line Detection Method for Unmanned Surface Vehicles Based on Gradient Saliency
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
A Robust Gradient Based Method for Building Extraction from LiDAR and Photogrammetric Imagery
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
A Robust Gradient Based Method for Building Extraction from LiDAR and Photogrammetric Imagery.
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
Ammann, Adrian A; Suter, Marc J-F
2016-07-22
Metabolomics or environmental investigations generate samples containing very large numbers of small molecular weight analytes. A single mode chromatographic separation excludes a substantial part of such complex analyte mixtures. For instance, a reversed-phase separation would not retain ionic species, resulting in a correspondingly huge front peak. To address this problem, we used two commercially available mixed-mode ion-exchange reversed-phase columns (WAX-1 and WCX-1) in sequence in a novel multimode separation method. After trapping hydrophobics on a C18-trap in loop position, hydrophilics passing the trap are separated by a simultaneous gradient for HILIC, anion and cation exchange chromatography. This gradient ends in a washout phase with a high percentage of water, the correct starting conditions for a reversed-phase gradient eluting hydrophobics from the trap in a second step of the run. Amino acids (9), organic acids (2), sugars (8), fatty acid derived compounds (11), antioxidants (4), miscellanea (6) and xenobiotics (4) were analyzed. Compounds were separated after a single sample injection during a 50min run. Lipids derived small fatty acids up to a chain length of 12 carbons were also accessible within this run time. PMID:27324626
Distortion Correction in EPI Using an Extended PSF Method with a Reversed Phase Gradient Approach
In, Myung-Ho; Posnansky, Oleg; Beall, Erik B.; Lowe, Mark J.; Speck, Oliver
2015-01-01
In echo-planar imaging (EPI), such as commonly used for functional MRI (fMRI) and diffusion-tensor imaging (DTI), compressed distortion is a more difficult challenge than local stretching as spatial information can be lost in strongly compressed areas. In addition, the effects are more severe at ultra-high field (UHF) such as 7T due to increased field inhomogeneity. To resolve this problem, two EPIs with opposite phase-encoding (PE) polarity were acquired and combined after distortion correction. For distortion correction, a point spread function (PSF) mapping method was chosen due to its high correction accuracy and extended to perform distortion correction of both EPIs with opposite PE polarity thus reducing the PSF reference scan time. Because the amount of spatial information differs between the opposite PE datasets, the method was further extended to incorporate a weighted combination of the two distortion-corrected images to maximize the spatial information content of a final corrected image. The correction accuracy of the proposed method was evaluated in distortion-corrected data using both forward and reverse phase-encoded PSF reference data and compared with the reversed gradient approaches suggested previously. Further we demonstrate that the extended PSF method with an improved weighted combination can recover local distortions and spatial information loss and be applied successfully not only to spin-echo EPI, but also to gradient-echo EPIs acquired with both PE directions to perform geometrically accurate image reconstruction. PMID:25707006
METHODS FOR STUDYING BACTERIAL GENE TRANSFER IN SOIL BY CONJUGATION AND TRANSDUCTION
The purpose of this document is to provide a series of protocols by which a trained technician can conduct studies on the transfer of genetic information by conjugation or transduction in soil, with emphasis on bacteria containing recombinant DNA. The level of the document is gea...
A rapid biosensor-based method for quantification of free and glucose-conjugated salicylic acid
Technology Transfer Automated Retrieval System (TEKTRAN)
Salicylic acid (SA) is an important signalling molecule in plant defenses against biotrophic pathogens. It is also involved in several other processes such as heat production, flowering, and germination. SA exists in the plant as free SA and as an inert glucose conjugate (salicylic acid 2-O-ß-D-...
Estimating Effective Vertical Diffusivity in Shallow Ponds by a Constrained Flux-Gradient Method
NASA Astrophysics Data System (ADS)
Bean, J. R.; Torgersen, T.
2004-12-01
Shallow ponds have been used to mitigate the deleterious effects of storm water run-off by acting as detention/retention basins that sequester run-off associated pollutants in sediments. Studies show that the retention efficiency of these systems can decrease over time as a result of the internal loading of nutrients/contaminants from the sediments back to the water column where they are available for export downstream. Quantifying the vertical transport of gases (down) and sediment derived materials (up) is vital to the modeling and understanding of the processes that contribute to the magnitude of internal loading. A critical parameter is the effective vertical diffusion coefficient: Kz=Dmolecular +Deddy (cm2 sec-1). The flux gradient method for estimating effective vertical thermal diffusivity has been applied with success in large lakes which undergo stratification cycles on seasonal or longer time scales. We offer a constrained version of the flux-gradient method that has been adapted for use in a shallow pond with a daily stratification cycle. The method employs heat as a tracer and assumes that transport in the face of a stable gradient is diffusive. By shrinking the spatial and temporal resolution of measurement to scales appropriate to the system of interest and carefully accounting for internal source and sink terms of heat (e.g solar radiation and sediment heat fluxes) we are able to calculate Kz as a function of time and depth during periods of stable stratification, i.e when the pond is not vertically well-mixed. Results show the magnitude of Kz varies from ca. 10-3 to 10-1 (cm2 sec-1) under stratified conditions depending primarily on the strength of stratification.
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
Rossi, Edmund A; Goldenberg, David M; Chang, Chien-Hsing
2012-03-21
Advances in recombinant protein technology have facilitated the production of increasingly complex fusion proteins with multivalent, multifunctional designs for use in various in vitro and in vivo applications. In addition, traditional chemical conjugation remains a primary choice for linking proteins with polyethylene glycol (PEG), biotin, fluorescent markers, drugs, and others. More recently, site-specific conjugation of two or more interactive modules has emerged as a valid approach to expand the existing repertoires produced by either recombinant engineering or chemical conjugation alone, thus advancing the range of potential applications. Five such methods, each involving a specific binding event, are highlighted in this review, with a particular focus on the Dock-and-Lock (DNL) method, which exploits the natural interaction between the dimerization and docking domain (DDD) of cAMP-dependent protein kinase (PKA) and the anchoring domain (AD) of A-kinase anchoring proteins (AKAP). The various enablements of DNL to date include trivalent, tetravalent, pentavalent, and hexavalent antibodies of monospecificity or bispecificity; immnocytokines comprising multiple copies of interferon-alpha (IFNα); and site-specific PEGylation. These achievements attest to the power of the DNL platform technology to develop novel therapeutic and diagnostic agents from both proteins and nonproteins for unmet medical needs. PMID:22168393
Gradient ROtating Outer Volume Excitation (GROOVE): A Novel Method for Single-Shot 2-D OVS
Powell, Nathaniel J.; Jang, Albert; Park, Jang-Yeon; Valette, Julien; Garwood, Michael; Marjańska, Małgorzata
2014-01-01
Purpose A new outer volume suppression (OVS) technique is introduced that uses a single pulse and rotating gradients to accomplish frequency-swept excitation. This new technique, which is called Gradient ROtating Outer Volume Excitation (GROOVE), produces a circular or elliptical suppression band rather than suppressing the entire outer volume. Methods Theoretical and k-space descriptions of GROOVE are provided. The properties of GROOVE were investigated with simulations, phantom, and human experiments performed using a 4 T horizontal bore magnet equipped with a TEM coil. Results Similar suppression performance was obtained in phantom and human brain using GROOVE with circular and elliptical shapes. Simulations indicate that GROOVE requires less SAR and time than traditional OVS schemes, but traditional schemes provide a sharper transition zone and less residual signal. Conclusion GROOVE represents a new way of performing OVS in which spins are excited temporally in space on a trajectory which can be tailored to fit the shape of the suppression region. In addition, GROOVE is capable of suppressing tailored regions of space with more flexibility and in a shorter period of time than conventional methods. GROOVE provides a fast, low SAR alternative to conventional OVS methods in some applications (e.g., scalp suppression). PMID:24478130
NASA Astrophysics Data System (ADS)
Ji, Hong-Fei; Jiao, Yi; Wang, Sheng; Ji, Da-Heng; Yu, Cheng-Hui; Zhang, Yuan; Huang, Xiao-Biao
2015-12-01
The robust conjugate direction search (RCDS) method has high tolerance to noise in beam experiments. It has been demonstrated that this method can be used to optimize the machine performance of a light source online. In our study, taking BEPCII as an example, the feasibility of online tuning of the luminosity in a circular collider is explored, through numerical simulation and preliminary online experiments. It is shown that the luminosity that is artificially decreased by a deviation of beam orbital offset from optimal trajectory can be recovered with this method. Supported by National Natural Science Foundation of China (11475202, 11405187) and Youth Innovation Promotion Association of Chinese Academy of Sciences (2015009)
Gradient and curvature from the photometric-stereo method, including local confidence estimation
Woodham, R.J.
1994-11-01
The photometric-stereo method is one technique for three-dimensional shape determination that has been implemented in a variety of experimental settings and that has produced consistently good results. The idea is to use intensity values recorded from multiple images obtained from the same viewpoint but under different conditions of illumination. The resulting radiometric constraint makes it possible to obtain local estimates of both surface orientation and surface curvature without requiring either global smoothness assumptions or prior image segmentation. Photometric stereo is moved one step closer to practical possibility by a description of an experimental setting in which surface gradient estimation is achieved on full-frame video data at near-video-frame rates (i.e., 15 Hz). The implementation uses commercially available hardware. Reflectance is modeled empirically with measurements obtained from a calibration sphere. Estimation of the gradient ({ital p},{ital q}) requires only simple table lookup. Curvature estimation additionally uses the reflectance map {ital R}({ital p},{ital q}). The required lookup table and reflectance maps are derived during calibration. Because reflectance is modeled empirically, no prior physical model of the reflectance characteristics of the objects to be analyzed is assumed. At the same time, if a good physical model is available, it can be retrofitted to the method for implementation purposes. Photometric stereo is subject to error in the presence of cast shadows and interreflection. No purely local technique can succeed because these phenomena are inherently nonlocal. Nevertheless, it is demonstrated that one can exploit the redundancy in three-light-source photometric stereo to detect locally, in most cases, the presence of cast shadows and interreflection. Detection is facilitated by the explicit inclusion of a local confidence estimate in the lookup table used for gradient estimation.
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.
Randomized gradient-free method for multiagent optimization over time-varying networks.
Yuan, Deming; Ho, Daniel W C
2015-06-01
In this brief, we consider the multiagent optimization over a network where multiple agents try to minimize a sum of nonsmooth but Lipschitz continuous functions, subject to a convex state constraint set. The underlying network topology is modeled as time varying. We propose a randomized derivative-free method, where in each update, the random gradient-free oracles are utilized instead of the subgradients (SGs). In contrast to the existing work, we do not require that agents are able to compute the SGs of their objective functions. We establish the convergence of the method to an approximate solution of the multiagent optimization problem within the error level depending on the smoothing parameter and the Lipschitz constant of each agent's objective function. Finally, a numerical example is provided to demonstrate the effectiveness of the method. PMID:25099738
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.
Application of the split-gradient method to 3D image deconvolution in fluorescence microscopy.
Vicidomini, G; Boccacci, P; Diaspro, A; Bertero, M
2009-04-01
The methods of image deconvolution are important for improving the quality of the detected images in the different modalities of fluorescence microscopy such as wide-field, confocal, two-photon excitation and 4Pi. Because deconvolution is an ill-posed problem, it is, in general, reformulated in a statistical framework such as maximum likelihood or Bayes and reduced to the minimization of a suitable functional, more precisely, to a constrained minimization, because non-negativity of the solution is an important requirement. Next, iterative methods are designed for approximating such a solution. In this paper, we consider the Bayesian approach based on the assumption that the noise is dominated by photon counting, so the likelihood is of the Poisson-type, and that the prior is edge-preserving, as derived from a simple Markov random field model. By considering the negative logarithm of the a posteriori probability distribution, the computation of the maximum a posteriori (MAP) estimate is reduced to the constrained minimization of a functional that is the sum of the Csiszár I-divergence and a regularization term. For the solution of this problem, we propose an iterative algorithm derived from a general approach known as split-gradient method (SGM) and based on a suitable decomposition of the gradient of the functional into a negative and positive part. The result is a simple modification of the standard Richardson-Lucy algorithm, very easily implementable and assuring automatically the non-negativity of the iterates. Next, we apply this method to the particular case of confocal microscopy for investigating the effect of several edge-preserving priors proposed in the literature using both synthetic and real confocal images. The quality of the restoration is estimated both by computation of the Kullback-Leibler divergence of the restored image from the detected one and by visual inspection. It is observed that the noise artefacts are considerably reduced and desired
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.
NASA Astrophysics Data System (ADS)
Shu, Yu-Chen; Chern, I.-Liang; Chang, Chien C.
2014-10-01
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.
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.
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
Demonstrating the Temperature Gradient Impact on Grain Growth in UO2 Using the Phase Field Method
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.
NASA Astrophysics Data System (ADS)
Park, J.-H.; Fares, S.; Weber, R.; Goldstein, A. H.
2012-09-01
The Biosphere Effects on AeRosols and Photochemistry EXperiment (BEARPEX) took place in Blodgett Forest, a Ponderosa pine forest in the Sierra Nevada Mountains of California, during summer 2009. We deployed a Proton Transfer Reaction - Mass Spectrometer (PTR-MS) to measure fluxes and concentrations of biogenic volatile organic compounds (BVOCs). Eighteen ion species including the major BVOC expected at the site were measured sequentially at 5 heights to observe their vertical gradient from the forest floor to above the canopy. Fluxes of the 3 dominant BVOCs methanol, 2-Methyl-3-butene-2-ol (MBO), and monoterpenes, were measured above the canopy by the eddy covariance method. Canopy scale fluxes were also determined by the flux-gradient similarity method (K-theory). A universal K (Kuniv) was determined as the mean of individual K's calculated from the measured fluxes divided by vertical gradients for methanol, MBO, and monoterpenes. This Kuniv was then multiplied by the gradients of each observed ion species to compute their fluxes. The flux-gradient similarity method showed very good agreement with the Eddy Covariance method. Fluxes are presented for all measured species and compared to historical measurements from the same site, and used to test emission algorithms used to model fluxes at the regional scale. MBO was the dominant emission observed followed by methanol, monoterpenes, acetone, and acetaldehyde. The flux-gradient similarity method is shown to be a useful, and we recommend its use especially in experimental conditions when fast measurement of BVOC species is not available.
Moriguchi, Kazuki; Yamamoto, Shinji; Ohmine, Yuta; Suzuki, Katsunori
2016-01-01
Trans-kingdom conjugation is a phenomenon by which DNA is transferred into a eukaryotic cell by a bacterial conjugal transfer system. Improvement in this method to facilitate the rapid co-cultivation of donor bacterial and recipient eukaryotic cell cultures could make it the simplest transformation method, requiring neither isolation of vector DNA nor preparation of competent recipient cells. To evaluate this potential advantage of trans-kingdom conjugation, we examined this simple transformation method using vector combinations, helper plasmids, and recipient Saccharomyces cerevisiae strains. Mixing donor Escherichia coli and recipient S. cerevisiae overnight cultures (50 μL each) consistently yielded on the order of 101 transformants using the popular experimental strain BY4742 derived from S288c and a shuttle vector for trans-kingdom conjugation. Transformation efficiency increased to the order of 102 using a high receptivity trans-kingdom conjugation strain. In addition, either increasing the amount of donor cells or pretreating the recipient cells with thiols such as dithiothreitol improved the transformation efficiency by one order of magnitude. This simple trans-kingdom conjugation-mediated transformation method could be used as a practical yeast transformation method upon enrichment of available vectors and donor E. coli strains. PMID:26849654
NASA Astrophysics Data System (ADS)
Casotto, S.; Fantino, E.
This work is concerned with the comparison of four of the best-known methods for the computation of the gravitational potential and its gradients: the traditional formulation in terms of Associated Legendre Functions in spherical coordinates; the non-singular method of Pines; the algorithm developed by Cunningham and extended by Metris and collaborators; and a variant of the first method based on the Clenshaw summation formula. Extensive numerical tests in double and quadruple floating point precision have been performed in order to assess and compare the efficiency and precision of these algorithms. Results show that when properly optimized the algorithm of Clenshaw is the most efficient, closely followed by the traditional Legendre formulation. All four methods are characterized by a high level of precision, although care should be taken when approaching the geographic poles due to the singularities which affect the methods of Legendre and Clenshaw. The methods of Cunningham-Metris and Pines are both characterized by some loss of relative precision at the equator, which is inherent in the choice of the coordinate system.
NASA Astrophysics Data System (ADS)
Furusawa, Masahiro; Ikeya, Motoji
1991-09-01
A new method for generating a highly linear field gradient in a large space is described. The coil system consists of N equispaced parallel current lines placed on a cylinder perpendicular to the static magnetic field. The wires generate a gradient of any accuracy depending on N and in any direction in a plane perpendicular to the cylinder axis by controlling the current of each wire independently. The accuracy of the gradient using 16 infinite-length wires is less than 0.3% in the 60% region in diameter of the cylinder. An ESR-CT image of a DPPH test sample was obtained using this system of 16 wires.
Soukup, Sebastian T; Al-Maharik, Nawaf; Botting, Nigel; Kulling, Sabine E
2014-09-01
The biotransformation of isoflavones by gut microbiota and by drug metabolizing enzymes plays a crucial role in the understanding of their potential health-promoting effects. The purpose of our work was to develop a simultaneous, sensitive, and robust automated ultra high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method to quantify the soy isoflavones daidzein and genistein, their conjugative metabolites, as well as their major microbial degradation products in order to provide a method for use in large clinical trials or animal studies. An automated, 96-well solid-phase extraction method was used to extract the isoflavone analytes from plasma and urine. Separation of genistein, daidzein, and 19 of its metabolites, including five glucuronides, seven sulfates, and two sulfoglucuronides, as well as five microbial metabolites, was achieved in less than 25 min using a sub-2 μm particle column and a gradient elution with acetonitrile/methanol/water as mobile phases. Analysis was performed under negative ionization electrospray MS via the multiple reaction monitoring (MRM). Validation was performed according to the analytical method validation guidelines of Food and Drug Administration (FDA) and International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH) consisting of selectivity, accuracy, precision, linearity, limit of detection, recovery, matrix effect, and robustness. All validated parameters essentially matched the FDA and ICH requirements. The application of this method to a pharmacokinetic study in postmenopausal women showed that isoflavones are extensively metabolized in vivo. A robust automated analytical approach was developed, which allows the handling of large sample sizes but nevertheless provides detailed information on the isoflavone metabolite profile leading to a better understanding and interpretation of clinical and animal studies. PMID:25103528
Flow instability of a centrifugal pump determined using the energy gradient method
NASA Astrophysics Data System (ADS)
Li, Yi; Dong, Wenlong; He, Zhaohui; Huang, Yuanmin; Jiang, Xiaojun
2015-02-01
The stability of the centrifugal pump has not been well revealed because of the complexity of internal flow. To analyze the flow characteristics of a centrifugal pump operating at low capacity, methods of numerical simulation and experimental research were adopted in this paper. Characteristics of the inner flow were obtained. Standard k-ɛ turbulence models were used to calculate the inner flow of the pump under off-design conditions. The distribution of the energy gradient function K was obtained by three-dimensional numerical simulation at different flow rates. The relative velocity component was acquired from the absolute velocity obtained in particle image velocimetry. By comparing with experimental results, it was found that flow instability occurs at the position of maximum K. The flow stability reduces with an increasing flow rate. The research results provide a theoretical basis for the optimization design of a centrifugal pump.
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.
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.
Hydrogel-based methods for engineering cellular microenvironment with spatiotemporal gradients.
Wang, Lin; Li, Yuhui; Huang, Guoyou; Zhang, Xiaohui; Pingguan-Murphy, Belinda; Gao, Bin; Lu, Tian Jian; Xu, Feng
2016-06-01
Natural cellular microenvironment consists of spatiotemporal gradients of multiple physical (e.g. extracellular matrix stiffness, porosity and stress/strain) and chemical cues (e.g. morphogens), which play important roles in regulating cell behaviors including spreading, proliferation, migration, differentiation and apoptosis, especially for pathological processes such as tumor formation and progression. Therefore, it is essential to engineer cellular gradient microenvironment incorporating various gradients for the fabrication of normal and pathological tissue models in vitro. In this article, we firstly review the development of engineering cellular physical and chemical gradients with cytocompatible hydrogels in both two-dimension and three-dimension formats. We then present current advances in the application of engineered gradient microenvironments for the fabrication of disease models in vitro. Finally, concluding remarks and future perspectives for engineering cellular gradients are given. PMID:25641330
Li, Yi; Gu, Christine; Gruenhagen, Jason; Yehl, Peter; Chetwyn, Nik P; Medley, Colin D
2016-01-01
Antibody-drug conjugates (ADCs) are complex therapeutic agents that use the specific targeting properties of antibodies and the highly potent cytotoxicity of small molecule drugs to selectively eliminate tumor cells while limiting the toxicity to normal healthy tissues. Two critical quality attributes of ADCs are the purity and stability of the active small molecule drug linked to the ADC, but these are difficult to assess once the drug is conjugated to the antibody. In this study, we report a enzyme deconjugation approach to cleave small molecule drugs from ADCs, which allows the drugs to be subsequently characterized by reversed-phase high performance liquid chromatography. The model ADC we used in this study utilizes a valine-citrulline linker that is designed to be sensitive to endoproteases after internalization by tumor cells. We screened several proteases to determine the most effective enzyme. Among the 3 cysteine proteases evaluated, papain had the best efficiency in cleaving the small molecule drug from the model ADC. The deconjugation conditions were further optimized to achieve complete cleavage of the small molecule drug. This papain deconjugation approach demonstrated excellent specificity and precision. The purity and stability of the active drug on an ADC drug product was evaluated and the major degradation products of the active drug were identified. The papain deconjugation method was also applied to several other ADCs, with the results suggesting it could be applied generally to ADCs containing a valine-citrulline linker. Our results indicate that the papain deconjugation method is a powerful tool for characterizing the active small molecule drug conjugated to an ADC, and may be useful in ensuring the product quality, efficacy and the safety of ADCs. PMID:26891281
Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient.
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
Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient
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
Depth Estimation Method Based on the Ratio of Gravity and Full Tensor Gradient Invariant
NASA Astrophysics Data System (ADS)
Zhou, Wenna
2016-02-01
In this paper, I present a new depth estimation method based on the ratio of gravity and full tensor gradient invariant. The new approach is designed to be stably and quickly interpret the gravity data and full tensor gravity data. First, we deduce two simple calculation equations using the particular models (sphere and horizontal cylinder model). The depths of the particular sources can be directly calculated using the simple equations. However, a shape factor similar to the structural index of Euler deconvolution is contained in the simple calculation equations. It directly relates to the accuracy of calculation depth. To calculate the depth of source accurately, the shape factor must be determined first. Thus, the application of the simple equations is very circumscribed. To overcome the limitation, I calculate the ratio of the simple equations of different altitudes to improve the original algorithm. It effectively eliminates the influence of the shape factor. I use different model to test the method and apply the method on real gravity data. It demonstrates that the new approach is stable, simple and effective depth estimation method. The new improved approach not only can be used to calculate the sphere and cylinder model depth, but also can be used to calculate other general models. It is a very useful tool to calculate the depth of gravity bodies.
A Novel Ultrasonic Method for Characterizing Microstructural Gradients in Tubular Structures
NASA Technical Reports Server (NTRS)
Roth, Don J.; Carney, Dorothy V.; Baaklini, George Y.; Bodis, James R.; Rauser, Richard W.
1998-01-01
Ultrasonic velocity and time-of-flight (TOF) imaging that uses back surface reflections to gage volumetric material quality is highly suited for quantitative characterization of microstructural gradients including those due to pore fraction, density, fiber fraction, and chemical composition variations. However, a weakness of conventional pulse echo ultrasonic velocity and TOF imaging is that the image shows the effects of thickness as well as microstructural variations, unless the part is uniformly thick. This limits this imaging method's usefulness in practical applications. Prior studies have described a pulse echo TOF based ultrasonic imaging method that requires using a single transducer in combination with a reflector plate placed behind samples which, eliminates the effect of thickness variation in the image. In those studies, this method was successful at isolating ultrasonic variations due to material in plate like samples of silicon nitride, metal matrix composite, and polymer matrix composite. In this study, the method is engineered for inspection of more complex shaped structures- those having (hollow) tubular or curved geometry. The experimental inspection technique and results are described as applied to a polymer matrix composite "proof of concept" tube that contains machined patches of various depths and an as manufactured monolithic silicon nitride ceramic tube that might be used in "real world" applications.
Direct measurement of sub-surface mass change using the variable-baseline gravity gradient method
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.
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).
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.
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.
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
NASA Astrophysics Data System (ADS)
Zou, Wenli; Filatov, Michael; Cremer, Dieter
2015-06-01
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 Hg2 and Cn2, which are due to the admixture of more bonding character to the highest occupied spinors.
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.
Zou, Wenli; Filatov, Michael; Cremer, Dieter
2015-06-01
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 Hg2 and Cn2, which are due to the admixture of more bonding character to the highest occupied spinors. PMID:26049478
Bozkaya, Uğur; 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. PMID:27155621
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.
Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient
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
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. PMID:26819907
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.
NASA Astrophysics Data System (ADS)
Park, J.-H.; Fares, S.; Weber, R.; Goldstein, A. H.
2014-01-01
The Biosphere Effects on AeRosols and Photochemistry EXperiment (BEARPEX) took place in Blodgett Forest, a Ponderosa pine forest in the Sierra Nevada of California, USA, during summer 2009. We deployed a proton transfer reaction-quadrupole mass spectrometer (PTR-QMS) to measure fluxes and concentrations of biogenic volatile organic compounds (BVOCs). Eighteen ion species, including the major BVOC expected at the site, were measured sequentially at 5 heights to observe their vertical gradient from the forest floor to above the canopy. Fluxes of the 3 dominant BVOCs methanol, 2-Methyl-3-butene-2-ol (MBO), and monoterpenes were measured above the canopy by the disjunct eddy covariance (EC) method. Canopy-scale fluxes were also determined by the flux-gradient similarity method (K-theory). A universal K (Kuniv) was determined as the mean of individual K's calculated from the measured fluxes divided by vertical gradients for methanol, MBO, and monoterpenes. This Kuniv was then multiplied by the gradients of each observed ion species to compute their fluxes. The flux-gradient similarity method showed very good agreement with the disjunct EC method. Fluxes are presented for all measured species and compared to historical measurements from the same site, and used to test emission algorithms used to model fluxes at the regional scale. MBO was the dominant emission observed, followed by methanol, monoterpenes, acetone, and acetaldehyde. The flux-gradient similarity method is shown to be tenable, and we recommend its use, especially in experimental conditions when fast measurement of BVOC species is not available.
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.
Gradients for two-component quasirelativistic methods. Application to dihalogenides of element 116.
van Wüllen, Christoph; Langermann, Norbert
2007-03-21
The authors report the implementation of geometry gradients for quasirelativistic two-component Hartree-Fock and density functional methods using either the zero-order regular approximation Hamiltonian or spin-dependent effective core potentials. The computational effort of the resulting program is comparable to that of corresponding nonrelativistic calculations, as it is dominated by the evaluation of derivative two-electron integrals, which is the same for both types of calculations. Besides the implementation of derivatives of matrix elements of the one-particle Hamiltonian with respect to nuclear displacements, the calculation of the derivative exchange-correlation energy for the open shell case involves complicated expressions because of the noncollinear approach chosen to define the spin density. A pilot application to dihalogenides of element 116 shows how spin-orbit coupling strongly affects the chemistry of the superheavy p-block elements. While these molecules are bent at a scalar-relativistic level, spin-orbit coupling is so strong that only the 7p3/2 atomic orbitals of element 116 are involved in bonding, which favors linear molecular geometries for dihalogenides with heavy terminal halogen atoms. PMID:17381195
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.
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.
Poblano v1.0 : a Matlab toolbox for gradient-based optimization.
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.
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.
Microencapsulation of conjugated linolenic acid-rich pomegranate seed oil by an emulsion method.
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
Tian, Zhiyong; Huang, Yingying; Zhang, Yan; Song, Lina; Qiao, Yan; Xu, Xuejun; Wang, Chaojie
2016-05-01
The effect of polyamine side chains on the interaction between naphthalimide-polyamine conjugates (1-7) and herring sperm DNA was studied by UV/vis absorption and fluorescent spectra under physiological conditions (pH=7.4). The diverse spectral data and further molecular docking simulation in silico indicated that the aromatic moiety of these compounds could intercalate into the DNA base pairs while the polyamine motif might simultaneously locate in the minor groove. The triamine compound 7 can interact more potently with DNA than the corresponding diamine compounds (1-6). The presence of the bulky terminal group in the diamine side chain reduced the binding strength of compound 1 with DNA, compared to other diamine compounds (2-6). In addition, the increasing methylene number in the diamine backbone generally results in the elevated binding constant of compounds-DNA complex. The fluorescent tests at different temperature revealed that the quenching mechanism was a static type. The binding constant and thermodynamic parameter showed that the binding strength and the type of interaction force, associated with the side chains, were mainly hydrogen bonding and hydrophobic force. And the calculated free binding energies of molecular docking are generally consistent with the stability of polyamine-DNA complexes. The circular dichroism assay about the impact of compounds 1-7 on DNA conformation testified the B to A-like conformational change. PMID:26926663
Cho, Hansol; Son, Young Mok; Kim, Mu Gyeom; Ra, Byoung Joo; Park, Joon-Yong; Lee, Seung Hui; Choi, Jin Sung; Song, Min Young; Park, O Ok; Kim, Youn Cheol; Hwang, Jin Taek
2006-10-01
We report a fabrication method for a gradient refractive-index polymeric object from a binary comonomer system, regardless of the monomers' reactivity ratio and the molar volume criteria of gradient refractive-index development. To fabricate a large gradient refractive-index rod consisting of a methyl methacrylate and 2,2,3,3-tetrafluoropropyl methacrylate comonomer pair that has not been used for fabrication of a copolymer gradient refractive-index rod by previous conventional methods because of chemical restrictions in molar volume and reactivity ratio difference, we use the so-called successive UV polymerization in a controlled radial volume in conjunction with an automatic refill reactor. Simultaneously and automatically, the volume shrinkage problem, an inevitable shortcoming for the fabrication of a large polymeric object in a commercial production scale, is overcome and exploited. The theoretical features of the refractive-index profile generation of this method are also compared with those of conventional methods for which the chemical restrictions of monomers are crucial for the shape of a refractive-index profile. PMID:16983409
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
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.
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
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.
A spreadsheet method of estimating best-fit hydraulic gradients using head data from multiple wells.
Devlin, J F
2003-01-01
Hydraulic gradients from planar water tables, or piezometric surfaces, and horizontal flow regimes can be quickly and conveniently calculated from data sets involving numerous wells. The matrix-solving functions of a modem spreadsheet program (Excel) were used to determine the equation of a water-table plane, Ax + By + Cz - D = 0, and the equation coefficients were then used to determine the magnitude of the hydraulic gradient, according to gradient = square root of A2 + B2/C2, and its direction, according to alpha = arctan B/A, where alpha is the angle measured from the x-axis. A pre-prepared Excel file constructed to handle data from up to 20 wells at once is available for free downloading at www.geo.ku.edu/hydro/KUHydro.html. PMID:12772824
Soviet phase conjugation research
Fisher, R.A.; Boyd, R.W.; Klein, M.B.; Kurnit, N.A.; Milonni, P.W.; Rockwell, D.A.; Yeh, P.
1990-09-01
Optical phase conjugation is a Soviet-discovered technique that applies nonlinear optical effects to automatically manipulate laser beams while automatically correcting for arbitrary distortions. Optical phase conjugation can aid in providing improved configurations for average-power and high-peak-power laser systems; it can provide nearly automatic pointing and tracking laser systems; and it can provide many other practical applications (both military and nonmilitary). Here it is important to note that 100- to 1000-watt systems are also of significant importance, not just ultra-high-energy or high-power lasers designed to do significant structural damage at significant distances. One class of phase conjugation techniques, namely, stimulated Brillouin scattering, along with its four-wave mixing counterpart, Brillioun-enhanced four-wave mixing, has been the hallmark of the Soviet effort -- with nearly all contributions (both theoretical and experimental) arising from the Soviet Union. Both stimulated Brillouin scattering and Brillouin-enhanced four-wave mixing arise from the same electrostrictive nonlinearity, where the presence of a gradient in the optical intensity produces a force on the fluid. Scientists in the United States started studying optical phase conjugation approximately five years after Soviet scientists, and initially concentrated on areas quite different from those of Soviet emphasis.
NASA Astrophysics Data System (ADS)
Gould, Harvey; Maddi, Jason; Dinneen, Timothy
2000-06-01
Time-invariant electric field gradients have long been used to deflect beams of molecules and neutral atoms. However, time-varying electric field gradients can also be used to accelerate, slow [1,2], cool [2], or bunch these same beams. The possible applications include slowing and cooling thermal beams of molecules and atoms, launching cold atoms from a trap into a fountain, beam transport, and measuring atomic dipole polarizabilities. [1] H.L. Bethlem, G. Berden, and G Meijer, Phys. Rev. Lett. 83, 1588 (1999). [2] J. A. Maddi, T.P. Dinneen, and H. Gould, Phys. Rev. A60, 3882 (1999).
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
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
NASA Astrophysics Data System (ADS)
Zou, Wenli; Filatov, Michael; Cremer, Dieter
2011-06-01
The analytical energy gradient of the normalized elimination of the small component (NESC) method is derived for the first time and implemented for the routine calculation of NESC geometries and other first order molecular properties. Essential for the derivation is the correct calculation of the transformation matrix U relating the small component to the pseudolarge component of the wavefunction. The exact form of {partial {U}}/{partial λ } is derived and its contribution to the analytical energy gradient is investigated. The influence of a finite nucleus model and that of the picture change is determined. Different ways of speeding up the calculation of the NESC gradient are tested. It is shown that first order properties can routinely be calculated in combination with Hartree-Fock, density functional theory (DFT), coupled cluster theory, or any electron correlation corrected quantum chemical method, provided the NESC Hamiltonian is determined in an efficient, but nevertheless accurate way. The general applicability of the analytical NESC gradient is demonstrated by benchmark calculations for NESC/CCSD (coupled cluster with all single and double excitation) and NESC/DFT involving up to 800 basis functions.
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
High-sensitivity in-plane vector magnetometry using the alternating gradient force method
NASA Astrophysics Data System (ADS)
Thomas, Luc; Rahmani, Anas; Renaudin, Patrice; Wack, André
2003-05-01
The alternating gradient force magnetometer is a highly sensitive tool particularly suited for thin films magnetometry. The measurement technique is based upon the alternating force generated on a magnetized sample by a set of field-gradient coils. The so-induced sample oscillation is directly proportional to the sample's magnetization. High sensitivity measurements are achieved by mounting the sample at the end of a cantilever attached to a piezoelectric bimorph element, and by tuning the excitation frequency close to the mechanical resonance of the sample-cantilever assembly. Here we describe a new design that allows to measure both in-plane components of the magnetization of a thin film sample, for any direction of the external magnetic field within the sample's plane. By rotating the sample-probe assembly, we find the output signal to be proportional to the projection of the alternating force along the sense axis of the piezoelectric bimorph. Besides, the resonance frequency of the system remains unchanged. Thus, hysteresis loops can be measured accurately for various angles between the applied field and an in-plane anisotropy axis. The signal only vanishes when the alternating force is orthogonal to the bimorph axis. Moreover, we have designed a set of two pairs of gradient coils, whose axis are orthogonal to one another. By varying the excitation current within these two pairs of coils, it is possible to rotate the alternating gradient direction, to detect magnetization components along or perpendicular to the external field.
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.
Birdsall, Robert E; McCarthy, Sean M; Janin-Bussat, Marie Claire; Perez, Michel; Haeuw, Jean-François; Chen, Weibin; Beck, Alain
2016-01-01
Conjugation processes and stability studies associated with the production and shelf life of antibody-drug conjugates (ADCs) can result in free (non-conjugated) drug species. These free drug species can increase the risk to patients and reduce the efficacy of the ADC. Despite stringent purification steps, trace levels of free drug species may be present in formulated ADCs, reducing the therapeutic window. The reduction of sample preparation steps through the incorporation of multidimensional techniques has afforded analysts more efficient methods to assess trace drug species. Multidimensional methods coupling size-exclusion and reversed phase liquid chromatography with ultra-violet detection (SEC-RPLC/UV) have been reported, but offer limited sensitivity and can limit method optimization. The current study addresses these challenges with a multidimensional method that is specific, sensitive, and enables method control in both dimensions via coupling of an on-line solid phase extraction column to RPLC with mass spectral detection (SPE-RPLC/MS). The proposed method was evaluated using an antibody-fluorophore conjugate (AFC) as an ADC surrogate to brentuximab vedotin and its associated parent maleimide-val-cit-DSEA payload and the derived N-acetylcysteine adduct formed during the conjugation process. Assay sensitivity was found to be 2 orders more sensitive using MS detection in comparison to UV-based detection with a nominal limit of quantitation of 0.30 ng/mL (1.5 pg on-column). Free-drug species were present in an unadulterated ADC surrogate sample at concentrations below 7 ng/mL, levels not detectable by UV alone. The proposed SPE-RPLC/MS method provides a high degree of specificity and sensitivity in the assessment of trace free drug species and offers improved control over each dimension, enabling straightforward integration into existing or novel workflows. PMID:26651262
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
Optimising a parallel conjugate gradient solver
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.
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.
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
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...
Shiono, Hiroyuki; Matsui, Takuya; Okada, Tadashi; Ito, Yoichiro
2016-08-01
We have developed a novel continuous flow-through cell separation method using a Percoll density gradient. This method can continuously separate a large number of cells into five fractions according to their densities. To apply this method to the separation of basophils, Percoll density gradients were modified to improve basophil enrichment. When a set of Percoll density gradients was prepared (1.071, 1.075, 1.080, 1.084, and 1.090 g/mL) the basophils in a healthy volunteer were enriched by an average of 23.1 and 63.5% at Percoll densities of 1.075 (fraction 3) and 1.080 g/mL (fraction 4), respectively. On average, the yield of basophils was 1.66 × 10(5) cells in fraction 3 and 1.61 × 10(5) cells in fraction 4 from 9 mL of peripheral blood. The expression of CD203c (cluster of differentiation 203c) on separated basophils was upregulated by anti-immunoglobulin E stimulation similar to basophils in whole blood. Histamine release induced by calcium ionophore was also observed in the separated basophils. The present method will be useful for basophil enrichment since it preserves their function without using counterflow elutriation and immunological reagents, and this method will be effective as a preparative separation for cell purification by flow cytometry. PMID:27293108
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.
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.
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. PMID:25273413
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.
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.
The Optimized Gradient Method for Full Waveform Inversion and its Spectral Implementation
NASA Astrophysics Data System (ADS)
Wu, Zedong; Alkhalifah, Tariq
2016-03-01
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 modeling 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 multi-scale 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.
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
Ye, Xingyou; Patil, Hemlata; Feng, Xin; Tiwari, Roshan V; Lu, Jiannan; Gryczke, Andreas; Kolter, Karl; Langley, Nigel; Majumdar, Soumyajit; Neupane, Dipesh; Mishra, Sanjay R; Repka, Michael A
2016-02-01
Over the past few decades, nanocrystal formulations have evolved as promising drug delivery systems owing to their ability to enhance the bioavailability and maintain the stability of poorly water-soluble drugs. However, conventional methods of preparing nanocrystal formulations, such as spray drying and freeze drying, have some drawbacks including high cost, time and energy inefficiency, traces of residual solvent, and difficulties in continuous operation. Therefore, new techniques for the production of nanocrystal formulations are necessary. The main objective of this study was to introduce a new technique for the production of nanocrystal solid dispersions (NCSDs) by combining high-pressure homogenization (HPH) and hot-melt extrusion (HME). Efavirenz (EFZ), a Biopharmaceutics Classification System class II drug, which is used for the treatment of human immunodeficiency virus (HIV) type I, was selected as the model drug for this study. A nanosuspension (NS) was first prepared by HPH using sodium lauryl sulfate (SLS) and Kollidon® 30 as a stabilizer system. The NS was then mixed with Soluplus® in the extruder barrel, and the water was removed by evaporation. The decreased particle size and crystalline state of EFZ were confirmed by scanning electron microscopy, zeta particle size analysis, and differential scanning calorimetry. The increased dissolution rate was also determined. EFZ NCSD was found to be highly stable after storage for 6 months. In summary, the conjugation of HPH with HME technology was demonstrated to be a promising novel method for the production of NCSDs. PMID:26283197
NASA Astrophysics Data System (ADS)
Kolgotin, Alexei; Müller, Detlef; Romanov, Anton; Chemyakin, Eduard
2016-06-01
Correlation relationships between aerosol microphysical parameters and optical data are investigated. The results show that surface-area concentrations and extinction coefficients are linearly correlated with a correlation coefficient above 0.99 for arbitrary particle size distribution. The correlation relationships that we obtained can be used as constraints in our inversion of optical lidar data. Simulation studies demonstrate a significant stabilization of aerosol microphysical data products if we apply the gradient correlation method in our traditional regularization technique.
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
ZHANG, ZHUOYUAN; WANG, CHENXING; LI, TANG; LIU, ZHE; LI, LONGJIANG
2014-01-01
The aim of the present study was to compare the method of ultracentrifugation and density gradient separation for isolating Tca8113 human tongue squamous cell carcinoma cell line-derived exosomes. The exosomes were obtained from the culture supernatant of cultured Tca8113 cells, respectively, followed by identification with transmission electron microscopy observation and western blot analysis. The two different methods were then compared by the morphology, the distribution range of the particle size and the concentration of proteins of the extracted exosomes. In vitro, Tca8113 cells can secrete a large amount of vesicle-like structures, which are identified as exosomes by the presence of the surface markers, Hsp-70 and Alix. The protein profile of the two products are almost the same, however the particle size distribution of the exosomes extracted with density gradient centrifugation are more limited, between 40–120 nm, and these have a higher protein concentration. The results indicate that Tca8113 cells can secrete exosomes in vitro, and the density gradient separation methods for purifying exosomes is improved, which is helpful for future research and application of exosomes. PMID:25202395
Calibration of the RPC charge readout in the ARGO-YBJ experiment with the iso-gradient method
NASA Astrophysics Data System (ADS)
Bartoli, B.; Bernardini, P.; Bi, X. J.; Branchini, P.; Budano, A.; Camarri, P.; Cao, Z.; Cardarelli, R.; Catalanotti, S.; Chen, S. Z.; Chen, T. L.; Creti, P.; Cui, S. W.; Dai, B. Z.; D`Amone, A.; Danzengluobu; De Mitri, I.; D`Ettorre Piazzoli, B.; Di Girolamo, T.; Di Sciascio, G.; Feng, C. F.; Feng, Zhaoyang; Feng, Zhenyong; Gou, Q. B.; Guo, Y. Q.; He, H. H.; Hu, Haibing; Hu, Hongbo; Iacovacci, M.; Iuppa, R.; Jia, H. Y.; Labaciren; Li, H. J.; Liguori, G.; Liu, C.; Liu, J.; Liu, M. Y.; Lu, H.; Ma, L. L.; Ma, X. H.; Mancarella, G.; Mari, S. M.; Marsella, G.; Martello, D.; Mastroianni, S.; Montini, P.; Ning, C. C.; Panareo, M.; Perrone, L.; Pistilli, P.; Ruggieri, F.; Salvini, P.; Santonico, R.; Shen, P. R.; Sheng, X. D.; Shi, F.; Surdo, A.; Tan, Y. H.; Vallania, P.; Vernetto, S.; Vigorito, C.; Wang, H.; Wu, C. Y.; Wu, H. R.; Xue, L.; Yang, Q. Y.; Yang, X. C.; Yao, Z. G.; Yuan, A. F.; Zha, M.; Zhang, H. M.; Zhang, L.; Zhang, X. Y.; Zhang, Y.; Zhao, J.; Zhaxiciren; Zhaxisangzhu; Zhou, X. X.; Zhu, F. R.; Zhu, Q. Q.; Zizzi, G.
2015-05-01
The ARGO-YBJ experiment is a full coverage array of Resistive Plate Chambers (RPCs) with an active area of 5800 m2. In order to eliminate the response difference of the charge readout from the RPCs, a calibration procedure is carried out with the iso-gradient method. This method also allows the extension of the absolute calibration with the muon telescope including scintillation detectors to all the RPCs in the array. The overall systematic uncertainty in measurements of the number of particles by the RPCs is 10.7%. In general, the method gives results consistent with those from a totally different approach also used in the experiment.
NASA Astrophysics Data System (ADS)
Perez Sanchez-Canete, Enrique; Scott, Russell L.; Barron-Gafford, Greg; van Haren, Joost
2016-04-01
Soil CO2 fluxes represent a major source of CO2 emissions, where small changes in their estimation provoke large changes in the quantification of the global carbon cycle. Recently, the gradient method that employs soil CO2 probes at multiple depths has been offered as a way to inexpensively and continuously measure soil CO2 flux. However, the use of the gradient method can yield inappropriate flux estimates due to the uncertainties mainly associated with the inappropriate determination of the soil diffusion coefficient. Therefore, in-situ methods to determine diffusion coefficient are necessary to obtain accurate CO2 fluxes. Here the data obtained during one year with two automatic soil CO2 chambers along with CO2 molar fraction data from 4 probes at 10 cm depth, were used to determine a model of soil diffusion coefficient (Ds), which was applied later to obtain the soil CO2 fluxes by the gradient method. Another Ds model was obtained by injection and sampling of SF6 during several campaigns with different soil water content levels. Both Ds models obtained in situ were compared with another 13 Ds models published. We addressed three questions: 1) Can we use a previously published model, or do we need to determine Ds in situ? 2) How accurate are the CO2 fluxes estimates obtained by the gradient method for different Ds models, compared with chamber-measured CO2 fluxes? 3) Can we take a limited number of chamber measurements to obtain a good Ds model, or we need longer calibration periods? Comparing the cumulative soil respiration for the different diffusion models, we found that the model with empirical calibration to the soil chambers had the best agreement with the chamber fluxes (<0.5% error). The SF6 model underestimated by chamber fluxes by 23% and the published models ranged from an underestimate of 78% to an overestimate of 14%. Most importantly, we found that a few days of measurements with a soil respiration chamber (with widely varying soil water content
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. PMID:26065425
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.
Cell interaction study method using novel 3D silica nanoneedle gradient arrays
Rajput, Deepak; Crowder, Spencer; Hofmeister, Lucas; Costa, Lino; Sung, Hak-Joon; Hofmeister, William
2012-01-01
Understanding cellular interactions with culture substrate features is important to advance cell biology and regenerative medicine. When surface topographical features are considerably larger in vertical dimension and are spaced at least one cell dimension apart, the features act as 3D physical barriers that can guide cell adhesion, thereby altering cell behavior. In the present study, we investigated competitive interactions of cells with neighboring cells and matrix using a novel nanoneedle gradient array. A gradient array of nanoholes was patterned at the surface of fused silica by single-pulse femtosecond laser machining. A negative replica of the pattern was extracted by nanoimprinting with a thin film of polymer. Silica was deposited on top of the polymer replica to form silica nanoneedles. NIH 3T3 fibroblasts were cultured on silica nanoneedles and their behavior was studied and compared with those cultured on a flat silica surface. The presence of silica nanoneedles was found to enhance the adhesion of fibroblasts while maintaining cell viability. The anisotropy in the arrangement of silica nanoneedles was found to affect the morphology and spreading of fibroblasts. Additionally, variations in nanoneedle spacing regulated cell-matrix and cell-cell interactions, effectively preventing cell aggregation in areas of tightly-packed nanoneedles. This proof-of-concept study provides a reproducible means for controlling competitive cell adhesion events and offers a novel system whose properties can be manipulated to intimately control cell behavior. PMID:23006558
COLLECTION OF AIRBORNE PARTICLES BY A HIGH-GRADIENT PERMANENT MAGNETIC METHOD
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.
Antibody-gold cluster conjugates
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.
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. PMID:27209196
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.
NASA Astrophysics Data System (ADS)
Kulkarni, Manish; Singh, Gurpreet; Karim, Alamgir
2012-02-01
Microphase morphologies of poly(styrene)-block-poly(methylmethacrylate) (PS-PMMA) block co-polymer (BCP) films coated on various tunable surface energy gradient (SEG) substrates were compared. Substrates were prepared by coating silane self assembled monolayer (SAM) and hydrophobic sol-gel based layer of silica (xerogel) on quartz and exposed to UV-ozone radiation by placing them on an accelerating stage that oxidizes the surface to generate SEG. The combinatorial thickness gradient samples of BCP film were prepared by flow coating the BCP solution orthogonal to the SEG. Samples were annealed using novel cold zone annealing (CZA) method with a sharp thermal gradient (50 ^oC/mm) to obtain highly ordered BCP morphologies. Effect of CZA annealing rate and film thickness on BCP morphologies of the SAM treated and untreated quartz as well as xerogel substrates were compared. It was observed that BCP films coated on the untreated quartz substrates exhibited hexagonally packed perpendicular cylindrical morphologies whereas higher area fraction of parallel cylinders was observed for SEG xerogel substrates for higher surface energies (>40 mJ/m^2). BCP 2D surface morphologies studied using AFM, were confirmed to extend to the interior of the film (3D) by GISAXS.
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.
Phase gradient algorithm method for three-dimensional holographic ladar imaging.
Stafford, Jason W; Duncan, Bradley D; Rabb, David J
2016-06-10
Three-dimensional (3D) holographic ladar uses digital holography with frequency diversity to add the ability to resolve targets in range. A key challenge is that since individual frequency samples are not recorded simultaneously, differential phase aberrations may exist between them, making it difficult to achieve range compression. We describe steps specific to this modality so that phase gradient algorithms (PGA) can be applied to 3D holographic ladar data for phase corrections across multiple temporal frequency samples. Substantial improvement of range compression is demonstrated with a laboratory experiment where our modified PGA technique is applied. Additionally, the PGA estimator is demonstrated to be efficient for this application, and the maximum entropy saturation behavior of the estimator is analytically described. PMID:27409018
NASA Astrophysics Data System (ADS)
Chen, Chong; Xu, Guoliang
2012-03-01
In this paper, we present a novel and effective L2-gradient-flow-based semi-implicit finite-element method for solving a variational problem of image reconstruction. The method is applicable to several data scenarios, especially for the contaminated data detected from uniformly sparse or randomly distributed projection directions. We also give a complete and rigorous proof for the convergence of the semi-implicit finite-element method, in which the convergence does not rely on the choices of the regularization parameter and the temporal step size. The experimental results show that our method has more desirable performance comparing with other reconstruction methods in solving a number of challenging reconstruction problems.
Elmendorf, Sarah C.; Henry, Gregory H. R.; Hollister, Robert D.; Fosaa, Anna Maria; Gould, William A.; Hermanutz, Luise; Hofgaard, Annika; Jónsdóttir, Ingibjörg S.; Jorgenson, Janet C.; Lévesque, Esther; Magnusson, Borgþór; Molau, Ulf; Myers-Smith, Isla H.; Oberbauer, Steven F.; Rixen, Christian; Tweedie, Craig E.; Walker, Marilyn D.
2015-01-01
Inference about future climate change impacts typically relies on one of three approaches: manipulative experiments, historical comparisons (broadly defined to include monitoring the response to ambient climate fluctuations using repeat sampling of plots, dendroecology, and paleoecology techniques), and space-for-time substitutions derived from sampling along environmental gradients. Potential limitations of all three approaches are recognized. Here we address the congruence among these three main approaches by comparing the degree to which tundra plant community composition changes (i) in response to in situ experimental warming, (ii) with interannual variability in summer temperature within sites, and (iii) over spatial gradients in summer temperature. We analyzed changes in plant community composition from repeat sampling (85 plant communities in 28 regions) and experimental warming studies (28 experiments in 14 regions) throughout arctic and alpine North America and Europe. Increases in the relative abundance of species with a warmer thermal niche were observed in response to warmer summer temperatures using all three methods; however, effect sizes were greater over broad-scale spatial gradients relative to either temporal variability in summer temperature within a site or summer temperature increases induced by experimental warming. The effect sizes for change over time within a site and with experimental warming were nearly identical. These results support the view that inferences based on space-for-time substitution overestimate the magnitude of responses to contemporary climate warming, because spatial gradients reflect long-term processes. In contrast, in situ experimental warming and monitoring approaches yield consistent estimates of the magnitude of response of plant communities to climate warming. PMID:25548195
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
NASA Astrophysics Data System (ADS)
Durand, M. T.; Molotch, N. P.; Kim, E. J.; Margulis, S. A.; Courville, Z.; Bateni, S.
2011-12-01
Snow microstructure is one of the fundamental controls on the propagation of radiation through the snowpack, at wavelengths ranging from visible to microwave. Objective characterization of snow microstructure for radiative transfer modeling has long been a difficult issue. Traditionally measurements of snow microstructure have been made via hand lens or stereology. Geometric grain size or the maximum linear extent of prevailing grains can be measured using a ruled card or a loupe- style hand lens, but these measurements are prone to observer error. In the stereology approach, snow samples are obtained in the field, preserved via a casting agent, cut with a microtome and photographed in the lab, then analyzed to obtain the specific surface area; these measurements are time and resource intensive. More recently, field-based techniques have been developed, including contact spectroscopy and NIR photography. Contact spectroscopy has a vertical resolution ~2 cm, while the NIR camera has a vertical resolution ~1mm. Contact spectroscopy measures direct reflectance across the entire visible/NIR spectrum, while the NIR camera measures diffuse reflectance within a single wavelength band. In this study, our goal was to evaluate how accurately the contact spectroscopy and NIR photography characterize specific surface area for four different types of snow. Our study took place in Steamboat Springs, Colorado in late March, 2011. We measured grain size at four different elevations, approximately at four locations spanning an elevation gradient of ~1000 meters. At the lowest elevation, liquid water was present in the snowpack on some days, and significant melt-refreeze crusts were present throughout the pack. At the highest elevation, no evidence of melt metamorphism was observed, except for a basal melt-refreeze crust from the beginning of the season. In addition to evaluating the accuracy of each technique, we evaluated the sensitivity of each technique to easily-made user
Yi, Jiang; Zhang, Yuzhu; Liang, Rong; Zhong, Fang; Ma, Jianguo
2015-01-14
Beta-lactoglobulin (BLG)–catechin conjugates were prepared by a free radical method and investigated with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), electrospray ionization–mass spectrometry (ESI-MS), and far-UV circular dichroism (CD). Covalent binding between BLG and catechin were confirmed with SDS-PAGE and ESI-MS. About 93% of beta-lactoglobulin was conjugated with catechin or catecin fragments according to the gel intensity analysis software. Far-UV CD results showed that the content of β-sheet decreased with a corresponding increase in unordered structures after grafting. Both nanoemulsions with mean particle size between 160 and 170 nm were prepared. Both the rate of particle growth and the total beta-carotene (BC) loss at 50 °C were significantly greater than at 4 and 25 °C. The retention rates of BC in nanoemulsions were 27.8% and 48.6% for BLG and BLG–catechin conjugates, respectively, after 30 days of storage at 50 °C. The BC retention encapsulated in nanoemulsion was significantly improved using BLG–catechin conjugates, compared with BLG alone. The increase of BC retention in nanoemulsions encapsulated with BLG–catechin conjugates was due to the significant improvement of antioxidative properties (reducing power, free radical scavenging activity, and hydroxyl radical scavenging activity) of BLG after covalent binding with catechin. The results indicated that the proteins modified with polyphenols can be widely used in a labile bioactive compounds encapsulation delivery system. PMID:25514513
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…
NASA Astrophysics Data System (ADS)
Fantino, E.; Casotto, S.
2009-07-01
Four widely used algorithms for the computation of the Earth’s gravitational potential and its first-, second- and third-order gradients are examined: the traditional increasing degree recursion in associated Legendre functions and its variant based on the Clenshaw summation, plus the methods of Pines and Cunningham-Metris, which are free from the singularities that distinguish the first two methods at the geographic poles. All four methods are reorganized with the lumped coefficients approach, which in the cases of Pines and Cunningham-Metris requires a complete revision of the algorithms. The characteristics of the four methods are studied and described, and numerical tests are performed to assess and compare their precision, accuracy, and efficiency. In general the performance levels of all four codes exhibit large improvements over previously published versions. From the point of view of numerical precision, away from the geographic poles Clenshaw and Legendre offer an overall better quality. Furthermore, Pines and Cunningham-Metris are affected by an intrinsic loss of precision at the equator and suffer from additional deterioration when the gravity gradients components are rotated into the East-North-Up topocentric reference system.
Ward, G.J. Ecole Polytechnique Federale, Lausanne ); Heckbert, P.S. . School of Computer Science Technische Hogeschool Delft . Dept. of Technical Mathematics and Informatics)
1992-04-01
A new method for improving the accuracy of a diffuse interreflection calculation is introduced in a ray tracing context. The information from a hemispherical sampling of the luminous environment is interpreted in a new way to predict the change in irradiance as a function of position and surface orientation. The additional computation involved is modest and the benefit is substantial. An improved interpolation of irradiance resulting from the gradient calculation produces smoother, more accurate renderings. This result is achieved through better utilization of ray samples rather than additional samples or alternate sampling strategies. Thus, the technique is applicable to a variety of global illumination algorithms that use hemicubes or Monte Carlo sampling techniques.
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.
Jagannath, Ravi Prasad K; Yalavarthy, Phaneendra K
2013-03-01
Typical image-guided diffuse optical tomographic image reconstruction procedures involve reduction of the number of optical parameters to be reconstructed equal to the number of distinct regions identified in the structural information provided by the traditional imaging modality. This makes the image reconstruction problem less ill-posed compared to traditional underdetermined cases. Still, the methods that are deployed in this case are same as those used for traditional diffuse optical image reconstruction, which involves a regularization term as well as computation of the Jacobian. A gradient-free Nelder-Mead simplex method is proposed here to perform the image reconstruction procedure and is shown to provide solutions that closely match ones obtained using established methods, even in highly noisy data. The proposed method also has the distinct advantage of being more efficient owing to being regularization free, involving only repeated forward calculations. PMID:23515862
NASA Astrophysics Data System (ADS)
Jagannath, Ravi Prasad K.; Yalavarthy, Phaneendra K.
2013-03-01
Typical image-guided diffuse optical tomographic image reconstruction procedures involve reduction of the number of optical parameters to be reconstructed equal to the number of distinct regions identified in the structural information provided by the traditional imaging modality. This makes the image reconstruction problem less ill-posed compared to traditional underdetermined cases. Still, the methods that are deployed in this case are same as those used for traditional diffuse optical image reconstruction, which involves a regularization term as well as computation of the Jacobian. A gradient-free Nelder-Mead simplex method is proposed here to perform the image reconstruction procedure and is shown to provide solutions that closely match ones obtained using established methods, even in highly noisy data. The proposed method also has the distinct advantage of being more efficient owing to being regularization free, involving only repeated forward calculations.
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
Design of a gradient-index beam shaping system via a genetic algorithm optimization method
NASA Astrophysics Data System (ADS)
Evans, Neal C.; Shealy, David L.
2000-10-01
Geometrical optics - the laws of reflection and refraction, ray tracing, conservation of energy within a bundle of rays, and the condition of constant optical path length - provides a foundation for design of laser beam shaping systems. This paper explores the use of machine learning techniques, concentrating on genetic algorithms, to design laser beam shaping systems using geometrical optics. Specifically, a three-element GRIN laser beam shaping system has been designed to expand and transform a Gaussian input beam profile into one with a uniform irradiance profile. Solution to this problem involves the constrained optimization of a merit function involving a mix of discrete and continuous parameters. The merit function involves terms that measure the deviation of the output beam diameter, divergence, and irradiance from target values. The continuous parameters include the distances between the lens elements, the thickness, and radii of the lens elements. The discrete parameters include the GRIN glass types from a manufacturer's database, the gradient direction of the GRIN elements (positive or negative), and the actual number of lens elements in the system (one to four).
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
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.
Giżyńska, Marta K.; Kukołowicz, Paweł F.; Kordowski, Paweł
2014-01-01
Aim The aim of this work is to present a method of beam weight and wedge angle optimization for patients with prostate cancer. Background 3D-CRT is usually realized with forward planning based on a trial and error method. Several authors have published a few methods of beam weight optimization applicable to the 3D-CRT. Still, none on these methods is in common use. Materials and methods Optimization is based on the assumption that the best plan is achieved if dose gradient at ICRU point is equal to zero. Our optimization algorithm requires beam quality index, depth of maximum dose, profiles of wedged fields and maximum dose to femoral heads. The method was tested for 10 patients with prostate cancer, treated with the 3-field technique. Optimized plans were compared with plans prepared by 12 experienced planners. Dose standard deviation in target volume, and minimum and maximum doses were analyzed. Results The quality of plans obtained with the proposed optimization algorithms was comparable to that prepared by experienced planners. Mean difference in target dose standard deviation was 0.1% in favor of the plans prepared by planners for optimization of beam weights and wedge angles. Introducing a correction factor for patient body outline for dose gradient at ICRU point improved dose distribution homogeneity. On average, a 0.1% lower standard deviation was achieved with the optimization algorithm. No significant difference in mean dose–volume histogram for the rectum was observed. Conclusions Optimization shortens very much time planning. The average planning time was 5 min and less than a minute for forward and computer optimization, respectively. PMID:25337411
Wan, B; Doumen, C; Duszynski, J; Salama, G; LaNoue, K F
1993-08-01
The electrical potential gradient across the mitochondrial membrane (delta psi m) in perfused rat hearts was estimated by calculating the equilibrium distribution of the lipophilic cation tetraphenylphosphonium (TPP+), using measured kinetic constants of uptake and release of TPP+. First-order rate constants of TPP+ uptake were measured during 30-min perfusions of intact rat hearts with tracer amounts (5.0 nM) of tritium-labeled TPP+ ([3H]TPP+) in the perfusate. This was followed by a 30-min washout, during which the first-order rate constant of efflux was estimated. Values of [3H]TPP+ outside the heart and total [3H]TPP+ inside the heart at equilibrium were calculated. From this information and separately estimated time-averaged plasma membrane potentials (delta psi c) it was possible to calculate free cytosolic [3H]TPP+ at equilibrium. It was also possible to calculate free intramitochondrial [3H]TPP+ at equilibrium as the difference between total tissue [3H]TPP+ minus free cytosolic TPP+ and the sum of all the bound [3H]TPP+. Bound [3H]TPP+ was determined from [3H]TPP+ binding constants measured in separate experiments, using both isolated mitochondria and isolated cardiac myocytes under conditions where both delta psi m and delta psi c were zero. Delta psi m was calculated from the intramitochondrial and cytosolic free TPP+ concentrations using the Nernst equation. Values of delta psi m were 144.9 +/- 2.0 mV in hearts perfused with 5 mM pyruvate and 118.2 +/- 1.4 mV in hearts perfused with 11 mM glucose, in good agreement with delta psi m obtained from isolated rat heart mitochondria.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8368347
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.
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.
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. PMID:26636071
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. PMID:26636071
Chemical Gradient-mediated Melting Curve Analysis for Genotyping of Single Nucleotide Polymorphisms
Russom, Aman; Irimia, Daniel; Toner, Mehmet
2009-01-01
This report describes a microfluidic solid-phase Chemical Gradient-mediated Melting Curve Analysis (CGMCA) method for single nucleotide polymorphism (SNP) analysis. The method is based on allele-specific denaturation to discriminate mismatched (MM) from perfectly matched (PM) DNA duplexes upon exposure to linear chemical gradient. PM and MM DNA duplexes conjugated on beads are captured in a microfluidic gradient generator device designed with dams, keeping the beads trapped perpendicular to a gradient generating channel. Two denaturants, formamide and urea, were tested for their ability to destabilize the DNA duplex by competing with Watson-Crick pairing. Upon exposure to the chemical gradient, rapid denaturing profile was monitored in real time using fluorescence microscopy. The results show that the two duplexes exhibit different kinetics of denaturation profiles, enabling discrimination of MM from PM DNA duplexes to score SNP. PMID:19593749
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. PMID:26838399
Minzioni, Paolo; Pusino, Vincenzo; Cristiani, Ilaria; Marazzi, Lucia; Martinelli, Mario; Langrock, Carsten; Fejer, M M; Degiorgio, Vittorio
2010-08-16
We experimentally compare the effectiveness of three different optical-phase-conjugation-based nonlinearity-compensation strategies on a transmission system employing phase-modulated signals, and hence affected by the Gordon-Mollenauer effect. We demonstrate that it is possible to obtain significant nonlinearity compensation, but that no improvement is obtained using configurations specifically aimed at the compensation of the nonlinear phase noise. PMID:20721200
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.
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.
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
Improvement of the variable storage coefficient method with water surface gradient as a variable
Technology Transfer Automated Retrieval System (TEKTRAN)
The variable storage coefficient (VSC) method has been used for streamflow routing in continuous hydrological simulation models such as the Agricultural Policy/Environmental eXtender (APEX) and the Soil and Water Assessment Tool (SWAT) for more than 30 years. APEX operates on a daily time step and ...
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
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.
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.
Huang, D; Chow, Tommy W S
2007-01-01
Microarray gene expression data usually consist of a large amount of genes. Among these genes, only a small fraction is informative for performing cancer diagnostic test. This paper focuses on effective identification of informative genes. We analyze gene selection models from the perspective of optimization theory. As a result, a new strategy is designed to modify conventional search engines. Also, as overfitting is likely to occur in microarray data because of their small sample set, a point injection technique is developed to address the problem of overfitting. The proposed strategies have been evaluated on three kinds of cancer diagnosis. Our results show that the proposed strategies can improve the performance of gene selection substantially. The experimental results also indicate that the proposed methods are very robust under all the investigated cases. PMID:17666766
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
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
NASA Astrophysics Data System (ADS)
Gonga-Saholiariliva, Nahossio; Gunnell, Yanni; Harbor, David; Mering, Catherine
2011-11-01
The study of abrupt changes in longitudinal river profiles, or knickpoints, is currently approached through an empirical power law: the slope-area relationship. Results based on digital elevation model (DEM) analyses and stream extractions are generally intended to determine crustal uplift rates and identify transient landscape conditions. In this article, we present an alternative geomorphometric method for locating knickpoints and knickzones based on local slope gradient and curvature attributes. Intended as a rapid, regional scale, automated knickpoint detection technique, the accuracy of this slope-curvature method is tested on two digital elevation grids, NASA's SRTM (ground resolution of 90 m, resampled here to 75 m) and the ASTER DEM (15 m) in the Sierra Nacimiento (New Mexico, USA), a basement-cored mountain range recently exhumed by waves of headward drainage integration in response to remote tectonic deformation in the adjacent Rio Grande rift. Out of every 10 gradient anomalies detected by the SRTM-derived numeric routine, up to 8 are certifiable knickpoints recognized among a population of georeferenced occurrences surveyed in the field. An independent comparison with the slope-area method provided a further accuracy test, which was particularly useful at sites that could not be validated in the field for practical reasons. Given the low tectonic activity of the study area, the majority of knickpoints was also found to coincide with lithologic boundaries, making it difficult without further geomorphological data to single out dynamic knickpoints directly caused by the upstream propagation of channel instabilities relating to base level change.
Correlated displacement- T2 MRI by means of a Pulsed Field Gradient-Multi Spin Echo method
NASA Astrophysics Data System (ADS)
Windt, Carel W.; Vergeldt, Frank J.; Van As, Henk
2007-04-01
A method for correlated displacement- T2 imaging is presented. A Pulsed Field Gradient-Multi Spin Echo (PFG-MSE) sequence is used to record T2 resolved propagators on a voxel-by-voxel basis, making it possible to perform single voxel correlated displacement- T2 analyses. In spatially heterogeneous media the method thus gives access to sub-voxel information about displacement and T2 relaxation. The sequence is demonstrated using a number of flow conducting model systems: a tube with flowing water of variable intrinsic T2's, mixing fluids of different T2's in an "X"-shaped connector, and an intact living plant. PFG-MSE can be applied to yield information about the relation between flow, pore size and exchange behavior, and can aid volume flow quantification by making it possible to correct for T2 relaxation during the displacement labeling period Δ in PFG displacement imaging methods. Correlated displacement- T2 imaging can be of special interest for a number of research subjects, such as the flow of liquids and mixtures of liquids or liquids and solids moving through microscopic conduits of different sizes (e.g., plants, porous media, bioreactors, biomats).
Correlated displacement-T2 MRI by means of a Pulsed Field Gradient-Multi Spin Echo Method.
Windt, Carel W; Vergeldt, Frank J; Van As, Henk
2007-04-01
A method for correlated displacement-T2 imaging is presented. A Pulsed Field Gradient-Multi Spin Echo (PFG-MSE) sequence is used to record T2 resolved propagators on a voxel-by-voxel basis, making it possible to perform single voxel correlated displacement-T2 analyses. In spatially heterogeneous media the method thus gives access to sub-voxel information about displacement and T2 relaxation. The sequence is demonstrated using a number of flow conducting model systems: a tube with flowing water of variable intrinsic T2's, mixing fluids of different T2's in an "X"-shaped connector, and an intact living plant. PFG-MSE can be applied to yield information about the relation between flow, pore size and exchange behavior, and can aid volume flow quantification by making it possible to correct for T2 relaxation during the displacement labeling period Delta in PFG displacement imaging methods. Correlated displacement-T2 imaging can be of special interest for a number of research subjects, such as the flow of liquids and mixtures of liquids or liquids and solids moving through microscopic conduits of different sizes (e.g., plants, porous media, bioreactors, biomats). PMID:17236795
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.
Guidez, Emilie B; Xu, Peng; Gordon, Mark S
2016-02-01
The dispersion interaction energy may be expressed as a sum over R(-n) terms, with n ≥ 6. Most implementations of the dispersion interaction in model potentials are terminated at n = 6. Those implementations that do include higher order contributions commonly only include even power terms, despite the fact that odd power terms can be important. Because the effective fragment potential (EFP) method contains no empirically fitted parameters, the EFP method provides a useful vehicle for examining the importance of the leading R(-7) odd power term in the dispersion expansion. To fully evaluate the importance of the R(-7) contribution to the dispersion energy, it is important to have analytic energy first derivatives for all terms. In the present work, the gradients of the term E7 ∼ R(-7) are derived analytically, implemented in the GAMESS software package, and evaluated relative to other terms in the dispersion expansion and relative to the total EFP interaction energy. Periodic boundary conditions in the minimum image convention are also implemented. A more accurate dispersion energy contribution can now be obtained during molecular dynamics simulations. PMID:26745447
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. PMID:25681736
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.
Al/Al-N/AlN compositional gradient film synthesized by ion-beam assisted deposition method
Amamoto, Yoshiki; Uchiyama, Shingo; Watanabe, Yoshihisa; Nakamura, Yoshikazu
1997-12-01
Al/Al-N-AlN compositional gradient thin film was deposited on a Si(100) substrate at room temperature by ion-beam assisted deposition method, with a diminishing ion beam current from 1.4 to 0 mA at increments of 0.3 mA in order to gradually decrease the nitrogen to aluminum ratio at the substrate. The gradual Al and AlN variation in composition was shown by the change of the Al/N atomic ratio analyzed by the energy dispersive X-ray spectroscopy (EDX) and the X-ray photoelectron spectroscopy (XPS) in the cross section of the film. The formation of crystalline Al metal and AlN ceramic layer on the Si substrate was revealed by X-ray diffraction (XRD). The cross sectional image taken by high resolution transmission electron microscope (HRTEM) showed a nano-sized crystalline Al-N ceramic material and the flat interface between the Si substrate and the AlN film.
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.
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.
Mohammadpour, Mozhdeh; Jamshidi, Zahra
2016-05-21
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. PMID:27208944
Walravens, Jeroen; Mikula, Hannes; Rychlik, Michael; Asam, Stefan; Ediage, Emmanuel Njumbe; Di Mavungu, José Diana; Van Landschoot, Anita; Vanhaecke, Lynn; De Saeger, Sarah
2014-10-31
A UPLC-ESI(+/-)-MS/MS method for the simultaneous determination of free (alternariol, alternariol monomethyl ether, altenuene, tenuazonic acid, tentoxin, altertoxin-I) and conjugated (sulfates and glucosides of alternariol and alternariol monomethyl ether) Alternaria toxins in cereals and cereal products (rice, oat flakes and barley) was developed. Optimization of the sample preparation and extraction methodology was achieved through experimental design, using full factorial design for extraction solvent composition optimization and fractional factorial design to identify the critical factors in the sample preparation protocol, which were in turn subjected to optimization. Final extracts were analysed using an Waters Acquity UPLC system coupled to a Quattro Premier XE mass spectrometer equipped with an electrospray interface operated in both positive and negative ionization mode. Chromatographic separation was achieved using an Acquity UPLC HSS T3 column, and the applied gradient elution programme allowed for the simultaneous determination of 10 Alternaria toxins in a one-step chromatographic run with a total run time of only 7min. Subsequently, the method, applying isotopically labelled internal standards ([(2)H4]-alternariol monomethyl ether and [(13)C6,(15)N]-tenuazonic acid), was validated for several parameters such as linearity, apparent recovery, limit of detection, limit of quantification, precision, measurement uncertainty and specificity (in agreement with the criteria mentioned in Commission Regulation No. 401/2006/EC and Commission Decision No. 2002/657/EC). During validation, quality of the bioanalytical data was improved by counteracting the observed heteroscedasticity through the application of weighted least squares linear regression (WLSLR). Finally, 24 commercially available cereal-based foodstuffs were subjected to analysis, revealing the presence of tenuazonic acid in both rice and oat flake samples (
HPLC-fluorescence determination of individual free and conjugated bile acids in human serum.
Gatti, R; Roda, A; Cerre, C; Bonazzi, D; Cavrini, V
1997-01-01
A method for the quantitative analysis of unconjugated and conjugated bile acids (BA) in serum of patients with primary biliary cirrhosis (PBC) before and after therapy with antibiotic or ursodeoxycholic acid (UDCA) is described. After separation of the free, glycine and taurine conjugated (F, G and T conjugated) fractions by solid-phase extraction, the isolated T conjugates were hydrolysed enzymatically using cholyglycine hydrolase. The BA fractions were derivatized using 2-bromoacetyl-6-methoxynaphthalene (Br-AMN) and detected fluorimetrically (lambda exc = 300 nm, lambda em = 460 nm). The derivatization reaction was performed under mild conditions (10 min at 40 degrees C) in an aqueous medium in the presence of tetrakis (decyl) ammonium bromide (TDeABr). The HPLC separation was achieved using an ODS column and with a mobile phase gradient mixture of A-B, where A is water and B is acetonitrile:methanol (60:40 v/v) for elution at a flow-rate of 1.2 mL/min. The reproducibility, recovery and separation of individual BA under gradient elution conditions were satisfactory, allowing a sensitive detection of each BA in serum samples with a detection limit of about 1-2 pmol. PMID:9051208
Wei, Wenbo; Jia, Guang; Flanigan, David; Zhou, Jinyuan; Knopp, Michael V
2014-01-01
Glycosaminoglycan Chemical Exchange Saturation Transfer (gagCEST) is an important molecular MRI methodology developed to assess changes in cartilage GAG concentrations. The correction for B0 field inhomogeneity is technically crucial in gagCEST imaging. This study evaluates the accuracy of the B0 estimation determined by the dual gradient echo method and the effect on gagCEST measurements. The results were compared with those from the commonly used z-spectrum method. Eleven knee patients and three healthy volunteers were scanned. Dual gradient echo B0 maps with different ∆TE values (1, 2, 4, 8, and 10 ms) were acquired. The asymmetry of the magnetization transfer ratio at 1 ppm offset referred to the bulk water frequency, MTRasym(1 ppm), was used to quantify cartilage GAG levels. The B0 shifts for all knee patients using the z-spectrum and dual gradient echo methods are strongly correlated for all ∆TE values used (r = 0.997 to 0.786, corresponding to ∆TE = 10 to 1 ms). The corrected MTRasym(1 ppm) values using the z-spectrum method (1.34% ± 0.74%) highly agree only with those using the dual gradient echo methods with ∆TE = 10 ms (1.72% ± 0.80%; r = 0.924) and 8 ms (1.50% ± 0.82%; r = 0.712). The dual gradient echo method with longer ∆TE values (more than 8 ms) has an excellent correlation with the z-spectrum method for gagCEST imaging at 3T. PMID:24119460
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.
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
Enhanced optical phase conjugation in nonlinear metamaterials.
Kim, Kihong
2014-12-15
Optical phase conjugation by degenerate four-wave mixing in nonlinear metamaterials is studied theoretically by solving the coupled wave equations using a generalized version of the invariant imbedding method. The phase-conjugate reflectance and the lateral shift of the phase-conjugate reflected beams are calculated and their dependencies on the frequency, the polarization, the incident angle, the material properties and the structure are investigated in detail. It is found that the efficiency of phase conjugation can be significantly enhanced due to the enhancement of electromagnetic fields in various metamaterial structures. PMID:25607488
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.
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.
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.
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.
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.
New Langevin and gradient thermostats for rigid body dynamics.
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
Engineering spatial gradients of signaling proteins using magnetic nanoparticles.
Bonnemay, L; Hostachy, S; Hoffmann, C; Gautier, J; Gueroui, Z
2013-11-13
Intracellular biochemical reactions are often localized in space and time, inducing gradients of enzymatic activity that may play decisive roles in determining cell's fate and functions. However, the techniques available to examine such enzymatic gradients of activity remain limited. Here, we propose a new method to engineer a spatial gradient of signaling protein concentration within Xenopus egg extracts using superparamagnetic nanoparticles. We show that, upon the application of a magnetic field, a concentration gradient of nanoparticles with a tunable length extension is established within confined egg extracts. We then conjugate the nanoparticles to RanGTP, a small G-protein controlling microtubule assembly. We found that the generation of an artificial gradient of Ran-nanoparticles modifies the spatial positioning of microtubule assemblies. Furthermore, the spatial control of the level of Ran concentration allows us to correlate the local fold increase in Ran-nanoparticle concentration with the spatial positioning of the microtubule-asters. Our assay provides a bottom-up approach to examine the minimum ingredients generating polarization and symmetry breaking within cells. More generally, these results show how magnetic nanoparticles and magnetogenetic tools can be used to control the spatiotemporal dynamics of signaling pathways. PMID:24111679
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. PMID:16485758
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.
Oligonucleotide conjugates for therapeutic applications
Winkler, Johannes
2013-01-01
Insufficient pharmacokinetic properties and poor cellular uptake are the main hurdles for successful therapeutic development of oligonucleotide agents. The covalent attachment of various ligands designed to influence the biodistribution and cellular uptake or for targeting specific tissues is an attractive possibility to advance therapeutic applications and to expand development options. In contrast to advanced formulations, which often consist of multiple reagents and are sensitive to a variety of preparation conditions, oligonucleotide conjugates are defined molecules, enabling structure-based analytics and quality control techniques. This review gives an overview of current developments of oligonucleotide conjugates for therapeutic applications. Attached ligands comprise peptides, proteins, carbohydrates, aptamers and small molecules, including cholesterol, tocopherol and folic acid. Important linkage types and conjugation methods are summarized. The distinct ligands directly influence biochemical parameters, uptake machanisms and pharmacokinetic properties. PMID:23883124
Burki, Umar; Keane, Jonathan; Blain, Alison; O'Donovan, Liz; Gait, Michael John; Laval, Steven H; Straub, Volker
2015-10-01
Antisense oligonucleotide (AON)-induced exon skipping is one of the most promising strategies for treating Duchenne muscular dystrophy (DMD) and other rare monogenic conditions. Phosphorodiamidate morpholino oligonucleotides (PMOs) and 2'-O-methyl phosphorothioate (2'OMe) are two of the most advanced AONs in development. The next generation of peptide-conjugated PMO (P-PMO) is also showing great promise, but to advance these therapies it is essential to determine the pharmacokinetic and biodistribution (PK/BD) profile using a suitable method to detect AON levels in blood and tissue samples. An enzyme-linked immunosorbent assay (ELISA)-based method, which shows greater sensitivity than the liquid chromatography-mass spectrometry method, is the method of choice for 2'OMe detection in preclinical and clinical studies. However, no such assay has been developed for PMO/P-PMO detection, and we have, therefore, developed an ultrasensitive hybridization-based ELISA for this purpose. The assay has a linear detection range of 5-250 pM (R(2)>0.99) in mouse serum and tissue lysates. The sensitivity was sufficient for determining the 24-h PK/BD profile of PMO and P-PMO injected at standard doses (12.5 mg/kg) in mdx mice, the dystrophin-deficient mouse model for DMD. The assay demonstrated an accuracy approaching 100% with precision values under 12%. This provides a powerful cost-effective assay for the purpose of accelerating the development of these emerging therapeutic agents. PMID:26176274
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.
Enhanced photophysics of conjugated polymers
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.
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
Momose, T; Mure, M; Iida, T; Goto, J; Nambara, T
1998-06-19
A simple and efficient method for the separation of individual unconjugated bile acids and their glycine- and taurine-amidated, 3-sulfated, 3-glucosylated and 3-glucuronidated conjugates is described. The method involves the use of a two-dimensional (2D) reversed-phase (RP) high-performance thin-layer chromatographic (HPTLC) technique with methyl beta-cyclodextrin (Me-beta-CD). Five major unconjugated bile acids, chenodeoxycholic acid (CDCA), deoxycholic acid (DCA), ursodeoxycholic acid and lithocholic acid, and their conjugates were examined as the solutes. A high degree of separation of individual bile acids in each homologous series was achieved on a RP-HPTLC plate by developing with aqueous methanol in the first dimension and the same solvent system containing Me-beta-CD in the second dimension. In particular, all of the six 'difficult-to-separate' pairs, unconjugated CDCA and DCA and their conjugated forms with glycine, taurine, sulfuric acid, D-glucose and D-glucuronic acid, were effectively resolved by adding Me-beta-CD in the aqueous mobile phases with the formers having larger mobilities than the latter. The application of this 2D inclusion RP-HPLC method to the separation of glycine-conjugated bile acids in human bile is also described. The present method would be useful for separating and characterizing these bile acids present in biological materials. PMID:9691303
Wang, Chunlei; Chen, Sike; Caceres-Cortes, Janet; Huang, Richard Y-C; Tymiak, Adrienne A; Zhang, Yingru
2016-07-15
UV spectrophotometry is widely used to determine the molar extinction coefficients (MECs) of cytotoxic drugs as well as the drug antibody ratios (DARs) of antibody drug conjugates (ADCs). However, the unknown purity of a drug due to interfering impurities can lead to erroneous MECs and DARs. Hence, reliable methods to accurately determine purity and the MECs of drugs with limited quantity is urgently needed in Drug Discovery. Such a method has been developed. It achieves absolute purity and accurate MEC determination by a single automated HPLC analysis that uses less than 5μg of material. Specifically, analytical HPLC separation with online UV detection was used to resolve impurities and measure absorbance from only the compound of interest. Simultaneously, an online chemiluminescence nitrogen detector (CLND) was used to determine the concentration of the analyte. The MECs were then calculated from the absorbance and concentration results. The accuracy of the method was demonstrated using caffeine and a commercial cytotoxic drug, DM1. This approach is particularly suited to analyzing mixtures or samples with low purities. Excellent reproducibility was demonstrated by analyzing a proprietary drug with linker synthesized from different batches with very different levels of purity. In addition, the MECs of drug with linker, along with ADC peak areas measured from size exclusion chromatography (SEC), were used to calculate DARs for 21 in-house ADCs. The DAR results were consistent with those obtained by MS analysis. PMID:27286648
Chung, Boram; Shin, Gi Won; Choi, Woong; Joo, Jinmyoung; Jeon, Sangmin; Jung, Gyoo Yeol
2014-12-01
Antibody-conjugated magnetic nanoparticles (Ab-MNPs) have potential in pathogen detection because they allow target cells to be easily separated from complex sample matrices. However, the sensitivity and specificity of pathogen capture by Ab-MNPs generally vary according to the types of MNPs, antibodies, and sample matrices, as well as preparation methods, including immobilization. Therefore, achieving a reproducible analysis utilizing Ab-MNPs as a pathogen detection method requires accurate characterization of Ab-MNP capture ability and standardization of all handling processes. In this study, we used high-resolution CE-single strand conformational polymorphism coupled with a stuffer-free multiplex ligation-dependent probe amplification system to characterize Ab-MNPs. The capture ability of Ab-MNPs targeting Salmonella enteritidis and nine pathogens, including S. enteritidis, was analyzed in phosphate buffer and milk. The effect of storage conditions on the stability of Ab-MNPs was also assessed. The results showed that the stuffer-free multiplex ligation-dependent probe amplification system has the potential to serve as a standard characterization method for Ab-MNPs. Moreover, the precise characterization of Ab-MNPs facilitated robust pathogen detection in various applications. PMID:25070923
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. PMID:17433454
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.
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).
Iterative methods for weighted least-squares
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.
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
Tessier, E; Neirinck, L; Zhu, Z
2003-12-25
A novel sensitive high-performance liquid chromatography-electrospray mass spectrometry method has been developed for the determination of ursodeoxycholic acid (UDCA) and its glycine and taurine conjugates, glycoursodeoxycholic acid (GDCA) and tauroursodeoxycholic acid (TDCA). The procedure involved a solid phase extraction of UDCA, GDCA, TDCA and the internal standard, 23-nordeoxycholic acid from human plasma on a C18 Bond Elut cartridge. Chromatography was performed by isocratic reverse phase separation with methanol/25 mM ammonium acetate (40/60, v/v) containing 0.05% acetic acid on a C18 column with embedded polar functional group. Detection was achieved using an LC-MS/MS system. The standard curve was linear over a working range of 10-3000 ng/ml for all analytes and gave an average correlation coefficient of 0.9992 or better during validation. The absolute recovery for UDCA, GDCA, TDCA and the internal standard was 87.3, 83.7, 79.5 and 95.8%, respectively. This method is simple, sensitive and suitable for pharmacokinetics, bioequivalence or clinical studies. PMID:14643509
Digital optical phase conjugation of fluorescence in turbid tissue
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.
Jensen, Stephanie M; Nguyen, Celina T; Jewett, John C
2016-09-01
Dengue virus (DENV) is a mosquito-transmitted flavivirus that infects approximately 100 million people annually. Multi-day protocols for purification of DENV reduce the infective titer due to viral sensitivity to both temperature and pH. Herein we describe a 5-h protocol for the purification of all DENV serotypes, utilizing traditional gradient-free ultracentrifugation followed by selective virion precipitation. This protocol allows for the separation of DENV from contaminating proteins - including intact C6/36 densovirus, for the production of infective virus at high concentration for protein-level analysis. PMID:27265428
Harris, C T; Haw, D W; Handler, W B; Chronik, B A
2013-06-21
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. PMID:23739174
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.
NASA Technical Reports Server (NTRS)
Rendell, Alistair P.; Lee, Timothy J.
1991-01-01
The analytic energy gradient for the single and double excitation coupled-cluster (CCSD) wave function has been reformulated and implemented in a new set of programs. The reformulated set of gradient equations have a smaller computational cost than any previously published. The iterative solution of the linear equations and the construction of the effective density matrices are fully vectorized, being based on matrix multiplications. The new method has been used to investigate the Cl2O2 molecule, which has recently been postulated as an important intermediate in the destruction of ozone in the stratosphere. In addition to reporting computational timings, the CCSD equilibrium geometries, harmonic vibrational frequencies, infrared intensities, and relative energetics of three isomers of Cl2O2 are presented.
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).
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.
NASA Astrophysics Data System (ADS)
Heßelmann, Andreas
2015-04-01
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.
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.
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.
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. PMID:26091609
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
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. PMID:27379913
Shen, W C; Ryser, H J
1978-01-01
The carbodiimide-catalyzed conjugation of a 6700 molecular weight fragment of poly-L-lysine to radiolabeled human serum albumin or to horseradish peroxidase enhances the membrane transport of each protein into cultured mouse fibroblasts approximately 11- and 200-fold, respectively. At least 50% of the peroxidase activity remained after conjugation. Trypsinization and carbamylation of the two conjugates demonstrates that the enhancement of their cellular uptake is related to their poly-L-lysine content. Simple addition to the medium of comparable amounts of free poly-L-lysine has no effect on the transport of either native protein. Addition of poly-L-ornithine (molecular weight 200,000) at 3-30 microgram/ml, a condition known to cause enhancement of 125I-labeled human serum albumin uptake by mouse sarcoma cells, has no visible effect on the cellular uptake of native horseradish peroxidase. The intracellular localization of the enzyme-poly-L-lysine conjugate can be demonstrated cytochemically by either light or transmission electron microscopy. A concentration of conjugate that increases the uptake more than 200-fold does not cause any detectable morphological change suggestive of cell toxicity. Furthermore, because poly-L-lysine is an excellent substrate for intracellular proteolytic enzymes, it can be expected to be broken down and reutilized in the cell. Images PMID:273916
Gradient boosting machines, a tutorial.
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
Gradient boosting machines, a tutorial
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
Fiber bundle phase conjugate mirror
Ward, Benjamin G.
2012-05-01
An improved method and apparatus for passively conjugating the phases of a distorted wavefronts resulting from optical phase mismatch between elements of a fiber laser array are disclosed. A method for passively conjugating a distorted wavefront comprises the steps of: multiplexing a plurality of probe fibers and a bundle pump fiber in a fiber bundle array; passing the multiplexed output from the fiber bundle array through a collimating lens and into one portion of a non-linear medium; passing the output from a pump collection fiber through a focusing lens and into another portion of the non-linear medium so that the output from the pump collection fiber mixes with the multiplexed output from the fiber bundle; adjusting one or more degrees of freedom of one or more of the fiber bundle array, the collimating lens, the focusing lens, the non-linear medium, or the pump collection fiber to produce a standing wave in the non-linear medium.
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.
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.
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.
Atomic phase conjugation from a Bose condensate
Goldstein, E.V.; Plaettner, K.; Meystre, P.
1996-08-01
The authors discuss the possibility of observing atomic phase conjugation from Bose condensates, and using it as a diagnostic tool to access the spatial coherence properties and to measure the lifetime of the condensate. They argue that since phase conjugation results from the scattering of a partial matter wave off the spatial grating produced by two other waves, it offers a natural way to directly measure such properties, and as such provides an attractive alternative to the optical methods proposed in the past.
Parameter-exploring policy gradients.
Sehnke, Frank; Osendorfer, Christian; Rückstiess, Thomas; Graves, Alex; Peters, Jan; Schmidhuber, Jürgen
2010-05-01
We present a model-free reinforcement learning method for partially observable Markov decision problems. Our method estimates a likelihood gradient by sampling directly in parameter space, which leads to lower variance gradient estimates than obtained by regular policy gradient methods. We show that for several complex control tasks, including robust standing with a humanoid robot, this method outperforms well-known algorithms from the fields of standard policy gradients, finite difference methods and population based heuristics. We also show that the improvement is largest when the parameter samples are drawn symmetrically. Lastly we analyse the importance of the individual components of our method by incrementally incorporating them into the other algorithms, and measuring the gain in performance after each step. PMID:20061118
Self-organizing conjugated polymers
NASA Astrophysics Data System (ADS)
Hong, Xiaoyong Michael
2000-10-01
A general and efficient synthetic route to semifluoroalkyl substituted thiophenes has been developed and a series of 3-semifluoroalkylthiophenes were synthesized. The lengths of the fluorocarbon chain and hydrocarbon spacer between thiophene and fluorocarbon were systematically altered to study their effect on the properties of the resulting polymers. Oxidative polymerization (FeCl3) and electrochemical polymerization of 3-semifluoroalkylthiophenes afforded regiorandom (head-to-tail coupling ˜70%) homopolymers. The solubility and thermal transition temperatures of the polymers are also dependent on the nature of side chains. The surface properties of the polymers are also a function of the length of fluoroalkyl side chains. From x-ray diffraction, the regiorandom polymers have low crystallinity. Two synthetic methods have been successfully utilized to prepare regioregular poly(3-semifluoroalkylthiophene)s (head-to-tail coupling >90%) and gave identical polymers. The regioregular polymers are highly conjugated and highly ordered. The long side chain substituted polythiophenes form a liquid crystal mesophase between the crystal solid and isotropic liquid phases. To prepare polymers bearing alternating 3-semifluoroalkylthiophene and alkylthiophene units, we developed synthetic methods to 3-semifluoroalkyl-4 '-alkyl-2,2'-bithiophenes. The 3-semifluoroalkyl-4 '-alkyl-2,2'-bithiophenes were polymerized to afford regiorandom and regioregular polymers. Regiorandom polymers have low crystallinity and conjugation. Regioregular, strictly alternating copolymer with 3-semifluoroalkylthiophene and alkylthiophene units are highly conjugated and ordered. The regioregular polymers self-assemble into bilayer structure in solid state due to phase separation between fluorocarbon and hydrocarbon. At high temperatures close to melting transition, the thiophene rings rotate and twist along the molecular axis to give a single layer structure. Methylene bridges were placed between the
Sakamaki, Hiroshi; Uchida, Takeharu; Lim, Lee Wah; Takeuchi, Toyohide
2015-01-01
Columns made of three different materials were evaluated with regard to the carryover of phosphorylated peptides and fumonisins in liquid chromatography/tandem mass spectrometry (LC/MS/MS). In order to eliminate carryover caused by the injection operation in the autosampler, the column carryover was calculated using the duplicated solvent gradient method. A column made of a glass-lined stainless-steel tube and polyethylene frits (GL-PE column) yielded the most significant improvements in the peak shape and the carryover as compared to the other columns. The carryover of fumonisin B1 (FB1) and HLADLSpK (T19p) in the GL-PE column could be reduced; the lower limit of quantitation of T19p, and the range of the calibration curve were also improved. Since carryover peaks with the GL-PE column were symmetrical peaks of the samples, carryover in the column did not occur. The carryover calculated by the duplicated solvent gradient method corresponded to those in the flow path from the injection port to the inlet frit of the column. The carryover value of FB1 in the column with a stainless-steel tube and stainless-steel frits (S-S column) was 1.70%, and that of the flow path was 0.23%. We found that the majority of the carryover in our system occurred in the S-S column. PMID:25746806
NASA Astrophysics Data System (ADS)
Scuseria, Gustavo E.
1991-01-01
The analytic energy gradient for the singles and doubles coupled cluster method including a perturbative correction due to triple excitations [CCSD(T)] is formulated and computationally implemented. Encouraged by the recent success in reproducing the experimental equilibrium structure and vibrational frequencies of ozone, the new CCSD(T) gradient method is tested with two other ``difficult'' quantum chemistry problems: FOOF and Cr2. With the largest basis set employed in this work [triple zeta plus two sets of polarization functions (TZ2Pf)] at the CCSD(T) level of theory, the predictions for the O-O and O-F bond lengths in FOOF are 1.218 and 1.589 Å, respectively. These figures are in good agreement with the experimental values 1.216 and 1.575 Å. Based on CCSD calculations with even larger basis sets, it is concluded that the error of 0.014 Å in the O-F bond length at the TZ2Pf/CCSD(T) level of theory is due to the remaining basis set deficiency. On the other hand, the CCSD(T) prediction for the equilibrium bond length of Cr2 (1.604 Å), obtained with a large (10s8p3d2f1g) basis set capable of achieving the Hartree-Fock limit, is still 0.075 Å shorter than experiment, clearly indicating the importance of higher than connected triple excitations in a single-reference treatment of this particular problem.
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
Conjugal amyotrophic lateral sclerosis
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
Gubernator, Jerzy; Lipka, Dominik; Korycińska, Mariola; Kempińska, Katarzyna; Milczarek, Magdalena; Wietrzyk, Joanna; Hrynyk, Rafał; Barnert, Sabine; Süss, Regine; Kozubek, Arkadiusz
2014-01-01
Liposomes act as efficient drug carriers. Recently, epirubicin (EPI) formulation was developed using a novel EDTA ion gradient method for drug encapsulation. This formulation displayed very good stability and drug retention in vitro in a two-year long-term stability experiment. The cryo-TEM images show drug precipitate structures different than ones formed with ammonium sulfate method, which is usually used to encapsulate anthracyclines. Its pharmacokinetic properties and its efficacy in the human breast MDA-MB-231 cancer xenograft model were also determined. The liposomal EPI formulation is eliminated slowly with an AUC of 7.6487, while the free drug has an AUC of only 0.0097. The formulation also had a much higher overall antitumor efficacy than the free drug. PMID:24621591
Full-waveform inversion in the time domain with an energy-weighted gradient
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.
NASA Technical Reports Server (NTRS)
Bertram, Mitchel H.; Feller, William V.
1959-01-01
A procedure based on the method of similar solutions is presented by which the skin friction, heat transfer, and boundary-layer thickness in a laminar hypersonic flow with pressure gradient may be rapidly evaluated if the pressure distribution is known. This solution, which at present is. restricted to power-law variations of pressure with surface distance, is presented for a wide range of exponents in the power law corresponding to both favorable and adverse pressure gradients. This theory has been compared to results from heat-transfer experiments on blunt-nose flat plates and a hemisphere cylinder at free-stream Mach numbers of 4 and 6.8. The flat-plate experiments included tests made at a Mach number of 6.8 over a range of angle of attack of +/- 10 deg. Reasonable agreement of the experimental and theoretical heat-transfer coefficients has been obtained as well as good correlation of the experimental results over the entire range of angle of attack studied. A similar comparison of theory with experiment was not feasible for boundary-layer-thickness data; however, the hypersonic similarity theory was found to account satisfactorily for the variation in boundary-layer thickness due to local pressure distribution for several sets of measurements.
Nagata, Takeshi; Fedorov, Dmitri G; Li, Hui; Kitaura, Kazuo
2012-05-28
A new energy expression is proposed for the fragment molecular orbital method interfaced with the polarizable continuum model (FMO/PCM). The solvation free energy is shown to be more accurate on a set of representative polypeptides with neutral and charged residues, in comparison to the original formulation at the same level of the many-body expansion of the electrostatic potential determining the apparent surface charges. The analytic first derivative of the energy with respect to nuclear coordinates is formulated at the second-order Møller-Plesset (MP2) perturbation theory level combined with PCM, for which we derived coupled perturbed Hartree-Fock equations. The accuracy of the analytic gradient is demonstrated on test calculations in comparison to numeric gradient. Geometry optimization of the small Trp-cage protein (PDB: 1L2Y) is performed with FMO/PCM/6-31(+)G(d) at the MP2 and restricted Hartree-Fock with empirical dispersion (RHF/D). The root mean square deviations between the FMO optimized and NMR experimental structure are found to be 0.414 and 0.426 Å for RHF/D and MP2, respectively. The details of the hydrogen bond network in the Trp-cage protein are revealed. PMID:22667545
Arcisauskaite, Vaida; Knecht, Stefan; Sauer, Stephan P A; Hemmingsen, Lars
2012-12-14
We examine the performance of Density Functional Theory (DFT) approaches based on the Zeroth-Order Regular Approximation (ZORA) Hamiltonian (with and without inclusion of spin-orbit coupling) for predictions of electric field gradients (EFGs) at the heavy atom Hg nucleus. This is achieved by comparing with benchmark DFT and CCSD-T data (Arcisauskaite et al., Phys. Chem. Chem. Phys., 2012, 14, 2651-2657) obtained from 4-component Dirac-Coulomb Hamiltonian calculations. The investigated set of molecules comprises linear HgL(2) (L = Cl, Br, I, CH(3)) and bent HgCl(2) mercury compounds as well as the trigonal planar [HgCl(3)](-) system. In 4-component calculations we used the dyall.cv3z basis set for Hg, Br, I and the cc-pCVTZ basis set for H, C, Cl, whereas in ZORA calculations we used the QZ4P basis set for all the atoms. ZORA-4 reproduces the fully relativistic 4-component DFT reference values within 6% for all studied Hg compounds and employed functionals (BH&H, BP86, PBE0), whereas scalar relativistic (SR)-ZORA-4 results show deviations of up to 15%. Compared to our 4-component CCSD-T benchmark the BH&H functional performs best at both 4-component and ZORA levels. We furthermore observe that changes in the largest component of the diagonalised EFG tensor, V(zz), of linear HgCl(2) show a slightly stronger dependence than the r(-3) scaling upon bond length r(Hg-Cl) alterations. The 4-component/BH&H V(zz) value of -9.26 a.u. for a bent HgCl(2) (∠Cl-Hg-Cl = 120°) is close to -9.60 a.u. obtained for the linear HgCl(2) structure. Thus a point charge model for EFG calculations completely fails in this case. By means of a projection analysis of molecular orbital (MO) contributions to V(zz) in terms of the atomic constituents, we conclude that this is due to the increased importance of the Hg 5d orbitals upon bending HgCl(2) compared to the linear HgCl(2) structure. Changing ligand leads to only minor changes in V(zz) (from -9.60 a.u. (HgCl(2)) to -8.85 a.u. (HgI(2)) at
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.
Conjugative Transfer in Staphylococcus aureus.
Halsey, Cortney R; Fey, Paul D
2016-01-01
The acquisition of plasmids has led to a significant increase in antimicrobial resistance within the staphylococci. In order to study these plasmids effectively, one must be able move the plasmid DNA into genetically clean backgrounds. While the smaller staphylococcal class I (1-5 kb) and class II (10-30 kb) plasmids are readily transferred using bacteriophage transduction or electroporation, these methods are inefficient at moving the larger class III (30-60 kb) plasmids. This review describes methods to transfer class III plasmids via conjugative mobilization. PMID:26194708
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.
Design, synthesis, characterization and study of novel conjugated polymers
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.
NASA Technical Reports Server (NTRS)
Heier, W. C. (Inventor)
1974-01-01
A method is described for compression molding of thermosetting plastics composition. Heat is applied to the compressed load in a mold cavity and adjusted to hold molding temperature at the interface of the cavity surface and the compressed compound to produce a thermal front. This thermal front advances into the evacuated compound at mean right angles to the compression load and toward a thermal fence formed at the opposite surface of the compressed compound.
Ishida, Mayumi; Toyota, Kazuo; Ehara, Masahiro; Frisch, Michael J; Nakatsuji, Hiroshi
2004-02-01
A method of calculating analytical energy gradients of the singlet and triplet excited states, ionized states, electron-attached states, and high-spin states from quartet to septet states by the symmetry-adapted-cluster configuration-interaction general-R method is developed and implemented. This method is a powerful tool in the studies of geometries, dynamics, and properties of the states of molecules in which not only one-electron processes but also two- and multielectron processes are involved. The performance of the present method was confirmed by calculating the geometries and the spectroscopic constants of the diatomic and polyatomic molecules in various electronic states involving the ground state and the one- to three-electron excited states. The accurate descriptions were obtained for the equilibrium geometries, vibrational frequencies, and adiabatic excitation energies, which show the potential usefulness of the present method. The particularly interesting applications were to the C' 1Ag state of acetylene, the A 2Deltau and B 2Sigmau+ states of CNC and the 4B1 and a 4Piu states of N3 radical. PMID:15268403
NASA Astrophysics Data System (ADS)
Pattanaboonmee, N.; Ramasamy, P.; Yimnirun, R.; Manyum, P.
2011-01-01
Single crystals of pure, L-arginine and glycine doped ammonium dihydrogen orthophosphate (ADP) were grown by both the slow solvent evaporation method and the temperature-gradient method of Sankaranarayanan-Ramasamy (SR). The metastable zone width for different saturation temperatures of pure glycine and L-arginine added solutions were carried out. The grown crystals were characterized by differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), powder X-ray diffraction (XRD), optical transmission, dielectric constant, dielectric loss, and Vickers microhardness. The DSC and TG curves of the grown crystals indicated that they were stable up to 200 °C. The XRD study confirmed the structure of the grown crystal. The optical transmission analysis revealed that the pure and doped ADP crystals had very high percentage of transmission in the entire visible region. The important optical parameters such as reflectance and extinction coefficients of the grown crystals were calculated. L-arginine and glycine were used as dopants to reduce dielectric constant of ADP. The a.c. resistivity and a.c. conductivity were calculated. Dielectric loss of the doped ADP crystals grown by the SR method is lower than the doped ADP crystals grown by the conventional method. Larger hardness value for the SR method grown crystals confirmed greater crystalline perfection.
Gradient zone boundary control in salt gradient solar ponds
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.
Greening, David W; Xu, Rong; Ji, Hong; Tauro, Bow J; Simpson, Richard J
2015-01-01
Exosomes are 40-150 nm extracellular vesicles that are released from a multitude of cell types, and perform diverse cellular functions including intercellular communication, antigen presentation, and transfer of tumorigenic proteins, mRNA and miRNA. Exosomes are important regulators of the cellular niche, and their altered characteristics in many diseases, such as cancer, suggest their importance for diagnostic and therapeutic applications, and as drug delivery vehicles. Exosomes have been purified from biological fluids and in vitro cell cultures using a variety of strategies and techniques. In this chapter, we reveal the protocol and key insights into the isolation, purification and characterization of exosomes, distinct from shed microvesicles and apoptotic blebs. Using the colorectal cancer cell line LIM1863 as a cell model, a comprehensive evaluation of exosome isolation methods including ultracentrifugation (UC-Exos), OptiPrep™ density-based separation (DG-Exos), and immunoaffinity capture using anti-EpCAM-coated magnetic beads (IAC-Exos) were examined. All exosome isolation methodologies contained 40-150 nm vesicles based on electron microscopy, and positive for exosome markers (Alix, TSG101, HSP70) based on immunoblotting. This protocol employed a proteomic profiling approach to characterize the protein composition of exosomes, and label-free spectral counting to evaluate the effectiveness of each method in exosome isolation. Based on the number of MS/MS spectra identified for exosome markers and proteins associated with their biogenesis, trafficking, and release, IAC-Exos was shown to be the most effective method to isolate exosomes. However, the use of density-based separation (DG-Exos) provides significant advantages for exosome isolation when the use of immunoaffinity capture is limited (due to antibody availability and suitability of exosome markers). PMID:25820723
Molecularly defined antibody conjugation through a selenocysteine interface†
Hofer, Thomas; Skeffington, Lauren R.; Chapman, Colby M.; Rader, Christoph
2009-01-01
Antibody conjugates have broad utility in basic, preclinical, and clinical applications. Conventional antibody conjugation through the amine group of lysine or the thiol group of cysteine residues yields heterogeneous products of undefined stoichiometry and considerable batch-to-batch variability. To preserve the two hallmarks of the antibody molecule, precision and predictability, methods that enable site-specific antibody conjugation are in high demand. Based on a mammalian cell expression system, we describe the utilization of the 21st natural amino acid selenocysteine for the generation of IgG and Fab molecules with unique nucleophilic reactivity that affords site-specific conjugation to electrophilic derivatives of biotin, fluorescein, and poly(ethylene glycol). The resulting antibody conjugates were found to fully retain their antigen binding capability and, in case of IgG, the ability to mediate effector functions. Gain-of-function was demonstrated in vitro and in vivo. While these antibody conjugates are relevant for a variety of proteomic, diagnostic, and therapeutic applications, they also constitute a proof-of-principle for the generation of molecularly defined antibody-drug conjugates and radioimmunoconjugates. Compared to other site-specific antibody conjugation methods, selenocysteine interface technology (i) only involves a minor modification at the C-terminus that does not interfere with disulfide bridges, (ii) does not require activation, and (iii) generates unique 1:1 stoichiometries of biological and chemical component. Collectively, our method affords the generation of highly defined antibody conjugates with broad utility from proteomic applications to therapeutic intervention. PMID:19894757
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.
Strategies and Advancement in Antibody-Drug Conjugate Optimization for Targeted Cancer Therapeutics
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
Nakajima, Yuya; Seino, Junji; Nakai, Hiromi
2016-05-10
An analytical energy gradient for the spin-dependent general Hartree-Fock method based on the infinite-order Douglas-Kroll-Hess (IODKH) method was developed. To treat realistic systems, the local unitary transformation (LUT) scheme was employed both in energy and energy gradient calculations. The present energy gradient method was numerically assessed to investigate the accuracy in several diatomic molecules containing fifth- and sixth-period elements and to examine the efficiency in one-, two-, and three-dimensional silver clusters. To arrive at a practical calculation, we also determined the geometrical parameters of fac-tris(2-phenylpyridine)iridium and investigated the efficiency. The numerical results confirmed that the present method describes a highly accurate relativistic effect with high efficiency. The present method can be a powerful scheme for determining geometries of large molecules, including heavy-element atoms. PMID:27045757
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
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.
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. PMID:27300107
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
Noh, Seam; Hong, Yong Seok; Han, Seunghee
2016-02-01
A diffusive gradient in thin films (DGT) is an in situ sampling technique for the quantitative analysis of contaminant concentrations that is based on the diffusion and adsorption of contaminants on to resin gels. In the present study, a DGT technique was applied to measure total mercury (Hg) and monomethylmercury (MMHg) concentrations in lake and coastal sediment porewaters and compare them with those from ex situ sediment centrifugation. To calculate the total Hg and MMHg concentrations in porewater using the DGT method, the diffusion coefficients of Hg species in a diffusive gel medium was first determined, and then total Hg and MMHg depth profiles were measured using the experimentally determined diffusion coefficients. Using the diffusion coefficients for artificial lake and estuarine waters containing inorganic salts, rather than those for lake and estuarine waters containing Suwannee River humic acid (∼5 mg C L(-1) ), the DGT method demonstrated similar Hg and MMHg profiles to those using the centrifugation method. Based on the need for fine vertical resolution and high metal concentrations to be collected, DGT is suggested to be a reliable method for determining Hg(II) and MMHg depth profiles in sediment porewater. PMID:26250361
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.
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.
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.
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.
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
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 image for
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
Stabilized polyacrylic saccharide protein conjugates
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.
Stabilized polyacrylic saccharide protein conjugates
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.
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
Woodcock, Steven R.; Salvatore, Sonia R.; Bonacci, Gustavo; Schopfer, Francisco J.; Freeman, Bruce A.
2014-01-01
Nitro-conjugated linoleic acids (NO2-cLA), endogenous nitrodiene lipids which act as inflammatory signaling mediators, were isolated and single isomers purified from the biomimetic acidic nitration products of conjugated linoleic acid (CLA). Structures were elucidated by means of detailed NMR and HPLC–MS/MS spectroscopic analysis and the relative double bond configurations assigned. Additional synthetic methods produced useful quantities and similar isomeric distributions of these unusual and reactive compounds for biological studies and isotopic standards, and the potential conversion of nitro-linoleic to nitro-conjugated linoleic acids was explored via a facile base-catalyzed isomerization. This represents one of the few descriptions of naturally occurring conjugated nitro dienes (in particular, 1-nitro 1,3-diene), an unusual and highly reactive motif with few biological examples extant. PMID:24350701
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.
Coughlin, John; Masci, Allyson; Gronke, Robert S; Bergelson, Svetlana; Co, Carl
2016-07-15
Immobilized protein receptors and enzymes are tools for isolating or enriching ligands and substrates based on affinity. For example, glutathione S-transferase (GST) is fused to proteins as a tag for binding to its substrate glutathione (GSH) linked to solid supports. One issue with this approach is that high-affinity interactions between receptors and ligands require harsh elution conditions such as low pH, which can result in leached receptor. Another issue is the inherent nonspecific chemical conjugation of reactive groups such as N-hydroxysuccinimide (NHS) that couple lysines to solid supports; the nonspecificity of NHS may result in residue modifications near the binding site(s) of the receptor that can affect ligand specificity. In this study, a simple conjugation procedure is presented that overcomes these limitations and results in immobilized GST fusion proteins that are functional and specific. Here, the affinity of GST for GSH was used to generate an enzyme-substrate site-specific cross-linking reaction; GSH-Sepharose was preactivated with 1-ethyl-3-(dimethylaminopropyl)carbodiimide (EDC) and then incubated Fc gamma receptor IIIa (FcγRIIIa)-GST. The immobilized FcγRIIIa-GST more specifically bound glycosylated immunoglobulin G1s (IgG1s) and was used to enrich nonfucosylated IgG1s from weaker binding species. This technique can be used when modifications of amino acids lead to changes in activity. PMID:27063248
Continuous gravity gradient logging
Fitch, J.L.; Lyle, W.D. Jr.
1986-07-29
A method is described for conducting a gravimetry survey of an earth formation, comprising the steps of: (a) continuously traversing the earth formation with a gravity logging tool having a column of fluid within the tool, (b) measuring a first pressure difference along a first interval within the column of fluid, (c) measuring a second pressure difference along a second interval within the column of fluid, (d) differencing the first and second pressure differences to determine the gravity gradient along the earth formation between the first and second intervals.
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
Spatial gradient tuning in metamaterials
NASA Astrophysics Data System (ADS)
Driscoll, Tom; Goldflam, Michael; Jokerst, Nan; Basov, Dimitri; Smith, David
2011-03-01
Gradient Index (GRIN) metamaterials have been used to create devices inspired by, but often surpassing the potential of, conventional GRIN optics. The unit-cell nature of metamaterials presents the opportunity to exert much greater control over spatial gradients than is possible in natural materials. This is true not only during the design phase but also offers the potential for real-time reconfiguration of the metamaterial gradient. This ability fits nicely into the picture of transformation-optics, in which spatial gradients can enable an impressive suite of innovative devices. We discuss methods to exert control over metamaterial response, focusing on our recent demonstrations using Vanadium Dioxide. We give special attention to role of memristance and mem-capacitance observed in Vanadium Dioxide, which simplify the demands of stimuli and addressing, as well as intersecting metamaterials with the field of memory-materials.
Cormier, V.F.
1990-08-10
The locked mode method of synthesizing complete regional seismograms (Harvey, 1981) was modified to include the Langer uniform asymptotic approximation to vertical wave-functions within layers having linear vertical velocity gradients. Good agreement is obtained in gradient models between synthetics computed using the Langer-locked mode method, the colocation method, and the conventional locked mode method in models parameterized by thin homogeneous layers. Errors in calculated displacement introduced by the use of the Langer approximation remain less than several percent for wavelengths lambda < or = 0.2V/nabla operator V. Whenever it is necessary to represent gradients accurately, the Langer-locked mode method is computationally more efficient than the locked mode method using thin homogeneous layers. By reducing the number of parameters needed to describe an Earth model, the Langer-locked method will also simplify the inverse problem of determining structure using observed and synthetic regional seismograms. Test calculations of regional seismograms confirm that the Pn and Sn phases are strongly affected by the magnitude of the velocity gradients beneath the Moho, but that Lg is only weakly affected by the details of crustal layering.
Solution assembly of conjugated polymers
NASA Astrophysics Data System (ADS)
Bokel, Felicia A.
This dissertation focuses on the solution-state polymer assembly of conjugated polymers with specific attention to nano- and molecular-scale morphology. Understanding how to control these structures holds potential for applications in polymer-based electronics. Optimization of conjugated polymer morphology was performed with three objectives: 1) segregation of donor and acceptor materials on the nanometer length-scale, 2) achieving molecular-scale ordering in terms of crystallinity within distinct domains, and 3) maximizing the number and quality of well-defined donor/acceptor interfaces. Chapter 1 introduces the development of a mixed solvent method to create crystalline poly(3-hexyl thiophene) (P3HT) fibrils in solution. Chapter 2 describes fibril purification and approaches to robust and functional fibrils, while chapters 3 and 4 demonstrate the formation of hybrid nanocomposite wires of P3HT and cadmium selenide (CdSe) nanoparticles by two methods: 1) co-crystallization of free and P3HT-grafted CdSe for composite nanowires and 2) direct attachment of CdSe nanoparticles at fibril edges to give superhighway structures. These composite structures show great potential in the application of optoelectronic devices, such as the active layer of solar cells. Finally, ultrafast photophysical characterization of these polymers, using time-resolved photoluminescence and transient absorption, was performed to determine the aggregation types present in suspended fibrils and monitor the formation and decay of charged species in fibrils and donor-acceptor systems.
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.
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
Filatov, Michael; Huix-Rotllant, Miquel
2014-07-14
Computational investigation of the longest wavelength excitations in a series of cyanines and linear n-acenes is undertaken with the use of standard spin-conserving linear response time-dependent density functional theory (TD-DFT) as well as its spin-flip variant and a ΔSCF method based on the ensemble DFT. The spin-conserving linear response TD-DFT fails to accurately reproduce the lowest excitation energy in these π-conjugated systems by strongly overestimating the excitation energies of cyanines and underestimating the excitation energies of n-acenes. The spin-flip TD-DFT is capable of correcting the underestimation of excitation energies of n-acenes by bringing in the non-dynamic electron correlation into the ground state; however, it does not fully correct for the overestimation of the excitation energies of cyanines, for which the non-dynamic correlation does not seem to play a role. The ensemble DFT method employed in this work is capable of correcting for the effect of missing non-dynamic correlation in the ground state of n-acenes and for the deficient description of differential correlation effects between the ground and excited states of cyanines and yields the excitation energies of both types of extended π-conjugated systems with the accuracy matching high-level ab initio multireference calculations.
Combining Step Gradients and Linear Gradients in Density.
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
[Conjugate vaccines against bacterial infections: typhoid fever].
Paniagua, J; García, J A; López, C R; González, C R; Isibasi, A; Kumate, J
1992-01-01
Capsular polysaccharides have been studied as possible vaccines against infectious diseases. However, they are capable to induce only short-run protection because of their T-independent properties and they would not be protective against infection in high-risk populations. The alternative to face this problem is to develop methods to join covalently the polysaccharide and proteins to both increase the immunogenicity of and to confer the property of T-dependence to this antigen. In order to obtain a conjugate vaccine against typhoid fever, in our laboratory we have tried to synthesize a conjugate immunogen between the Vi antigen and porins from Salmonella typhi. PMID:1377407
Tajeddin, E; Sherafat, S J; Majidi, M R S; Alebouyeh, M; Alizadeh, A H M; Zali, M R
2016-08-01
Bacterial infection is considered a predisposing factor for disorders of the biliary tract. This study aimed to determine the diversity of bacterial communities in bile samples and their involvement in the occurrence of biliary tract diseases. A total of 102 bile samples were collected during endoscopic retrograde cholangiopancreatography (ERCP). Characterization of bacteria was done using culture and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) methods. Antimicrobial susceptibility of the isolates was determined based on the Clinical and Laboratory Standards Institute (CLSI) guidelines and identity of the nucleotide sequences of differentiated bands from the DGGE gels was determined based on GenBank data. In total, 41.2 % (42/102) of the patients showed bacterial infection in their bile samples. This infection was detected in 21 % (4/19), 45.4 % (5/11), 53.5 % (15/28), and 54.5 % (24/44) of patients with common bile duct stone, microlithiasis, malignancy, and gallbladder stone, respectively. Escherichia coli showed a significant association with gallstones. Polymicrobial infection was detected in 48 % of the patients. While results of the culture method established coexistence of biofilm-forming bacteria (Pseudomonas aeruginosa, E. coli, Klebsiella pneumoniae, Enterococcus spp., and Acinetobacter spp.) in different combinations, the presence of Capnocytophaga spp., Lactococcus spp., Bacillus spp., Staphylococcus haemolyticus, Enterobacter or Citrobacter spp., Morganella spp., Salmonella spp., and Helicobacter pylori was also characterized in these samples by the PCR-DGGE method. Multidrug resistance phenotypes (87.5 %) and resistance to third- and fourth-generation cephalosporins and quinolones were common in these strains, which could evolve through their selection by bile components. Ability for biofilm formation seems to be a need for polymicrobial infection in this organ. PMID:27193890
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
NASA Astrophysics Data System (ADS)
Schäfer, K.; Jahn, C.; Emeis, S.; Wiwiorra, M.; von der Heide, C.; Böttcher, J.; Deurer, M.; Weymann, D.; Schleichardt, A.; Raabe, A.
2009-09-01
For up-scaling the emissions of N2O, CO2 and CH4 (GHG) from arable field soils a measuring tunnel for controlled enrichment of released gases was installed at the soil surface covering an area of 495 or 306 m2. The concentrations of GHG and humidity were measured by the path-averaging, multi-component Fourier Transform Infrared (FTIR) absorption spectrometry at an open path of 100 m length across the whole measuring tunnel. During a 2-years-time frame the N2O fluxes between the soil and the atmosphere at the agricultural field varied between 1.0 and 21 µg N2O-N m-2 h-1. These results were compared with N2O emission rates that were simultaneously measured with a conventional closed chamber technique. The resulting N2O fluxes between the soil and the atmosphere of both methods had the same order of magnitude. However, we found an extreme spatial variability of N2O fluxes at the scale of the closed chambers. The hypothesis that an enlargement of the measured soil surface area is an appropriate measure to avoid the problems of up-scaling results of small scale chamber measurements was confirmed by the results obtained with the measuring tunnel. Currently, a non-intrusive emission and flux measurement method at a scale from 100 m up to. 27.000 m2 on the basis of the flux-gradient method (0.50 and 2.70 m height above surface) is developed and tested by means of open-path multi-component measurement methods (FTIR, GHG) and area averaging meteorological measurements (determination of horizontal winds, friction velocity using acoustic tomography). Two campaigns in October 2007 and June 2008 were performed with this new methodology when wind speeds were low. Due to the very low wind speeds and insufficient turbulence for the application of the usual flux-gradient method a new concept introducing the viscosity instead of stability corrections was developed. It requires a direct measurement of the friction velocity and the vertical gradient of the horizontal wind speeds by
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.
Conjugate flow action functionals
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.
Conjugate flow action functionals
NASA Astrophysics Data System (ADS)
Venturi, Daniele
2013-11-01
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.
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.
Diviš, Pavel; Kadlecová, Milada; Ouddane, Baghdad
2016-05-01
The distribution of mercury in surface water and in sediment from Deûle River in Northern France was studied by application of conventional sampling methods and by diffusive gradients in thin films technique (DGT). Concentration of total dissolved mercury in surface water was 20.8 ± 0.8 ng l(-1). The particulate mercury concentration was 6.2 ± 0.6 µg g(-1). The particulate mercury was accumulated in sediment (9.9 ± 2.3 mg kg(-1)), and it was transformed by methylating bacteria to methylmercury, mainly in the first 2-cm layer of the sediment. Total dissolved concentration of mercury in sediment pore water obtained by application of centrifugation extraction was 17.6 ± 4.1 ng l(-1), and it was comparable with total dissolved pore water mercury concentration measured by DGT probe containing Duolite GT-73 resin gel (18.2 ± 4.3 ng l(-1)), taking the sediment heterogeneity and different principles of the applied methods into account. By application of two DGT probes with different resin gels specific for mercury, it was found that approximately 30 % of total dissolved mercury in sediment pore water was present in labile forms easy available for biota. The resolution of mercury DGT depth profiles was 0.5 cm, which allows, unlike conventional techniques, to study the connection of the geochemical cycle of mercury with geochemical cycles of iron and manganese. PMID:26428003
Photorefractive phase-conjugation digital holographic microscopy
NASA Astrophysics Data System (ADS)
Chang, Chi-Ching; Chan, Huang-Tian; Shiu, Min-Tzung; Chew, Yang-Kun
2015-05-01
In this work, we propose an innovative method for digital holographic microscopy named as photorefractive phaseconjugation digital holographic microscopy (PPCDHM) technique based on the phase conjugation dynamic holographic process in photorefractive BaTiO3 crystal and the retrieval of phase and amplitude of the object wave were performed by a reflection-type digital holographic method. Both amplitude and phase reconstruction benefit from the prior amplification by self-pumped conjugation (SPPC) as they have an increased SNR. The interest of the PPCDHM is great, because its hologram is created by interfered the amplified phase-conjugate wave field generated from a photorefractive phase conjugator (PPC) correcting the phase aberration of the imaging system and the reference wave onto the digital CCD camera. Therefore, a precise three-dimensional description of the object with high SNR can be obtained digitally with only one hologram acquisition. The method requires the acquisition of a single hologram from which the phase distribution can be obtained simultaneously with distribution of intensity at the surface of the object.
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
Phase conjugation by four-wave mixing in inhomogeneous plasmas
NASA Technical Reports Server (NTRS)
Williams, Edward A.; Lininger, Diana M.; Goldman, Martin V.
1989-01-01
The effects of density, temperature, and velocity gradients on four-wave mixing (FWM) in a plasma are investigated. A fluid model is used in which the stimulated Brillouin terms are included, but pump depletion is neglected. The steady state phase conjugate reflectivity and signal transmission coefficients are calculated and discussed for both degenerate and resonant FWM. The substantial effects of inhomogeneity on the use of FWM as a plasma diagnostic are discussed.