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.

Beyond the functional matrix hypothesis: a network null model of human skull growth for the formation of bone articulations

PubMed Central

Esteve-Altava, Borja; Rasskin-Gutman, Diego

2014-01-01

Craniofacial sutures and synchondroses form the boundaries among bones in the human skull, providing functional, developmental and evolutionary information. Bone articulations in the skull arise due to interactions between genetic regulatory mechanisms and epigenetic factors such as functional matrices (soft tissues and cranial cavities), which mediate bone growth. These matrices are largely acknowledged for their influence on shaping the bones of the skull; however, it is not fully understood to what extent functional matrices mediate the formation of bone articulations. Aiming to identify whether or not functional matrices are key developmental factors guiding the formation of bone articulations, we have built a network null model of the skull that simulates unconstrained bone growth. This null model predicts bone articulations that arise due to a process of bone growth that is uniform in rate, direction and timing. By comparing predicted articulations with the actual bone articulations of the human skull, we have identified which boundaries specifically need the presence of functional matrices for their formation. We show that functional matrices are necessary to connect facial bones, whereas an unconstrained bone growth is sufficient to connect non-facial bones. This finding challenges the role of the brain in the formation of boundaries between bones in the braincase without neglecting its effect on skull shape. Ultimately, our null model suggests where to look for modified developmental mechanisms promoting changes in bone growth patterns that could affect the development and evolution of the head skeleton. PMID:24975579

Invertible flexible matrices

NASA Astrophysics Data System (ADS)

Justino, Júlia

2017-06-01

Matrices with coefficients having uncertainties of type o (.) or O (.), called flexible matrices, are studied from the point of view of nonstandard analysis. The uncertainties of the afore-mentioned kind will be given in the form of the so-called neutrices, for instance the set of all infinitesimals. Since flexible matrices have uncertainties in their coefficients, it is not possible to define the identity matrix in an unique way and so the notion of spectral identity matrix arises. Not all nonsingular flexible matrices can be turned into a spectral identity matrix using Gauss-Jordan elimination method, implying that that not all nonsingular flexible matrices have the inverse matrix. Under certain conditions upon the size of the uncertainties appearing in a nonsingular flexible matrix, a general theorem concerning the boundaries of its minors is presented which guarantees the existence of the inverse matrix of a nonsingular flexible matrix.

Further Development of HS Field Theory

NASA Astrophysics Data System (ADS)

Abdurrahman, Abdulmajeed; Faridani, Jacqueline; Gassem, Mahmoud

2006-04-01

We present a systematic treatment of the HS Field theory of the open bosonic string and discuss its relationship to other full string field theories of the open bosonic string such as Witten's theory and the CVS theory. In the development of the HS field theory we encounter infinite dimensional matrices arising from the change of representation between the two theories, i.e., the HS field theory and the full string field theory. We give a general procedure of how to invert these gigantic matrices. The inversion of these matrices involves the computation of many infinite sums. We give the values of these sums and state their generalizations arising from considering higher order vertices (i.e., more than three strings) in string field theory. Moreover, we give a general procedure, on how to evaluate the generalized sums, that can be extended to many generic sums of similar properties. We also discuss the conformal operator connecting the HS field theory to that of the CVS string field theory.

Efficient Computation of Sparse Matrix Functions for Large-Scale Electronic Structure Calculations: The CheSS Library.

PubMed

Mohr, Stephan; Dawson, William; Wagner, Michael; Caliste, Damien; Nakajima, Takahito; Genovese, Luigi

2017-10-10

We present CheSS, the "Chebyshev Sparse Solvers" library, which has been designed to solve typical problems arising in large-scale electronic structure calculations using localized basis sets. The library is based on a flexible and efficient expansion in terms of Chebyshev polynomials and presently features the calculation of the density matrix, the calculation of matrix powers for arbitrary powers, and the extraction of eigenvalues in a selected interval. CheSS is able to exploit the sparsity of the matrices and scales linearly with respect to the number of nonzero entries, making it well-suited for large-scale calculations. The approach is particularly adapted for setups leading to small spectral widths of the involved matrices and outperforms alternative methods in this regime. By coupling CheSS to the DFT code BigDFT, we show that such a favorable setup is indeed possible in practice. In addition, the approach based on Chebyshev polynomials can be massively parallelized, and CheSS exhibits excellent scaling up to thousands of cores even for relatively small matrix sizes.

Wavelets in electronic structure calculations

NASA Astrophysics Data System (ADS)

Modisette, Jason Perry

1997-09-01

Ab initio calculations of the electronic structure of bulk materials and large clusters are not possible on today's computers using current techniques. The storage and diagonalization of the Hamiltonian matrix are the limiting factors in both memory and execution time. The scaling of both quantities with problem size can be reduced by using approximate diagonalization or direct minimization of the total energy with respect to the density matrix in conjunction with a localized basis. Wavelet basis members are much more localized than conventional bases such as Gaussians or numerical atomic orbitals. This localization leads to sparse matrices of the operators that arise in SCF multi-electron calculations. We have investigated the construction of the one-electron Hamiltonian, and also the effective one- electron Hamiltonians that appear in density-functional and Hartree-Fock theories. We develop efficient methods for the generation of the kinetic energy and potential matrices, the Hartree and exchange potentials, and the local exchange-correlation potential of the LDA. Test calculations are performed on one-electron problems with a variety of potentials in one and three dimensions.

Beyond the functional matrix hypothesis: a network null model of human skull growth for the formation of bone articulations.

PubMed

Esteve-Altava, Borja; Rasskin-Gutman, Diego

2014-09-01

Craniofacial sutures and synchondroses form the boundaries among bones in the human skull, providing functional, developmental and evolutionary information. Bone articulations in the skull arise due to interactions between genetic regulatory mechanisms and epigenetic factors such as functional matrices (soft tissues and cranial cavities), which mediate bone growth. These matrices are largely acknowledged for their influence on shaping the bones of the skull; however, it is not fully understood to what extent functional matrices mediate the formation of bone articulations. Aiming to identify whether or not functional matrices are key developmental factors guiding the formation of bone articulations, we have built a network null model of the skull that simulates unconstrained bone growth. This null model predicts bone articulations that arise due to a process of bone growth that is uniform in rate, direction and timing. By comparing predicted articulations with the actual bone articulations of the human skull, we have identified which boundaries specifically need the presence of functional matrices for their formation. We show that functional matrices are necessary to connect facial bones, whereas an unconstrained bone growth is sufficient to connect non-facial bones. This finding challenges the role of the brain in the formation of boundaries between bones in the braincase without neglecting its effect on skull shape. Ultimately, our null model suggests where to look for modified developmental mechanisms promoting changes in bone growth patterns that could affect the development and evolution of the head skeleton. © 2014 Anatomical Society.

Structure preserving noise and dissipation in the Toda lattice

NASA Astrophysics Data System (ADS)

Arnaudon, Alexis

2018-05-01

In this paper, we use Flaschka’s change of variables of the open Toda lattice and its interpretation in terms of the group structure of the LU factorisation as a coadjoint motion on a certain dual of the Lie algebra to implement a structure preserving noise and dissipation. Both preserve the structure of the coadjoint orbit, that is the space of symmetric tri-diagonal matrices and arise as a new type of multiplicative noise and nonlinear dissipation of the Toda lattice. We investigate some of the properties of these deformations and, in particular, the continuum limit as a stochastic Burger equation with a nonlinear viscosity. This work is meant to be exploratory, and open more questions that we can answer with simple mathematical tools and without numerical simulations.

Eigenmode computation of cavities with perturbed geometry using matrix perturbation methods applied on generalized eigenvalue problems

NASA Astrophysics Data System (ADS)

Gorgizadeh, Shahnam; Flisgen, Thomas; van Rienen, Ursula

2018-07-01

Generalized eigenvalue problems are standard problems in computational sciences. They may arise in electromagnetic fields from the discretization of the Helmholtz equation by for example the finite element method (FEM). Geometrical perturbations of the structure under concern lead to a new generalized eigenvalue problems with different system matrices. Geometrical perturbations may arise by manufacturing tolerances, harsh operating conditions or during shape optimization. Directly solving the eigenvalue problem for each perturbation is computationally costly. The perturbed eigenpairs can be approximated using eigenpair derivatives. Two common approaches for the calculation of eigenpair derivatives, namely modal superposition method and direct algebraic methods, are discussed in this paper. Based on the direct algebraic methods an iterative algorithm is developed for efficiently calculating the eigenvalues and eigenvectors of the perturbed geometry from the eigenvalues and eigenvectors of the unperturbed geometry.

Mismatch and resolution in compressive imaging

NASA Astrophysics Data System (ADS)

Fannjiang, Albert; Liao, Wenjing

2011-09-01

Highly coherent sensing matrices arise in discretization of continuum problems such as radar and medical imaging when the grid spacing is below the Rayleigh threshold as well as in using highly coherent, redundant dictionaries as sparsifying operators. Algorithms (BOMP, BLOOMP) based on techniques of band exclusion and local optimization are proposed to enhance Orthogonal Matching Pursuit (OMP) and deal with such coherent sensing matrices. BOMP and BLOOMP have provably performance guarantee of reconstructing sparse, widely separated objects independent of the redundancy and have a sparsity constraint and computational cost similar to OMP's. Numerical study demonstrates the effectiveness of BLOOMP for compressed sensing with highly coherent, redundant sensing matrices.

Properties of networks with partially structured and partially random connectivity

NASA Astrophysics Data System (ADS)

Ahmadian, Yashar; Fumarola, Francesco; Miller, Kenneth D.

2015-01-01

Networks studied in many disciplines, including neuroscience and mathematical biology, have connectivity that may be stochastic about some underlying mean connectivity represented by a non-normal matrix. Furthermore, the stochasticity may not be independent and identically distributed (iid) across elements of the connectivity matrix. More generally, the problem of understanding the behavior of stochastic matrices with nontrivial mean structure and correlations arises in many settings. We address this by characterizing large random N ×N matrices of the form A =M +L J R , where M ,L , and R are arbitrary deterministic matrices and J is a random matrix of zero-mean iid elements. M can be non-normal, and L and R allow correlations that have separable dependence on row and column indices. We first provide a general formula for the eigenvalue density of A . For A non-normal, the eigenvalues do not suffice to specify the dynamics induced by A , so we also provide general formulas for the transient evolution of the magnitude of activity and frequency power spectrum in an N -dimensional linear dynamical system with a coupling matrix given by A . These quantities can also be thought of as characterizing the stability and the magnitude of the linear response of a nonlinear network to small perturbations about a fixed point. We derive these formulas and work them out analytically for some examples of M ,L , and R motivated by neurobiological models. We also argue that the persistence as N →∞ of a finite number of randomly distributed outlying eigenvalues outside the support of the eigenvalue density of A , as previously observed, arises in regions of the complex plane Ω where there are nonzero singular values of L-1(z 1 -M ) R-1 (for z ∈Ω ) that vanish as N →∞ . When such singular values do not exist and L and R are equal to the identity, there is a correspondence in the normalized Frobenius norm (but not in the operator norm) between the support of the spectrum of A for J of norm σ and the σ pseudospectrum of M .

Metal-inorganic-organic matrices as efficient sorbents for hydrogen storage.

PubMed

Azzouz, Abdelkrim; Nousir, Saadia; Bouazizi, Nabil; Roy, René

2015-03-01

Stabilization of metal nanoparticles (MNPs) without re-aggregation is a major challenge. An unprecedented strategy is developed for achieving high dispersion of copper(0) or palladium(0) on montmorillonite-supported diethanolamine or thioglycerol. This results in novel metal-inorganic-organic matrices (MIOM) that readily capture hydrogen at ambient conditions, with easy release under air stream. Hydrogen retention appears to involve mainly physical interactions, slightly stronger on thioglycerol-based MIOM (S-MIOM). Thermal enhancement of desorption suggests also a contribution of chemical interactions. The increase of hydrogen uptake with prolonged contact times arises from diffusion hindrance, which appears to be beneficial by favoring hydrogen entrapment. Even with compact structures, MIOMs act as efficient sorbents with much higher efficiency factor (1.14-1.17 mmol H 2 m(-2)) than many other sophisticated adsorbents reported in the literature. This opens new prospects for hydrogen storage and potential applications in microfluidic hydrogenation reactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Regularized matrix regression

PubMed Central

Zhou, Hua; Li, Lexin

2014-01-01

Summary Modern technologies are producing a wealth of data with complex structures. For instance, in two-dimensional digital imaging, flow cytometry and electroencephalography, matrix-type covariates frequently arise when measurements are obtained for each combination of two underlying variables. To address scientific questions arising from those data, new regression methods that take matrices as covariates are needed, and sparsity or other forms of regularization are crucial owing to the ultrahigh dimensionality and complex structure of the matrix data. The popular lasso and related regularization methods hinge on the sparsity of the true signal in terms of the number of its non-zero coefficients. However, for the matrix data, the true signal is often of, or can be well approximated by, a low rank structure. As such, the sparsity is frequently in the form of low rank of the matrix parameters, which may seriously violate the assumption of the classical lasso. We propose a class of regularized matrix regression methods based on spectral regularization. A highly efficient and scalable estimation algorithm is developed, and a degrees-of-freedom formula is derived to facilitate model selection along the regularization path. Superior performance of the method proposed is demonstrated on both synthetic and real examples. PMID:24648830

Exploiting Data Sparsity in Parallel Matrix Powers Computations

DTIC Science & Technology

2013-05-03

2013 Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of information is estimated to average 1 hour...matrices of the form A = D+USV H, where D is sparse and USV H has low rank but may be dense. Matrices of this form arise in many practical applications...methods numerical partial di erential equation solvers, and preconditioned iterative methods. If A has this form , our algorithm enables a communication

A split band-Cholesky equation solving strategy for finite element analysis of transient field problems. [in fluid mechanics

NASA Technical Reports Server (NTRS)

Cooke, C. H.

1978-01-01

The paper describes the split-Cholesky strategy for banded matrices arising from the large systems of equations in certain fluid mechanics problems. The basic idea is that for a banded matrix the computation can be carried out in pieces, with only a small portion of the matrix residing in core. Mesh considerations are discussed by demonstrating the manner in which the assembly of finite element equations proceeds for linear trial functions on a triangular mesh. The FORTRAN code which implements the out-of-core decomposition strategy for banded symmetric positive definite matrices (mass matrices) of a coupled initial value problem is given.

The failing measurement of attitudes: How semantic determinants of individual survey responses come to replace measures of attitude strength.

PubMed

Arnulf, Jan Ketil; Larsen, Kai Rune; Martinsen, Øyvind Lund; Egeland, Thore

2018-01-12

The traditional understanding of data from Likert scales is that the quantifications involved result from measures of attitude strength. Applying a recently proposed semantic theory of survey response, we claim that survey responses tap two different sources: a mixture of attitudes plus the semantic structure of the survey. Exploring the degree to which individual responses are influenced by semantics, we hypothesized that in many cases, information about attitude strength is actually filtered out as noise in the commonly used correlation matrix. We developed a procedure to separate the semantic influence from attitude strength in individual response patterns, and compared these results to, respectively, the observed sample correlation matrices and the semantic similarity structures arising from text analysis algorithms. This was done with four datasets, comprising a total of 7,787 subjects and 27,461,502 observed item pair responses. As we argued, attitude strength seemed to account for much information about the individual respondents. However, this information did not seem to carry over into the observed sample correlation matrices, which instead converged around the semantic structures offered by the survey items. This is potentially disturbing for the traditional understanding of what survey data represent. We argue that this approach contributes to a better understanding of the cognitive processes involved in survey responses. In turn, this could help us make better use of the data that such methods provide.

Quantization of an electromagnetic field in two-dimensional photonic structures based on the scattering matrix formalism ( S-quantization)

NASA Astrophysics Data System (ADS)

Ivanov, K. A.; Nikolaev, V. V.; Gubaydullin, A. R.; Kaliteevski, M. A.

2017-10-01

Based on the scattering matrix formalism, we have developed a method of quantization of an electromagnetic field in two-dimensional photonic nanostructures ( S-quantization in the two-dimensional case). In this method, the fields at the boundaries of the quantization box are expanded into a Fourier series and are related with each other by the scattering matrix of the system, which is the product of matrices describing the propagation of plane waves in empty regions of the quantization box and the scattering matrix of the photonic structure (or an arbitrary inhomogeneity). The quantization condition (similarly to the onedimensional case) is formulated as follows: the eigenvalues of the scattering matrix are equal to unity, which corresponds to the fact that the set of waves that are incident on the structure (components of the expansion into the Fourier series) is equal to the set of waves that travel away from the structure (outgoing waves). The coefficients of the matrix of scattering through the inhomogeneous structure have been calculated using the following procedure: the structure is divided into parallel layers such that the permittivity in each layer varies only along the axis that is perpendicular to the layers. Using the Fourier transform, the Maxwell equations have been written in the form of a matrix that relates the Fourier components of the electric field at the boundaries of neighboring layers. The product of these matrices is the transfer matrix in the basis of the Fourier components of the electric field. Represented in a block form, it is composed by matrices that contain the reflection and transmission coefficients for the Fourier components of the field, which, in turn, constitute the scattering matrix. The developed method considerably simplifies the calculation scheme for the analysis of the behavior of the electromagnetic field in structures with a two-dimensional inhomogeneity. In addition, this method makes it possible to obviate difficulties that arise in the analysis of the Purcell effect because of the divergence of the integral describing the effective volume of the mode in open systems.

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

PubMed

Fessler, J A; Booth, S D

1999-01-01

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

Topological and kinetic determinants of the modal matrices of dynamic models of metabolism

PubMed Central

2017-01-01

Large-scale kinetic models of metabolism are becoming increasingly comprehensive and accurate. A key challenge is to understand the biochemical basis of the dynamic properties of these models. Linear analysis methods are well-established as useful tools for characterizing the dynamic response of metabolic networks. Central to linear analysis methods are two key matrices: the Jacobian matrix (J) and the modal matrix (M-1) arising from its eigendecomposition. The modal matrix M-1 contains dynamically independent motions of the kinetic model near a reference state, and it is sparse in practice for metabolic networks. However, connecting the structure of M-1 to the kinetic properties of the underlying reactions is non-trivial. In this study, we analyze the relationship between J, M-1, and the kinetic properties of the underlying network for kinetic models of metabolism. Specifically, we describe the origin of mode sparsity structure based on features of the network stoichiometric matrix S and the reaction kinetic gradient matrix G. First, we show that due to the scaling of kinetic parameters in real networks, diagonal dominance occurs in a substantial fraction of the rows of J, resulting in simple modal structures with clear biological interpretations. Then, we show that more complicated modes originate from topologically-connected reactions that have similar reaction elasticities in G. These elasticities represent dynamic equilibrium balances within reactions and are key determinants of modal structure. The work presented should prove useful towards obtaining an understanding of the dynamics of kinetic models of metabolism, which are rooted in the network structure and the kinetic properties of reactions. PMID:29267329

A Performance Comparison of the Parallel Preconditioners for Iterative Methods for Large Sparse Linear Systems Arising from Partial Differential Equations on Structured Grids

NASA Astrophysics Data System (ADS)

Ma, Sangback

In this paper we compare various parallel preconditioners such as Point-SSOR (Symmetric Successive OverRelaxation), ILU(0) (Incomplete LU) in the Wavefront ordering, ILU(0) in the Multi-color ordering, Multi-Color Block SOR (Successive OverRelaxation), SPAI (SParse Approximate Inverse) and pARMS (Parallel Algebraic Recursive Multilevel Solver) for solving large sparse linear systems arising from two-dimensional PDE (Partial Differential Equation)s on structured grids. Point-SSOR is well-known, and ILU(0) is one of the most popular preconditioner, but it is inherently serial. ILU(0) in the Wavefront ordering maximizes the parallelism in the natural order, but the lengths of the wave-fronts are often nonuniform. ILU(0) in the Multi-color ordering is a simple way of achieving a parallelism of the order N, where N is the order of the matrix, but its convergence rate often deteriorates as compared to that of natural ordering. We have chosen the Multi-Color Block SOR preconditioner combined with direct sparse matrix solver, since for the Laplacian matrix the SOR method is known to have a nondeteriorating rate of convergence when used with the Multi-Color ordering. By using block version we expect to minimize the interprocessor communications. SPAI computes the sparse approximate inverse directly by least squares method. Finally, ARMS is a preconditioner recursively exploiting the concept of independent sets and pARMS is the parallel version of ARMS. Experiments were conducted for the Finite Difference and Finite Element discretizations of five two-dimensional PDEs with large meshsizes up to a million on an IBM p595 machine with distributed memory. Our matrices are real positive, i. e., their real parts of the eigenvalues are positive. We have used GMRES(m) as our outer iterative method, so that the convergence of GMRES(m) for our test matrices are mathematically guaranteed. Interprocessor communications were done using MPI (Message Passing Interface) primitives. The results show that in general ILU(0) in the Multi-Color ordering ahd ILU(0) in the Wavefront ordering outperform the other methods but for symmetric and nearly symmetric 5-point matrices Multi-Color Block SOR gives the best performance, except for a few cases with a small number of processors.

Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences.

PubMed

Tan, Yen Hock; Huang, He; Kihara, Daisuke

2006-08-15

Aligning distantly related protein sequences is a long-standing problem in bioinformatics, and a key for successful protein structure prediction. Its importance is increasing recently in the context of structural genomics projects because more and more experimentally solved structures are available as templates for protein structure modeling. Toward this end, recent structure prediction methods employ profile-profile alignments, and various ways of aligning two profiles have been developed. More fundamentally, a better amino acid similarity matrix can improve a profile itself; thereby resulting in more accurate profile-profile alignments. Here we have developed novel amino acid similarity matrices from knowledge-based amino acid contact potentials. Contact potentials are used because the contact propensity to the other amino acids would be one of the most conserved features of each position of a protein structure. The derived amino acid similarity matrices are tested on benchmark alignments at three different levels, namely, the family, the superfamily, and the fold level. Compared to BLOSUM45 and the other existing matrices, the contact potential-based matrices perform comparably in the family level alignments, but clearly outperform in the fold level alignments. The contact potential-based matrices perform even better when suboptimal alignments are considered. Comparing the matrices themselves with each other revealed that the contact potential-based matrices are very different from BLOSUM45 and the other matrices, indicating that they are located in a different basin in the amino acid similarity matrix space.

Properties of Zero-Free Transfer Function Matrices

NASA Astrophysics Data System (ADS)

D. O. Anderson, Brian; Deistler, Manfred

Transfer functions of linear, time-invariant finite-dimensional systems with more outputs than inputs, as arise in factor analysis (for example in econometrics), have, for state-variable descriptions with generic entries in the relevant matrices, no finite zeros. This paper gives a number of characterizations of such systems (and indeed square discrete-time systems with no zeros), using state-variable, impulse response, and matrix-fraction descriptions. Key properties include the ability to recover the input values at any time from a bounded interval of output values, without any knowledge of an initial state, and an ability to verify the no-zero property in terms of a property of the impulse response coefficient matrices. Results are particularized to cases where the transfer function matrix in question may or may not have a zero at infinity or a zero at zero.

Multivariable frequency domain identification via 2-norm minimization

NASA Technical Reports Server (NTRS)

Bayard, David S.

1992-01-01

The author develops a computational approach to multivariable frequency domain identification, based on 2-norm minimization. In particular, a Gauss-Newton (GN) iteration is developed to minimize the 2-norm of the error between frequency domain data and a matrix fraction transfer function estimate. To improve the global performance of the optimization algorithm, the GN iteration is initialized using the solution to a particular sequentially reweighted least squares problem, denoted as the SK iteration. The least squares problems which arise from both the SK and GN iterations are shown to involve sparse matrices with identical block structure. A sparse matrix QR factorization method is developed to exploit the special block structure, and to efficiently compute the least squares solution. A numerical example involving the identification of a multiple-input multiple-output (MIMO) plant having 286 unknown parameters is given to illustrate the effectiveness of the algorithm.

Digital Maps, Matrices and Computer Algebra

ERIC Educational Resources Information Center

Knight, D. G.

2005-01-01

The way in which computer algebra systems, such as Maple, have made the study of complex problems accessible to undergraduate mathematicians with modest computational skills is illustrated by some large matrix calculations, which arise from representing the Earth's surface by digital elevation models. Such problems are often considered to lie in…

The ELPA library: scalable parallel eigenvalue solutions for electronic structure theory and computational science.

PubMed

Marek, A; Blum, V; Johanni, R; Havu, V; Lang, B; Auckenthaler, T; Heinecke, A; Bungartz, H-J; Lederer, H

2014-05-28

Obtaining the eigenvalues and eigenvectors of large matrices is a key problem in electronic structure theory and many other areas of computational science. The computational effort formally scales as O(N(3)) with the size of the investigated problem, N (e.g. the electron count in electronic structure theory), and thus often defines the system size limit that practical calculations cannot overcome. In many cases, more than just a small fraction of the possible eigenvalue/eigenvector pairs is needed, so that iterative solution strategies that focus only on a few eigenvalues become ineffective. Likewise, it is not always desirable or practical to circumvent the eigenvalue solution entirely. We here review some current developments regarding dense eigenvalue solvers and then focus on the Eigenvalue soLvers for Petascale Applications (ELPA) library, which facilitates the efficient algebraic solution of symmetric and Hermitian eigenvalue problems for dense matrices that have real-valued and complex-valued matrix entries, respectively, on parallel computer platforms. ELPA addresses standard as well as generalized eigenvalue problems, relying on the well documented matrix layout of the Scalable Linear Algebra PACKage (ScaLAPACK) library but replacing all actual parallel solution steps with subroutines of its own. For these steps, ELPA significantly outperforms the corresponding ScaLAPACK routines and proprietary libraries that implement the ScaLAPACK interface (e.g. Intel's MKL). The most time-critical step is the reduction of the matrix to tridiagonal form and the corresponding backtransformation of the eigenvectors. ELPA offers both a one-step tridiagonalization (successive Householder transformations) and a two-step transformation that is more efficient especially towards larger matrices and larger numbers of CPU cores. ELPA is based on the MPI standard, with an early hybrid MPI-OpenMPI implementation available as well. Scalability beyond 10,000 CPU cores for problem sizes arising in the field of electronic structure theory is demonstrated for current high-performance computer architectures such as Cray or Intel/Infiniband. For a matrix of dimension 260,000, scalability up to 295,000 CPU cores has been shown on BlueGene/P.

Fibronectin alters the rate of formation and structure of the fibrin matrix.

PubMed

Ramanathan, Anand; Karuri, Nancy

2014-01-10

Plasma fibronectin is a vital component of the fibrin clot; however its role on clot structure is not clearly understood. The goal of this study was to examine the influence of fibronectin on the kinetics of formation, structural characteristics and composition of reconstituted fibrin clots or fibrin matrices. Fibrin matrices were formed by adding thrombin to 1, 2 or 4 mg/ml fibrinogen supplemented with 0-0.4 mg/ml fibronectin. The rate of fibrin matrix formation was then monitored by measuring light absorbance properties at different time points. Confocal microscopy of fluorescein conjugated fibrinogen was used to visualize the structural characteristics of fibrin matrices. The amount of fibronectin in fibrin matrices was determined through electrophoresis and immunoblotting of solubilized matrices. Fibronectin concentration positively correlated with the initial rate of fibrin matrix formation and with steady state light absorbance values of fibrin matrices. An increase in fibronectin concentration resulted in thinner and denser fibers in the fibrin matrices. Electrophoresis and immunoblotting showed that fibronectin was covalently and non-covalently bound to fibrin matrices and in the form of high molecular weight multimers. The formation of fibronectin multimers was attributed to cross-linking of fibronectin by trace amounts Factor XIIIa. These findings are novel because they link results from light absorbance studies to microcopy analyses and demonstrate an influence of fibronectin on fibrin matrix structural characteristics. This data is important in developing therapies that destabilize fibrin clots. Copyright © 2014. Published by Elsevier Inc.

Exploring homogeneity of correlation structures of gene expression datasets within and between etiological disease categories.

PubMed

Jong, Victor L; Novianti, Putri W; Roes, Kit C B; Eijkemans, Marinus J C

2014-12-01

The literature shows that classifiers perform differently across datasets and that correlations within datasets affect the performance of classifiers. The question that arises is whether the correlation structure within datasets differ significantly across diseases. In this study, we evaluated the homogeneity of correlation structures within and between datasets of six etiological disease categories; inflammatory, immune, infectious, degenerative, hereditary and acute myeloid leukemia (AML). We also assessed the effect of filtering; detection call and variance filtering on correlation structures. We downloaded microarray datasets from ArrayExpress for experiments meeting predefined criteria and ended up with 12 datasets for non-cancerous diseases and six for AML. The datasets were preprocessed by a common procedure incorporating platform-specific recommendations and the two filtering methods mentioned above. Homogeneity of correlation matrices between and within datasets of etiological diseases was assessed using the Box's M statistic on permuted samples. We found that correlation structures significantly differ between datasets of the same and/or different etiological disease categories and that variance filtering eliminates more uncorrelated probesets than detection call filtering and thus renders the data highly correlated.

Laminin active peptide/agarose matrices as multifunctional biomaterials for tissue engineering.

PubMed

Yamada, Yuji; Hozumi, Kentaro; Aso, Akihiro; Hotta, Atsushi; Toma, Kazunori; Katagiri, Fumihiko; Kikkawa, Yamato; Nomizu, Motoyoshi

2012-06-01

Cell adhesive peptides derived from extracellular matrix components are potential candidates to afford bio-adhesiveness to cell culture scaffolds for tissue engineering. Previously, we covalently conjugated bioactive laminin peptides to polysaccharides, such as chitosan and alginate, and demonstrated their advantages as biomaterials. Here, we prepared functional polysaccharide matrices by mixing laminin active peptides and agarose gel. Several laminin peptide/agarose matrices showed cell attachment activity. In particular, peptide AG73 (RKRLQVQLSIRT)/agarose matrices promoted strong cell attachment and the cell behavior depended on the stiffness of agarose matrices. Fibroblasts formed spheroid structures on the soft AG73/agarose matrices while the cells formed a monolayer with elongated morphologies on the stiff matrices. On the stiff AG73/agarose matrices, neuronal cells extended neuritic processes and endothelial cells formed capillary-like networks. In addition, salivary gland cells formed acini-like structures on the soft matrices. These results suggest that the peptide/agarose matrices are useful for both two- and three-dimensional cell culture systems as a multifunctional biomaterial for tissue engineering. Copyright © 2012 Elsevier Ltd. All rights reserved.

Evaluation of an Approximate Method for Synthesizing Covariance Matrices for Use in Meta-Analytic SEM

ERIC Educational Resources Information Center

Beretvas, S. Natasha; Furlow, Carolyn F.

2006-01-01

Meta-analytic structural equation modeling (MA-SEM) is increasingly being used to assess model-fit for variables' interrelations synthesized across studies. MA-SEM researchers have analyzed synthesized correlation matrices using structural equation modeling (SEM) estimation that is designed for covariance matrices. This can produce incorrect…

An experimental study on Sodalite and SAP matrices for immobilization of spent chloride salt waste

NASA Astrophysics Data System (ADS)

Giacobbo, Francesca; Da Ros, Mirko; Macerata, Elena; Mariani, Mario; Giola, Marco; De Angelis, Giorgio; Capone, Mauro; Fedeli, Carlo

2018-02-01

In the frame of Generation IV reactors a renewed interest in pyro-processing of spent nuclear fuel is underway. Molten chloride salt waste arising from the recovering of uranium and plutonium through pyro-processing is one of the problematic wastes for direct application of vitrification or ceramization. In this work, Sodalite and SAP have been evaluated and compared as potential matrices for confinement of spent chloride salt waste coming from pyro-processing. To this aim Sodalite and SAP were synthesized both in pure form and mixed with different glass matrices, i.e. commercially available glass frit and borosilicate glass. The confining matrices were loaded with mixed chloride salts to study their retention capacities with respect to the elements of interest. The matrices were characterized and leached for contact times up to 150 days at room temperature and at 90 °C. SEM analyses were also performed in order to compare the matrix surface before and after leaching. Leaching results are discussed and compared in terms of normalized releases with similar results reported in literature. According to this comparative study the SAP matrix with glass frit binder resulted in the best matrix among the ones studied, with respect to retention capacities for both matrix and spent fuel elements.

SAR matrices: automated extraction of information-rich SAR tables from large compound data sets.

PubMed

Wassermann, Anne Mai; Haebel, Peter; Weskamp, Nils; Bajorath, Jürgen

2012-07-23

We introduce the SAR matrix data structure that is designed to elucidate SAR patterns produced by groups of structurally related active compounds, which are extracted from large data sets. SAR matrices are systematically generated and sorted on the basis of SAR information content. Matrix generation is computationally efficient and enables processing of large compound sets. The matrix format is reminiscent of SAR tables, and SAR patterns revealed by different categories of matrices are easily interpretable. The structural organization underlying matrix formation is more flexible than standard R-group decomposition schemes. Hence, the resulting matrices capture SAR information in a comprehensive manner.

Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST.

PubMed

Goonesekere, Nalin Cw

2009-01-01

The large numbers of protein sequences generated by whole genome sequencing projects require rapid and accurate methods of annotation. The detection of homology through computational sequence analysis is a powerful tool in determining the complex evolutionary and functional relationships that exist between proteins. Homology search algorithms employ amino acid substitution matrices to detect similarity between proteins sequences. The substitution matrices in common use today are constructed using sequences aligned without reference to protein structure. Here we present amino acid substitution matrices constructed from the alignment of a large number of protein domain structures from the structural classification of proteins (SCOP) database. We show that when incorporated into the homology search algorithms BLAST and PSI-blast, the structure-based substitution matrices enhance the efficacy of detecting remote homologs.

Periodic GMP Matrices

NASA Astrophysics Data System (ADS)

Eichinger, Benjamin

2016-07-01

We recall criteria on the spectrum of Jacobi matrices such that the corresponding isospectral torus consists of periodic operators. Motivated by those known results for Jacobi matrices, we define a new class of operators called GMP matrices. They form a certain Generalization of matrices related to the strong Moment Problem. This class allows us to give a parametrization of almost periodic finite gap Jacobi matrices by periodic GMP matrices. Moreover, due to their structural similarity we can carry over numerous results from the direct and inverse spectral theory of periodic Jacobi matrices to the class of periodic GMP matrices. In particular, we prove an analogue of the remarkable ''magic formula'' for this new class.

A robust direct-integration method for rotorcraft maneuver and periodic response

NASA Technical Reports Server (NTRS)

Panda, Brahmananda

1992-01-01

The Newmark-Beta method and the Newton-Raphson iteration scheme are combined to develop a direct-integration method for evaluating the maneuver and periodic-response expressions for rotorcraft. The method requires the generation of Jacobians and includes higher derivatives in the formulation of the geometric stiffness matrix to enhance the convergence of the system. The method leads to effective convergence with nonlinear structural dynamics and aerodynamic terms. Singularities in the matrices can be addressed with the method as they arise from a Lagrange multiplier approach for coupling equations with nonlinear constraints. The method is also shown to be general enough to handle singularities from quasisteady control-system models. The method is shown to be more general and robust than the similar 2GCHAS method for analyzing rotorcraft dynamics.

Research on numerical algorithms for large space structures

NASA Technical Reports Server (NTRS)

Denman, E. D.

1982-01-01

Numerical algorithms for large space structures were investigated with particular emphasis on decoupling method for analysis and design. Numerous aspects of the analysis of large systems ranging from the algebraic theory to lambda matrices to identification algorithms were considered. A general treatment of the algebraic theory of lambda matrices is presented and the theory is applied to second order lambda matrices.

Tensor Sparse Coding for Positive Definite Matrices.

PubMed

Sivalingam, Ravishankar; Boley, Daniel; Morellas, Vassilios; Papanikolopoulos, Nikos

2013-08-02

In recent years, there has been extensive research on sparse representation of vector-valued signals. In the matrix case, the data points are merely vectorized and treated as vectors thereafter (for e.g., image patches). However, this approach cannot be used for all matrices, as it may destroy the inherent structure of the data. Symmetric positive definite (SPD) matrices constitute one such class of signals, where their implicit structure of positive eigenvalues is lost upon vectorization. This paper proposes a novel sparse coding technique for positive definite matrices, which respects the structure of the Riemannian manifold and preserves the positivity of their eigenvalues, without resorting to vectorization. Synthetic and real-world computer vision experiments with region covariance descriptors demonstrate the need for and the applicability of the new sparse coding model. This work serves to bridge the gap between the sparse modeling paradigm and the space of positive definite matrices.

Tensor sparse coding for positive definite matrices.

PubMed

Sivalingam, Ravishankar; Boley, Daniel; Morellas, Vassilios; Papanikolopoulos, Nikolaos

2014-03-01

In recent years, there has been extensive research on sparse representation of vector-valued signals. In the matrix case, the data points are merely vectorized and treated as vectors thereafter (for example, image patches). However, this approach cannot be used for all matrices, as it may destroy the inherent structure of the data. Symmetric positive definite (SPD) matrices constitute one such class of signals, where their implicit structure of positive eigenvalues is lost upon vectorization. This paper proposes a novel sparse coding technique for positive definite matrices, which respects the structure of the Riemannian manifold and preserves the positivity of their eigenvalues, without resorting to vectorization. Synthetic and real-world computer vision experiments with region covariance descriptors demonstrate the need for and the applicability of the new sparse coding model. This work serves to bridge the gap between the sparse modeling paradigm and the space of positive definite matrices.

Controllable reflection properties of nanocomposite photonic crystals constructed by semiconductor nanocrystallites and natural periodic bio-matrices.

PubMed

Han, Jie; Su, Huilan; Song, Fang; Zhang, Di; Chen, Zhixin

2010-10-01

In this contribution, the subtle periodic nanostructures in butterfly wings and peacock feathers are applied as natural PhC matrices to in situ embed CdS nanocrystallites (nano-CdS) on the structure surface via a convenient solution process. The resulting nano-CdS/natural PhCs nanocomposites show typical 1D, quasi 1D and 2D PhC structures at the nanoscale, which is inherited from the corresponding natural periodic bio-matrices. Moreover, their reflection properties are investigated and show dependence on PhC type, structure parameter, loading amount, as well as collecting angle. This work suggests that natural periodic bio-structures could be perfect matrices to construct novel nanocomposite PhCs, whose photonic band structures are tunable and thus achieve controllable optical properties. Related ideas could inspire the design and synthesis of future nanocomposite PhCs.

Atom and Bond Fukui Functions and Matrices: A Hirshfeld-I Atoms-in-Molecule Approach.

PubMed

Oña, Ofelia B; De Clercq, Olivier; Alcoba, Diego R; Torre, Alicia; Lain, Luis; Van Neck, Dimitri; Bultinck, Patrick

2016-09-19

The Fukui function is often used in its atom-condensed form by isolating it from the molecular Fukui function using a chosen weight function for the atom in the molecule. Recently, Fukui functions and matrices for both atoms and bonds separately were introduced for semiempirical and ab initio levels of theory using Hückel and Mulliken atoms-in-molecule models. In this work, a double partitioning method of the Fukui matrix is proposed within the Hirshfeld-I atoms-in-molecule framework. Diagonalizing the resulting atomic and bond matrices gives eigenvalues and eigenvectors (Fukui orbitals) describing the reactivity of atoms and bonds. The Fukui function is the diagonal element of the Fukui matrix and may be resolved in atom and bond contributions. The extra information contained in the atom and bond resolution of the Fukui matrices and functions is highlighted. The effect of the choice of weight function arising from the Hirshfeld-I approach to obtain atom- and bond-condensed Fukui functions is studied. A comparison of the results with those generated by using the Mulliken atoms-in-molecule approach shows low correlation between the two partitioning schemes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A two-dimensional Riemann solver with self-similar sub-structure - Alternative formulation based on least squares projection

NASA Astrophysics Data System (ADS)

Balsara, Dinshaw S.; Vides, Jeaniffer; Gurski, Katharine; Nkonga, Boniface; Dumbser, Michael; Garain, Sudip; Audit, Edouard

2016-01-01

Just as the quality of a one-dimensional approximate Riemann solver is improved by the inclusion of internal sub-structure, the quality of a multidimensional Riemann solver is also similarly improved. Such multidimensional Riemann problems arise when multiple states come together at the vertex of a mesh. The interaction of the resulting one-dimensional Riemann problems gives rise to a strongly-interacting state. We wish to endow this strongly-interacting state with physically-motivated sub-structure. The self-similar formulation of Balsara [16] proves especially useful for this purpose. While that work is based on a Galerkin projection, in this paper we present an analogous self-similar formulation that is based on a different interpretation. In the present formulation, we interpret the shock jumps at the boundary of the strongly-interacting state quite literally. The enforcement of the shock jump conditions is done with a least squares projection (Vides, Nkonga and Audit [67]). With that interpretation, we again show that the multidimensional Riemann solver can be endowed with sub-structure. However, we find that the most efficient implementation arises when we use a flux vector splitting and a least squares projection. An alternative formulation that is based on the full characteristic matrices is also presented. The multidimensional Riemann solvers that are demonstrated here use one-dimensional HLLC Riemann solvers as building blocks. Several stringent test problems drawn from hydrodynamics and MHD are presented to show that the method works. Results from structured and unstructured meshes demonstrate the versatility of our method. The reader is also invited to watch a video introduction to multidimensional Riemann solvers on http://www.nd.edu/ dbalsara/Numerical-PDE-Course.

Direct system parameter identification of mechanical structures with application to modal analysis

NASA Technical Reports Server (NTRS)

Leuridan, J. M.; Brown, D. L.; Allemang, R. J.

1982-01-01

In this paper a method is described to estimate mechanical structure characteristics in terms of mass, stiffness and damping matrices using measured force input and response data. The estimated matrices can be used to calculate a consistent set of damped natural frequencies and damping values, mode shapes and modal scale factors for the structure. The proposed technique is attractive as an experimental modal analysis method since the estimation of the matrices does not require previous estimation of frequency responses and since the method can be used, without any additional complications, for multiple force input structure testing.

On the buckling of hexagonal boron nitride nanoribbons via structural mechanics

NASA Astrophysics Data System (ADS)

Giannopoulos, Georgios I.

2018-03-01

Monolayer hexagonal boron nitride nanoribbons have similar crystal structure as graphene nanoribbons, have excellent mechanical, thermal insulating and dielectric properties and additionally present chemical stability. These allotropes of boron nitride can be used in novel applications, in which graphene is not compatible, to achieve remarkable performance. The purpose of the present work is to provide theoretical estimations regarding the buckling response of hexagonal boron nitride monolayer under compressive axial loadings. For this reason, a structural mechanics method is formulated which employs the exact equilibrium atomistic structure of the specific two-dimensional nanomaterial. In order to represent the interatomic interactions appearing between boron and nitrogen atoms, the Dreiding potential model is adopted which is realized by the use of three-dimensional, two-noded, spring-like finite elements of appropriate stiffness matrices. The critical compressive loads that cause the buckling of hexagonal boron nitride nanoribbons are computed with respect to their size and chirality while some indicative buckled shapes of them are illustrated. Important conclusions arise regarding the effect of the size and chirality on the structural stability of the hexagonal boron nitride monolayers. An analytical buckling formula, which provides good fitting of the numerical outcome, is proposed.

Deployable structures using bistable reeled composites

NASA Astrophysics Data System (ADS)

Daton-Lovett, Andrew J.; Compton-Bishop, Quentin M.; Curry, Richard G.

2000-06-01

This paper describes an innovative, patented use of composite materials developed by RolaTube Technology Ltd. to make smart deployable structures. Bi-stable reeled composites (BRCs) can alternate between two stable forms; that of a strong, rigid structure and that of a compact coil of flat-wound material. Bi-stability arises as a result of the manipulation of Poisson's ratio and isotropy in the various layers of the material. BRCs are made of fiber- reinforced composite materials, most often with a thermoplastic matrix. A range of fibers and polymer matrices can be used according to the requirements of the operating environment. Samples of a BRC structure were constructed using layers of unidirectional, fiber-reinforced thermoplastic sheet with the layers at different angles. The whole assembly was then consolidated under conditions of elevated temperature and pressure. The properties of the BRC are described and the result of a series of experiments performed on the sample to determine the tensile strength of the BRC structure are reported. A full analysis using finite element methods is being undertaken in collaboration with the University of Cambridge, England. The first commercial use has been to fabricate boom and drive mechanisms for the remote inspection of industrial plant.

Spatial-temporal-covariance-based modeling, analysis, and simulation of aero-optics wavefront aberrations.

PubMed

Vogel, Curtis R; Tyler, Glenn A; Wittich, Donald J

2014-07-01

We introduce a framework for modeling, analysis, and simulation of aero-optics wavefront aberrations that is based on spatial-temporal covariance matrices extracted from wavefront sensor measurements. Within this framework, we present a quasi-homogeneous structure function to analyze nonhomogeneous, mildly anisotropic spatial random processes, and we use this structure function to show that phase aberrations arising in aero-optics are, for an important range of operating parameters, locally Kolmogorov. This strongly suggests that the d5/3 power law for adaptive optics (AO) deformable mirror fitting error, where d denotes actuator separation, holds for certain important aero-optics scenarios. This framework also allows us to compute bounds on AO servo lag error and predictive control error. In addition, it provides us with the means to accurately simulate AO systems for the mitigation of aero-effects, and it may provide insight into underlying physical processes associated with turbulent flow. The techniques introduced here are demonstrated using data obtained from the Airborne Aero-Optics Laboratory.

Study on vulnerability matrices of masonry buildings of mainland China

NASA Astrophysics Data System (ADS)

Sun, Baitao; Zhang, Guixin

2018-04-01

The degree and distribution of damage to buildings subjected to earthquakes is a concern of the Chinese Government and the public. Seismic damage data indicates that seismic capacities of different types of building structures in various regions throughout mainland China are different. Furthermore, the seismic capacities of the same type of structure in different regions may vary. The contributions of this research are summarized as follows: 1) Vulnerability matrices and earthquake damage matrices of masonry structures in mainland China were chosen as research samples. The aim was to analyze the differences in seismic capacities of sample matrices and to present general rules for categorizing seismic resistance. 2) Curves relating the percentage of damaged masonry structures with different seismic resistances subjected to seismic demand in different regions of seismic intensity (VI to X) have been developed. 3) A method has been proposed to build vulnerability matrices of masonry structures. The damage ratio for masonry structures under high-intensity events such as the Ms 6.1 Panzhihua earthquake in Sichuan province on 30 August 2008, was calculated to verify the applicability of this method. This research offers a significant theoretical basis for predicting seismic damage and direct loss assessment of groups of buildings, as well as for earthquake disaster insurance.

Unusual square roots in the ghost-free theory of massive gravity

NASA Astrophysics Data System (ADS)

Golovnev, Alexey; Smirnov, Fedor

2017-06-01

A crucial building block of the ghost free massive gravity is the square root function of a matrix. This is a problematic entity from the viewpoint of existence and uniqueness properties. We accurately describe the freedom of choosing a square root of a (non-degenerate) matrix. It has discrete and (in special cases) continuous parts. When continuous freedom is present, the usual perturbation theory in terms of matrices can be critically ill defined for some choices of the square root. We consider the new formulation of massive and bimetric gravity which deals directly with eigenvalues (in disguise of elementary symmetric polynomials) instead of matrices. It allows for a meaningful discussion of perturbation theory in such cases, even though certain non-analytic features arise.

High-throughput screening of dye-ligands for chromatography.

PubMed

Kumar, Sunil; Punekar, Narayan S

2014-01-01

Dye-ligand-based chromatography has become popular after Cibacron Blue, the first reactive textile dye, found application for protein purification. Many other textile dyes have since been successfully used to purify a number of proteins and enzymes. While the exact nature of their interaction with target proteins is often unclear, dye-ligands are thought to mimic the structural features of their corresponding substrates, cofactors, etc. The dye-ligand affinity matrices are therefore considered pseudo-affinity matrices. In addition, dye-ligands may simply bind with proteins due to electrostatic, hydrophobic, and hydrogen-bonding interactions. Because of their low cost, ready availability, and structural stability, dye-ligand affinity matrices have gained much popularity. Choice of a large number of dye structures offers a range of matrices to be prepared and tested. When presented in the high-throughput screening mode, these dye-ligand matrices provide a formidable tool for protein purification. One could pick from the list of dye-ligands already available or build a systematic library of such structures for use. A high-throughput screen may be set up to choose best dye-ligand matrix as well as ideal conditions for binding and elution, for a given protein. The mode of operation could be either manual or automated. The technology is available to test the performance of dye-ligand matrices in small volumes in an automated liquid-handling workstation. Screening a systematic library of dye-ligand structures can help establish a structure-activity relationship. While the origins of dye-ligand chromatography lay in exploiting pseudo-affinity, it is now possible to design very specific biomimetic dye structures. High-throughput screening will be of value in this endeavor as well.

Structures and textures of the Murchison and Mighei carbonaceous chondrite matrices

NASA Technical Reports Server (NTRS)

Mackinnon, I. D. R.

1980-01-01

High-resolution transmission electron microscopy has confirmed earlier observations that the character of the Murchison and Mighei fine-grained matrices is complex in mineralogy and texture. Layer structure minerals occur as planar laths, rounded grains or subhedral grains, and range in size from less than 100 A to about 1 micrometer. Serpentine-type and brucite-type structures predominate in the CM matrices. The occurrence of Povlen chrysolite and a vein of disordered mixed-layer and brucite-type material cutting a large lizardite-type grain suggests that at least some of the matrix materials were formed by alteration of preexisting material.

RGD peptide-displaying M13 bacteriophage/PLGA nanofibers as cell-adhesive matrices for smooth muscle cells

NASA Astrophysics Data System (ADS)

Shin, Yong Cheol; Lee, Jong Ho; Jin, Oh Seong; Lee, Eun Ji; Jin, Lin Hua; Kim, Chang-Seok; Hong, Suck Won; Han, Dong-Wook; Kim, Chuntae; Oh, Jin-Woo

2015-01-01

Extracellular matrices (ECMs) are network structures that play an essential role in regulating cellular growth and differentiation. In this study, novel nanofibrous matrices were fabricated by electrospinning M13 bacteriophage and poly(lactic- co-glycolic acid) (PLGA) and were shown to be structurally and functionally similar to natural ECMs. A genetically-engineered M13 bacteriophage was constructed to display Arg-Gly-Asp (RGD) peptides on its surface. The physicochemical properties of RGD peptide-displaying M13 bacteriophage (RGD-M13 phage)/PLGA nanofibers were characterized by using scanning electron microscopy and Fourier-transform infrared spectroscopy. We used immunofluorescence staining to confirm that M13 bacteriophages were homogenously distributed in RGD-M13 phage/PLGA matrices. Furthermore, RGD-M13 phage/PLGA nanofibrous matrices, having excellent biocompatibility, can enhance the behaviors of vascular smooth muscle cells. This result suggests that RGD-M13 phage/PLGA nanofibrous matrices have potentials to serve as tissue engineering scaffolds.

Invariant Poisson-Nijenhuis structures on Lie groups and classification

NASA Astrophysics Data System (ADS)

Ravanpak, Zohreh; Rezaei-Aghdam, Adel; Haghighatdoost, Ghorbanali

We study right-invariant (respectively, left-invariant) Poisson-Nijenhuis structures (P-N) on a Lie group G and introduce their infinitesimal counterpart, the so-called r-n structures on the corresponding Lie algebra 𝔤. We show that r-n structures can be used to find compatible solutions of the classical Yang-Baxter equation (CYBE). Conversely, two compatible r-matrices from which one is invertible determine an r-n structure. We classify, up to a natural equivalence, all r-matrices and all r-n structures with invertible r on four-dimensional symplectic real Lie algebras. The result is applied to show that a number of dynamical systems which can be constructed by r-matrices on a phase space whose symmetry group is Lie group a G, can be specifically determined.

An improved approach to the analysis of drug-protein binding by distance geometry

NASA Technical Reports Server (NTRS)

Goldblum, A.; Kieber-Emmons, T.; Rein, R.

1986-01-01

The calculation of side chain centers of coordinates and the subsequent generation of side chain-side chain and side chain-backbone distance matrices is suggested as an improved method for viewing interactions inside proteins and for the comparison of protein structures. The use of side chain distance matrices is demonstrated with free PTI, and the use of difference distance matrices for side chains is shown for free and trypsin-bound PTI as well as for the X-ray structures of trypsin complexes with PTI and with benzamidine. It is found that conformational variations are reflected in the side chain distance matrices much more than in the standard C-C distance representations.

On the representation matrices of the spin permutation group. [for atomic and molecular electronic structures

NASA Technical Reports Server (NTRS)

Wilson, S.

1977-01-01

A method is presented for the determination of the representation matrices of the spin permutation group (symmetric group), a detailed knowledge of these matrices being required in the study of the electronic structure of atoms and molecules. The method is characterized by the use of two different coupling schemes. Unlike the Yamanouchi spin algebraic scheme, the method is not recursive. The matrices for the fundamental transpositions can be written down directly in one of the two bases. The method results in a computationally significant reduction in the number of matrix elements that have to be stored when compared with, say, the standard Young tableaux group theoretical approach.

Approaches to optimization of SS/TDMA time slot assignment. [satellite switched time division multiple access

NASA Technical Reports Server (NTRS)

Wade, T. O.

1984-01-01

Reduction techniques for traffic matrices are explored in some detail. These matrices arise in satellite switched time-division multiple access (SS/TDMA) techniques whereby switching of uplink and downlink beams is required to facilitate interconnectivity of beam zones. A traffic matrix is given to represent that traffic to be transmitted from n uplink beams to n downlink beams within a TDMA frame typically of 1 ms duration. The frame is divided into segments of time and during each segment a portion of the traffic is represented by a switching mode. This time slot assignment is characterized by a mode matrix in which there is not more than a single non-zero entry on each line (row or column) of the matrix. Investigation is confined to decomposition of an n x n traffic matrix by mode matrices with a requirement that the decomposition be 100 percent efficient or, equivalently, that the line(s) in the original traffic matrix whose sum is maximal (called critical line(s)) remain maximal as mode matrices are subtracted throughout the decomposition process. A method of decomposition of an n x n traffic matrix by mode matrices results in a number of steps that is bounded by n(2) - 2n + 2. It is shown that this upper bound exists for an n x n matrix wherein all the lines are maximal (called a quasi doubly stochastic (QDS) matrix) or for an n x n matrix that is completely arbitrary. That is, the fact that no method can exist with a lower upper bound is shown for both QDS and arbitrary matrices, in an elementary and straightforward manner.

Tolerant compressed sensing with partially coherent sensing matrices

NASA Astrophysics Data System (ADS)

Birnbaum, Tobias; Eldar, Yonina C.; Needell, Deanna

2017-08-01

Most of compressed sensing (CS) theory to date is focused on incoherent sensing, that is, columns from the sensing matrix are highly uncorrelated. However, sensing systems with naturally occurring correlations arise in many applications, such as signal detection, motion detection and radar. Moreover, in these applications it is often not necessary to know the support of the signal exactly, but instead small errors in the support and signal are tolerable. Despite the abundance of work utilizing incoherent sensing matrices, for this type of tolerant recovery we suggest that coherence is actually beneficial . We promote the use of coherent sampling when tolerant support recovery is acceptable, and demonstrate its advantages empirically. In addition, we provide a first step towards theoretical analysis by considering a specific reconstruction method for selected signal classes.

An Efficient Multicore Implementation of a Novel HSS-Structured Multifrontal Solver Using Randomized Sampling

DOE PAGES

Ghysels, Pieter; Li, Xiaoye S.; Rouet, Francois -Henry; ...

2016-10-27

Here, we present a sparse linear system solver that is based on a multifrontal variant of Gaussian elimination and exploits low-rank approximation of the resulting dense frontal matrices. We use hierarchically semiseparable (HSS) matrices, which have low-rank off-diagonal blocks, to approximate the frontal matrices. For HSS matrix construction, a randomized sampling algorithm is used together with interpolative decompositions. The combination of the randomized compression with a fast ULV HSS factoriz ation leads to a solver with lower computational complexity than the standard multifrontal method for many applications, resulting in speedups up to 7 fold for problems in our test suite.more » The implementation targets many-core systems by using task parallelism with dynamic runtime scheduling. Numerical experiments show performance improvements over state-of-the-art sparse direct solvers. The implementation achieves high performance and good scalability on a range of modern shared memory parallel systems, including the Intel Xeon Phi (MIC). The code is part of a software package called STRUMPACK - STRUctured Matrices PACKage, which also has a distributed memory component for dense rank-structured matrices.« less

Planck 2015 results. VI. LFI mapmaking

NASA Astrophysics Data System (ADS)

Planck Collaboration; Ade, P. A. R.; Aghanim, N.; Ashdown, M.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Bartolo, N.; Battaner, E.; Benabed, K.; Benoît, A.; Benoit-Lévy, A.; Bernard, J.-P.; Bersanelli, M.; Bielewicz, P.; Bonaldi, A.; Bonavera, L.; Bond, J. R.; Borrill, J.; Bouchet, F. R.; Bucher, M.; Burigana, C.; Butler, R. C.; Calabrese, E.; Cardoso, J.-F.; Catalano, A.; Chamballu, A.; Chary, R.-R.; Christensen, P. R.; Colombi, S.; Colombo, L. P. L.; Crill, B. P.; Curto, A.; Cuttaia, F.; Danese, L.; Davies, R. D.; Davis, R. J.; de Bernardis, P.; de Rosa, A.; de Zotti, G.; Delabrouille, J.; Dickinson, C.; Diego, J. M.; Dole, H.; Donzelli, S.; Doré, O.; Douspis, M.; Ducout, A.; Dupac, X.; Efstathiou, G.; Elsner, F.; Enßlin, T. A.; Eriksen, H. K.; Fergusson, J.; Finelli, F.; Forni, O.; Frailis, M.; Franceschi, E.; Frejsel, A.; Galeotta, S.; Galli, S.; Ganga, K.; Giard, M.; Giraud-Héraud, Y.; Gjerløw, E.; González-Nuevo, J.; Górski, K. M.; Gratton, S.; Gregorio, A.; Gruppuso, A.; Hansen, F. K.; Hanson, D.; Harrison, D. L.; Henrot-Versillé, S.; Herranz, D.; Hildebrandt, S. R.; Hivon, E.; Hobson, M.; Holmes, W. A.; Hornstrup, A.; Hovest, W.; Huffenberger, K. M.; Hurier, G.; Jaffe, A. H.; Jaffe, T. R.; Juvela, M.; Keihänen, E.; Keskitalo, R.; Kiiveri, K.; Kisner, T. S.; Knoche, J.; Kunz, M.; Kurki-Suonio, H.; Lähteenmäki, A.; Lamarre, J.-M.; Lasenby, A.; Lattanzi, M.; Lawrence, C. R.; Leahy, J. P.; Leonardi, R.; Lesgourgues, J.; Levrier, F.; Liguori, M.; Lilje, P. B.; Linden-Vørnle, M.; Lindholm, V.; López-Caniego, M.; Lubin, P. M.; Macías-Pérez, J. F.; Maggio, G.; Maino, D.; Mandolesi, N.; Mangilli, A.; Martin, P. G.; Martínez-González, E.; Masi, S.; Matarrese, S.; Mazzotta, P.; McGehee, P.; Meinhold, P. R.; Melchiorri, A.; Mendes, L.; Mennella, A.; Migliaccio, M.; Mitra, S.; Montier, L.; Morgante, G.; Mortlock, D.; Moss, A.; Munshi, D.; Murphy, J. A.; Naselsky, P.; Nati, F.; Natoli, P.; Netterfield, C. B.; Nørgaard-Nielsen, H. U.; Novikov, D.; Novikov, I.; Paci, F.; Pagano, L.; Paoletti, D.; Partridge, B.; Pasian, F.; Patanchon, G.; Pearson, T. J.; Perdereau, O.; Perotto, L.; Perrotta, F.; Pettorino, V.; Pierpaoli, E.; Pietrobon, D.; Pointecouteau, E.; Polenta, G.; Pratt, G. W.; Prézeau, G.; Prunet, S.; Puget, J.-L.; Rachen, J. P.; Rebolo, R.; Reinecke, M.; Remazeilles, M.; Renzi, A.; Rocha, G.; Rosset, C.; Rossetti, M.; Roudier, G.; Rubiño-Martín, J. A.; Rusholme, B.; Sandri, M.; Santos, D.; Savelainen, M.; Scott, D.; Seiffert, M. D.; Shellard, E. P. S.; Spencer, L. D.; Stolyarov, V.; Stompor, R.; Sutton, D.; Suur-Uski, A.-S.; Sygnet, J.-F.; Tauber, J. A.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tristram, M.; Tucci, M.; Tuovinen, J.; Valenziano, L.; Valiviita, J.; Van Tent, B.; Vassallo, T.; Vielva, P.; Villa, F.; Wade, L. A.; Wandelt, B. D.; Watson, R.; Wehus, I. K.; Yvon, D.; Zacchei, A.; Zonca, A.

2016-09-01

This paper describes the mapmaking procedure applied to Planck Low Frequency Instrument (LFI) data. The mapmaking step takes as input the calibrated timelines and pointing information. The main products are sky maps of I, Q, and U Stokes components. For the first time, we present polarization maps at LFI frequencies. The mapmaking algorithm is based on a destriping technique, which is enhanced with a noise prior. The Galactic region is masked to reduce errors arising from bandpass mismatch and high signal gradients. We apply horn-uniform radiometer weights to reduce the effects of beam-shape mismatch. The algorithm is the same as used for the 2013 release, apart from small changes in parameter settings. We validate the procedure through simulations. Special emphasis is put on the control of systematics, which is particularly important for accurate polarization analysis. We also produce low-resolution versions of the maps and corresponding noise covariance matrices. These serve as input in later analysis steps and parameter estimation. The noise covariance matrices are validated through noise Monte Carlo simulations. The residual noise in the map products is characterized through analysis of half-ring maps, noise covariance matrices, and simulations.

Quantum formalism for classical statistics

NASA Astrophysics Data System (ADS)

Wetterich, C.

2018-06-01

In static classical statistical systems the problem of information transport from a boundary to the bulk finds a simple description in terms of wave functions or density matrices. While the transfer matrix formalism is a type of Heisenberg picture for this problem, we develop here the associated Schrödinger picture that keeps track of the local probabilistic information. The transport of the probabilistic information between neighboring hypersurfaces obeys a linear evolution equation, and therefore the superposition principle for the possible solutions. Operators are associated to local observables, with rules for the computation of expectation values similar to quantum mechanics. We discuss how non-commutativity naturally arises in this setting. Also other features characteristic of quantum mechanics, such as complex structure, change of basis or symmetry transformations, can be found in classical statistics once formulated in terms of wave functions or density matrices. We construct for every quantum system an equivalent classical statistical system, such that time in quantum mechanics corresponds to the location of hypersurfaces in the classical probabilistic ensemble. For suitable choices of local observables in the classical statistical system one can, in principle, compute all expectation values and correlations of observables in the quantum system from the local probabilistic information of the associated classical statistical system. Realizing a static memory material as a quantum simulator for a given quantum system is not a matter of principle, but rather of practical simplicity.

Preconditioned Mixed Spectral Element Methods for Elasticity and Stokes Problems

NASA Technical Reports Server (NTRS)

Pavarino, Luca F.

1996-01-01

Preconditioned iterative methods for the indefinite systems obtained by discretizing the linear elasticity and Stokes problems with mixed spectral elements in three dimensions are introduced and analyzed. The resulting stiffness matrices have the structure of saddle point problems with a penalty term, which is associated with the Poisson ratio for elasticity problems or with stabilization techniques for Stokes problems. The main results of this paper show that the convergence rate of the resulting algorithms is independent of the penalty parameter, the number of spectral elements Nu and mildly dependent on the spectral degree eta via the inf-sup constant. The preconditioners proposed for the whole indefinite system are block-diagonal and block-triangular. Numerical experiments presented in the final section show that these algorithms are a practical and efficient strategy for the iterative solution of the indefinite problems arising from mixed spectral element discretizations of elliptic systems.

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.

The Development of Novel Nanodiamond Based MALDI Matrices for the Analysis of Small Organic Pharmaceuticals

NASA Astrophysics Data System (ADS)

Chitanda, Jackson M.; Zhang, Haixia; Pahl, Erica; Purves, Randy W.; El-Aneed, Anas

2016-10-01

The utility of novel functionalized nanodiamonds (NDs) as matrices for matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) is described herein. MALDI-MS analysis of small organic compounds (<1000 Da) is typically complex because of interferences from numerous cluster ions formed when using conventional matrices. To expand the use of MALDI for the analysis of small molecules, novel matrices were designed by covalently linking conventional matrices (or a lysine moiety) to detonated NDs. Four new functionalized NDs were evaluated for their ionization capabilities using five pharmaceuticals with varying molecular structures. Two ND matrices were able to ionize all tested pharmaceuticals in the negative ion mode, producing the deprotonated ions [M - H]-. Ion intensity for target analytes was generally strong with enhanced signal-to-noise ratios compared with conventional matrices. The negative ion mode is of great importance for biological samples as interference from endogenous compounds is inherently minimized in the negative ion mode. Since the molecular structures of the tested pharmaceuticals did not suggest that negative ion mode would be preferable, this result magnifies the importance of these findings. On the other hand, conventional matrices primarily facilitated the ionization as expected in the positive ion mode, producing either the protonated molecules [M + H]+ or cationic adducts (typically producing complex spectra with numerous adduct peaks). The data presented in this study suggests that these matrices may offer advantages for the analysis of low molecular weight pharmaceuticals/metabolites.

The Development of Novel Nanodiamond Based MALDI Matrices for the Analysis of Small Organic Pharmaceuticals.

PubMed

Chitanda, Jackson M; Zhang, Haixia; Pahl, Erica; Purves, Randy W; El-Aneed, Anas

2016-10-01

The utility of novel functionalized nanodiamonds (NDs) as matrices for matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) is described herein. MALDI-MS analysis of small organic compounds (<1000 Da) is typically complex because of interferences from numerous cluster ions formed when using conventional matrices. To expand the use of MALDI for the analysis of small molecules, novel matrices were designed by covalently linking conventional matrices (or a lysine moiety) to detonated NDs. Four new functionalized NDs were evaluated for their ionization capabilities using five pharmaceuticals with varying molecular structures. Two ND matrices were able to ionize all tested pharmaceuticals in the negative ion mode, producing the deprotonated ions [M - H](-). Ion intensity for target analytes was generally strong with enhanced signal-to-noise ratios compared with conventional matrices. The negative ion mode is of great importance for biological samples as interference from endogenous compounds is inherently minimized in the negative ion mode. Since the molecular structures of the tested pharmaceuticals did not suggest that negative ion mode would be preferable, this result magnifies the importance of these findings. On the other hand, conventional matrices primarily facilitated the ionization as expected in the positive ion mode, producing either the protonated molecules [M + H](+) or cationic adducts (typically producing complex spectra with numerous adduct peaks). The data presented in this study suggests that these matrices may offer advantages for the analysis of low molecular weight pharmaceuticals/metabolites. Graphical Abstract ᅟ.

The Graphic Representation of Structure in Similarity/Dissimilarity Matrices: Alternative Methods.

ERIC Educational Resources Information Center

Rudnitsky, Alan N.

Three approaches to the graphic representation of similarity and dissimilarity matrices are compared and contrasted. Specifically, Kruskal's multidimensional scaling, Johnson's hierarchical clustering, and Waern's graphing techniques are employed to depict, in two dimensions, data representing the structure of a set of botanical concepts. Each of…

Noisy covariance matrices and portfolio optimization II

NASA Astrophysics Data System (ADS)

Pafka, Szilárd; Kondor, Imre

2003-03-01

Recent studies inspired by results from random matrix theory (Galluccio et al.: Physica A 259 (1998) 449; Laloux et al.: Phys. Rev. Lett. 83 (1999) 1467; Risk 12 (3) (1999) 69; Plerou et al.: Phys. Rev. Lett. 83 (1999) 1471) found that covariance matrices determined from empirical financial time series appear to contain such a high amount of noise that their structure can essentially be regarded as random. This seems, however, to be in contradiction with the fundamental role played by covariance matrices in finance, which constitute the pillars of modern investment theory and have also gained industry-wide applications in risk management. Our paper is an attempt to resolve this embarrassing paradox. The key observation is that the effect of noise strongly depends on the ratio r= n/ T, where n is the size of the portfolio and T the length of the available time series. On the basis of numerical experiments and analytic results for some toy portfolio models we show that for relatively large values of r (e.g. 0.6) noise does, indeed, have the pronounced effect suggested by Galluccio et al. (1998), Laloux et al. (1999) and Plerou et al. (1999) and illustrated later by Laloux et al. (Int. J. Theor. Appl. Finance 3 (2000) 391), Plerou et al. (Phys. Rev. E, e-print cond-mat/0108023) and Rosenow et al. (Europhys. Lett., e-print cond-mat/0111537) in a portfolio optimization context, while for smaller r (around 0.2 or below), the error due to noise drops to acceptable levels. Since the length of available time series is for obvious reasons limited in any practical application, any bound imposed on the noise-induced error translates into a bound on the size of the portfolio. In a related set of experiments we find that the effect of noise depends also on whether the problem arises in asset allocation or in a risk measurement context: if covariance matrices are used simply for measuring the risk of portfolios with a fixed composition rather than as inputs to optimization, the effect of noise on the measured risk may become very small.

Bayes linear covariance matrix adjustment

NASA Astrophysics Data System (ADS)

Wilkinson, Darren J.

1995-12-01

In this thesis, a Bayes linear methodology for the adjustment of covariance matrices is presented and discussed. A geometric framework for quantifying uncertainties about covariance matrices is set up, and an inner-product for spaces of random matrices is motivated and constructed. The inner-product on this space captures aspects of our beliefs about the relationship between covariance matrices of interest to us, providing a structure rich enough for us to adjust beliefs about unknown matrices in the light of data such as sample covariance matrices, exploiting second-order exchangeability and related specifications to obtain representations allowing analysis. Adjustment is associated with orthogonal projection, and illustrated with examples of adjustments for some common problems. The problem of adjusting the covariance matrices underlying exchangeable random vectors is tackled and discussed. Learning about the covariance matrices associated with multivariate time series dynamic linear models is shown to be amenable to a similar approach. Diagnostics for matrix adjustments are also discussed.

A Distributed-Memory Package for Dense Hierarchically Semi-Separable Matrix Computations Using Randomization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rouet, François-Henry; Li, Xiaoye S.; Ghysels, Pieter

In this paper, we present a distributed-memory library for computations with dense structured matrices. A matrix is considered structured if its off-diagonal blocks can be approximated by a rank-deficient matrix with low numerical rank. Here, we use Hierarchically Semi-Separable (HSS) representations. Such matrices appear in many applications, for example, finite-element methods, boundary element methods, and so on. Exploiting this structure allows for fast solution of linear systems and/or fast computation of matrix-vector products, which are the two main building blocks of matrix computations. The compression algorithm that we use, that computes the HSS form of an input dense matrix, reliesmore » on randomized sampling with a novel adaptive sampling mechanism. We discuss the parallelization of this algorithm and also present the parallelization of structured matrix-vector product, structured factorization, and solution routines. The efficiency of the approach is demonstrated on large problems from different academic and industrial applications, on up to 8,000 cores. Finally, this work is part of a more global effort, the STRUctured Matrices PACKage (STRUMPACK) software package for computations with sparse and dense structured matrices. Hence, although useful on their own right, the routines also represent a step in the direction of a distributed-memory sparse solver.« less

A Distributed-Memory Package for Dense Hierarchically Semi-Separable Matrix Computations Using Randomization

DOE PAGES

Rouet, François-Henry; Li, Xiaoye S.; Ghysels, Pieter; ...

2016-06-30

In this paper, we present a distributed-memory library for computations with dense structured matrices. A matrix is considered structured if its off-diagonal blocks can be approximated by a rank-deficient matrix with low numerical rank. Here, we use Hierarchically Semi-Separable (HSS) representations. Such matrices appear in many applications, for example, finite-element methods, boundary element methods, and so on. Exploiting this structure allows for fast solution of linear systems and/or fast computation of matrix-vector products, which are the two main building blocks of matrix computations. The compression algorithm that we use, that computes the HSS form of an input dense matrix, reliesmore » on randomized sampling with a novel adaptive sampling mechanism. We discuss the parallelization of this algorithm and also present the parallelization of structured matrix-vector product, structured factorization, and solution routines. The efficiency of the approach is demonstrated on large problems from different academic and industrial applications, on up to 8,000 cores. Finally, this work is part of a more global effort, the STRUctured Matrices PACKage (STRUMPACK) software package for computations with sparse and dense structured matrices. Hence, although useful on their own right, the routines also represent a step in the direction of a distributed-memory sparse solver.« less

Applications of multiple-constraint matrix updates to the optimal control of large structures

NASA Technical Reports Server (NTRS)

Smith, S. W.; Walcott, B. L.

1992-01-01

Low-authority control or vibration suppression in large, flexible space structures can be formulated as a linear feedback control problem requiring computation of displacement and velocity feedback gain matrices. To ensure stability in the uncontrolled modes, these gain matrices must be symmetric and positive definite. In this paper, efficient computation of symmetric, positive-definite feedback gain matrices is accomplished through the use of multiple-constraint matrix update techniques originally developed for structural identification applications. Two systems were used to illustrate the application: a simple spring-mass system and a planar truss. From these demonstrations, use of this multiple-constraint technique is seen to provide a straightforward approach for computing the low-authority gains.

Example-Based Learning: Exploring the Use of Matrices and Problem Variability

ERIC Educational Resources Information Center

Hancock-Niemic, Mary A.; Lin, Lijia; Atkinson, Robert K.; Renkl, Alexander; Wittwer, Joerg

2016-01-01

The purpose of the study was to investigate the efficacy of using faded worked examples presented in matrices with problem structure variability to enhance learners' ability to recognize the underlying structure of the problems. Specifically, this study compared the effects of matrix-format versus linear-format faded worked examples combined with…

ATLAS, an integrated structural analysis and design system. Volume 4: Random access file catalog

NASA Technical Reports Server (NTRS)

Gray, F. P., Jr. (Editor)

1979-01-01

A complete catalog is presented for the random access files used by the ATLAS integrated structural analysis and design system. ATLAS consists of several technical computation modules which output data matrices to corresponding random access file. A description of the matrices written on these files is contained herein.

Texture zero neutrino models and their connection with resonant leptogenesis

NASA Astrophysics Data System (ADS)

Achelashvili, Avtandil; Tavartkiladze, Zurab

2018-04-01

Within the low scale resonant leptogenesis scenario, the cosmological CP asymmetry may arise by radiative corrections through the charged lepton Yukawa couplings. While in some cases, as one expects, decisive role is played by the λτ coupling, we show that in specific neutrino textures only by inclusion of the λμ the cosmological CP violation is generated at 1-loop level. With the purpose to relate the cosmological CP violation to the leptonic CP phase δ, we consider an extension of MSSM with two right handed neutrinos (RHN), which are degenerate in mass at high scales. Together with this, we first consider two texture zero 3 × 2 Dirac Yukawa matrices of neutrinos. These via see-saw generated neutrino mass matrices augmented by single ΔL = 2 dimension five (d = 5) operator give predictive neutrino sectors with calculable CP asymmetries. The latter is generated through λμ,τ coupling(s) at 1-loop level. Detailed analysis of the leptogenesis is performed. We also revise some one texture zero Dirac Yukawa matrices, considered earlier, and show that addition of a single ΔL = 2, d = 5 entry in the neutrino mass matrices, together with newly computed 1-loop corrections to the CP asymmetries, give nice accommodation of the neutrino sector and desirable amount of the baryon asymmetry via the resonant leptogenesis even for rather low RHN masses (∼few TeV-107 GeV).

Histopathologic study of human vocal fold mucosa unphonated over a decade.

PubMed

Sato, Kiminori; Umeno, Hirohito; Ono, Takeharu; Nakashima, Tadashi

2011-12-01

Mechanotransduction caused by vocal fold vibration could possibly be an important factor in the maintenance of extracellular matrices and layered structure of the human adult vocal fold mucosa as a vibrating tissue after the layered structure has been completed. Vocal fold stellate cells (VFSCs) in the human maculae flavae of the vocal fold mucosa are inferred to be involved in the metabolism of extracellular matrices of the vocal fold mucosa. Maculae flavae are also considered to be an important structure in the growth and development of the human vocal fold mucosa. Tension caused by phonation (vocal fold vibration) is hypothesized to stimulate the VFSCs to accelerate production of extracellular matrices. A human adult vocal fold mucosa unphonated over a decade was investigated histopathologically. Vocal fold mucosa unphonated for 11 years and 2 months of a 64-year-old male with cerebral hemorrhage was investigated by light and electron microscopy. The vocal fold mucosae (including maculae flavae) were atrophic. The vocal fold mucosa did not have a vocal ligament, Reinke's space or a layered structure. The lamina propria appeared as a uniform structure. Morphologically, the VFSCs synthesized fewer extracellular matrices, such as fibrous protein and glycosaminoglycan. Consequently, VFSCs appeared to decrease their level of activity.

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

PubMed

Ghosh, A

1988-08-01

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

Rotational 3D printing of damage-tolerant composites with programmable mechanics

PubMed Central

Raney, Jordan R.; Compton, Brett G.; Ober, Thomas J.; Shea, Kristina; Lewis, Jennifer A.

2018-01-01

Natural composites exhibit exceptional mechanical performance that often arises from complex fiber arrangements within continuous matrices. Inspired by these natural systems, we developed a rotational 3D printing method that enables spatially controlled orientation of short fibers in polymer matrices solely by varying the nozzle rotation speed relative to the printing speed. Using this method, we fabricated carbon fiber–epoxy composites composed of volume elements (voxels) with programmably defined fiber arrangements, including adjacent regions with orthogonally and helically oriented fibers that lead to nonuniform strain and failure as well as those with purely helical fiber orientations akin to natural composites that exhibit enhanced damage tolerance. Our approach broadens the design, microstructural complexity, and performance space for fiber-reinforced composites through site-specific optimization of their fiber orientation, strain, failure, and damage tolerance. PMID:29348206

Fast Algorithms for Structured Least Squares and Total Least Squares Problems

PubMed Central

Kalsi, Anoop; O’Leary, Dianne P.

2006-01-01

We consider the problem of solving least squares problems involving a matrix M of small displacement rank with respect to two matrices Z1 and Z2. We develop formulas for the generators of the matrix M HM in terms of the generators of M and show that the Cholesky factorization of the matrix M HM can be computed quickly if Z1 is close to unitary and Z2 is triangular and nilpotent. These conditions are satisfied for several classes of matrices, including Toeplitz, block Toeplitz, Hankel, and block Hankel, and for matrices whose blocks have such structure. Fast Cholesky factorization enables fast solution of least squares problems, total least squares problems, and regularized total least squares problems involving these classes of matrices. PMID:27274922

Fast Algorithms for Structured Least Squares and Total Least Squares Problems.

PubMed

Kalsi, Anoop; O'Leary, Dianne P

2006-01-01

We consider the problem of solving least squares problems involving a matrix M of small displacement rank with respect to two matrices Z 1 and Z 2. We develop formulas for the generators of the matrix M (H) M in terms of the generators of M and show that the Cholesky factorization of the matrix M (H) M can be computed quickly if Z 1 is close to unitary and Z 2 is triangular and nilpotent. These conditions are satisfied for several classes of matrices, including Toeplitz, block Toeplitz, Hankel, and block Hankel, and for matrices whose blocks have such structure. Fast Cholesky factorization enables fast solution of least squares problems, total least squares problems, and regularized total least squares problems involving these classes of matrices.

Partial Quark-Lepton Universality and Neutrino CP Violation

DOE PAGES

Liao, Jiajun; Marfatia, D.; Whisnant, K.

2015-01-01

We smore » tudy a model with partial quark-lepton universality that can naturally arise in grand unified theories. We find that constraints on the model can be reduced to a single condition on the Dirac CP phase δ in the neutrino sector. Using our current knowledge of the CKM and PMNS mixing matrices, we predict - 32 . 4 ° ≤ δ ≤ 32 . 0 ° at 2 σ .« less

Structure-performance relationships of phenyl cinnamic acid derivatives as MALDI-MS matrices for sulfatide detection.

PubMed

Tambe, Suparna; Blott, Henning; Fülöp, Annabelle; Spang, Nils; Flottmann, Dirk; Bräse, Stefan; Hopf, Carsten; Junker, Hans-Dieter

2017-02-01

A key aspect for the further development of matrix-assisted laser desorption ionization (MALDI)-mass spectrometry (MS) is a better understanding of the working principles of MALDI matrices. To address this issue, a chemical compound library of 59 structurally related cinnamic acid derivatives was synthesized. Potential MALDI matrices were evaluated with sulfatides, a class of anionic lipids which are abundant in complex brain lipid mixtures. For each matrix relative mean S/N ratios of sulfatides were determined against 9-aminoacridine as a reference matrix using negative ion mass spectrometry with 355 and 337 nm laser systems. The comparison of matrix features with their corresponding relative mean S/N ratios for sulfatide detection identified correlations between matrix substitution patterns, their chemical functionality, and their MALDI-MS performance. Crystal structures of six selected matrices provided structural insight in hydrogen bond interactions in the solid state. Principal component analysis allowed the additional identification of correlation trends between structural and physical matrix properties like number of exchangeable protons at the head group, MW, logP, UV-Vis, and sulfatide detection sensitivity. Graphical abstract Design, synthesis and mass spectrometric evaluation of MALDI-MS matrix compound libraries allows the identification of matrix structure - MALDI-MS performance relationships using multivariate statistics as a tool.

Statistical model for the mechanical behavior of the tissue engineering non-woven fibrous matrices under large deformation.

PubMed

Rizvi, Mohd Suhail; Pal, Anupam

2014-09-01

The fibrous matrices are widely used as scaffolds for the regeneration of load-bearing tissues due to their structural and mechanical similarities with the fibrous components of the extracellular matrix. These scaffolds not only provide the appropriate microenvironment for the residing cells but also act as medium for the transmission of the mechanical stimuli, essential for the tissue regeneration, from macroscopic scale of the scaffolds to the microscopic scale of cells. The requirement of the mechanical loading for the tissue regeneration requires the fibrous scaffolds to be able to sustain the complex three-dimensional mechanical loading conditions. In order to gain insight into the mechanical behavior of the fibrous matrices under large amount of elongation as well as shear, a statistical model has been formulated to study the macroscopic mechanical behavior of the electrospun fibrous matrix and the transmission of the mechanical stimuli from scaffolds to the cells via the constituting fibers. The study establishes the load-deformation relationships for the fibrous matrices for different structural parameters. It also quantifies the changes in the fiber arrangement and tension generated in the fibers with the deformation of the matrix. The model reveals that the tension generated in the fibers on matrix deformation is not homogeneous and hence the cells located in different regions of the fibrous scaffold might experience different mechanical stimuli. The mechanical response of fibrous matrices was also found to be dependent on the aspect ratio of the matrix. Therefore, the model establishes a structure-mechanics interdependence of the fibrous matrices under large deformation, which can be utilized in identifying the appropriate structure and external mechanical loading conditions for the regeneration of load-bearing tissues. Copyright © 2014 Elsevier Ltd. All rights reserved.

Planck 2015 results: VI. LFI mapmaking

DOE PAGES

Ade, P. A. R.; Aghanim, N.; Ashdown, M.; ...

2016-09-20

This article describes the mapmaking procedure applied to Planck Low Frequency Instrument (LFI) data. The mapmaking step takes as input the calibrated timelines and pointing information. The main products are sky maps of I, Q, and U Stokes components. For the first time, we present polarization maps at LFI frequencies. The mapmaking algorithm is based on a destriping technique, which is enhanced with a noise prior. The Galactic region is masked to reduce errors arising from bandpass mismatch and high signal gradients. We apply horn-uniform radiometer weights to reduce the effects of beam-shape mismatch. The algorithm is the same asmore » used for the 2013 release, apart from small changes in parameter settings. We validate the procedure through simulations. Special emphasis is put on the control of systematics, which is particularly important for accurate polarization analysis. We also produce low-resolution versions of the maps and corresponding noise covariance matrices. These serve as input in later analysis steps and parameter estimation. The noise covariance matrices are validated through noise Monte Carlo simulations. The residual noise in the map products is characterized through analysis of half-ring maps, noise covariance matrices, and simulations.« less

Direct structural parameter identification by modal test results

NASA Technical Reports Server (NTRS)

Chen, J.-C.; Kuo, C.-P.; Garba, J. A.

1983-01-01

A direct identification procedure is proposed to obtain the mass and stiffness matrices based on the test measured eigenvalues and eigenvectors. The method is based on the theory of matrix perturbation in which the correct mass and stiffness matrices are expanded in terms of analytical values plus a modification matrix. The simplicity of the procedure enables real time operation during the structural testing.

Big and small: menisci in soil pores affect water pressures, dynamics of groundwater levels, and catchment-scale average matric potentials

NASA Astrophysics Data System (ADS)

de Rooij, G. H.

2010-09-01

Soil water is confined behind the menisci of its water-air interface. Catchment-scale fluxes (groundwater recharge, evaporation, transpiration, precipitation, etc.) affect the matric potential, and thereby the interface curvature and the configuration of the phases. In turn, these affect the fluxes (except precipitation), creating feedbacks between pore-scale and catchment-scale processes. Tracking pore-scale processes beyond the Darcy scale is not feasible. Instead, for a simplified system based on the classical Darcy's Law and Laplace-Young Law we i) clarify how menisci transfer pressure from the atmosphere to the soil water, ii) examine large-scale phenomena arising from pore-scale processes, and iii) analyze the relationship between average meniscus curvature and average matric potential. In stagnant water, changing the gravitational potential or the curvature of the air-water interface changes the pressure throughout the water. Adding small amounts of water can thus profoundly affect water pressures in a much larger volume. The pressure-regulating effect of the interface curvature showcases the meniscus as a pressure port that transfers the atmospheric pressure to the water with an offset directly proportional to its curvature. This property causes an extremely rapid rise of phreatic levels in soils once the capillary fringe extends to the soil surface and the menisci flatten. For large bodies of subsurface water, the curvature and vertical position of any meniscus quantify the uniform hydraulic potential under hydrostatic equilibrium. During unit-gradient flow, the matric potential corresponding to the mean curvature of the menisci should provide a good approximation of the intrinsic phase average of the matric potential.

Nouvelles bornes et estimations pour les milieux poreux à matrice rigide parfaitement plastique

NASA Astrophysics Data System (ADS)

Bilger, Nicolas; Auslender, François; Bornert, Michel; Masson, Renaud

We derive new rigorous bounds and self-consistent estimates for the effective yield surface of porous media with a rigid perfectly plastic matrix and a microstructure similar to Hashin's composite spheres assemblage. These results arise from a homogenisation technique that combines a pattern-based modelling for linear composite materials and a variational formulation for nonlinear media. To cite this article: N. Bilger et al., C. R. Mecanique 330 (2002) 127-132.

Toric Networks, Geometric R-Matrices and Generalized Discrete Toda Lattices

NASA Astrophysics Data System (ADS)

Inoue, Rei; Lam, Thomas; Pylyavskyy, Pavlo

2016-11-01

We use the combinatorics of toric networks and the double affine geometric R-matrix to define a three-parameter family of generalizations of the discrete Toda lattice. We construct the integrals of motion and a spectral map for this system. The family of commuting time evolutions arising from the action of the R-matrix is explicitly linearized on the Jacobian of the spectral curve. The solution to the initial value problem is constructed using Riemann theta functions.

Aztec user`s guide. Version 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hutchinson, S.A.; Shadid, J.N.; Tuminaro, R.S.

1995-10-01

Aztec is an iterative library that greatly simplifies the parallelization process when solving the linear systems of equations Ax = b where A is a user supplied n x n sparse matrix, b is a user supplied vector of length n and x is a vector of length n to be computed. Aztec is intended as a software tool for users who want to avoid cumbersome parallel programming details but who have large sparse linear systems which require an efficiently utilized parallel processing system. A collection of data transformation tools are provided that allow for easy creation of distributed sparsemore » unstructured matrices for parallel solution. Once the distributed matrix is created, computation can be performed on any of the parallel machines running Aztec: nCUBE 2, IBM SP2 and Intel Paragon, MPI platforms as well as standard serial and vector platforms. Aztec includes a number of Krylov iterative methods such as conjugate gradient (CG), generalized minimum residual (GMRES) and stabilized biconjugate gradient (BICGSTAB) to solve systems of equations. These Krylov methods are used in conjunction with various preconditioners such as polynomial or domain decomposition methods using LU or incomplete LU factorizations within subdomains. Although the matrix A can be general, the package has been designed for matrices arising from the approximation of partial differential equations (PDEs). In particular, the Aztec package is oriented toward systems arising from PDE applications.« less

Large leptonic Dirac CP phase from broken democracy with random perturbations

NASA Astrophysics Data System (ADS)

Ge, Shao-Feng; Kusenko, Alexander; Yanagida, Tsutomu T.

2018-06-01

A large value of the leptonic Dirac CP phase can arise from broken democracy, where the mass matrices are democratic up to small random perturbations. Such perturbations are a natural consequence of broken residual S3 symmetries that dictate the democratic mass matrices at leading order. With random perturbations, the leptonic Dirac CP phase has a higher probability to attain a value around ± π / 2. Comparing with the anarchy model, broken democracy can benefit from residual S3 symmetries, and it can produce much better, realistic predictions for the mass hierarchy, mixing angles, and Dirac CP phase in both quark and lepton sectors. Our approach provides a general framework for a class of models in which a residual symmetry determines the general features at leading order, and where, in the absence of other fundamental principles, the symmetry breaking appears in the form of random perturbations.

Infrared and density functional theory studies of isoprene-water complexes in noble gas matrices

NASA Astrophysics Data System (ADS)

Ito, Fumiyuki

2017-11-01

The interaction of 2-methyl-1,3-butadiene (isoprene) with a H2O molecule in low-temperature noble gas matrices (Ar or Kr) was investigated using infrared absorption spectroscopy. Vibrational peaks arising from 1:1 isoprene-H2O adducts were assigned and compared with the results of quantum chemical calculations. The comparison led to the conclusion that the H2O molecule in the complex preferentially H-bonds to one of the two unsaturated Cdbnd C bonds, and that the binding energy of the complex is comparable to that of the C6H6-H2O complex. The present study suggests that the change in the charge distribution of isoprene due to the formation of a complex with H2O may lead to alteration of the reactivity with respect to the insertion of OH radicals, thereby influencing the formation of aerosols in the atmosphere.

Rotational 3D printing of damage-tolerant composites with programmable mechanics.

PubMed

Raney, Jordan R; Compton, Brett G; Mueller, Jochen; Ober, Thomas J; Shea, Kristina; Lewis, Jennifer A

2018-02-06

Natural composites exhibit exceptional mechanical performance that often arises from complex fiber arrangements within continuous matrices. Inspired by these natural systems, we developed a rotational 3D printing method that enables spatially controlled orientation of short fibers in polymer matrices solely by varying the nozzle rotation speed relative to the printing speed. Using this method, we fabricated carbon fiber-epoxy composites composed of volume elements (voxels) with programmably defined fiber arrangements, including adjacent regions with orthogonally and helically oriented fibers that lead to nonuniform strain and failure as well as those with purely helical fiber orientations akin to natural composites that exhibit enhanced damage tolerance. Our approach broadens the design, microstructural complexity, and performance space for fiber-reinforced composites through site-specific optimization of their fiber orientation, strain, failure, and damage tolerance. Copyright © 2018 the Author(s). Published by PNAS.

A user's guide to the SUDAN computer program for determining the vibration modes of structural systems. Ph.D. Thesis - Case Western Reserve Univ., Jun. 1963

NASA Technical Reports Server (NTRS)

Kvaternik, R. G.; Durling, B. J.

1978-01-01

The use of the SUDAN computer program for analyzing structural systems for their natural modes and frequencies of vibration is described. SUDAN is intended for structures which can be represented as an equivalent system of beam, spring, and rigid-body substructures. User-written constraint equations are used to analytically join the mass and stiffness matrices of the substructures to form the mass and stiffness matrices of the complete structure from which all the frequencies and modes of the system are determined. The SUDAN program can treat the case in which both the mass and stiffness matrices of the coupled system may be singular simultaneously. A general description of the FORTRAN IV program is given, the computer hardware and software specifications are indicated, and the input required by the program is described.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghysels, Pieter; Li, Xiaoye S.; Rouet, Francois -Henry

Here, we present a sparse linear system solver that is based on a multifrontal variant of Gaussian elimination and exploits low-rank approximation of the resulting dense frontal matrices. We use hierarchically semiseparable (HSS) matrices, which have low-rank off-diagonal blocks, to approximate the frontal matrices. For HSS matrix construction, a randomized sampling algorithm is used together with interpolative decompositions. The combination of the randomized compression with a fast ULV HSS factoriz ation leads to a solver with lower computational complexity than the standard multifrontal method for many applications, resulting in speedups up to 7 fold for problems in our test suite.more » The implementation targets many-core systems by using task parallelism with dynamic runtime scheduling. Numerical experiments show performance improvements over state-of-the-art sparse direct solvers. The implementation achieves high performance and good scalability on a range of modern shared memory parallel systems, including the Intel Xeon Phi (MIC). The code is part of a software package called STRUMPACK - STRUctured Matrices PACKage, which also has a distributed memory component for dense rank-structured matrices.« less

The spectra of reducible matrices over complete commutative idempotent semifields and their spectral lattices

NASA Astrophysics Data System (ADS)

José Valverde-Albacete, Francisco; Peláez-Moreno, Carmen

2016-02-01

Previous work has shown a relation between L-valued extensions of Formal Concept Analysis and the spectra of some matrices related to L-valued contexts. To clarify this relation, we investigated elsewhere the nature of the spectra of irreducible matrices over idempotent semifields in the framework of dioids, naturally ordered semirings, that encompass several of those extensions. This initial work already showed many differences with respect to their counterparts over incomplete idempotent semifields, in what concerns the definition of the spectrum and the eigenvectors. Considering special sets of eigenvectors also brought out complete lattices in the picture and we argue that such structure may be more important than standard eigenspace structure for matrices over completed idempotent semifields. In this paper, we complete that investigation in the sense that we consider the spectra of reducible matrices over completed idempotent semifields and dioids, giving, as a result, a constructive solution to the all-eigenvectors problem in this setting. This solution shows that the relation of complete lattices to eigenspaces is even tighter than suspected.

Multimodal approach to characterization of hydrophilic matrices manufactured by wet and dry granulation or direct compression methods.

PubMed

Kulinowski, Piotr; Woyna-Orlewicz, Krzysztof; Obrał, Jadwiga; Rappen, Gerd-Martin; Haznar-Garbacz, Dorota; Węglarz, Władysław P; Jachowicz, Renata; Wyszogrodzka, Gabriela; Klaja, Jolanta; Dorożyński, Przemysław P

2016-02-29

The purpose of the research was to investigate the effect of the manufacturing process of the controlled release hydrophilic matrix tablets on their hydration behavior, internal structure and drug release. Direct compression (DC) quetiapine hemifumarate matrices and matrices made of powders obtained by dry granulation (DG) and high shear wet granulation (HS) were prepared. They had the same quantitative composition and they were evaluated using X-ray microtomography, magnetic resonance imaging and biorelevant stress test dissolution. Principal results concerned matrices after 2 h of hydration: (i) layered structure of the DC and DG hydrated tablets with magnetic resonance image intensity decreasing towards the center of the matrix was observed, while in HS matrices layer of lower intensity appeared in the middle of hydrated part; (ii) the DC and DG tablets retained their core and consequently exhibited higher resistance to the physiological stresses during simulation of small intestinal passage than HS formulation. Comparing to DC, HS granulation changed properties of the matrix in terms of hydration pattern and resistance to stress in biorelevant dissolution apparatus. Dry granulation did not change these properties-similar hydration pattern and dissolution in biorelevant conditions were observed for DC and DG matrices. Copyright © 2015 Elsevier B.V. All rights reserved.

Estimating and Identifying Unspecified Correlation Structure for Longitudinal Data

PubMed Central

Hu, Jianhua; Wang, Peng; Qu, Annie

2014-01-01

Identifying correlation structure is important to achieving estimation efficiency in analyzing longitudinal data, and is also crucial for drawing valid statistical inference for large size clustered data. In this paper, we propose a nonparametric method to estimate the correlation structure, which is applicable for discrete longitudinal data. We utilize eigenvector-based basis matrices to approximate the inverse of the empirical correlation matrix and determine the number of basis matrices via model selection. A penalized objective function based on the difference between the empirical and model approximation of the correlation matrices is adopted to select an informative structure for the correlation matrix. The eigenvector representation of the correlation estimation is capable of reducing the risk of model misspecification, and also provides useful information on the specific within-cluster correlation pattern of the data. We show that the proposed method possesses the oracle property and selects the true correlation structure consistently. The proposed method is illustrated through simulations and two data examples on air pollution and sonar signal studies. PMID:26361433

Complex eigenvalue analysis of rotating structures

NASA Technical Reports Server (NTRS)

Patel, J. S.; Seltzer, S. M.

1972-01-01

A FORTRAN subroutine to NASTRAN which constructs coriolis and centripetal acceleration matrices, and a centrifugal load vector due to spin about a selected point or about the mass center of the structure is discussed. The rigid translational degrees of freedom can be removed by using a transformation matrix T and its explicitly given inverse. These matrices are generated in the subroutine and their explicit expressions are given.

Performance analysis of distributed symmetric sparse matrix vector multiplication algorithm for multi-core architectures

DOE PAGES

Oryspayev, Dossay; Aktulga, Hasan Metin; Sosonkina, Masha; ...

2015-07-14

In this article, sparse matrix vector multiply (SpMVM) is an important kernel that frequently arises in high performance computing applications. Due to its low arithmetic intensity, several approaches have been proposed in literature to improve its scalability and efficiency in large scale computations. In this paper, our target systems are high end multi-core architectures and we use messaging passing interface + open multiprocessing hybrid programming model for parallelism. We analyze the performance of recently proposed implementation of the distributed symmetric SpMVM, originally developed for large sparse symmetric matrices arising in ab initio nuclear structure calculations. We also study important featuresmore » of this implementation and compare with previously reported implementations that do not exploit underlying symmetry. Our SpMVM implementations leverage the hybrid paradigm to efficiently overlap expensive communications with computations. Our main comparison criterion is the "CPU core hours" metric, which is the main measure of resource usage on supercomputers. We analyze the effects of topology-aware mapping heuristic using simplified network load model. Furthermore, we have tested the different SpMVM implementations on two large clusters with 3D Torus and Dragonfly topology. Our results show that the distributed SpMVM implementation that exploits matrix symmetry and hides communication yields the best value for the "CPU core hours" metric and significantly reduces data movement overheads.« less

Cell-adhesive RGD peptide-displaying M13 bacteriophage/PLGA nanofiber matrices for growth of fibroblasts.

PubMed

Shin, Yong Cheol; Lee, Jong Ho; Jin, Linhua; Kim, Min Jeong; Oh, Jin-Woo; Kim, Tai Wan; Han, Dong-Wook

2014-01-01

M13 bacteriophages can be readily fabricated as nanofibers due to non-toxic bacterial virus with a nanofiber-like shape. In the present study, we prepared hybrid nanofiber matrices composed of poly(lactic-co-glycolic acid, PLGA) and M13 bacteriophages which were genetically modified to display the RGD peptide on their surface (RGD-M13 phage). The surface morphology and chemical composition of hybrid nanofiber matrices were characterized by scanning electron microscopy (SEM) and Raman spectroscopy, respectively. Immunofluorescence staining was conducted to investigate the existence of M13 bacteriophages in RGD-M13 phage/PLGA hybrid nanofibers. In addition, the attachment and proliferation of three different types of fibroblasts on RGD-M13 phage/PLGA nanofiber matrices were evaluated to explore how fibroblasts interact with these matrices. SEM images showed that RGD-M13 phage/PLGA hybrid matrices had the non-woven porous structure, quite similar to that of natural extracellular matrices, having an average fiber diameter of about 190 nm. Immunofluorescence images and Raman spectra revealed that RGD-M13 phages were homogeneously distributed in entire matrices. Moreover, the attachment and proliferation of fibroblasts cultured on RGD-M13 phage/PLGA matrices were significantly enhanced due to enriched RGD moieties on hybrid matrices. These results suggest that RGD-M13 phage/PLGA matrices can be efficiently used as biomimetic scaffolds for tissue engineering applications.

Prediction of Ras-effector interactions using position energy matrices.

PubMed

Kiel, Christina; Serrano, Luis

2007-09-01

One of the more challenging problems in biology is to determine the cellular protein interaction network. Progress has been made to predict protein-protein interactions based on structural information, assuming that structural similar proteins interact in a similar way. In a previous publication, we have determined a genome-wide Ras-effector interaction network based on homology models, with a high accuracy of predicting binding and non-binding domains. However, for a prediction on a genome-wide scale, homology modelling is a time-consuming process. Therefore, we here successfully developed a faster method using position energy matrices, where based on different Ras-effector X-ray template structures, all amino acids in the effector binding domain are sequentially mutated to all other amino acid residues and the effect on binding energy is calculated. Those pre-calculated matrices can then be used to score for binding any Ras or effector sequences. Based on position energy matrices, the sequences of putative Ras-binding domains can be scanned quickly to calculate an energy sum value. By calibrating energy sum values using quantitative experimental binding data, thresholds can be defined and thus non-binding domains can be excluded quickly. Sequences which have energy sum values above this threshold are considered to be potential binding domains, and could be further analysed using homology modelling. This prediction method could be applied to other protein families sharing conserved interaction types, in order to determine in a fast way large scale cellular protein interaction networks. Thus, it could have an important impact on future in silico structural genomics approaches, in particular with regard to increasing structural proteomics efforts, aiming to determine all possible domain folds and interaction types. All matrices are deposited in the ADAN database (http://adan-embl.ibmc.umh.es/). Supplementary data are available at Bioinformatics online.

Parallel iterative methods for sparse linear and nonlinear equations

NASA Technical Reports Server (NTRS)

Saad, Youcef

1989-01-01

As three-dimensional models are gaining importance, iterative methods will become almost mandatory. Among these, preconditioned Krylov subspace methods have been viewed as the most efficient and reliable, when solving linear as well as nonlinear systems of equations. There has been several different approaches taken to adapt iterative methods for supercomputers. Some of these approaches are discussed and the methods that deal more specifically with general unstructured sparse matrices, such as those arising from finite element methods, are emphasized.

On Asymptotic Properties of a Number Theoretic Function Arising out of a Spin Chain Modelin Statistical Mechanics

NASA Astrophysics Data System (ADS)

Kallies, J.; Özlük, A.; Peter, M.; Snyder, C.

Let Let N be a positive integer and define Φ(N) as the number of matrices, C, which are products of A and B, where both A and B must occur, such that the trace, Tr(C)=N. It has been conjectured that see [10]. In this note we consider the summatory function and show that

Fate of Thallium(I) in Reverse Osmosis and Chlorinated Water Matrices

DTIC Science & Technology

2014-02-01

pKa of 13 for aquated Tl + , and that the precise nature of the hydrated ion in solution is not well established. 7 No further reactions of the Tl...of Tl + may be viewed as arising from a physical phenomenon. Because of the nature of the vial containing the thallium salt solution, it may be that...loss of thallium concentration was a result of adsorption of Tl + on the vial walls. Plastic vials are known to have significant adsorption

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.

Nonequilibrium thermo-chemical calculations using a diagonal implicit scheme

NASA Technical Reports Server (NTRS)

Imlay, Scott T.; Roberts, Donald W.; Soetrisno, Moeljo; Eberhardt, Scott

1991-01-01

A recently developed computer program for hypersonic vehicle flow analysis is described. The program uses a diagonal implicit algorithm to solve the equations of viscous flow for a gas in thermochemical nonequilibrium. The diagonal scheme eliminates the expense of inverting large block matrices that arise when species conservation equations are introduced. The program uses multiple zones of grids patched together and includes radiation wall and rarefied gas boundary conditions. Solutions are presented for hypersonic flows of air and hydrogen air mixtures.

Fine structure of spectral properties for random correlation matrices: An application to financial markets

NASA Astrophysics Data System (ADS)

Livan, Giacomo; Alfarano, Simone; Scalas, Enrico

2011-07-01

We study some properties of eigenvalue spectra of financial correlation matrices. In particular, we investigate the nature of the large eigenvalue bulks which are observed empirically, and which have often been regarded as a consequence of the supposedly large amount of noise contained in financial data. We challenge this common knowledge by acting on the empirical correlation matrices of two data sets with a filtering procedure which highlights some of the cluster structure they contain, and we analyze the consequences of such filtering on eigenvalue spectra. We show that empirically observed eigenvalue bulks emerge as superpositions of smaller structures, which in turn emerge as a consequence of cross correlations between stocks. We interpret and corroborate these findings in terms of factor models, and we compare empirical spectra to those predicted by random matrix theory for such models.

Structural phase transitions in isotropic magnetic elastomers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meilikhov, E. Z., E-mail: meilikhov@yandex.ru; Farzetdinova, R. M.

Magnetic elastomers represent a new type of materials that are “soft” matrices with “hard” magnetic granules embedded in them. The elastic forces of the matrix and the magnetic forces acting between granules are comparable in magnitude even under small deformations. As a result, these materials acquire a number of new properties; in particular, their mechanical and/or magnetic characteristics can depend strongly on the polymer matrix filling with magnetic particles and can change under the action of an external magnetic field, pressure, and temperature. To describe the properties of elastomers, we use a model in which the interaction of magnetic granulesmore » randomly arranged in space with one another is described in the dipole approximation by the distribution function of dipole fields, while their interaction with the matrix is described phenomenologically. A multitude of deformation, magnetic-field, and temperature effects that are described in this paper and are quite accessible to experimental observation arise within this model.« less

Multitasking the Davidson algorithm for the large, sparse eigenvalue problem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Umar, V.M.; Fischer, C.F.

1989-01-01

The authors report how the Davidson algorithm, developed for handling the eigenvalue problem for large and sparse matrices arising in quantum chemistry, was modified for use in atomic structure calculations. To date these calculations have used traditional eigenvalue methods, which limit the range of feasible calculations because of their excessive memory requirements and unsatisfactory performance attributed to time-consuming and costly processing of zero valued elements. The replacement of a traditional matrix eigenvalue method by the Davidson algorithm reduced these limitations. Significant speedup was found, which varied with the size of the underlying problem and its sparsity. Furthermore, the range ofmore » matrix sizes that can be manipulated efficiently was expended by more than one order or magnitude. On the CRAY X-MP the code was vectorized and the importance of gather/scatter analyzed. A parallelized version of the algorithm obtained an additional 35% reduction in execution time. Speedup due to vectorization and concurrency was also measured on the Alliant FX/8.« less

The detection of flaws in austenitic welds using the decomposition of the time-reversal operator

NASA Astrophysics Data System (ADS)

Cunningham, Laura J.; Mulholland, Anthony J.; Tant, Katherine M. M.; Gachagan, Anthony; Harvey, Gerry; Bird, Colin

2016-04-01

The non-destructive testing of austenitic welds using ultrasound plays an important role in the assessment of the structural integrity of safety critical structures. The internal microstructure of these welds is highly scattering and can lead to the obscuration of defects when investigated by traditional imaging algorithms. This paper proposes an alternative objective method for the detection of flaws embedded in austenitic welds based on the singular value decomposition of the time-frequency domain response matrices. The distribution of the singular values is examined in the cases where a flaw exists and where there is no flaw present. A lower threshold on the singular values, specific to austenitic welds, is derived which, when exceeded, indicates the presence of a flaw. The detection criterion is successfully implemented on both synthetic and experimental data. The datasets arising from welds containing a flaw are further interrogated using the decomposition of the time-reversal operator (DORT) method and the total focusing method (TFM), and it is shown that images constructed via the DORT algorithm typically exhibit a higher signal-to-noise ratio than those constructed by the TFM algorithm.

The detection of flaws in austenitic welds using the decomposition of the time-reversal operator

PubMed Central

Cunningham, Laura J.; Mulholland, Anthony J.; Gachagan, Anthony; Harvey, Gerry; Bird, Colin

2016-01-01

The non-destructive testing of austenitic welds using ultrasound plays an important role in the assessment of the structural integrity of safety critical structures. The internal microstructure of these welds is highly scattering and can lead to the obscuration of defects when investigated by traditional imaging algorithms. This paper proposes an alternative objective method for the detection of flaws embedded in austenitic welds based on the singular value decomposition of the time-frequency domain response matrices. The distribution of the singular values is examined in the cases where a flaw exists and where there is no flaw present. A lower threshold on the singular values, specific to austenitic welds, is derived which, when exceeded, indicates the presence of a flaw. The detection criterion is successfully implemented on both synthetic and experimental data. The datasets arising from welds containing a flaw are further interrogated using the decomposition of the time-reversal operator (DORT) method and the total focusing method (TFM), and it is shown that images constructed via the DORT algorithm typically exhibit a higher signal-to-noise ratio than those constructed by the TFM algorithm. PMID:27274683

Application’s Method of Quadratic Programming for Optimization of Portfolio Selection

NASA Astrophysics Data System (ADS)

Kawamoto, Shigeru; Takamoto, Masanori; Kobayashi, Yasuhiro

Investors or fund-managers face with optimization of portfolio selection, which means that determine the kind and the quantity of investment among several brands. We have developed a method to obtain optimal stock’s portfolio more rapidly from twice to three times than conventional method with efficient universal optimization. The method is characterized by quadratic matrix of utility function and constrained matrices divided into several sub-matrices by focusing on structure of these matrices.

Correlations of multiscale entropy in the FX market

NASA Astrophysics Data System (ADS)

Stosic, Darko; Stosic, Dusan; Ludermir, Teresa; Stosic, Tatijana

2016-09-01

The regularity of price fluctuations in exchange rates plays a crucial role in FX market dynamics. Distinct variations in regularity arise from economic, social and political events, such as interday trading and financial crisis. This paper applies a multiscale time-dependent entropy method on thirty-three exchange rates to analyze price fluctuations in the FX. Correlation matrices of entropy values, termed entropic correlations, are in turn used to describe global behavior of the market. Empirical results suggest a weakly correlated market with pronounced collective behavior at bi-weekly trends. Correlations arise from cycles of low and high regularity in long-term trends. Eigenvalues of the correlation matrix also indicate a dominant European market, followed by shifting American, Asian, African, and Pacific influences. As a result, we find that entropy is a powerful tool for extracting important information from the FX market.

Pharmacological Interventions for the MATRICS Cognitive Domains in Schizophrenia: What’s the Evidence?

PubMed Central

Vingerhoets, Wilhelmina A. M.; Bloemen, Oswald J. N.; Bakker, Geor; van Amelsvoort, Therese A. M. J.

2013-01-01

Schizophrenia is a disabling, chronic psychiatric disorder with a prevalence rate of 0.5–1% in the general population. Symptoms include positive (e.g., delusions, hallucinations), negative (e.g., blunted affect, social withdrawal), as well as cognitive symptoms (e.g., memory and attention problems). Although 75–85% of patients with schizophrenia report cognitive impairments, the underlying neuropharmacological mechanisms are not well understood and currently no effective treatment is available for these impairments. This has led to the Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) initiative, which established seven cognitive domains that are fundamentally impaired in schizophrenia. These domains include verbal learning and memory, visual learning and memory, working memory, attention and vigilance, processing speed, reasoning and problem solving, and social cognition. Recently, a growing number of studies have been conducted trying to identify the underlying neuropharmacological mechanisms of cognitive impairments in schizophrenia patients. Specific cognitive impairments seem to arise from different underlying neuropharmacological mechanisms. However, most review articles describe cognition in general and an overview of the mechanisms involved in these seven separate cognitive domains is currently lacking. Therefore, we reviewed the underlying neuropharmacological mechanisms focusing on the domains as established by the MATRICS initiative which are considered most crucial in schizophrenia. PMID:24363646

Structural analysis and design of multivariable control systems: An algebraic approach

NASA Technical Reports Server (NTRS)

Tsay, Yih Tsong; Shieh, Leang-San; Barnett, Stephen

1988-01-01

The application of algebraic system theory to the design of controllers for multivariable (MV) systems is explored analytically using an approach based on state-space representations and matrix-fraction descriptions. Chapters are devoted to characteristic lambda matrices and canonical descriptions of MIMO systems; spectral analysis, divisors, and spectral factors of nonsingular lambda matrices; feedback control of MV systems; and structural decomposition theories and their application to MV control systems.

Partitioning Rectangular and Structurally Nonsymmetric Sparse Matrices for Parallel Processing

DOE Office of Scientific and Technical Information (OSTI.GOV)

B. Hendrickson; T.G. Kolda

1998-09-01

A common operation in scientific computing is the multiplication of a sparse, rectangular or structurally nonsymmetric matrix and a vector. In many applications the matrix- transpose-vector product is also required. This paper addresses the efficient parallelization of these operations. We show that the problem can be expressed in terms of partitioning bipartite graphs. We then introduce several algorithms for this partitioning problem and compare their performance on a set of test matrices.

Excipient foods: designing food matrices that improve the oral bioavailability of pharmaceuticals and nutraceuticals.

PubMed

McClements, David Julian; Xiao, Hang

2014-07-25

The oral bioavailability of many lipophilic bioactive agents (pharmaceuticals and nutraceuticals) is limited due to various physicochemical and physiological processes: poor release from food or drug matrices; low solubility in gastrointestinal fluids; metabolism or chemical transformation within the gastrointestinal tract; low epithelium cell permeability. The bioavailability of these agents can be improved by specifically designing food matrices that control their release, solubilization, transport, metabolism, and absorption within the gastrointestinal tract. This article discusses the impact of food composition and structure on oral bioavailability, and how this knowledge can be used to design excipient foods for improving the oral bioavailability of lipophilic bioactives. Excipient foods contain ingredients or structures that may have no bioactivity themselves, but that are able to promote the bioactivity of co-ingested bioactives. These bioactives may be lipophilic drugs in pharmaceutical preparations (such as capsules, pills, or syrups) or nutraceuticals present within food matrices (such as natural or processed foods and beverages).

The algebraic theory of latent projectors in lambda matrices

NASA Technical Reports Server (NTRS)

Denman, E. D.; Leyva-Ramos, J.; Jeon, G. J.

1981-01-01

Multivariable systems such as a finite-element model of vibrating structures, control systems, and large-scale systems are often formulated in terms of differential equations which give rise to lambda matrices. The present investigation is concerned with the formulation of the algebraic theory of lambda matrices and the relationship of latent roots, latent vectors, and latent projectors to the eigenvalues, eigenvectors, and eigenprojectors of the companion form. The chain rule for latent projectors and eigenprojectors for the repeated latent root or eigenvalues is given.

Comparative analysis of different weight matrices in subspace system identification for structural health monitoring

NASA Astrophysics Data System (ADS)

Shokravi, H.; Bakhary, NH

2017-11-01

Subspace System Identification (SSI) is considered as one of the most reliable tools for identification of system parameters. Performance of a SSI scheme is considerably affected by the structure of the associated identification algorithm. Weight matrix is a variable in SSI that is used to reduce the dimensionality of the state-space equation. Generally one of the weight matrices of Principle Component (PC), Unweighted Principle Component (UPC) and Canonical Variate Analysis (CVA) are used in the structure of a SSI algorithm. An increasing number of studies in the field of structural health monitoring are using SSI for damage identification. However, studies that evaluate the performance of the weight matrices particularly in association with accuracy, noise resistance, and time complexity properties are very limited. In this study, the accuracy, noise-robustness, and time-efficiency of the weight matrices are compared using different qualitative and quantitative metrics. Three evaluation metrics of pole analysis, fit values and elapsed time are used in the assessment process. A numerical model of a mass-spring-dashpot and operational data is used in this research paper. It is observed that the principal components obtained using PC algorithms are more robust against noise uncertainty and give more stable results for the pole distribution. Furthermore, higher estimation accuracy is achieved using UPC algorithm. CVA had the worst performance for pole analysis and time efficiency analysis. The superior performance of the UPC algorithm in the elapsed time is attributed to using unit weight matrices. The obtained results demonstrated that the process of reducing dimensionality in CVA and PC has not enhanced the time efficiency but yield an improved modal identification in PC.

Isolated glyoxylic acid-water 1:1 complexes in low temperature argon matrices.

PubMed

Lundell, Jan; Olbert-Majkut, Adriana

2015-02-05

The 1:1 hydrogen bonded complexes between glyoxylic acid (GA) and water are studied in low temperature argon matrices. Four different complex structures were found in deposited matrices. The lowest energy conformer (T1) of GA was found to form complex, where the water molecule was attached to the opposite side of the intramolecular hydrogen bond in the molecule (T1B). Interestingly, this complex was estimated to be+8.0 kJ mol(-1) higher in energy than the most stable structure (T1A), where the water is inserted into the internal hydrogen bond, and also found in solid argon but in smaller abundance. For the second-lowest energy conformer of GA (T2), the two lowest-energy complex structures were identified, with the most stable complex structure (T2A) also being the most abundant in the matrices. The difference between experiment and computational energetic order of the two complex structures of the same GA conformer is explained by contributions of deformation energy upon complexation and the effect of the environment. The computed BSSE-corrected interaction energies are for the two most stable complexes of the two GA conformers for T1A and T2A -42.11 and -45.03 kJ mol(-1), respectively, at the CCSD(T)/aug-cc-pVTZ//B3LYP/aug-cc-pVTZ level of theory. Copyright © 2013 Elsevier B.V. All rights reserved.

The food matrix affects the anthocyanin profile of fortified egg and dairy matrices during processing and in vitro digestion.

PubMed

Pineda-Vadillo, Carlos; Nau, Françoise; Guerin-Dubiard, Catherin; Jardin, Julien; Lechevalier, Valérie; Sanz-Buenhombre, Marisa; Guadarrama, Alberto; Tóth, Tamás; Csavajda, Éva; Hingyi, Hajnalka; Karakaya, Sibel; Sibakov, Juhani; Capozzi, Francesco; Bordoni, Alessandra; Dupont, Didier

2017-01-01

The aim of the present study was to understand to what extent the inclusion of anthocyanins into dairy and egg matrices could affect their stability after processing and their release and solubility during digestion. For this purpose, individual and total anthocyanin content of four different enriched matrices, namely custard dessert, milkshake, pancake and omelettete, was determined after their manufacturing and during in vitro digestion. Results showed that anthocyanin recovery after processing largely varied among matrices, mainly due to the treatments applied and the interactions developed with other food components. In terms of digestion, the present study showed that the inclusion of anthocyanins into food matrices could be an effective way to protect them against intestinal degradation, and also the incorporation of anthocyanins into matrices with different compositions and structures could represent an interesting and effective method to control the delivery of anthocyanins within the different compartments of the digestive tract. Copyright © 2016 Elsevier Ltd. All rights reserved.

Two-dimensional integrating matrices on rectangular grids. [solving differential equations associated with rotating structures

NASA Technical Reports Server (NTRS)

Lakin, W. D.

1981-01-01

The use of integrating matrices in solving differential equations associated with rotating beam configurations is examined. In vibration problems, by expressing the equations of motion of the beam in matrix notation, utilizing the integrating matrix as an operator, and applying the boundary conditions, the spatial dependence is removed from the governing partial differential equations and the resulting ordinary differential equations can be cast into standard eigenvalue form. Integrating matrices are derived based on two dimensional rectangular grids with arbitrary grid spacings allowed in one direction. The derivation of higher dimensional integrating matrices is the initial step in the generalization of the integrating matrix methodology to vibration and stability problems involving plates and shells.

Nano-Fiber Reinforced Enhancements in Composite Polymer Matrices

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

2009-01-01

Nano-fibers are used to reinforce polymer matrices to enhance the matrix dependent properties that are subsequently used in conventional structural composites. A quasi isotropic configuration is used in arranging like nano-fibers through the thickness to ascertain equiaxial enhanced matrix behavior. The nano-fiber volume ratios are used to obtain the enhanced matrix strength properties for 0.01,0.03, and 0.05 nano-fiber volume rates. These enhanced nano-fiber matrices are used with conventional fiber volume ratios of 0.3 and 0.5 to obtain the composite properties. Results show that nano-fiber enhanced matrices of higher than 0.3 nano-fiber volume ratio are degrading the composite properties.

Discrete Kalman filtering equations of second-order form for control-structure interaction simulations

NASA Technical Reports Server (NTRS)

Park, K. C.; Alvin, K. F.; Belvin, W. Keith

1991-01-01

A second-order form of discrete Kalman filtering equations is proposed as a candidate state estimator for efficient simulations of control-structure interactions in coupled physical coordinate configurations as opposed to decoupled modal coordinates. The resulting matrix equation of the present state estimator consists of the same symmetric, sparse N x N coupled matrices of the governing structural dynamics equations as opposed to unsymmetric 2N x 2N state space-based estimators. Thus, in addition to substantial computational efficiency improvement, the present estimator can be applied to control-structure design optimization for which the physical coordinates associated with the mass, damping and stiffness matrices of the structure are needed instead of modal coordinates.

Chemical Reactions Triggered Using Electrons Photodetached from "Clean" Distributions of Anions Deposited in Cryogenic Matrices via Counterion Codeposition.

PubMed

Ludwig, Ryan M; Moore, David T

2014-09-04

Application of matrix isolation spectroscopy to ionic species is typically complicated by the presence of neutral contaminants during matrix deposition. Herein we demonstrate that simultaneous deposition of balanced currents of counterions with mass-selected ions of interest generates "clean" distributions of matrix-isolated metal carbonyl anions, where the only bands appearing in the CO-stretching region of the vibrational spectrum arise from ions. (Neutrals are initially absent.) Photodetachment by mild irradiation with visible light leads to complete conversion of the anions into their corresponding neutral species. The photodetached electrons, in turn, initiate covalent chemistry, inducing C-C bond formation following electron-capture by CO van der Waals dimers to produce trans-OCCO(-). The initial clean distribution of ions enables clear connections to be drawn between the spectral changes occurring at each experimental step, thus demonstrating the potential of the counterion codeposition technique to facilitate detailed studies of chemistry involving ions and electron transfer in cryogenic matrices.

A Partitioning Algorithm for Block-Diagonal Matrices With Overlap

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guy Antoine Atenekeng Kahou; Laura Grigori; Masha Sosonkina

2008-02-02

We present a graph partitioning algorithm that aims at partitioning a sparse matrix into a block-diagonal form, such that any two consecutive blocks overlap. We denote this form of the matrix as the overlapped block-diagonal matrix. The partitioned matrix is suitable for applying the explicit formulation of Multiplicative Schwarz preconditioner (EFMS) described in [3]. The graph partitioning algorithm partitions the graph of the input matrix into K partitions, such that every partition {Omega}{sub i} has at most two neighbors {Omega}{sub i-1} and {Omega}{sub i+1}. First, an ordering algorithm, such as the reverse Cuthill-McKee algorithm, that reduces the matrix profile ismore » performed. An initial overlapped block-diagonal partition is obtained from the profile of the matrix. An iterative strategy is then used to further refine the partitioning by allowing nodes to be transferred between neighboring partitions. Experiments are performed on matrices arising from real-world applications to show the feasibility and usefulness of this approach.« less

Multivariate statistics of the Jacobian matrices in tensor based morphometry and their application to HIV/AIDS.

PubMed

Lepore, Natasha; Brun, Caroline A; Chiang, Ming-Chang; Chou, Yi-Yu; Dutton, Rebecca A; Hayashi, Kiralee M; Lopez, Oscar L; Aizenstein, Howard J; Toga, Arthur W; Becker, James T; Thompson, Paul M

2006-01-01

Tensor-based morphometry (TBM) is widely used in computational anatomy as a means to understand shape variation between structural brain images. A 3D nonlinear registration technique is typically used to align all brain images to a common neuroanatomical template, and the deformation fields are analyzed statistically to identify group differences in anatomy. However, the differences are usually computed solely from the determinants of the Jacobian matrices that are associated with the deformation fields computed by the registration procedure. Thus, much of the information contained within those matrices gets thrown out in the process. Only the magnitude of the expansions or contractions is examined, while the anisotropy and directional components of the changes are ignored. Here we remedy this problem by computing multivariate shape change statistics using the strain matrices. As the latter do not form a vector space, means and covariances are computed on the manifold of positive-definite matrices to which they belong. We study the brain morphology of 26 HIV/AIDS patients and 14 matched healthy control subjects using our method. The images are registered using a high-dimensional 3D fluid registration algorithm, which optimizes the Jensen-Rényi divergence, an information-theoretic measure of image correspondence. The anisotropy of the deformation is then computed. We apply a manifold version of Hotelling's T2 test to the strain matrices. Our results complement those found from the determinants of the Jacobians alone and provide greater power in detecting group differences in brain structure.

Structure and stability of genetic variance-covariance matrices: A Bayesian sparse factor analysis of transcriptional variation in the three-spined stickleback.

PubMed

Siren, J; Ovaskainen, O; Merilä, J

2017-10-01

The genetic variance-covariance matrix (G) is a quantity of central importance in evolutionary biology due to its influence on the rate and direction of multivariate evolution. However, the predictive power of empirically estimated G-matrices is limited for two reasons. First, phenotypes are high-dimensional, whereas traditional statistical methods are tuned to estimate and analyse low-dimensional matrices. Second, the stability of G to environmental effects and over time remains poorly understood. Using Bayesian sparse factor analysis (BSFG) designed to estimate high-dimensional G-matrices, we analysed levels variation and covariation in 10,527 expressed genes in a large (n = 563) half-sib breeding design of three-spined sticklebacks subject to two temperature treatments. We found significant differences in the structure of G between the treatments: heritabilities and evolvabilities were higher in the warm than in the low-temperature treatment, suggesting more and faster opportunity to evolve in warm (stressful) conditions. Furthermore, comparison of G and its phenotypic equivalent P revealed the latter is a poor substitute of the former. Most strikingly, the results suggest that the expected impact of G on evolvability-as well as the similarity among G-matrices-may depend strongly on the number of traits included into analyses. In our results, the inclusion of only few traits in the analyses leads to underestimation in the differences between the G-matrices and their predicted impacts on evolution. While the results highlight the challenges involved in estimating G, they also illustrate that by enabling the estimation of large G-matrices, the BSFG method can improve predicted evolutionary responses to selection. © 2017 John Wiley & Sons Ltd.

FPGA architecture and implementation of sparse matrix vector multiplication for the finite element method

NASA Astrophysics Data System (ADS)

Elkurdi, Yousef; Fernández, David; Souleimanov, Evgueni; Giannacopoulos, Dennis; Gross, Warren J.

2008-04-01

The Finite Element Method (FEM) is a computationally intensive scientific and engineering analysis tool that has diverse applications ranging from structural engineering to electromagnetic simulation. The trends in floating-point performance are moving in favor of Field-Programmable Gate Arrays (FPGAs), hence increasing interest has grown in the scientific community to exploit this technology. We present an architecture and implementation of an FPGA-based sparse matrix-vector multiplier (SMVM) for use in the iterative solution of large, sparse systems of equations arising from FEM applications. FEM matrices display specific sparsity patterns that can be exploited to improve the efficiency of hardware designs. Our architecture exploits FEM matrix sparsity structure to achieve a balance between performance and hardware resource requirements by relying on external SDRAM for data storage while utilizing the FPGAs computational resources in a stream-through systolic approach. The architecture is based on a pipelined linear array of processing elements (PEs) coupled with a hardware-oriented matrix striping algorithm and a partitioning scheme which enables it to process arbitrarily big matrices without changing the number of PEs in the architecture. Therefore, this architecture is only limited by the amount of external RAM available to the FPGA. The implemented SMVM-pipeline prototype contains 8 PEs and is clocked at 110 MHz obtaining a peak performance of 1.76 GFLOPS. For 8 GB/s of memory bandwidth typical of recent FPGA systems, this architecture can achieve 1.5 GFLOPS sustained performance. Using multiple instances of the pipeline, linear scaling of the peak and sustained performance can be achieved. Our stream-through architecture provides the added advantage of enabling an iterative implementation of the SMVM computation required by iterative solution techniques such as the conjugate gradient method, avoiding initialization time due to data loading and setup inside the FPGA internal memory.

Discrete integration of continuous Kalman filtering equations for time invariant second-order structural systems

NASA Technical Reports Server (NTRS)

Park, K. C.; Belvin, W. Keith

1990-01-01

A general form for the first-order representation of the continuous second-order linear structural-dynamics equations is introduced to derive a corresponding form of first-order continuous Kalman filtering equations. Time integration of the resulting equations is carried out via a set of linear multistep integration formulas. It is shown that a judicious combined selection of computational paths and the undetermined matrices introduced in the general form of the first-order linear structural systems leads to a class of second-order discrete Kalman filtering equations involving only symmetric sparse N x N solution matrices.

Compound matrices

NASA Astrophysics Data System (ADS)

Kravvaritis, Christos; Mitrouli, Marilena

2009-02-01

This paper studies the possibility to calculate efficiently compounds of real matrices which have a special form or structure. The usefulness of such an effort lies in the fact that the computation of compound matrices, which is generally noneffective due to its high complexity, is encountered in several applications. A new approach for computing the Singular Value Decompositions (SVD's) of the compounds of a matrix is proposed by establishing the equality (up to a permutation) between the compounds of the SVD of a matrix and the SVD's of the compounds of the matrix. The superiority of the new idea over the standard method is demonstrated. Similar approaches with some limitations can be adopted for other matrix factorizations, too. Furthermore, formulas for the n - 1 compounds of Hadamard matrices are derived, which dodge the strenuous computations of the respective numerous large determinants. Finally, a combinatorial counting technique for finding the compounds of diagonal matrices is illustrated.

Analysing generator matrices G of similar state but varying minimum determinants

NASA Astrophysics Data System (ADS)

Harun, H.; Razali, M. F.; Rahman, N. A. Abdul

2016-10-01

Since Tarokh discovered Space-Time Trellis Code (STTC) in 1998, a considerable effort has been done to improve the performance of the original STTC. One way of achieving enhancement is by focusing on the generator matrix G, which represents the encoder structure for STTC. Until now, researchers have only concentrated on STTCs of different states in analyzing the performance of generator matrix G. No effort has been made on different generator matrices G of similar state. The reason being, it is difficult to produce a wide variety of generator matrices G with diverse minimum determinants. In this paper a number of generator matrices G with minimum determinant of four (4), eight (8) and sixteen (16) of the same state (i.e., 4-PSK) have been successfully produced. The performance of different generator matrices G in term of their bit error rate and signal-to-noise ratio for a Rayleigh fading environment are compared and evaluated. It is found from the MATLAB simulation that at low SNR (<8), the BER of generator matrices G with smaller minimum determinant is comparatively lower than those of higher minimum determinant. However, at high SNR (>14) there is no significant difference between the BER of these generator matrices G.

Sparse Matrices in MATLAB: Design and Implementation

NASA Technical Reports Server (NTRS)

Gilbert, John R.; Moler, Cleve; Schreiber, Robert

1992-01-01

The matrix computation language and environment MATLAB is extended to include sparse matrix storage and operations. The only change to the outward appearance of the MATLAB language is a pair of commands to create full or sparse matrices. Nearly all the operations of MATLAB now apply equally to full or sparse matrices, without any explicit action by the user. The sparse data structure represents a matrix in space proportional to the number of nonzero entries, and most of the operations compute sparse results in time proportional to the number of arithmetic operations on nonzeros.

SPARSKIT: A basic tool kit for sparse matrix computations

NASA Technical Reports Server (NTRS)

Saad, Youcef

1990-01-01

Presented here are the main features of a tool package for manipulating and working with sparse matrices. One of the goals of the package is to provide basic tools to facilitate the exchange of software and data between researchers in sparse matrix computations. The starting point is the Harwell/Boeing collection of matrices for which the authors provide a number of tools. Among other things, the package provides programs for converting data structures, printing simple statistics on a matrix, plotting a matrix profile, and performing linear algebra operations with sparse matrices.

Dynamics of Quantum Causal Structures

NASA Astrophysics Data System (ADS)

Castro-Ruiz, Esteban; Giacomini, Flaminia; Brukner, Časlav

2018-01-01

It was recently suggested that causal structures are both dynamical, because of general relativity, and indefinite, because of quantum theory. The process matrix formalism furnishes a framework for quantum mechanics on indefinite causal structures, where the order between operations of local laboratories is not definite (e.g., one cannot say whether operation in laboratory A occurs before or after operation in laboratory B ). Here, we develop a framework for "dynamics of causal structures," i.e., for transformations of process matrices into process matrices. We show that, under continuous and reversible transformations, the causal order between operations is always preserved. However, the causal order between a subset of operations can be changed under continuous yet nonreversible transformations. An explicit example is that of the quantum switch, where a party in the past affects the causal order of operations of future parties, leading to a transition from a channel from A to B , via superposition of causal orders, to a channel from B to A . We generalize our framework to construct a hierarchy of quantum maps based on transformations of process matrices and transformations thereof.

Classifying Correlation Matrices into Relatively Homogeneous Subgroups: A Cluster Analytic Approach

ERIC Educational Resources Information Center

Cheung, Mike W.-L.; Chan, Wai

2005-01-01

Researchers are becoming interested in combining meta-analytic techniques and structural equation modeling to test theoretical models from a pool of studies. Most existing procedures are based on the assumption that all correlation matrices are homogeneous. Few studies have addressed what the next step should be when studies being analyzed are…

Encoders for block-circulant LDPC codes

NASA Technical Reports Server (NTRS)

Divsalar, Dariush (Inventor); Abbasfar, Aliazam (Inventor); Jones, Christopher R. (Inventor); Dolinar, Samuel J. (Inventor); Thorpe, Jeremy C. (Inventor); Andrews, Kenneth S. (Inventor); Yao, Kung (Inventor)

2009-01-01

Methods and apparatus to encode message input symbols in accordance with an accumulate-repeat-accumulate code with repetition three or four are disclosed. Block circulant matrices are used. A first method and apparatus make use of the block-circulant structure of the parity check matrix. A second method and apparatus use block-circulant generator matrices.

Trans- and cis-stilbene isolated in cryogenic argon and xenon matrices.

PubMed

Ünsalan, Ozan; Kuş, Nihal; Jarmelo, Susana; Fausto, Rui

2015-02-05

Monomers of trans- (TS) and cis-stilbene (CS) were isolated in cryogenic argon and xenon matrices, and their infrared (IR) spectra were fully assigned and interpreted. The interpretation of the vibrational spectra received support from theoretical calculations undertaken at the DFT(B3LYP)/6-311++G(d,p) level of theory. In situ broadband UV irradiation of the matrix-isolated CS led to its isomerization to TS, which appeared in the photolysed matrices in both non-planar and planar configurations. The non-planar species was found to convert into the more stable planar form upon subsequent annealing of the matrices at higher temperature. TS was found to be photostable under the used experimental conditions. The structure of the non-planar TS form was assigned based on the comparison of its observed IR spectrum with those theoretically predicted for different conformations of TS. Chemometrics was used to make this assignment. Additional reasoning on the structure of the studied stilbenes is presented taking as basis results of the Natural Bond Orbital analysis. Copyright © 2013 Elsevier B.V. All rights reserved.

Graph Theoretic Foundations of Multibody Dynamics Part I: Structural Properties

PubMed Central

Jain, Abhinandan

2011-01-01

This is the first part of two papers that use concepts from graph theory to obtain a deeper understanding of the mathematical foundations of multibody dynamics. The key contribution is the development of a unifying framework that shows that key analytical results and computational algorithms in multibody dynamics are a direct consequence of structural properties and require minimal assumptions about the specific nature of the underlying multibody system. This first part focuses on identifying the abstract graph theoretic structural properties of spatial operator techniques in multibody dynamics. The second part paper exploits these structural properties to develop a broad spectrum of analytical results and computational algorithms. Towards this, we begin with the notion of graph adjacency matrices and generalize it to define block-weighted adjacency (BWA) matrices and their 1-resolvents. Previously developed spatial operators are shown to be special cases of such BWA matrices and their 1-resolvents. These properties are shown to hold broadly for serial and tree topology multibody systems. Specializations of the BWA and 1-resolvent matrices are referred to as spatial kernel operators (SKO) and spatial propagation operators (SPO). These operators and their special properties provide the foundation for the analytical and algorithmic techniques developed in the companion paper. We also use the graph theory concepts to study the topology induced sparsity structure of these operators and the system mass matrix. Similarity transformations of these operators are also studied. While the detailed development is done for the case of rigid-link multibody systems, the extension of these techniques to a broader class of systems (e.g. deformable links) are illustrated. PMID:22102790

An efficient solver for large structured eigenvalue problems in relativistic quantum chemistry

NASA Astrophysics Data System (ADS)

Shiozaki, Toru

2017-01-01

We report an efficient program for computing the eigenvalues and symmetry-adapted eigenvectors of very large quaternionic (or Hermitian skew-Hamiltonian) matrices, using which structure-preserving diagonalisation of matrices of dimension N > 10, 000 is now routine on a single computer node. Such matrices appear frequently in relativistic quantum chemistry owing to the time-reversal symmetry. The implementation is based on a blocked version of the Paige-Van Loan algorithm, which allows us to use the Level 3 BLAS subroutines for most of the computations. Taking advantage of the symmetry, the program is faster by up to a factor of 2 than state-of-the-art implementations of complex Hermitian diagonalisation; diagonalising a 12, 800 × 12, 800 matrix took 42.8 (9.5) and 85.6 (12.6) minutes with 1 CPU core (16 CPU cores) using our symmetry-adapted solver and Intel Math Kernel Library's ZHEEV that is not structure-preserving, respectively. The source code is publicly available under the FreeBSD licence.

Normal response function method for mass and stiffness matrix updating using complex FRFs

NASA Astrophysics Data System (ADS)

Pradhan, S.; Modak, S. V.

2012-10-01

Quite often a structural dynamic finite element model is required to be updated so as to accurately predict the dynamic characteristics like natural frequencies and the mode shapes. Since in many situations undamped natural frequencies and mode shapes need to be predicted, it has generally been the practice in these situations to seek updating of only mass and stiffness matrix so as to obtain a reliable prediction model. Updating using frequency response functions (FRFs) has been one of the widely used approaches for updating, including updating of mass and stiffness matrices. However, the problem with FRF based methods, for updating mass and stiffness matrices, is that these methods are based on use of complex FRFs. Use of complex FRFs to update mass and stiffness matrices is not theoretically correct as complex FRFs are not only affected by these two matrices but also by the damping matrix. Therefore, in situations where updating of only mass and stiffness matrices using FRFs is required, the use of complex FRFs based updating formulation is not fully justified and would lead to inaccurate updated models. This paper addresses this difficulty and proposes an improved FRF based finite element model updating procedure using the concept of normal FRFs. The proposed method is a modified version of the existing response function method that is based on the complex FRFs. The effectiveness of the proposed method is validated through a numerical study of a simple but representative beam structure. The effect of coordinate incompleteness and robustness of method under presence of noise is investigated. The results of updating obtained by the improved method are compared with the existing response function method. The performance of the two approaches is compared for cases of light, medium and heavily damped structures. It is found that the proposed improved method is effective in updating of mass and stiffness matrices in all the cases of complete and incomplete data and with all levels and types of damping.

Covariance structure in the skull of Catarrhini: a case of pattern stasis and magnitude evolution.

PubMed

de Oliveira, Felipe Bandoni; Porto, Arthur; Marroig, Gabriel

2009-04-01

The study of the genetic variance/covariance matrix (G-matrix) is a recent and fruitful approach in evolutionary biology, providing a window of investigating for the evolution of complex characters. Although G-matrix studies were originally conducted for microevolutionary timescales, they could be extrapolated to macroevolution as long as the G-matrix remains relatively constant, or proportional, along the period of interest. A promising approach to investigating the constancy of G-matrices is to compare their phenotypic counterparts (P-matrices) in a large group of related species; if significant similarity is found among several taxa, it is very likely that the underlying G-matrices are also equivalent. Here we study the similarity of covariance and correlation structure in a broad sample of Old World monkeys and apes (Catarrhini). We made phylogenetically structured comparisons of correlation and covariance matrices derived from 39 skull traits, ranging from between species to the superfamily level. We also compared the overall magnitude of integration between skull traits (r2) for all Catarrhini genera. Our results show that P-matrices were not strictly constant among catarrhines, but the amount of divergence observed among taxa was generally low. There was significant and positive correlation between the amount of divergence in correlation and covariance patterns among the 30 genera and their phylogenetic distances derived from a recently proposed phylogenetic hypothesis. Our data demonstrate that the P-matrices remained relatively similar along the evolutionary history of catarrhines, and comparisons with the G-matrix available for a New World monkey genus (Saguinus) suggests that the same holds for all anthropoids. The magnitude of integration, in contrast, varied considerably among genera, indicating that evolution of the magnitude, rather than the pattern of inter-trait correlations, might have played an important role in the diversification of the catarrhine skull.

Chitosan-Based Matrices Prepared by Gamma Irradiation for Tissue Regeneration: Structural Properties vs. Preparation Method.

PubMed

Casimiro, Maria Helena; Lancastre, Joana J H; Rodrigues, Alexandra P; Gomes, Susana R; Rodrigues, Gabriela; Ferreira, Luís M

2017-02-01

In the last decade, new generations of biopolymer-based materials have attracted attention, aiming its application as scaffolds for tissue engineering. These engineered three-dimensional scaffolds are designed to improve or replace damaged, missing, or otherwise compromised tissues or organs. Despite the number of promising methods that can be used to generate 3D cell-instructive matrices, the innovative nature of the present work relies on the application of ionizing radiation technology to form and modify surfaces and matrices with advantage over more conventional technologies (room temperature reaction, absence of harmful initiators or solvents, high penetration through the bulk materials, etc.), and the possibility of preparation and sterilization in one single step. The current chapter summarizes the work done by the authors in the gamma radiation processing of biocompatible and biodegradable chitosan-based matrices for skin regeneration. Particular attention is given to the correlation between the different preparation conditions and the final polymeric matrices' properties. We therefore expect to demonstrate that instructive matrices produced and improved by radiation technology bring to the field of skin regenerative medicine a supplemental advantage over more conservative techniques.

Introducing capillary electrophoresis with laser-induced fluorescence (CE-LIF) as a potential analysis and quantification tool for galactooligosaccharides extracted from complex food matrices.

PubMed

Albrecht, Simone; Schols, Henk A; Klarenbeek, Bert; Voragen, Alphons G J; Gruppen, Harry

2010-03-10

The analysis and quantification of (galacto)oligosaccharides from food matrices demands both a reproducible extraction method as well as a sensitive and accurate analytical method. Three typical matrices, namely, infant formula, fruit juice, and a maltodextrin-rich preparation, to which a commercial galactooligosaccharide mixture was added in a product concentration range from 1.25 to 30%, served as model substrates. Solid-phase extraction on graphitized carbon material upon enzymatic amyloglucosidase pretreatment enabled a good recovery and a selective purification of the different galactooligosaccharide structures from the exceeding amounts of particularly lactose and maltodextrins. With the implementation of capillary electrophoresis in combination with laser-induced fluorescence (CE-LIF) detection, a new possibility facilitating a sensitive qualitative and quantitative determination of the galactooligosaccharide contents in the different food matrices is outlined. Simultaneous monitoring and quantifying prebiotic oligosaccharides embedded in food matrices presents a promising and important step toward an efficient monitoring of individual oligosaccharides and is of interest for research areas dealing with small quantities of oligosaccharides embedded in complex matrices, e.g., body liquids.

Spectrophotometric versus NIR-MIR assessments of cowpea pods for discriminating the impact of freezing.

PubMed

Machado, Nelson; Domínguez-Perles, Raúl; Ramos, Ana; Rosa, Eduardo As; Barros, Ana Irna

2017-10-01

Freezing represents an important storage method for vegetal foodstuffs, such as cowpea pods, and thus the impact of this process on the chemical composition of these matrices arises as a prominent issue. In this sense, the phytochemical contents in frozen cowpea pods (i.e. at 6 and 9 months) have been compared with fresh cowpea pods material, with the samples being concomitantly assessed by Fourier-transform infrared spectroscopy (FTIR), both mid-infrared (MIR) and near infrared (NIR), aiming to evaluate the potential of these techniques as a rapid tool for the traceability of these matrices. A decrease in phytochemical contents during freezing was observed, allowing the classification of samples according to the freezing period based on such variations. Also, MIR and NIR allowed discrimination of samples: the use of the first derivative demonstrated a better performance for this purpose, whereas the use of the normalized spectra gave the best correlations between the spectra and specific contents. In both cases, NIR displayed the best performance. Freezing of cowpea pods leads to a decrease of phytochemical contents, which can be monitored by FTIR spectroscopy, both within the MIR and NIR ranges, whereas the use of this technique, in tandem with chemometrics, constitutes a suitable methodology for the traceability of these matrices. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

A computer package for the design and eigenproblem solution of damped linear multidegree of freedom systems

NASA Technical Reports Server (NTRS)

Ahmadian, M.; Inman, D. J.

1982-01-01

Systems described by the matrix differental equation are considered. An interactive design routine is presented for positive definite mass, damping, and stiffness matrices. Designing is accomplished by adjusting the mass, damping, and stiffness matrices to obtain a desired oscillation behavior. The algorithm also features interactively modifying the physical structure of the system, obtaining the matrix structure and a number of other system properties. In case of a general system, where the M, C, and K matrices lack any special properties, a routine for the eigenproblem solution of the system is developed. The latent roots are obtained by computing the characteristic polynomial of the system and solving for its roots. The above routines are prepared in FORTRAN IV and prove to be usable for the machines with low core memory.

Chemiluminescence in cryogenic matrices

NASA Astrophysics Data System (ADS)

Lotnik, S. V.; Kazakov, Valeri P.

1989-04-01

The literature data on chemiluminescence (CL) in cryogenic matrices have been classified and correlated for the first time. The role of studies on phosphorescence and CL at low temperatures in the development of cryochemistry is shown. The features of low-temperature CL in matrices of nitrogen and inert gases (fine structure of spectra, matrix effects) and the data on the mobility and reactivity of atoms and radicals at very low temperatures are examined. The trends in the development of studies on CL in cryogenic matrices, such as the search for systems involving polyatomic molecules and extending the forms of CL reactions, are followed. The reactions of active nitrogen with hydrocarbons that are accompanied by light emission and CL in the oxidation of carbenes at T >= 77 K are examined. The bibliography includes 112 references.

Synthesis of high performance ceramic fibers by chemical vapor deposition for advanced metallics reinforcing

NASA Technical Reports Server (NTRS)

Revankar, Vithal; Hlavacek, Vladimir

1991-01-01

The chemical vapor deposition (CVD) synthesis of fibers capable of effectively reinforcing intermetallic matrices at elevated temperatures which can be used for potential applications in high temperature composite materials is described. This process was used due to its advantage over other fiber synthesis processes. It is extremely important to produce these fibers with good reproducible and controlled growth rates. However, the complex interplay of mass and energy transfer, blended with the fluid dynamics makes this a formidable task. The design and development of CVD reactor assembly and system to synthesize TiB2, CrB, B4C, and TiC fibers was performed. Residual thermal analysis for estimating stresses arising form thermal expansion mismatch were determined. Various techniques to improve the mechanical properties were also performed. Various techniques for improving the fiber properties were elaborated. The crystal structure and its orientation for TiB2 fiber is discussed. An overall view of the CVD process to develop CrB2, TiB2, and other high performance ceramic fibers is presented.

Analysis of cross-correlations between financial markets after the 2008 crisis

NASA Astrophysics Data System (ADS)

Sensoy, A.; Yuksel, S.; Erturk, M.

2013-10-01

We analyze the cross-correlation matrix C of the index returns of the main financial markets after the 2008 crisis using methods of random matrix theory. We test the eigenvalues of C for universal properties of random matrices and find that the majority of the cross-correlation coefficients arise from randomness. We show that the eigenvector of the largest deviating eigenvalue of C represents a global market itself. We reveal that high volatility of financial markets is observed at the same times with high correlations between them which lowers the risk diversification potential even if one constructs a widely internationally diversified portfolio of stocks. We identify and compare the connection and cluster structure of markets before and after the crisis using minimal spanning and ultrametric hierarchical trees. We find that after the crisis, the co-movement degree of the markets increases. We also highlight the key financial markets of pre and post crisis using main centrality measures and analyze the changes. We repeat the study using rank correlation and compare the differences. Further implications are discussed.

Positron annihilation lifetime spectroscopy (PALS): a probe for molecular organisation in self-assembled biomimetic systems.

PubMed

Fong, Celesta; Dong, Aurelia W; Hill, Anita J; Boyd, Ben J; Drummond, Calum J

2015-07-21

Positron annihilation lifetime spectroscopy (PALS) has been shown to be highly sensitive to conformational, structural and microenvironmental transformations arising from subtle geometric changes in molecular geometry in self-assembling biomimetic systems. The ortho-positronium (oPs) may be considered an active probe that can provide information on intrinsic packing and mobility within low molecular weight solids, viscous liquids, and soft matter systems. In this perspective we provide a critical overview of the literature in this field, including the evolution of analysis software and experimental protocols with commentary upon the practical utility of PALS. In particular, we discuss how PALS can provide unique insight into the macroscopic transport properties of several porous biomembrane-like nanostructures and suggest how this insight may provide information on the release of drugs from these matrices to aid in developing therapeutic interventions. We discuss the potentially exciting and fruitful application of this technique to membrane dynamics, diffusion and permeability. We propose that PALS can provide novel molecular level information that is complementary to conventional characterisation techniques.

Studies in tilt rotor VTOL aircraft aeroelasticity, volume 2. Ph.D. Thesis - Case Western Reserve Univ.

NASA Technical Reports Server (NTRS)

Kvaternik, R. G.

1973-01-01

Two methods for natural mode vibration analysis are discussed. The first consists of a direct approach based on a finite element representation of the complete structure as an entity. The mass and stiffness matrices for the complete structure are assembled by properly combining the mass and stiffness matrices of the individual elements into which the structure has been divided. The second approach is that of component mode synthesis. This method is based on the concept of synthesizing the natural modes of the complete structure from modes of conveniently difined substructures, or components, into which the structure has been partitioned. In this way the expedient of reducing the system degrees of freedom, and thus the size of the eigenvalue problem, can be introduced by partial modal synthesis.

Attenuated Total Reflection Fourier Transform Infrared (ATR FT-IR) Spectroscopy as an Analytical Method to Investigate the Secondary Structure of a Model Protein Embedded in Solid Lipid Matrices.

PubMed

Zeeshan, Farrukh; Tabbassum, Misbah; Jorgensen, Lene; Medlicott, Natalie J

2018-02-01

Protein drugs may encounter conformational perturbations during the formulation processing of lipid-based solid dosage forms. In aqueous protein solutions, attenuated total reflection Fourier transform infrared (ATR FT-IR) spectroscopy can investigate these conformational changes following the subtraction of spectral interference of solvent with protein amide I bands. However, in solid dosage forms, the possible spectral contribution of lipid carriers to protein amide I band may be an obstacle to determine conformational alterations. The objective of this study was to develop an ATR FT-IR spectroscopic method for the analysis of protein secondary structure embedded in solid lipid matrices. Bovine serum albumin (BSA) was chosen as a model protein, while Precirol AT05 (glycerol palmitostearate, melting point 58 ℃) was employed as the model lipid matrix. Bovine serum albumin was incorporated into lipid using physical mixing, melting and mixing, or wet granulation mixing methods. Attenuated total reflection FT-IR spectroscopy and size exclusion chromatography (SEC) were performed for the analysis of BSA secondary structure and its dissolution in aqueous media, respectively. The results showed significant interference of Precirol ATO5 with BSA amide I band which was subtracted up to 90% w/w lipid content to analyze BSA secondary structure. In addition, ATR FT-IR spectroscopy also detected thermally denatured BSA solid alone and in the presence of lipid matrix indicating its suitability for the detection of denatured protein solids in lipid matrices. Despite being in the solid state, conformational changes occurred to BSA upon incorporation into solid lipid matrices. However, the extent of these conformational alterations was found to be dependent on the mixing method employed as indicated by area overlap calculations. For instance, the melting and mixing method imparted negligible effect on BSA secondary structure, whereas the wet granulation mixing method promoted more changes. Size exclusion chromatography analysis depicted the complete dissolution of BSA in the aqueous media employed in the wet granulation method. In conclusion, an ATR FT-IR spectroscopic method was successfully developed to investigate BSA secondary structure in solid lipid matrices following the subtraction of lipid spectral interference. The ATR FT-IR spectroscopy could further be applied to investigate the secondary structure perturbations of therapeutic proteins during their formulation development.

Structure and optical properties of noble metal and oxide nanoparticles dispersed in various polysaccharide biopolymers

NASA Astrophysics Data System (ADS)

Djoković, V.; Božanic, D. K.; Vodnik, V. V.; Krsmanović, R. M.; Trandafilovic, L. V.; Dimitrijević-Branković, S.

2011-10-01

We present the results on the structure and the optical properties of noble metal (Ag, Au) and oxide (ZnO) nanoparticles synthesized by various methods in different polysaccharide matrices such as chitosan, glycogen, alginate and starch. The structure of the obtained nanoparticles was studied in detail with microscopic techniques (TEM, SEM), while the XPS spectroscopy was used to investigate the effects at the nanoparticle-biomolecule interfaces. The antimicrobial activity of the nanocomposite films with Ag nanoparticles was tested against the Staphylococcus aureus, Escherichia coli and Candida albicans pathogens. In addition, we will present the results on the structure and optical properties of the tryptophan amino acid functionalized silver nanoparticles dispersed in water soluble polymer matrices.

Quantitative structure-retention relationships for gas chromatographic retention indices of alkylbenzenes with molecular graph descriptors.

PubMed

Ivanciuc, O; Ivanciuc, T; Klein, D J; Seitz, W A; Balaban, A T

2001-02-01

Quantitative structure-retention relationships (QSRR) represent statistical models that quantify the connection between the molecular structure and the chromatographic retention indices of organic compounds, allowing the prediction of retention indices of novel, not yet synthesized compounds, solely from their structural descriptors. Using multiple linear regression, QSRR models for the gas chromatographic Kováts retention indices of 129 alkylbenzenes are generated using molecular graph descriptors. The correlational ability of structural descriptors computed from 10 molecular matrices is investigated, showing that the novel reciprocal matrices give numerical indices with improved correlational ability. A QSRR equation with 5 graph descriptors gives the best calibration and prediction results, demonstrating the usefulness of the molecular graph descriptors in modeling chromatographic retention parameters. The sequential orthogonalization of descriptors suggests simpler QSRR models by eliminating redundant structural information.

Structure-Function Network Mapping and Its Assessment via Persistent Homology

PubMed Central

2017-01-01

Understanding the relationship between brain structure and function is a fundamental problem in network neuroscience. This work deals with the general method of structure-function mapping at the whole-brain level. We formulate the problem as a topological mapping of structure-function connectivity via matrix function, and find a stable solution by exploiting a regularization procedure to cope with large matrices. We introduce a novel measure of network similarity based on persistent homology for assessing the quality of the network mapping, which enables a detailed comparison of network topological changes across all possible thresholds, rather than just at a single, arbitrary threshold that may not be optimal. We demonstrate that our approach can uncover the direct and indirect structural paths for predicting functional connectivity, and our network similarity measure outperforms other currently available methods. We systematically validate our approach with (1) a comparison of regularized vs. non-regularized procedures, (2) a null model of the degree-preserving random rewired structural matrix, (3) different network types (binary vs. weighted matrices), and (4) different brain parcellation schemes (low vs. high resolutions). Finally, we evaluate the scalability of our method with relatively large matrices (2514x2514) of structural and functional connectivity obtained from 12 healthy human subjects measured non-invasively while at rest. Our results reveal a nonlinear structure-function relationship, suggesting that the resting-state functional connectivity depends on direct structural connections, as well as relatively parsimonious indirect connections via polysynaptic pathways. PMID:28046127

Storage strategies of eddy-current FE-BI model for GPU implementation

NASA Astrophysics Data System (ADS)

Bardel, Charles; Lei, Naiguang; Udpa, Lalita

2013-01-01

In the past few years graphical processing units (GPUs) have shown tremendous improvements in computational throughput over standard CPU architecture. However, this comes at the cost of restructuring the algorithms to meet the strengths and drawbacks of this GPU architecture. A major drawback is the state of limited memory, and hence storage of FE stiffness matrices on the GPU is important. In contrast to storage on CPU the GPU storage format has significant influence on the overall performance. This paper presents an investigation of a storage strategy in the implementation of a two-dimensional finite element-boundary integral (FE-BI) model for Eddy current NDE applications, on GPU architecture. Specifically, the high dimensional matrices are manipulated by examining the matrix structure and optimally splitting into structurally independent component matrices for efficient storage and retrieval of each component. Results obtained using the proposed approach are compared to those of conventional CPU implementation for validating the method.

Rank-Optimized Logistic Matrix Regression toward Improved Matrix Data Classification.

PubMed

Zhang, Jianguang; Jiang, Jianmin

2018-02-01

While existing logistic regression suffers from overfitting and often fails in considering structural information, we propose a novel matrix-based logistic regression to overcome the weakness. In the proposed method, 2D matrices are directly used to learn two groups of parameter vectors along each dimension without vectorization, which allows the proposed method to fully exploit the underlying structural information embedded inside the 2D matrices. Further, we add a joint [Formula: see text]-norm on two parameter matrices, which are organized by aligning each group of parameter vectors in columns. This added co-regularization term has two roles-enhancing the effect of regularization and optimizing the rank during the learning process. With our proposed fast iterative solution, we carried out extensive experiments. The results show that in comparison to both the traditional tensor-based methods and the vector-based regression methods, our proposed solution achieves better performance for matrix data classifications.

A fast isogeometric BEM for the three dimensional Laplace- and Helmholtz problems

NASA Astrophysics Data System (ADS)

Dölz, Jürgen; Harbrecht, Helmut; Kurz, Stefan; Schöps, Sebastian; Wolf, Felix

2018-03-01

We present an indirect higher order boundary element method utilising NURBS mappings for exact geometry representation and an interpolation-based fast multipole method for compression and reduction of computational complexity, to counteract the problems arising due to the dense matrices produced by boundary element methods. By solving Laplace and Helmholtz problems via a single layer approach we show, through a series of numerical examples suitable for easy comparison with other numerical schemes, that one can indeed achieve extremely high rates of convergence of the pointwise potential through the utilisation of higher order B-spline-based ansatz functions.

A diagonal implicit scheme for computing flows with finite-rate chemistry

NASA Technical Reports Server (NTRS)

Eberhardt, Scott; Imlay, Scott

1990-01-01

A new algorithm for solving steady, finite-rate chemistry, flow problems is presented. The new scheme eliminates the expense of inverting large block matrices that arise when species conservation equations are introduced. The source Jacobian matrix is replaced by a diagonal matrix which is tailored to account for the fastest reactions in the chemical system. A point-implicit procedure is discussed and then the algorithm is included into the LU-SGS scheme. Solutions are presented for hypervelocity reentry and Hydrogen-Oxygen combustion. For the LU-SGS scheme a CFL number in excess of 10,000 has been achieved.

A new preconditioner update strategy for the solution of sequences of linear systems in structural mechanics: application to saddle point problems in elasticity

NASA Astrophysics Data System (ADS)

Mercier, Sylvain; Gratton, Serge; Tardieu, Nicolas; Vasseur, Xavier

2017-12-01

Many applications in structural mechanics require the numerical solution of sequences of linear systems typically issued from a finite element discretization of the governing equations on fine meshes. The method of Lagrange multipliers is often used to take into account mechanical constraints. The resulting matrices then exhibit a saddle point structure and the iterative solution of such preconditioned linear systems is considered as challenging. A popular strategy is then to combine preconditioning and deflation to yield an efficient method. We propose an alternative that is applicable to the general case and not only to matrices with a saddle point structure. In this approach, we consider to update an existing algebraic or application-based preconditioner, using specific available information exploiting the knowledge of an approximate invariant subspace or of matrix-vector products. The resulting preconditioner has the form of a limited memory quasi-Newton matrix and requires a small number of linearly independent vectors. Numerical experiments performed on three large-scale applications in elasticity highlight the relevance of the new approach. We show that the proposed method outperforms the deflation method when considering sequences of linear systems with varying matrices.

Submerged Shock Response of a Linearly Elastic Shell of Revolution Containing Internal Structure. User’s Manual for the ELSHOK Code.

DTIC Science & Technology

1982-05-01

execution of PICRUST, influence coefficients corresponding to the base or support motions of a substructure (the gji of Eq. (10) or the constraint...stiffness matrices (M and K, respectively) are also determined. These matrices are required for the calculation of the constraint modes gji of Eq.(lO) and

Derivation of improved load transformation matrices for launchers-spacecraft coupled analysis, and direct computation of margins of safety

NASA Technical Reports Server (NTRS)

Klein, M.; Reynolds, J.; Ricks, E.

1989-01-01

Load and stress recovery from transient dynamic studies are improved upon using an extended acceleration vector in the modal acceleration technique applied to structural analysis. Extension of the normal LTM (load transformation matrices) stress recovery to automatically compute margins of safety is presented with an application to the Hubble space telescope.

From deep TLS validation to ensembles of atomic models built from elemental motions

DOE PAGES

Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.; ...

2015-07-28

The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy severalmore » conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.« less

Sparse Gaussian elimination with controlled fill-in on a shared memory multiprocessor

NASA Technical Reports Server (NTRS)

Alaghband, Gita; Jordan, Harry F.

1989-01-01

It is shown that in sparse matrices arising from electronic circuits, it is possible to do computations on many diagonal elements simultaneously. A technique for obtaining an ordered compatible set directly from the ordered incompatible table is given. The ordering is based on the Markowitz number of the pivot candidates. This technique generates a set of compatible pivots with the property of generating few fills. A novel heuristic algorithm is presented that combines the idea of an order-compatible set with a limited binary tree search to generate several sets of compatible pivots in linear time. An elimination set for reducing the matrix is generated and selected on the basis of a minimum Markowitz sum number. The parallel pivoting technique presented is a stepwise algorithm and can be applied to any submatrix of the original matrix. Thus, it is not a preordering of the sparse matrix and is applied dynamically as the decomposition proceeds. Parameters are suggested to obtain a balance between parallelism and fill-ins. Results of applying the proposed algorithms on several large application matrices using the HEP multiprocessor (Kowalik, 1985) are presented and analyzed.

Atomistic simulation of graphene-based polymer nanocomposites

NASA Astrophysics Data System (ADS)

Rissanou, Anastassia N.; Bačová, Petra; Harmandaris, Vagelis

2016-05-01

Polymer/graphene nanostructured systems are hybrid materials which have attracted great attention the last years both for scientific and technological reasons. In the present work atomistic Molecular Dynamics simulations are performed for the study of graphene-based polymer nanocomposites composed of pristine, hydrogenated and carboxylated graphene sheets dispersed in polar (PEO) and nonpolar (PE) short polymer matrices (i.e., matrices containing chains of low molecular weight). Our focus is twofold; the one is the study of the structural and dynamical properties of short polymer chains and the way that they are affected by functionalized graphene sheets while the other is the effect of the polymer matrices on the behavior of graphene sheets.

Statistical mechanics of complex neural systems and high dimensional data

NASA Astrophysics Data System (ADS)

Advani, Madhu; Lahiri, Subhaneil; Ganguli, Surya

2013-03-01

Recent experimental advances in neuroscience have opened new vistas into the immense complexity of neuronal networks. This proliferation of data challenges us on two parallel fronts. First, how can we form adequate theoretical frameworks for understanding how dynamical network processes cooperate across widely disparate spatiotemporal scales to solve important computational problems? Second, how can we extract meaningful models of neuronal systems from high dimensional datasets? To aid in these challenges, we give a pedagogical review of a collection of ideas and theoretical methods arising at the intersection of statistical physics, computer science and neurobiology. We introduce the interrelated replica and cavity methods, which originated in statistical physics as powerful ways to quantitatively analyze large highly heterogeneous systems of many interacting degrees of freedom. We also introduce the closely related notion of message passing in graphical models, which originated in computer science as a distributed algorithm capable of solving large inference and optimization problems involving many coupled variables. We then show how both the statistical physics and computer science perspectives can be applied in a wide diversity of contexts to problems arising in theoretical neuroscience and data analysis. Along the way we discuss spin glasses, learning theory, illusions of structure in noise, random matrices, dimensionality reduction and compressed sensing, all within the unified formalism of the replica method. Moreover, we review recent conceptual connections between message passing in graphical models, and neural computation and learning. Overall, these ideas illustrate how statistical physics and computer science might provide a lens through which we can uncover emergent computational functions buried deep within the dynamical complexities of neuronal networks.

Matrices and scaffolds for drug delivery in dental, oral and craniofacial tissue engineering☆

PubMed Central

Moioli, Eduardo K.; Clark, Paul A.; Xin, Xuejun; Lal, Shan; Mao, Jeremy J.

2010-01-01

Current treatments for diseases and trauma of dental, oral and craniofacial (DOC) structures rely on durable materials such as amalgam and synthetic materials, or autologous tissue grafts. A paradigm shift has taken place to utilize tissue engineering and drug delivery approaches towards the regeneration of these structures. Several prototypes of DOC structures have been regenerated such as temporomandibular joint (TMJ) condyle, cranial sutures, tooth structures and periodontium components. However, many challenges remain when taking in consideration the high demand for esthetics of DOC structures, the complex environment and yet minimal scar formation in the oral cavity, and the need for accommodating multiple tissue phenotypes. This review highlights recent advances in the regeneration of DOC structures, including the tooth, periodontium, TMJ, cranial sutures and implant dentistry, with specific emphasis on controlled release of signaling cues for stem cells, biomaterial matrices and scaffolds, and integrated tissue engineering approaches. PMID:17499385

Polyhedral Oligomeric Silsesquioxane (POSS)-Containing Polymer Nanocomposites

PubMed Central

Ayandele, Ebunoluwa; Sarkar, Biswajit; Alexandridis, Paschalis

2012-01-01

Hybrid materials with superior structural and functional properties can be obtained by incorporating nanofillers into polymer matrices. Polyhedral oligomeric silsesquioxane (POSS) nanoparticles have attracted much attention recently due to their nanometer size, the ease of which these particles can be incorporated into polymeric materials and the unique capability to reinforce polymers. We review here the state of POSS-containing polymer nanocomposites. We discuss the influence of the incorporation of POSS into polymer matrices via chemical cross-linking or physical blending on the structure of nanocomposites, as affected by surface functional groups, and the POSS concentration. PMID:28348318

Biocompatible polyurethane/thiacalix[4]arenes functionalized Fe3O4 magnetic nanocomposites: Synthesis and properties.

PubMed

Mohammadi, Abbas; Barikani, Mehdi; Lakouraj, Moslem Mansour

2016-09-01

In this study, a series of magnetic polyurethane/Fe3O4 elastomer nanocomposites were prepared by covalently embedding novel thiacalix[4]arenes (TC4As) functionalized Fe3O4 nanoparticles (TC4As-Fe3O4) which contain macrocycles with reactive hydroxyl groups. Surface functionalization of Fe3O4 nanoparticles with TC4As macrocycles as unique reactive surface modifier not only gives specific characteristics to Fe3O4 nanoparticles but also improves the interphase interaction between nanoparticles and the polyurethane matrices through covalent attachment of polymer chains to nanoparticle surfaces. The novel synthesized TC4As-Fe3O4 nanoparticles were characterized by FTIR, XRD, TGA, VSM and SEM analysis. Furthermore, the effect of functionalization of Fe3O4 nanoparticles on the various properties of resulting nanocomposites was studied by XRD, TGA, DMTA, SEM, and a universal tensile tester. It was found that the functionalization of nanoparticles with TC4As affords better mechanical and thermal properties to polyurethane nanocomposites in comparison with unmodified nanoparticles. The SEM analysis showed finer dispersion of TC4As-Fe3O4 nanoparticles than unmodified Fe3O4 nanoparticles within the polyurethane matrices, which arising from formation of covalent bonding between TC4As functionalized Fe3O4 nanoparticles and polyurethane matrices. Moreover, the investigation of in vitro biocompatibility of novel nanocomposites showed that these samples are excellent candidate for biomedical use. Copyright © 2016 Elsevier B.V. All rights reserved.

The "invisible caregiver": multicaregiving among diabetic African-American grandmothers.

PubMed

Carthron, Dana L; Bailey, Donald E; Anderson, Ruth A

2014-01-01

To explore the multicaregiving roles African-American grandmothers assume while self-managing their diabetes. This longitudinal, qualitative pilot study explored the challenges of self-managing diabetes among six African-American caregiving grandmothers. Data were collected at 5 times points across 18 months. Content analysis, guided by the Adaptive Leadership framework, was conducted using data matrices to facilitate within-case and cross-case analyses. Although participants initially stated they cared only for grandchildren, all had additional caregiving responsibilities. Four themes emerged which illustrated how African-American caregiving grandmothers put the care of dependent children, extended family and community before themselves. Using the Adaptive Leadership framework, technical and adaptive challenges arising from multicaregiving were described as barriers to diabetes self-management. When assisting these women to self-manage their diabetes, clinicians must assess challenges arising from multicaregiving. This might require developing collaborative work relationships with the client to develop meaningful and attainable goals. Copyright © 2014 Mosby, Inc. All rights reserved.

A stochastic asymptotic-preserving scheme for a kinetic-fluid model for disperse two-phase flows with uncertainty

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Shi, E-mail: sjin@wisc.edu; Institute of Natural Sciences, School of Mathematical Science, MOELSEC and SHL-MAC, Shanghai Jiao Tong University, Shanghai 200240; Shu, Ruiwen, E-mail: rshu2@math.wisc.edu

In this paper we consider a kinetic-fluid model for disperse two-phase flows with uncertainty. We propose a stochastic asymptotic-preserving (s-AP) scheme in the generalized polynomial chaos stochastic Galerkin (gPC-sG) framework, which allows the efficient computation of the problem in both kinetic and hydrodynamic regimes. The s-AP property is proved by deriving the equilibrium of the gPC version of the Fokker–Planck operator. The coefficient matrices that arise in a Helmholtz equation and a Poisson equation, essential ingredients of the algorithms, are proved to be positive definite under reasonable and mild assumptions. The computation of the gPC version of a translation operatormore » that arises in the inversion of the Fokker–Planck operator is accelerated by a spectrally accurate splitting method. Numerical examples illustrate the s-AP property and the efficiency of the gPC-sG method in various asymptotic regimes.« less

Non-Hermitian localization in biological networks.

PubMed

Amir, Ariel; Hatano, Naomichi; Nelson, David R

2016-04-01

We explore the spectra and localization properties of the N-site banded one-dimensional non-Hermitian random matrices that arise naturally in sparse neural networks. Approximately equal numbers of random excitatory and inhibitory connections lead to spatially localized eigenfunctions and an intricate eigenvalue spectrum in the complex plane that controls the spontaneous activity and induced response. A finite fraction of the eigenvalues condense onto the real or imaginary axes. For large N, the spectrum has remarkable symmetries not only with respect to reflections across the real and imaginary axes but also with respect to 90^{∘} rotations, with an unusual anisotropic divergence in the localization length near the origin. When chains with periodic boundary conditions become directed, with a systematic directional bias superimposed on the randomness, a hole centered on the origin opens up in the density-of-states in the complex plane. All states are extended on the rim of this hole, while the localized eigenvalues outside the hole are unchanged. The bias-dependent shape of this hole tracks the bias-independent contours of constant localization length. We treat the large-N limit by a combination of direct numerical diagonalization and using transfer matrices, an approach that allows us to exploit an electrostatic analogy connecting the "charges" embodied in the eigenvalue distribution with the contours of constant localization length. We show that similar results are obtained for more realistic neural networks that obey "Dale's law" (each site is purely excitatory or inhibitory) and conclude with perturbation theory results that describe the limit of large directional bias, when all states are extended. Related problems arise in random ecological networks and in chains of artificial cells with randomly coupled gene expression patterns.

Non-Hermitian localization in biological networks

NASA Astrophysics Data System (ADS)

Amir, Ariel; Hatano, Naomichi; Nelson, David R.

2016-04-01

We explore the spectra and localization properties of the N -site banded one-dimensional non-Hermitian random matrices that arise naturally in sparse neural networks. Approximately equal numbers of random excitatory and inhibitory connections lead to spatially localized eigenfunctions and an intricate eigenvalue spectrum in the complex plane that controls the spontaneous activity and induced response. A finite fraction of the eigenvalues condense onto the real or imaginary axes. For large N , the spectrum has remarkable symmetries not only with respect to reflections across the real and imaginary axes but also with respect to 90∘ rotations, with an unusual anisotropic divergence in the localization length near the origin. When chains with periodic boundary conditions become directed, with a systematic directional bias superimposed on the randomness, a hole centered on the origin opens up in the density-of-states in the complex plane. All states are extended on the rim of this hole, while the localized eigenvalues outside the hole are unchanged. The bias-dependent shape of this hole tracks the bias-independent contours of constant localization length. We treat the large-N limit by a combination of direct numerical diagonalization and using transfer matrices, an approach that allows us to exploit an electrostatic analogy connecting the "charges" embodied in the eigenvalue distribution with the contours of constant localization length. We show that similar results are obtained for more realistic neural networks that obey "Dale's law" (each site is purely excitatory or inhibitory) and conclude with perturbation theory results that describe the limit of large directional bias, when all states are extended. Related problems arise in random ecological networks and in chains of artificial cells with randomly coupled gene expression patterns.

3d interaction homology: The structurally known rotamers of tyrosine derive from a surprisingly limited set of information-rich hydropathic interaction environments described by maps.

PubMed

Ahmed, Mostafa H; Koparde, Vishal N; Safo, Martin K; Neel Scarsdale, J; Kellogg, Glen E

2015-06-01

Sidechain rotamer libraries are obtained through exhaustive statistical analysis of existing crystallographic structures of proteins and have been applied in multiple aspects of structural biology, for example, crystallography of relatively low-resolution structures, in homology model building and in biomolecular NMR. Little is known, however, about the driving forces that lead to the preference or suitability of one rotamer over another. Construction of 3D hydropathic interaction maps for nearly 30,000 tyrosines reveals the environment around each, in terms of hydrophobic (π-π stacking, etc.) and polar (hydrogen bonding, etc.) interactions. After partitioning the tyrosines into backbone-dependent (ϕ, ψ) bins, a map similarity metric based on the correlation coefficient was applied to each map-map pair to build matrices suitable for clustering with k-means. The first bin (-200° ≤ ϕ < -155°; -205° ≤ ψ < -160°), representing 631 tyrosines, reduced to 14 unique hydropathic environments, with most diversity arising from favorable hydrophobic interactions with many different residue partner types. Polar interactions for tyrosine include surprisingly ubiquitous hydrogen bonding with the phenolic OH and a handful of unique environments surrounding the tyrosine backbone. The memberships of all but one of the 14 environments are dominated (>50%) by a single χ(1)/χ(2) rotamer. The last environment has weak or no interactions with the tyrosine ring and its χ(1)/χ(2) rotamer is indeterminate, which is consistent with it being composed of mostly surface residues. Each tyrosine residue attempts to fulfill its hydropathic valence and thus, structural water molecules are seen in a variety of roles throughout protein structure. © 2015 Wiley Periodicals, Inc.

Reinforcement of polymeric structures with asbestos fibrils

NASA Technical Reports Server (NTRS)

Rader, C. A.; Schwartz, A. M.

1970-01-01

Investigation determines structural potential of asbestos fibrils. Methods are developed for dispersing macrofibers of the asbestos into colloidal-sized ultimate fibrils and incorporating these fibrils in matrices without causing reagglomeration.

Encoding the structure of many-body localization with matrix product operators

NASA Astrophysics Data System (ADS)

Pekker, David; Clark, Bryan K.

2017-01-01

Anderson insulators are noninteracting disordered systems which have localized single-particle eigenstates. The interacting analog of Anderson insulators are the many-body localized (MBL) phases. The spectrum of the many-body eigenstates of an Anderson insulator is efficiently represented as a set of product states over the single-particle modes. We show that product states over matrix product operators of small bond dimension is the corresponding efficient description of the spectrum of an MBL insulator. In this language all of the many-body eigenstates are encoded by matrix product states (i.e., density matrix renormalization group wave functions) consisting of only two sets of low bond dimension matrices per site: the Gi matrices corresponding to the local ground state on site i and the Ei matrices corresponding to the local excited state. All 2n eigenstates can be generated from all possible combinations of these sets of matrices.

Asymmetric correlation matrices: an analysis of financial data

NASA Astrophysics Data System (ADS)

Livan, G.; Rebecchi, L.

2012-06-01

We analyse the spectral properties of correlation matrices between distinct statistical systems. Such matrices are intrinsically non-symmetric, and lend themselves to extend the spectral analyses usually performed on standard Pearson correlation matrices to the realm of complex eigenvalues. We employ some recent random matrix theory results on the average eigenvalue density of this type of matrix to distinguish between noise and non-trivial correlation structures, and we focus on financial data as a case study. Namely, we employ daily prices of stocks belonging to the American and British stock exchanges, and look for the emergence of correlations between two such markets in the eigenvalue spectrum of their non-symmetric correlation matrix. We find several non trivial results when considering time-lagged correlations over short lags, and we corroborate our findings by additionally studying the asymmetric correlation matrix of the principal components of our datasets.

Broken flavor 2↔3 symmetry and phenomenological approach for universal quark and lepton mass matrices

NASA Astrophysics Data System (ADS)

Matsuda, Koichi; Nishiura, Hiroyuki

2006-01-01

A phenomenological approach for the universal mass matrix model with a broken flavor 2↔3 symmetry is explored by introducing the 2↔3 antisymmetric parts of mass matrices for quarks and charged leptons. We present explicit texture components of the mass matrices, which are consistent with all the neutrino oscillation experiments and quark mixing data. The mass matrices have a common structure for quarks and leptons, while the large lepton mixings and the small quark mixings are derived with no fine-tuning due to the difference of the phase factors. The model predicts a value 2.4×10-3 for the lepton mixing matrix element square |U13|2, and also ⟨mν⟩=(0.89-1.4)×10-4eV for the averaged neutrino mass which appears in the neutrinoless double beta decay.

Porous matrix structures for alkaline electrolyte fuel cells

NASA Technical Reports Server (NTRS)

Vine, R. W.; Narsavage, S. T.

1975-01-01

A number of advancements have been realized by a continuing research program to develop higher chemically stable porous matrix structures with high bubble pressure (crossover resistance) for use as separators in potassium hydroxide electrolyte fuel cells. More uniform, higher-bubble-pressure asbestos matrices were produced by reconstituting Johns-Manville asbestos paper; Fybex potassium titanate which was found compatible with 42% KOH at 250 F for up to 3000 hr; good agreement was found between bubble pressures predicted by an analytical study and those measured with filtered structures; Teflon-bonded Fybex matrices with bubble pressures greater than 30 psi were obtained by filtering a water slurry of the mixture directly onto fuel cell electrodes; and PBI fibers have satisfactory compatibility with 42% KOH at 250 F.

TiO₂-Based Photocatalytic Geopolymers for Nitric Oxide Degradation.

PubMed

Strini, Alberto; Roviello, Giuseppina; Ricciotti, Laura; Ferone, Claudio; Messina, Francesco; Schiavi, Luca; Corsaro, Davide; Cioffi, Raffaele

2016-06-24

This study presents an experimental overview for the development of photocatalytic materials based on geopolymer binders as catalyst support matrices. Particularly, geopolymer matrices obtained from different solid precursors (fly ash and metakaolin), composite systems (siloxane-hybrid, foamed hybrid), and curing temperatures (room temperature and 60 °C) were investigated for the same photocatalyst content (i.e., 3% TiO₂ by weight of paste). The geopolymer matrices were previously designed for different applications, ranging from insulating (foam) to structural materials. The photocatalytic activity was evaluated as NO degradation in air, and the results were compared with an ordinary Portland cement reference. The studied matrices demonstrated highly variable photocatalytic performance depending on both matrix constituents and the curing temperature, with promising activity revealed by the geopolymers based on fly ash and metakaolin. Furthermore, microstructural features and titania dispersion in the matrices were assessed by scanning electron microscopy (SEM) and energy dispersive X-ray (EDS) analyses. Particularly, EDS analyses of sample sections indicated segregation effects of titania in the surface layer, with consequent enhancement or depletion of the catalyst concentration in the active sample region, suggesting non-negligible transport phenomena during the curing process. The described results demonstrated that geopolymer binders can be interesting catalyst support matrices for the development of photocatalytic materials and indicated a large potential for the exploitation of their peculiar features.

Construction of type-II QC-LDPC codes with fast encoding based on perfect cyclic difference sets

NASA Astrophysics Data System (ADS)

Li, Ling-xiang; Li, Hai-bing; Li, Ji-bi; Jiang, Hua

2017-09-01

In view of the problems that the encoding complexity of quasi-cyclic low-density parity-check (QC-LDPC) codes is high and the minimum distance is not large enough which leads to the degradation of the error-correction performance, the new irregular type-II QC-LDPC codes based on perfect cyclic difference sets (CDSs) are constructed. The parity check matrices of these type-II QC-LDPC codes consist of the zero matrices with weight of 0, the circulant permutation matrices (CPMs) with weight of 1 and the circulant matrices with weight of 2 (W2CMs). The introduction of W2CMs in parity check matrices makes it possible to achieve the larger minimum distance which can improve the error- correction performance of the codes. The Tanner graphs of these codes have no girth-4, thus they have the excellent decoding convergence characteristics. In addition, because the parity check matrices have the quasi-dual diagonal structure, the fast encoding algorithm can reduce the encoding complexity effectively. Simulation results show that the new type-II QC-LDPC codes can achieve a more excellent error-correction performance and have no error floor phenomenon over the additive white Gaussian noise (AWGN) channel with sum-product algorithm (SPA) iterative decoding.

Composites reinforced via mechanical interlocking of surface-roughened microplatelets within ductile and brittle matrices.

PubMed

Libanori, R; Carnelli, D; Rothfuchs, N; Binelli, M R; Zanini, M; Nicoleau, L; Feichtenschlager, B; Albrecht, G; Studart, A R

2016-04-12

Load-bearing reinforcing elements in a continuous matrix allow for improved mechanical properties and can reduce the weight of structural composites. As the mechanical performance of composite systems are heavily affected by the interfacial properties, tailoring the interactions between matrices and reinforcing elements is a crucial problem. Recently, several studies using bio-inspired model systems suggested that interfacial mechanical interlocking is an efficient mechanism for energy dissipation in platelet-reinforced composites. While cheap and effective solutions are available at the macroscale, the modification of surface topography in micron-sized reinforcing elements still represents a challenging task. Here, we report a simple method to create nanoasperities with tailored sizes and densities on the surface of alumina platelets and investigate their micromechanical effect on the energy dissipation mechanisms of nacre-like materials. Composites reinforced with roughened platelets exhibit improved mechanical properties for both organic ductile epoxy and inorganic brittle cement matrices. Mechanical interlocking increases the modulus of toughness (area under the stress-strain curve) by 110% and 56% in epoxy and cement matrices, respectively, as compared to those reinforced with flat platelets. This interlocking mechanism can potentially lead to a significant reduction in the weight of mechanical components while retaining the structural performance required in the application field.

Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization

PubMed Central

Lasala, R.; Coudray, N.; Abdine, A.; Zhang, Z.; Lopez-Redondo, M.; Kirshenbaum, R.; Alexopoulos, J.; Zolnai, Z.; Stokes, D.L.; Ubarretxena-Belandia, I.

2014-01-01

Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1,300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization. PMID:25478971

Quantum-inspired algorithm for estimating the permanent of positive semidefinite matrices

NASA Astrophysics Data System (ADS)

Chakhmakhchyan, L.; Cerf, N. J.; Garcia-Patron, R.

2017-08-01

We construct a quantum-inspired classical algorithm for computing the permanent of Hermitian positive semidefinite matrices by exploiting a connection between these mathematical structures and the boson sampling model. Specifically, the permanent of a Hermitian positive semidefinite matrix can be expressed in terms of the expected value of a random variable, which stands for a specific photon-counting probability when measuring a linear-optically evolved random multimode coherent state. Our algorithm then approximates the matrix permanent from the corresponding sample mean and is shown to run in polynomial time for various sets of Hermitian positive semidefinite matrices, achieving a precision that improves over known techniques. This work illustrates how quantum optics may benefit algorithm development.

Recursive inverse factorization.

PubMed

Rubensson, Emanuel H; Bock, Nicolas; Holmström, Erik; Niklasson, Anders M N

2008-03-14

A recursive algorithm for the inverse factorization S(-1)=ZZ(*) of Hermitian positive definite matrices S is proposed. The inverse factorization is based on iterative refinement [A.M.N. Niklasson, Phys. Rev. B 70, 193102 (2004)] combined with a recursive decomposition of S. As the computational kernel is matrix-matrix multiplication, the algorithm can be parallelized and the computational effort increases linearly with system size for systems with sufficiently sparse matrices. Recent advances in network theory are used to find appropriate recursive decompositions. We show that optimization of the so-called network modularity results in an improved partitioning compared to other approaches. In particular, when the recursive inverse factorization is applied to overlap matrices of irregularly structured three-dimensional molecules.

Amino Acid Properties Conserved in Molecular Evolution

PubMed Central

Rudnicki, Witold R.; Mroczek, Teresa; Cudek, Paweł

2014-01-01

That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts – one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications. PMID:24967708

Structural damage detection based on stochastic subspace identification and statistical pattern recognition: I. Theory

NASA Astrophysics Data System (ADS)

Ren, W. X.; Lin, Y. Q.; Fang, S. E.

2011-11-01

One of the key issues in vibration-based structural health monitoring is to extract the damage-sensitive but environment-insensitive features from sampled dynamic response measurements and to carry out the statistical analysis of these features for structural damage detection. A new damage feature is proposed in this paper by using the system matrices of the forward innovation model based on the covariance-driven stochastic subspace identification of a vibrating system. To overcome the variations of the system matrices, a non-singularity transposition matrix is introduced so that the system matrices are normalized to their standard forms. For reducing the effects of modeling errors, noise and environmental variations on measured structural responses, a statistical pattern recognition paradigm is incorporated into the proposed method. The Mahalanobis and Euclidean distance decision functions of the damage feature vector are adopted by defining a statistics-based damage index. The proposed structural damage detection method is verified against one numerical signal and two numerical beams. It is demonstrated that the proposed statistics-based damage index is sensitive to damage and shows some robustness to the noise and false estimation of the system ranks. The method is capable of locating damage of the beam structures under different types of excitations. The robustness of the proposed damage detection method to the variations in environmental temperature is further validated in a companion paper by a reinforced concrete beam tested in the laboratory and a full-scale arch bridge tested in the field.

Nonparaxial wave beams and packets with general astigmatism

NASA Astrophysics Data System (ADS)

Kiselev, A. P.; Plachenov, A. B.; Chamorro-Posada, P.

2012-04-01

We present exact solutions of the wave equation involving an arbitrary wave form with a phase closely similar to the general astigmatic phase of paraxial wave optics. Special choices of the wave form allow general astigmatic beamlike and pulselike waves with a Gaussian-type unrestricted localization in space and time. These solutions are generalizations of the known Bateman-type waves obtained from the connection existing between beamlike solutions of the paraxial parabolic equation and relatively undistorted wave solutions of the wave equation. As a technical tool, we present a full description of parametrizations of 2×2 symmetric matrices with positive imaginary part, which arise in the theory of Gaussian beams.

Loop suppressed light fermion masses with U (1 )R gauge symmetry

NASA Astrophysics Data System (ADS)

Nomura, Takaaki; Okada, Hiroshi

2017-07-01

We propose a model with a two-Higgs doublet, where quark and charged-lepton masses in the first and second families are induced at one-loop level, and neutrino masses are induced at the two-loop level. In our model, we introduce an extra U (1 )R gauge symmetry that plays a crucial role in achieving desired terms in no conflict with anomaly cancellation. We show the mechanism to generate fermion masses, the resultant mass matrices, and Yukawa interactions in mass eigenstates, and we discuss several interesting phenomenologies such as the muon anomalous magnetic dipole moment and the dark matter candidate that arise from this model.

Bi-dimensional null model analysis of presence-absence binary matrices.

PubMed

Strona, Giovanni; Ulrich, Werner; Gotelli, Nicholas J

2018-01-01

Comparing the structure of presence/absence (i.e., binary) matrices with those of randomized counterparts is a common practice in ecology. However, differences in the randomization procedures (null models) can affect the results of the comparisons, leading matrix structural patterns to appear either "random" or not. Subjectivity in the choice of one particular null model over another makes it often advisable to compare the results obtained using several different approaches. Yet, available algorithms to randomize binary matrices differ substantially in respect to the constraints they impose on the discrepancy between observed and randomized row and column marginal totals, which complicates the interpretation of contrasting patterns. This calls for new strategies both to explore intermediate scenarios of restrictiveness in-between extreme constraint assumptions, and to properly synthesize the resulting information. Here we introduce a new modeling framework based on a flexible matrix randomization algorithm (named the "Tuning Peg" algorithm) that addresses both issues. The algorithm consists of a modified swap procedure in which the discrepancy between the row and column marginal totals of the target matrix and those of its randomized counterpart can be "tuned" in a continuous way by two parameters (controlling, respectively, row and column discrepancy). We show how combining the Tuning Peg with a wise random walk procedure makes it possible to explore the complete null space embraced by existing algorithms. This exploration allows researchers to visualize matrix structural patterns in an innovative bi-dimensional landscape of significance/effect size. We demonstrate the rational and potential of our approach with a set of simulated and real matrices, showing how the simultaneous investigation of a comprehensive and continuous portion of the null space can be extremely informative, and possibly key to resolving longstanding debates in the analysis of ecological matrices. © 2017 The Authors. Ecology, published by Wiley Periodicals, Inc., on behalf of the Ecological Society of America.

A systematic linear space approach to solving partially described inverse eigenvalue problems

NASA Astrophysics Data System (ADS)

Hu, Sau-Lon James; Li, Haujun

2008-06-01

Most applications of the inverse eigenvalue problem (IEP), which concerns the reconstruction of a matrix from prescribed spectral data, are associated with special classes of structured matrices. Solving the IEP requires one to satisfy both the spectral constraint and the structural constraint. If the spectral constraint consists of only one or few prescribed eigenpairs, this kind of inverse problem has been referred to as the partially described inverse eigenvalue problem (PDIEP). This paper develops an efficient, general and systematic approach to solve the PDIEP. Basically, the approach, applicable to various structured matrices, converts the PDIEP into an ordinary inverse problem that is formulated as a set of simultaneous linear equations. While solving simultaneous linear equations for model parameters, the singular value decomposition method is applied. Because of the conversion to an ordinary inverse problem, other constraints associated with the model parameters can be easily incorporated into the solution procedure. The detailed derivation and numerical examples to implement the newly developed approach to symmetric Toeplitz and quadratic pencil (including mass, damping and stiffness matrices of a linear dynamic system) PDIEPs are presented. Excellent numerical results for both kinds of problem are achieved under the situations that have either unique or infinitely many solutions.

Hemimorphite as a natural sink for arsenic in zinc deposits and related mine tailings: Evidence from single-crystal EPR spectroscopy and hydrothermal synthesis

NASA Astrophysics Data System (ADS)

Mao, Mao; Lin, Jinru; Pan, Yuanming

2010-05-01

Hemimorphite is a refractory mineral in surface environments and occurs commonly in supergene non-sulfide Zn deposits and Zn mine tailings. Single-crystal electron paramagnetic resonance (EPR) spectra of gamma-ray-irradiated hemimorphite from Mapimi (Durango, Mexico) reveal two arsenic-associated oxyradicals: [AsO 4] 4- and [AsO 4] 2-. Inductively coupled plasma mass spectrometry analyses confirm this sample to contain 270 ppm As and that hemimorphite from other Zn deposits has appreciable amounts of arsenic as well. Spin Hamiltonian parameters, including matrices g, A ( 75As) and P( 75As), show that the [AsO 4] 4- radical formed from electron trapping by a locally uncompensated [AsO 4] 3- ion substituting for [SiO 4] 4-. Matrices g, A( 75As) and P( 75As) of the [AsO 4] 2- radical show it to have the unpaired spin on the bridging oxygen of an [AsO 4] 3- ion at a Si site and linked to a monovalent impurity ion. This structural model for the [AsO 4] 2- radical is further supported by observed 29Si and 1H superhyperfine structures arising from interactions with a single Si atom (A/g eβe = ˜1 mT at B// c) and two equivalent H atoms (A/g eβe = ˜0.3 mT at B∧ b = 10°), respectively. Hydrothermal experiments at 200 °C and ˜9.5 MPa show that hemimorphite contains up to ˜2.5 wt% As 2O 5 and suggest that both the arsenate concentration and the pH value in the solution affect the As content in hemimorphite. These results demonstrate that hemimorphite is capable of sequestering arsenate in its crystal lattice, hence is a natural sink for attenuating As in supergene non-sulfide Zn deposits and Zn mine tailings. Moreover, results from hemimorphite potentially have more far-reaching implications for major silicates such as zeolites in the immobilization and removal of arsenic in surface environments.

Why is it so difficult to classify Renazzo-type (CR) carbonaceous chondrites? - Implications from TEM observations of matrices for the sequences of aqueous alteration

NASA Astrophysics Data System (ADS)

Abreu, Neyda M.

2016-12-01

A number of different classifications have been proposed for the CR chondrites; this study aims at reconciling these different schemes. Mineralogy-based classification has proved particularly challenging for weakly to moderately altered CRs because incipient mineral replacement and elemental mobilization arising from aqueous alteration only affected the most susceptible primary phases, which are generally located in the matrix. Secondary matrix phases are extremely fine-grained (generally sub-micron) and heterogeneously mixed with primary nebular materials. Compositional and isotopic classification parameters are fraught with confounding factors, such as terrestrial weathering, impact processes, and variable abundance of clasts from different regions of the CR parent body or from altogether different planetary bodies. Here, detailed TEM observations from eighteen FIB sections retrieved from the matrices of nine Antarctic CR chondrites (EET 96259, GRA 95229, GRO 95577, GRO 03116, LAP 02342, LAP 04516, LAP 04720, MIL 07525, and MIL 090001) are presented, representing a range of petrologic types. Amorphous Fe-Mg silicates are found to be the dominant phase in all but the most altered CR chondrite matrices, which still retain significant amounts of these amorphous materials. Amorphous Fe-Mg silicates are mixed with phyllosilicates at the nanometer scale. The ratio of amorphous Fe-Mg silicates to phyllosilicates decreases as: (1) the size of phyllosilicates, (2) abundance of magnetite, and (3) replacement of Fe-Ni sulfides increase. Carbonates are only abundant in the most altered CR chondrite, GRO 95577. Nanophase Fe-Ni metal and tochilinite are present small abundances in most CR matrices. Based on the presence, abundance and size of phyllosilicates with respect to amorphous Fe-Mg silicates, the sub-micron features of CR chondrites have been linked to existing classification sequences, and possible reasons for inconsistencies among classification schemes are discussed.

Reading off the nongeometric scalar potentials via the topological data of the compactifying Calabi-Yau manifolds

NASA Astrophysics Data System (ADS)

Shukla, Pramod

2016-10-01

In the context of studying the 4D-effective potentials of type IIB nongeometric flux compactifications, this article has a twofold goal. First, we present a modular invariant symplectic rearrangement of the tree level nongeometric scalar potential arising from a flux superpotential which includes the S-dual pairs of nongeometric fluxes (Q , P ), the standard NS-NS and RR three-form fluxes (F3 , H3 ), and the geometric flux (ω ). This "symplectic formulation" is valid for arbitrary numbers of Kähler moduli, and the complex structure moduli which are implicitly encoded in a set of symplectic matrices. In the second part, we further explicitly rewrite all the symplectic ingredients in terms of saxionic and axionic components of the complex structure moduli. The same leads to a compact form of the generic scalar potential being explicitly written out in terms of all the real moduli/axions. Moreover, the final form of the scalar potential needs only the knowledge of some topological data (such as Hodge numbers and the triple-intersection numbers) of the compactifying threefolds and their respective mirrors. Finally, we demonstrate how the same is equivalent to say that, for a given concrete example, various pieces of the scalar potential can be directly read off from our generic proposal, without the need of starting from the Kähler and superpotentials.

Cell-Adhesive Matrices Composed of RGD Peptide-Displaying M13 Bacteriophage/Poly(lactic-co-glycolic acid) Nanofibers Beneficial to Myoblast Differentiation.

PubMed

Shin, Yong Cheol; Lee, Jong Ho; Jin, Linhua; Kim, Min Jeong; Kim, Chuntae; Hong, Suck Won; Oh, Jin Woo; Han, Dong-Wook

2015-10-01

Recently, there has been considerable effort to develop suitable scaffolds for tissue engineering applications. Cell adhesion is a prerequisite for cells to survive. In nature, the extracellular matrix (ECM) plays this role. Therefore, an ideal scaffold should be structurally similar to the natural ECM and have biocompatibility and biodegradability. In addition, the scaffold should have biofunctionality, which provides the potent ability to enhance the cellular behaviors, such as adhesion, proliferation and differentiation. This study concentrates on fabricating cell-adhesive matrices composed of RGD peptide-displaying M13 bacteriophage (RGD-M13 phage) and poly(lactic-co-glycolic acid, PLGA) nanofibers. Long rod-shaped M13 bacteriophages are non-toxic and can express many desired proteins on their surface. A genetically engineered M13 phage was constructed to display RGD peptides on its surface. PLGA is a biodegradable polymer with excellent biocompatibility and suitable physicochemical property for adhesive matrices. In this study, RGD-M13 phage/PLGA hybrid nanofiber matrices were fabricated by electrospinning. The physicochemical properties of these matrices were characterized by scanning electron microscopy, atomic force microscopy, Raman spectroscopy, and contact angle measurement. In addition, the cellular behaviors, such as the initial attachment, proliferation and differentiation, were analyzed by a CCK-8 assay and immunofluorescence staining to evaluate the potential application of these matrices to tissue engineering scaffolds. The RGD-M13 phage/PLGA nanofiber matrices could enhance the cellular behaviors and promote the differentiation of C2C12 myoblasts. These results suggest that the RGD-M13 phage/PLGA nanofiber matrices are beneficial to myoblast differentiation and can serve as effective tissue engineering scaffolds.

Exact evaluations of some Meijer G-functions and probability of all eigenvalues real for the product of two Gaussian matrices

NASA Astrophysics Data System (ADS)

Kumar, Santosh

2015-11-01

We provide a proof to a recent conjecture by Forrester (2014 J. Phys. A: Math. Theor. 47 065202) regarding the algebraic and arithmetic structure of Meijer G-functions which appear in the expression for probability of all eigenvalues real for the product of two real Gaussian matrices. In the process we come across several interesting identities involving Meijer G-functions.

Reorganization of chromosome architecture in replicative cellular senescence.

PubMed

Criscione, Steven W; De Cecco, Marco; Siranosian, Benjamin; Zhang, Yue; Kreiling, Jill A; Sedivy, John M; Neretti, Nicola

2016-02-01

Replicative cellular senescence is a fundamental biological process characterized by an irreversible arrest of proliferation. Senescent cells accumulate a variety of epigenetic changes, but the three-dimensional (3D) organization of their chromatin is not known. We applied a combination of whole-genome chromosome conformation capture (Hi-C), fluorescence in situ hybridization, and in silico modeling methods to characterize the 3D architecture of interphase chromosomes in proliferating, quiescent, and senescent cells. Although the overall organization of the chromatin into active (A) and repressive (B) compartments and topologically associated domains (TADs) is conserved between the three conditions, a subset of TADs switches between compartments. On a global level, the Hi-C interaction matrices of senescent cells are characterized by a relative loss of long-range and gain of short-range interactions within chromosomes. Direct measurements of distances between genetic loci, chromosome volumes, and chromatin accessibility suggest that the Hi-C interaction changes are caused by a significant reduction of the volumes occupied by individual chromosome arms. In contrast, centromeres oppose this overall compaction trend and increase in volume. The structural model arising from our study provides a unique high-resolution view of the complex chromosomal architecture in senescent cells.

Closed-form eigensolutions of nonviscously, nonproportionally damped systems based on continuous damping sensitivity

NASA Astrophysics Data System (ADS)

Lázaro, Mario

2018-01-01

In this paper, nonviscous, nonproportional, vibrating structures are considered. Nonviscously damped systems are characterized by dissipative mechanisms which depend on the history of the response velocities via hereditary kernel functions. Solutions of the free motion equation lead to a nonlinear eigenvalue problem involving mass, stiffness and damping matrices. Viscoelasticity leads to a frequency dependence of this latter. In this work, a novel closed-form expression to estimate complex eigenvalues is derived. The key point is to consider the damping model as perturbed by a continuous fictitious parameter. Assuming then the eigensolutions as function of this parameter, the computation of the eigenvalues sensitivity leads to an ordinary differential equation, from whose solution arises the proposed analytical formula. The resulting expression explicitly depends on the viscoelasticity (frequency derivatives of the damping function), the nonproportionality (influence of the modal damping matrix off-diagonal terms). Eigenvectors are obtained using existing methods requiring only the corresponding eigenvalue. The method is validated using a numerical example which compares proposed with exact ones and with those determined from the linear first order approximation in terms of the damping matrix. Frequency response functions are also plotted showing that the proposed approach is valid even for moderately or highly damped systems.

Human collagen produced in plants: more than just another molecule.

PubMed

Shoseyov, Oded; Posen, Yehudit; Grynspan, Frida

2014-01-01

Consequential to its essential role as a mechanical support and affinity regulator in extracellular matrices, collagen constitutes a highly sought after scaffolding material for regeneration and healing applications. However, substantiated concerns have been raised with regard to quality and safety of animal tissue-extracted collagen, particularly in relation to its immunogenicity, risk of disease transmission and overall quality and consistency. In parallel, contamination with undesirable cellular factors can significantly impair its bioactivity, vis-a-vis its impact on cell recruitment, proliferation and differentiation. High-scale production of recombinant human collagen Type I (rhCOL1) in the tobacco plant provides a source of an homogenic, heterotrimeric, thermally stable "virgin" collagen which self assembles to fine homogenous fibrils displaying intact binding sites and has been applied to form numerous functional scaffolds for tissue engineering and regenerative medicine. In addition, rhCOL1 can form liquid crystal structures, yielding a well-organized and mechanically strong membrane, two properties indispensable to extracellular matrix (ECM) mimicry. Overall, the shortcomings of animal- and cadaver-derived collagens arising from their source diversity and recycled nature are fully overcome in the plant setting, constituting a collagen source ideal for tissue engineering and regenerative medicine applications.

Fibrous nonlinear elasticity enables positive mechanical feedback between cells and ECMs

PubMed Central

Hall, Matthew S.; Alisafaei, Farid; Ban, Ehsan; Feng, Xinzeng; Hui, Chung-Yuen; Shenoy, Vivek B.; Wu, Mingming

2016-01-01

In native states, animal cells of many types are supported by a fibrous network that forms the main structural component of the ECM. Mechanical interactions between cells and the 3D ECM critically regulate cell function, including growth and migration. However, the physical mechanism that governs the cell interaction with fibrous 3D ECM is still not known. In this article, we present single-cell traction force measurements using breast tumor cells embedded within 3D collagen matrices. We recreate the breast tumor mechanical environment by controlling the microstructure and density of type I collagen matrices. Our results reveal a positive mechanical feedback loop: cells pulling on collagen locally align and stiffen the matrix, and stiffer matrices, in return, promote greater cell force generation and a stiffer cell body. Furthermore, cell force transmission distance increases with the degree of strain-induced fiber alignment and stiffening of the collagen matrices. These findings highlight the importance of the nonlinear elasticity of fibrous matrices in regulating cell–ECM interactions within a 3D context, and the cell force regulation principle that we uncover may contribute to the rapid mechanical tissue stiffening occurring in many diseases, including cancer and fibrosis. PMID:27872289

Human elastin polypeptides improve the biomechanical properties of three-dimensional matrices through the regulation of elastogenesis.

PubMed

Boccafoschi, Francesca; Ramella, Martina; Sibillano, Teresa; De Caro, Liberato; Giannini, Cinzia; Comparelli, Roberto; Bandiera, Antonella; Cannas, Mario

2015-03-01

The replacement of diseased tissues with biological substitutes with suitable biomechanical properties is one of the most important goal in tissue engineering. Collagen represents a satisfactory choice for scaffolds. Unfortunately, the lack of elasticity represents a restriction to a wide use of collagen for several applications. In this work, we studied the effect of human elastin-like polypeptide (HELP) as hybrid collagen-elastin matrices. In particular, we studied the biomechanical properties of collagen/HELP scaffolds considering several components involved in ECM remodeling (elastin, collagen, fibrillin, lectin-like receptor, metalloproteinases) and cell phenotype (myogenin, myosin heavy chain) with particular awareness for vascular tissue engineering applications. Elastin and collagen content resulted upregulated in collagen-HELP matrices, even showing an improved structural remodeling through the involvement of proteins to a ECM remodeling activity. Moreover, the hybrid matrices enhanced the contractile activity of C2C12 cells concurring to improve the mechanical properties of the scaffold. Finally, small-angle X-ray scattering analyses were performed to enable a very detailed analysis of the matrices at the nanoscale, comparing the scaffolds with native blood vessels. In conclusion, our work shows the use of recombinant HELP, as a very promising complement able to significantly improve the biomechanical properties of three-dimensional collagen matrices in terms of tensile stress and elastic modulus. © 2014 Wiley Periodicals, Inc.

TiO2-Based Photocatalytic Geopolymers for Nitric Oxide Degradation

PubMed Central

Strini, Alberto; Roviello, Giuseppina; Ricciotti, Laura; Ferone, Claudio; Messina, Francesco; Schiavi, Luca; Corsaro, Davide; Cioffi, Raffaele

2016-01-01

This study presents an experimental overview for the development of photocatalytic materials based on geopolymer binders as catalyst support matrices. Particularly, geopolymer matrices obtained from different solid precursors (fly ash and metakaolin), composite systems (siloxane-hybrid, foamed hybrid), and curing temperatures (room temperature and 60 °C) were investigated for the same photocatalyst content (i.e., 3% TiO2 by weight of paste). The geopolymer matrices were previously designed for different applications, ranging from insulating (foam) to structural materials. The photocatalytic activity was evaluated as NO degradation in air, and the results were compared with an ordinary Portland cement reference. The studied matrices demonstrated highly variable photocatalytic performance depending on both matrix constituents and the curing temperature, with promising activity revealed by the geopolymers based on fly ash and metakaolin. Furthermore, microstructural features and titania dispersion in the matrices were assessed by scanning electron microscopy (SEM) and energy dispersive X-ray (EDS) analyses. Particularly, EDS analyses of sample sections indicated segregation effects of titania in the surface layer, with consequent enhancement or depletion of the catalyst concentration in the active sample region, suggesting non-negligible transport phenomena during the curing process. The described results demonstrated that geopolymer binders can be interesting catalyst support matrices for the development of photocatalytic materials and indicated a large potential for the exploitation of their peculiar features. PMID:28773634

Characterisation of volatile organic compounds (VOCs) released by the composting of different waste matrices.

PubMed

Schiavon, Marco; Martini, Luca Matteo; Corrà, Cesare; Scapinello, Marco; Coller, Graziano; Tosi, Paolo; Ragazzi, Marco

2017-12-01

The complaints arising from the problem of odorants released by composting plants may impede the construction of new composting facilities, preclude the proper activity of existing facilities or even lead to their closure, with negative implications for waste management and local economy. Improving the knowledge on VOC emissions from composting processes is of particular importance since different VOCs imply different odour impacts. To this purpose, three different organic matrices were studied in this work: dewatered sewage sludge (M1), digested organic fraction of municipal solid waste (M2) and untreated food waste (M3). The three matrices were aerobically biodegraded in a bench-scale bioreactor simulating composting conditions. A homemade device sampled the process air from each treatment at defined time intervals. The samples were analysed for VOC detection. The information on the concentrations of the detected VOCs was combined with the VOC-specific odour thresholds to estimate the relative weight of each biodegraded matrix in terms of odour impact. When the odour formation was at its maximum, the waste gas from the composting of M3 showed a total odour concentration about 60 and 15,000 times higher than those resulting from the composting of M1 and M2, respectively. Ethyl isovalerate showed the highest contribution to the total odour concentration (>99%). Terpenes (α-pinene, β-pinene, p-cymene and limonene) were abundantly present in M2 and M3, while sulphides (dimethyl sulphide and dimethyl disulphide) were the dominant components of M1. Copyright © 2017 Elsevier Ltd. All rights reserved.

Theoretical study of local structure for Ni2+ ions at tetragonal sites in K2ZnF4:Ni2+ system.

PubMed

Wang, Su-Juan; Kuang, Xiao-Yu; Lu, Cheng

2008-12-15

A theoretical method for studying the local lattice structure of Ni2+ ions in (NiF6)(4-) coordination complex is presented. Using the ligand-field model, the formulas relating the microscopic spin Hamiltonian parameters with the crystal structure parameters are derived. Based on the theoretical formulas, the 45 x 45 complete energy matrices for d8 (d2) configuration ions in a tetragonal ligand-field are constructed. By diagonalizing the complete energy matrices, the local distortion structure parameters (R perpendicular and R || ) of Ni2+ ions in K2ZnF4:Ni2+ system have been investigated. The theoretical results are accorded well with the experimental values. Moreover, to understand the detailed physical and chemical properties of the fluoroperovskite crystals, the theoretical values of the g factor of K2ZnF4:Ni2+ system at 78 and 290 K are reported first.

Theoretical study of local structure for Ni 2+ ions at tetragonal sites in K 2ZnF 4:Ni 2+ system

NASA Astrophysics Data System (ADS)

Wang, Su-Juan; Kuang, Xiao-Yu; Lu, Cheng

2008-12-01

A theoretical method for studying the local lattice structure of Ni 2+ ions in (NiF 6) 4- coordination complex is presented. Using the ligand-field model, the formulas relating the microscopic spin Hamiltonian parameters with the crystal structure parameters are derived. Based on the theoretical formulas, the 45 × 45 complete energy matrices for d8 ( d2) configuration ions in a tetragonal ligand-field are constructed. By diagonalizing the complete energy matrices, the local distortion structure parameters ( R⊥ and R||) of Ni 2+ ions in K 2ZnF 4:Ni 2+ system have been investigated. The theoretical results are accorded well with the experimental values. Moreover, to understand the detailed physical and chemical properties of the fluoroperovskite crystals, the theoretical values of the g factor of K 2ZnF 4:Ni 2+ system at 78 and 290 K are reported first.

Symmetric tridiagonal structure preserving finite element model updating problem for the quadratic model

NASA Astrophysics Data System (ADS)

Rakshit, Suman; Khare, Swanand R.; Datta, Biswa Nath

2018-07-01

One of the most important yet difficult aspect of the Finite Element Model Updating Problem is to preserve the finite element inherited structures in the updated model. Finite element matrices are in general symmetric, positive definite (or semi-definite) and banded (tridiagonal, diagonal, penta-diagonal, etc.). Though a large number of papers have been published in recent years on various aspects of solutions of this problem, papers dealing with structure preservation almost do not exist. A novel optimization based approach that preserves the symmetric tridiagonal structures of the stiffness and damping matrices is proposed in this paper. An analytical expression for the global minimum solution of the associated optimization problem along with the results of numerical experiments obtained by both the analytical expressions and by an appropriate numerical optimization algorithm are presented. The results of numerical experiments support the validity of the proposed method.

Robust prediction of consensus secondary structures using averaged base pairing probability matrices.

PubMed

Kiryu, Hisanori; Kin, Taishin; Asai, Kiyoshi

2007-02-15

Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures. We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs. The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available at http://www.ncrna.org/papers/McCaskillMEA/. Supplementary data are available at Bioinformatics online.

An efficient approach for the assembly of mass and stiffness matrices of structures with modifications

NASA Astrophysics Data System (ADS)

Wagner, Andreas; Spelsberg-Korspeter, Gottfried

2013-09-01

The finite element method is one of the most common tools for the comprehensive analysis of structures with applications reaching from static, often nonlinear stress-strain, to transient dynamic analyses. For single calculations the expense to generate an appropriate mesh is often insignificant compared to the analysis time even for complex geometries and therefore negligible. However, this is not the case for certain other applications, most notably structural optimization procedures, where the (re-)meshing effort is very important with respect to the total runtime of the procedure. Thus it is desirable to find methods to efficiently generate mass and stiffness matrices allowing to reduce this effort, especially for structures with modifications of minor complexity, e.g. panels with cutouts. Therefore, a modeling approach referred to as Energy Modification Method is proposed in this paper. The underlying idea is to model and discretize the basis structure, e.g. a plate, and the modifications, e.g. holes, separately. The discretized energy expressions of the modifications are then subtracted from (or added to) the energy expressions of the basis structure and the coordinates are related to each other by kinematical constraints leading to the mass and stiffness matrices of the complete structure. This approach will be demonstrated by two simple examples, a rod with varying material properties and a rectangular plate with a rectangular or circular hole, using a finite element discretization as basis. Convergence studies of the method based on the latter example follow demonstrating the rapid convergence and efficiency of the method. Finally, the Energy Modification Method is successfully used in the structural optimization of a circular plate with holes, with the objective to split all its double eigenfrequencies.

PALS: A unique probe for the molecular organisation of biopolymer matrices

NASA Astrophysics Data System (ADS)

Roussenova, M.; Alam, M. A.

2013-06-01

This short review aims to illustrate the versatility of Positron Annihilation Lifetime Spectroscopy (PALS) when utilized for the characterization of biopolymers (e.g.: starch, fractionated maltooligomers, gelatin and cellulose derivatives) commonly used for the formulation of pharmaceutical encapsulants. By showing examples from a number of recent PALS studies, we illustrate that this technique can be used to probe the changes in thermodynamic state and molecular packing for a wide range of biopolymer matrices as a function of temperature, matrix composition and water content. This provides a basis for establishing composition-structure-property relationships for these materials, which would eventually enable the rational control of their macroscopic properties and the design of optimal encapsulating matrices and intelligent drug delivery systems.

Effects of polyurethane matrices on fungal tannase and gallic acid production under solid state culture*

PubMed Central

Treviňo, Lucia; Contreras-Esquivel, Juan C.; Rodríguez-Herrera, Raul; Aguilar, Cristóbal Noé

2007-01-01

The influence of the physical structure of polyurethane matrix as a support in a solid state culture in tannase production and gallic acid accumulation by Aspergillus niger Aa-20 was evaluated. Three different polyurethane matrices were used as the support: continuous, semi-discontinuous and discontinuous. The highest tannase production at 2479.59 U/L during the first 12 h of culture was obtained using the discontinuous matrix. The gallic acid was accumulated at 7.64 g/L at the discontinuous matrix. The results show that the discontinuous matrix of polyurethane is better for tannase production and gallic acid accumulation in a solid state culture bioprocess than the continuous and semi-discontinuous matrices. PMID:17910122

Task Parallel Incomplete Cholesky Factorization using 2D Partitioned-Block Layout

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Kyungjoo; Rajamanickam, Sivasankaran; Stelle, George Widgery

We introduce a task-parallel algorithm for sparse incomplete Cholesky factorization that utilizes a 2D sparse partitioned-block layout of a matrix. Our factorization algorithm follows the idea of algorithms-by-blocks by using the block layout. The algorithm-byblocks approach induces a task graph for the factorization. These tasks are inter-related to each other through their data dependences in the factorization algorithm. To process the tasks on various manycore architectures in a portable manner, we also present a portable tasking API that incorporates different tasking backends and device-specific features using an open-source framework for manycore platforms i.e., Kokkos. A performance evaluation is presented onmore » both Intel Sandybridge and Xeon Phi platforms for matrices from the University of Florida sparse matrix collection to illustrate merits of the proposed task-based factorization. Experimental results demonstrate that our task-parallel implementation delivers about 26.6x speedup (geometric mean) over single-threaded incomplete Choleskyby- blocks and 19.2x speedup over serial Cholesky performance which does not carry tasking overhead using 56 threads on the Intel Xeon Phi processor for sparse matrices arising from various application problems.« less

Tuning the structural and electronic properties of heterogeneous chalcogenide nanostructures

NASA Astrophysics Data System (ADS)

Giberti, Federico; Voros, Marton; Galli, Giulia

Heterogeneous nanostructures, such as quantum dots (QDs) embedded in solid matrices, are promising platforms for solar energy conversion. Unfortunately, there is scarce information on the structure of the interface between the dots and their embedding matrix, thus hampering the design of functional materials with desired optoelectronic properties. Here, we developed a hierarchical computational strategy to obtain realistic models of semiconductor QDs embedded in matrices using enhanced sampling classical molecular dynamics simulations and predicted their electronic structure using first-principles electronic structure methods. We investigated PbSe/CdSe systems which are promising materials for solar cell applications and found a favorable quasi-type-II band alignments both for PbSe QDs in CdSe matrices and for CdSe embedded in PbSe. However, in the former case, we found the presence of detrimental intra-gap states, while in the latter no defect states are present. Hence we predict that embedding CdSe in PbSe leads to a more efficient platform for solar energy conversion. In addition, we showed that the structure of CdSe QD and in turn its band gap might be tuned by applying pressure to the PbSe matrix, providing a way to engineer the properties of new functional materials. Work by F. Giberti was supported by MICCoM funded by the U.S. Department of Energy (DOE), DOE/BES 5J-30161-0010A; work by M. Voros was supported by the U.S. DOE, under Award DE-AC02-06CH11357.

Fabrication of chemically cross-linked porous gelatin matrices.

PubMed

Bozzini, Sabrina; Petrini, Paola; Altomare, Lina; Tanzi, Maria Cristina

2009-01-01

The aim of this study was to chemically cross-link gelatin, by reacting its free amino groups with an aliphatic diisocyanate. To produce hydrogels with controllable properties, the number of reacting amino groups was carefully determined. Porosity was introduced into the gelatin-based hydrogels through the lyophilization process. Porous and non-porous matrices were characterized with respect to their chemical structure, morphology, water uptake and mechanical properties. The physical, chemical and mechanical properties of the porous matrices are related to the extent of their cross-linking, showing that they can be controlled by varying the reaction parameters. Water uptake values (24 hours) vary between 160% and 200% as the degree of cross-linking increases. The flexibility of the samples also decreases by changing the extent of cross-linking. Young's modulus shows values between 0.188 KPa, for the highest degree, and 0.142 KPa for the lowest degree. The matrices are potential candidates for use as tissue-engineering scaffolds by modulating their physical chemical properties according to the specific application.

Large-deviation theory for diluted Wishart random matrices

NASA Astrophysics Data System (ADS)

Castillo, Isaac Pérez; Metz, Fernando L.

2018-03-01

Wishart random matrices with a sparse or diluted structure are ubiquitous in the processing of large datasets, with applications in physics, biology, and economy. In this work, we develop a theory for the eigenvalue fluctuations of diluted Wishart random matrices based on the replica approach of disordered systems. We derive an analytical expression for the cumulant generating function of the number of eigenvalues IN(x ) smaller than x ∈R+ , from which all cumulants of IN(x ) and the rate function Ψx(k ) controlling its large-deviation probability Prob[IN(x ) =k N ] ≍e-N Ψx(k ) follow. Explicit results for the mean value and the variance of IN(x ) , its rate function, and its third cumulant are discussed and thoroughly compared to numerical diagonalization, showing very good agreement. The present work establishes the theoretical framework put forward in a recent letter [Phys. Rev. Lett. 117, 104101 (2016), 10.1103/PhysRevLett.117.104101] as an exact and compelling approach to deal with eigenvalue fluctuations of sparse random matrices.

A new measure based on degree distribution that links information theory and network graph analysis

PubMed Central

2012-01-01

Background Detailed connection maps of human and nonhuman brains are being generated with new technologies, and graph metrics have been instrumental in understanding the general organizational features of these structures. Neural networks appear to have small world properties: they have clustered regions, while maintaining integrative features such as short average pathlengths. Results We captured the structural characteristics of clustered networks with short average pathlengths through our own variable, System Difference (SD), which is computationally simple and calculable for larger graph systems. SD is a Jaccardian measure generated by averaging all of the differences in the connection patterns between any two nodes of a system. We calculated SD over large random samples of matrices and found that high SD matrices have a low average pathlength and a larger number of clustered structures. SD is a measure of degree distribution with high SD matrices maximizing entropic properties. Phi (Φ), an information theory metric that assesses a system’s capacity to integrate information, correlated well with SD - with SD explaining over 90% of the variance in systems above 11 nodes (tested for 4 to 13 nodes). However, newer versions of Φ do not correlate well with the SD metric. Conclusions The new network measure, SD, provides a link between high entropic structures and degree distributions as related to small world properties. PMID:22726594

Meta-Analytic Structural Equation Modeling (MASEM): Comparison of the Multivariate Methods

ERIC Educational Resources Information Center

Zhang, Ying

2011-01-01

Meta-analytic Structural Equation Modeling (MASEM) has drawn interest from many researchers recently. In doing MASEM, researchers usually first synthesize correlation matrices across studies using meta-analysis techniques and then analyze the pooled correlation matrix using structural equation modeling techniques. Several multivariate methods of…

Random-Effects Models for Meta-Analytic Structural Equation Modeling: Review, Issues, and Illustrations

ERIC Educational Resources Information Center

Cheung, Mike W.-L.; Cheung, Shu Fai

2016-01-01

Meta-analytic structural equation modeling (MASEM) combines the techniques of meta-analysis and structural equation modeling for the purpose of synthesizing correlation or covariance matrices and fitting structural equation models on the pooled correlation or covariance matrix. Both fixed-effects and random-effects models can be defined in MASEM.…

Joining of Components of Complex Structures for Improved Dynamic Response

DTIC Science & Technology

2011-10-28

system- level mass and stiffness matrices and force vector (at each frequency in the range of interest). To address this issue a series of complex...displacements of all candidate joint locations by using the system- level mass and stiffness matrices and force vector (at each frequency in the range of...joints. In contrast, Li et al. [10] proposed a fastener layout/topology that achieves an almost uniform stress level in each joint, and adopted

Low-rank matrix fitting based on subspace perturbation analysis with applications to structure from motion.

PubMed

Jia, Hongjun; Martinez, Aleix M

2009-05-01

The task of finding a low-rank (r) matrix that best fits an original data matrix of higher rank is a recurring problem in science and engineering. The problem becomes especially difficult when the original data matrix has some missing entries and contains an unknown additive noise term in the remaining elements. The former problem can be solved by concatenating a set of r-column matrices that share a common single r-dimensional solution space. Unfortunately, the number of possible submatrices is generally very large and, hence, the results obtained with one set of r-column matrices will generally be different from that captured by a different set. Ideally, we would like to find that solution that is least affected by noise. This requires that we determine which of the r-column matrices (i.e., which of the original feature points) are less influenced by the unknown noise term. This paper presents a criterion to successfully carry out such a selection. Our key result is to formally prove that the more distinct the r vectors of the r-column matrices are, the less they are swayed by noise. This key result is then combined with the use of a noise model to derive an upper bound for the effect that noise and occlusions have on each of the r-column matrices. It is shown how this criterion can be effectively used to recover the noise-free matrix of rank r. Finally, we derive the affine and projective structure-from-motion (SFM) algorithms using the proposed criterion. Extensive validation on synthetic and real data sets shows the superiority of the proposed approach over the state of the art.

Electronic-topological study of the structure-activity relationships in a series of steroids with mineralocorticoid binding affinity.

PubMed

Kandemirli, Fatma; Tokay, Nesrin; Shvets, Nataly M; Dimoglo, Anatoly S

2003-01-01

Conformational analysis and quantum chemical calculations were carried out using molecular mechanics (MMP2) and semi-empirical quantum chemistry (CNDO/2) methods for 51 steroid homologues belonging to a series of 17-spirolactones. Matrices called Electronic-Topological Matrices of Conjunction (ETMCs) were formed using data obtained from quantum chemical calculations. A structural fragment of activity was identified in the series of steroids. As seen from the fragment's properties, active compounds are characterized by the presence of two atoms of oxygen, O1 and O3, which are situated at a distance of 13.5 A and possess high negative charges (-0.29 to -0.31 e).

System identification of analytical models of damped structures

NASA Technical Reports Server (NTRS)

Fuh, J.-S.; Chen, S.-Y.; Berman, A.

1984-01-01

A procedure is presented for identifying linear nonproportionally damped system. The system damping is assumed to be representable by a real symmetric matrix. Analytical mass, stiffness and damping matrices which constitute an approximate representation of the system are assumed to be available. Given also are an incomplete set of measured natural frequencies, damping ratios and complex mode shapes of the structure, normally obtained from test data. A method is developed to find the smallest changes in the analytical model so that the improved model can exactly predict the measured modal parameters. The present method uses the orthogonality relationship to improve mass and damping matrices and the dynamic equation to find the improved stiffness matrix.

Brief announcement: Hypergraph parititioning for parallel sparse matrix-matrix multiplication

DOE PAGES

Ballard, Grey; Druinsky, Alex; Knight, Nicholas; ...

2015-01-01

The performance of parallel algorithms for sparse matrix-matrix multiplication is typically determined by the amount of interprocessor communication performed, which in turn depends on the nonzero structure of the input matrices. In this paper, we characterize the communication cost of a sparse matrix-matrix multiplication algorithm in terms of the size of a cut of an associated hypergraph that encodes the computation for a given input nonzero structure. Obtaining an optimal algorithm corresponds to solving a hypergraph partitioning problem. Furthermore, our hypergraph model generalizes several existing models for sparse matrix-vector multiplication, and we can leverage hypergraph partitioners developed for that computationmore » to improve application-specific algorithms for multiplying sparse matrices.« less

Structural Analysis of Covariance and Correlation Matrices.

ERIC Educational Resources Information Center

Joreskog, Karl G.

1978-01-01

A general approach to analysis of covariance structures is considered, in which the variances and covariances or correlations of the observed variables are directly expressed in terms of the parameters of interest. The statistical problems of identification, estimation and testing of such covariance or correlation structures are discussed.…

Structural and Spectroscopic Studies of Sm3+/CdS Nanocrystallites in Sol-Gel TiO2-ZrO2 Matrix

NASA Astrophysics Data System (ADS)

Karthika, S.; Prathibha, Vasudevan; Ann, Mary K. A.; Viji, Vidyadharan; Biju, P. R.; Unnikrishnan, N. V.

2014-02-01

A sol-gel method was used to prepare titania-zirconia matrices doped with Sm3+/CdS nanocrystallites. The structural properties of the matrices were characterized using transmission electron microscopy (TEM), thermogravimetric analysis (TGA), differential thermal analysis (DTA), and Fourier-transform infrared spectroscopy studies. The thermal stability of the material was determined by TGA/DTA analysis. The absorption spectrum shows the characteristic peaks of the Sm3+ ions and the absorption peak corresponding to the CdS nanocrystallites. The optical bandgap and size of the CdS nanoparticles were calculated from the absorption spectrum. From TEM, the interplanar distance ( d) was estimated to be 3.533 Å, which matches with the (1 0 0) plane of bulk CdS. The measurements yield a nanocrystallite size of around 7.8 nm. The optical absorption and emission spectra confirmed the formation of CdS nanoparticles along with samarium ions in the titania-zirconia matrices. The fluorescence intensity of the samarium ions was found to be greatly enhanced by codoping with CdS nanocrystallites.

Riemannian multi-manifold modeling and clustering in brain networks

NASA Astrophysics Data System (ADS)

Slavakis, Konstantinos; Salsabilian, Shiva; Wack, David S.; Muldoon, Sarah F.; Baidoo-Williams, Henry E.; Vettel, Jean M.; Cieslak, Matthew; Grafton, Scott T.

2017-08-01

This paper introduces Riemannian multi-manifold modeling in the context of brain-network analytics: Brainnetwork time-series yield features which are modeled as points lying in or close to a union of a finite number of submanifolds within a known Riemannian manifold. Distinguishing disparate time series amounts thus to clustering multiple Riemannian submanifolds. To this end, two feature-generation schemes for brain-network time series are put forth. The first one is motivated by Granger-causality arguments and uses an auto-regressive moving average model to map low-rank linear vector subspaces, spanned by column vectors of appropriately defined observability matrices, to points into the Grassmann manifold. The second one utilizes (non-linear) dependencies among network nodes by introducing kernel-based partial correlations to generate points in the manifold of positivedefinite matrices. Based on recently developed research on clustering Riemannian submanifolds, an algorithm is provided for distinguishing time series based on their Riemannian-geometry properties. Numerical tests on time series, synthetically generated from real brain-network structural connectivity matrices, reveal that the proposed scheme outperforms classical and state-of-the-art techniques in clustering brain-network states/structures.

Modeling of trim panels in the energy finite element analysis

NASA Astrophysics Data System (ADS)

Moravaeji, Seyed-Javid

Modeling a trim panel is divided into finding the power exchange through two different paths: (i) the connection of the outer and inner panels (ii) through the layers directly. The vibrational power exchanged through the mounts is modeled as the connection of two parallel plates connected via a beam. Wave matrices representing plates and beams are derived separately; then a matrix method is proposed to solve for the wave amplitudes and hence the vibrational power exchange between the plates accordingly. A closed form formula for the case of connection of two identical plates is derived. For the power transmission loss directly through the layers, first transfer matrices representing layers made of different materials is considered. New matrices for a porous layer are derived. A method of finding the layered structure transfer matrix is proposed. It is concluded that in general a single isotropic layer cannot replace a structure accurately. Finally, on the basis of an equivalent transfer matrix, an optimization process for is proposed to replace the panel by a suitable set of layers.

Empirical Bayes method for reducing false discovery rates of correlation matrices with block diagonal structure.

PubMed

Pacini, Clare; Ajioka, James W; Micklem, Gos

2017-04-12

Correlation matrices are important in inferring relationships and networks between regulatory or signalling elements in biological systems. With currently available technology sample sizes for experiments are typically small, meaning that these correlations can be difficult to estimate. At a genome-wide scale estimation of correlation matrices can also be computationally demanding. We develop an empirical Bayes approach to improve covariance estimates for gene expression, where we assume the covariance matrix takes a block diagonal form. Our method shows lower false discovery rates than existing methods on simulated data. Applied to a real data set from Bacillus subtilis we demonstrate it's ability to detecting known regulatory units and interactions between them. We demonstrate that, compared to existing methods, our method is able to find significant covariances and also to control false discovery rates, even when the sample size is small (n=10). The method can be used to find potential regulatory networks, and it may also be used as a pre-processing step for methods that calculate, for example, partial correlations, so enabling the inference of the causal and hierarchical structure of the networks.

In Situ Porous Structures: A Unique Polymer Erosion Mechanism in Biodegradable Dipeptide-based Polyphosphazene and Polyester Blends Producing Matrices for Regenerative Engineering

PubMed Central

Deng, Meng; Nair, Lakshmi S.; Nukavarapu, Syam P.; Kumbar, Sangamesh G.; Jiang, Tao; Weikel, Arlin L.; Krogman, Nicholas R.; Allcock, Harry R.; Laurencin, Cato T.

2011-01-01

Synthetic biodegradable polymers serve as temporary substrates that accommodate cell infiltration and tissue in-growth in regenerative medicine. To allow tissue in-growth and nutrient transport, traditional three-dimensional (3D) scaffolds must be prefabricated with an interconnected porous structure. Here we demonstrated for the first time a unique polymer erosion process through which polymer matrices evolve from a solid coherent film to an assemblage of microspheres with an interconnected 3D porous structure. This polymer system was developed on the highly versatile platform of polyphosphazene-polyester blends. Co-substituting a polyphosphazene backbone with both hydrophilic glycylglycine dipeptide and hydrophobic 4-phenylphenoxy group generated a polymer with strong hydrogen bonding capacity. Rapid hydrolysis of the polyester component permitted the formation of 3D void space filled with self-assembled polyphosphazene spheres. Characterization of such self-assembled porous structures revealed macropores (10-100 μm) between spheres as well as micro- and nanopores on the sphere surface. A similar degradation pattern was confirmed in vivo using a rat subcutaneous implantation model. 12 weeks of implantation resulted in an interconnected porous structure with 82-87% porosity. Cell infiltration and collagen tissue in-growth between microspheres observed by histology confirmed the formation of an in situ 3D interconnected porous structure. It was determined that the in situ porous structure resulted from unique hydrogen bonding in the blend promoting a three-stage degradation mechanism. The robust tissue in-growth of this dynamic pore forming scaffold attests to the utility of this system as a new strategy in regenerative medicine for developing solid matrices that balance degradation with tissue formation. PMID:21789036

Histopathologic investigations of the unphonated human child vocal fold mucosa.

PubMed

Sato, Kiminori; Umeno, Hirohito; Nakashima, Tadashi; Nonaka, Satoshi; Harabuchi, Yasuaki

2012-01-01

Vocal fold stellate cells (VFSCs) in the maculae flavae (MFe) located at both ends of the vocal fold mucosa are inferred to be involved in the metabolism of extracellular matrices. MFe are also considered to be an important structure in the growth and development of the human vocal fold mucosa. Tension caused by phonation (vocal fold vibration) is hypothesized to stimulate VFSCs to accelerate production of extracellular matrices. Human child vocal fold mucosae unphonated since birth were investigated histologically. Histologic analysis of human child vocal fold mucosa. Vocal fold mucosae, which have remained unphonated since birth, of two children (7 and 12 years old) with cerebral palsy were investigated by light and electron microscopy and compared with normal subjects. Vocal fold mucosae and MFe were hypoplastic and rudimentary and did not have a vocal ligament, Reinke's space, or the layered structure. The lamina propria appeared as a uniform structure. Some VFSCs in the MFe showed degeneration and not many vesicles were present at the periphery of the cytoplasm. The VFSCs synthesized fewer extracellular matrices, such as fibrous protein and glycosaminoglycan. The VFSCs appeared to have decreased activity. Vocal fold vibration (phonation) after birth is an important factor in the growth and development of the human vocal fold mucosa. Copyright © 2012 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

Model reduction and frequency residuals for a robust estimation of nonlinearities in subspace identification

NASA Astrophysics Data System (ADS)

De Filippis, G.; Noël, J. P.; Kerschen, G.; Soria, L.; Stephan, C.

2017-09-01

The introduction of the frequency-domain nonlinear subspace identification (FNSI) method in 2013 constitutes one in a series of recent attempts toward developing a realistic, first-generation framework applicable to complex structures. If this method showed promising capabilities when applied to academic structures, it is still confronted with a number of limitations which needs to be addressed. In particular, the removal of nonphysical poles in the identified nonlinear models is a distinct challenge. In the present paper, it is proposed as a first contribution to operate directly on the identified state-space matrices to carry out spurious pole removal. A modal-space decomposition of the state and output matrices is examined to discriminate genuine from numerical poles, prior to estimating the extended input and feedthrough matrices. The final state-space model thus contains physical information only and naturally leads to nonlinear coefficients free of spurious variations. Besides spurious variations due to nonphysical poles, vibration modes lying outside the frequency band of interest may also produce drifts of the nonlinear coefficients. The second contribution of the paper is to include residual terms, accounting for the existence of these modes. The proposed improved FNSI methodology is validated numerically and experimentally using a full-scale structure, the Morane-Saulnier Paris aircraft.

Globally altered structural brain network topology in grapheme-color synesthesia.

PubMed

Hänggi, Jürgen; Wotruba, Diana; Jäncke, Lutz

2011-04-13

Synesthesia is a perceptual phenomenon in which stimuli in one particular modality elicit a sensation within the same or another sensory modality (e.g., specific graphemes evoke the perception of particular colors). Grapheme-color synesthesia (GCS) has been proposed to arise from abnormal local cross-activation between grapheme and color areas because of their hyperconnectivity. Recently published studies did not confirm such a hyperconnectivity, although morphometric alterations were found in occipitotemporal, parietal, and frontal regions of synesthetes. We used magnetic resonance imaging surface-based morphometry and graph-theoretical network analyses to investigate the topology of structural brain networks in 24 synesthetes and 24 nonsynesthetes. Connectivity matrices were derived from region-wise cortical thickness correlations of 2366 different cortical parcellations across the whole cortex and from 154 more common brain divisions as well. Compared with nonsynesthetes, synesthetes revealed a globally altered structural network topology as reflected by reduced small-worldness, increased clustering, increased degree, and decreased betweenness centrality. Connectivity of the fusiform gyrus (FuG) and intraparietal sulcus (IPS) was changed as well. Hierarchical modularity analysis revealed increased intramodular and intermodular connectivity of the IPS in GCS. However, connectivity differences in the FuG and IPS showed a low specificity because of global changes. We provide first evidence that GCS is rooted in a reduced small-world network organization that is driven by increased clustering suggesting global hyperconnectivity within the synesthetes' brain. Connectivity alterations were widespread and not restricted to the FuG and IPS. Therefore, synesthetic experience might be only one phenotypic manifestation of the globally altered network architecture in GCS.

Discrimination Power of Polynomial-Based Descriptors for Graphs by Using Functional Matrices.

PubMed

Dehmer, Matthias; Emmert-Streib, Frank; Shi, Yongtang; Stefu, Monica; Tripathi, Shailesh

2015-01-01

In this paper, we study the discrimination power of graph measures that are based on graph-theoretical matrices. The paper generalizes the work of [M. Dehmer, M. Moosbrugger. Y. Shi, Encoding structural information uniquely with polynomial-based descriptors by employing the Randić matrix, Applied Mathematics and Computation, 268(2015), 164-168]. We demonstrate that by using the new functional matrix approach, exhaustively generated graphs can be discriminated more uniquely than shown in the mentioned previous work.

Discrimination Power of Polynomial-Based Descriptors for Graphs by Using Functional Matrices

PubMed Central

Dehmer, Matthias; Emmert-Streib, Frank; Shi, Yongtang; Stefu, Monica; Tripathi, Shailesh

2015-01-01

In this paper, we study the discrimination power of graph measures that are based on graph-theoretical matrices. The paper generalizes the work of [M. Dehmer, M. Moosbrugger. Y. Shi, Encoding structural information uniquely with polynomial-based descriptors by employing the Randić matrix, Applied Mathematics and Computation, 268(2015), 164–168]. We demonstrate that by using the new functional matrix approach, exhaustively generated graphs can be discriminated more uniquely than shown in the mentioned previous work. PMID:26479495

Photochemistry of pyrene with water at low temperature: study of atmospherical and astrochemical interest.

PubMed

Guennoun, Zohra; Aupetit, Christian; Mascetti, Joëlle

2011-03-17

Photochemistry of a polyaromatic hydrocarbon, pyrene C(16)H(10), with water has been investigated at cryogenic temperatures. Photoprocessing of this species, performed at λ > 235 nm, in argon matrices, adsorbed onto amorphous water surfaces, and trapped in solid water, led to the formation of ketonic isomers, C(16)H(10)O, and possibly quinones. These species have been identified for the first time by infrared spectroscopy with the support of isotopic substitution experiments and DFT calculations. These oxidized pyrene-like species, of atmospherical and astrochemical interest, most likely arise from a tautomeric rearrangement of their analogous hydroxylated molecules, these latter being formed by reaction of water with pyrene cations.

Calculation of spherical harmonics and Wigner d functions by FFT. Applications to fast rotational matching in molecular replacement and implementation into AMoRe.

PubMed

Trapani, Stefano; Navaza, Jorge

2006-07-01

The FFT calculation of spherical harmonics, Wigner D matrices and rotation function has been extended to all angular variables in the AMoRe molecular replacement software. The resulting code avoids singularity issues arising from recursive formulas, performs faster and produces results with at least the same accuracy as the original code. The new code aims at permitting accurate and more rapid computations at high angular resolution of the rotation function of large particles. Test calculations on the icosahedral IBDV VP2 subviral particle showed that the new code performs on the average 1.5 times faster than the original code.

Substructure-based control of flexible structures

NASA Technical Reports Server (NTRS)

Babuska, Vit; Craig, Roy R., Jr.

1993-01-01

A decentralized procedure is presented for the design of controllers for flexible structures. Spatially significant components are created which approximate the response of a specific part of the complete structure. For each component, the controller and observer gain matrices which are used in a controller for the complete structure. The proposed method is illustrated on a model of NASA Langley's CSI testbed structure.

A Note on the Factor Analysis of Partial Covariance Matrices

ERIC Educational Resources Information Center

McDonald, Roderick P.

1978-01-01

The relationship between the factor structure of a convariance matrix and the factor structure of a partial convariance matrix when one or more variables are partialled out of the original matrix is given in this brief note. (JKS)

Matrix density alters zyxin phosphorylation, which limits peripheral process formation and extension in endothelial cells invading 3D collagen matrices.

PubMed

Abbey, Colette A; Bayless, Kayla J

2014-09-01

This study was designed to determine the optimal conditions required for known pro-angiogenic stimuli to elicit successful endothelial sprouting responses. We used an established, quantifiable model of endothelial cell (EC) sprout initiation where ECs were tested for invasion in low (1 mg/mL) and high density (5 mg/mL) 3D collagen matrices. Sphingosine 1-phosphate (S1P) alone, or S1P combined with stromal derived factor-1α (SDF) and phorbol ester (TPA), elicited robust sprouting responses. The ability of these factors to stimulate sprouting was more effective in higher density collagen matrices. S1P stimulation resulted in a significant increase in invasion distance, and with the exception of treatment groups containing phorbol ester, invasion distance was longer in 1mg/mL compared to 5mg/mL collagen matrices. Closer examination of cell morphology revealed that increasing matrix density and supplementing with SDF and TPA enhanced the formation of multicellular structures more closely resembling capillaries. TPA enhanced the frequency and size of lumen formation and correlated with a robust increase in phosphorylation of p42/p44 Erk kinase, while S1P and SDF did not. Also, a higher number of significantly longer extended processes formed in 5mg/mL compared to 1mg/mL collagen matrices. Because collagen matrices at higher density have been reported to be stiffer, we tested for changes in the mechanosensitive protein, zyxin. Interestingly, zyxin phosphorylation levels inversely correlated with matrix density, while levels of total zyxin did not change significantly. Immunofluorescence and localization studies revealed that total zyxin was distributed evenly throughout invading structures, while phosphorylated zyxin was slightly more intense in extended peripheral processes. Silencing zyxin expression increased extended process length and number of processes, while increasing zyxin levels decreased extended process length. Altogether these data indicate that ECs integrate signals from multiple exogenous factors, including changes in matrix density, to accomplish successful sprouting responses. We show here for the first time that zyxin limited the formation and extension of fine peripheral processes used by ECs for matrix interrogation, providing a molecular explanation for altered EC responses to high and low density collagen matrices. Copyright © 2014 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

Encoding of low-quality DNA profiles as genotype probability matrices for improved profile comparisons, relatedness evaluation and database searches.

PubMed

Ryan, K; Williams, D Gareth; Balding, David J

2016-11-01

Many DNA profiles recovered from crime scene samples are of a quality that does not allow them to be searched against, nor entered into, databases. We propose a method for the comparison of profiles arising from two DNA samples, one or both of which can have multiple donors and be affected by low DNA template or degraded DNA. We compute likelihood ratios to evaluate the hypothesis that the two samples have a common DNA donor, and hypotheses specifying the relatedness of two donors. Our method uses a probability distribution for the genotype of the donor of interest in each sample. This distribution can be obtained from a statistical model, or we can exploit the ability of trained human experts to assess genotype probabilities, thus extracting much information that would be discarded by standard interpretation rules. Our method is compatible with established methods in simple settings, but is more widely applicable and can make better use of information than many current methods for the analysis of mixed-source, low-template DNA profiles. It can accommodate uncertainty arising from relatedness instead of or in addition to uncertainty arising from noisy genotyping. We describe a computer program GPMDNA, available under an open source licence, to calculate LRs using the method presented in this paper. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A program for calculating load coefficient matrices utilizing the force summation method, L218 (LOADS). Volume 1: Engineering and usage

NASA Technical Reports Server (NTRS)

Miller, R. D.; Anderson, L. R.

1979-01-01

The LOADS program L218, a digital computer program that calculates dynamic load coefficient matrices utilizing the force summation method, is described. The load equations are derived for a flight vehicle in straight and level flight and excited by gusts and/or control motions. In addition, sensor equations are calculated for use with an active control system. The load coefficient matrices are calculated for the following types of loads: translational and rotational accelerations, velocities, and displacements; panel aerodynamic forces; net panel forces; shears and moments. Program usage and a brief description of the analysis used are presented. A description of the design and structure of the program to aid those who will maintain and/or modify the program in the future is included.

Electronic and magnetic properties of Ni nanoparticles embedded in various organic semiconductor matrices.

PubMed

Bräuer, Björn; Vaynzof, Yana; Zhao, Wei; Kahn, Antoine; Li, Wen; Zahn, Dietrich R T; Fernández, César de Julián; Sangregorio, Claudio; Salvan, Georgeta

2009-04-09

Ni nanoparticles with a size distribution from 2 to 6 nm, embedded in various organic matrices, were fabricated in ultrahigh vacuum. For this purpose metal free and Ni phthalocyanine, fullerene C(60), and pentacene were coevaporated with Ni. When coevaporated, Ni and H(2)Pc react, leading to the formation of NiPc and Ni nanoparticles. The molecular structure of the matrix was found to have negligible effect on the size of the nanoparticles but to influence the magnetic anisotropy of the nanoparticles: Ni nanoparticles formed in the buckyball matrix have a cubic symmetry, while nanoparticles formed in matrices consisting of planar molecules exhibit a uniaxial symmetry. After exposure to atmosphere, photoelectron spectroscopy investigations demonstrate the presence of metallic Ni nanoparticles accompanied by Ni oxide and the existence of a charge transfer from the organic matrix to the particles in all investigated systems. The oxidized Ni nanoparticles exhibit a larger magnetic anisotropy compared to the freshly prepared particles which show superparamagnetic properties above 17 K. Moreover, photoelectron spectroscopy was used to probe the oxidation process of the Ni nanoparticles in different organic matrices. It could thus be shown that a matrix consisting of spherical molecules like C(60) prevent the particles much better from oxidation compared to matrices of flat molecules.

Beam splitter phase shifts: Wave optics approach

NASA Astrophysics Data System (ADS)

Agnesi, Antonio; Degiorgio, Vittorio

2017-10-01

We investigate the phase relationships between transmitted and reflected waves in a lossless beam splitter having a multilayer structure, using the matrix approach as outlined in classical optics books. Contrarily to the case of the quantum optics formalism generally employed to describe beam splitters, these matrices are not unitary. In this note we point out the existence of general relations among the elements of the transfer matrix that describes the multilayer beam splitter. Such relations, which are independent of the detailed structure of the beam splitter, fix the phase shifts between reflected and transmitted waves. It is instructive to see how the results obtained by Zeilinger by using spinor algebra and Pauli matrices can be easily derived from our general relations.

A special form of SPD covariance matrix for interpretation and visualization of data manipulated with Riemannian geometry

NASA Astrophysics Data System (ADS)

Congedo, Marco; Barachant, Alexandre

2015-01-01

Currently the Riemannian geometry of symmetric positive definite (SPD) matrices is gaining momentum as a powerful tool in a wide range of engineering applications such as image, radar and biomedical data signal processing. If the data is not natively represented in the form of SPD matrices, typically we may summarize them in such form by estimating covariance matrices of the data. However once we manipulate such covariance matrices on the Riemannian manifold we lose the representation in the original data space. For instance, we can evaluate the geometric mean of a set of covariance matrices, but not the geometric mean of the data generating the covariance matrices, the space of interest in which the geometric mean can be interpreted. As a consequence, Riemannian information geometry is often perceived by non-experts as a "black-box" tool and this perception prevents a wider adoption in the scientific community. Hereby we show that we can overcome this limitation by constructing a special form of SPD matrix embedding both the covariance structure of the data and the data itself. Incidentally, whenever the original data can be represented in the form of a generic data matrix (not even square), this special SPD matrix enables an exhaustive and unique description of the data up to second-order statistics. This is achieved embedding the covariance structure of both the rows and columns of the data matrix, allowing naturally a wide range of possible applications and bringing us over and above just an interpretability issue. We demonstrate the method by manipulating satellite images (pansharpening) and event-related potentials (ERPs) of an electroencephalography brain-computer interface (BCI) study. The first example illustrates the effect of moving along geodesics in the original data space and the second provides a novel estimation of ERP average (geometric mean), showing that, in contrast to the usual arithmetic mean, this estimation is robust to outliers. In conclusion, we are able to show that the Riemannian concepts of distance, geometric mean, moving along a geodesic, etc. can be readily transposed into a generic data space, whatever this data space represents.

Carcinogenesis: alterations in reciprocal interactions of normal functional structure of biologic systems.

PubMed

Davydyan, Garri

2015-12-01

The evolution of biologic systems (BS) includes functional mechanisms that in some conditions may lead to the development of cancer. Using mathematical group theory and matrix analysis, previously, it was shown that normally functioning BS are steady functional structures regulated by three basis regulatory components: reciprocal links (RL), negative feedback (NFB) and positive feedback (PFB). Together, they form an integrative unit maintaining system's autonomy and functional stability. It is proposed that phylogenetic development of different species is implemented by the splitting of "rudimentary" characters into two relatively independent functional parts that become encoded in chromosomes. The functional correlate of splitting mechanisms is RL. Inversion of phylogenetic mechanisms during ontogenetic development leads cell differentiation until cells reach mature states. Deterioration of reciprocal structure in the genome during ontogenesis gives rise of pathological conditions characterized by unsteadiness of the system. Uncontrollable cell proliferation and invasive cell growth are the leading features of the functional outcomes of malfunctioning systems. The regulatory element responsible for these changes is RL. In matrix language, pathological regulation is represented by matrices having positive values of diagonal elements ( TrA  > 0) and also positive values of matrix determinant ( detA  > 0). Regulatory structures of that kind can be obtained if the negative entry of the matrix corresponding to RL is replaced with the positive one. To describe not only normal but also pathological states of BS, a unit matrix should be added to the basis matrices representing RL, NFB and PFB. A mathematical structure corresponding to the set of these four basis functional patterns (matrices) is a split quaternion (coquaternion). The structure and specific role of basis elements comprising four-dimensional linear space of split quaternions help to understand what changes in mechanism of cell differentiation may lead to cancer development.

Spine and test skeletal matrices of the Mediterranean sea urchin Arbacia lixula--a comparative characterization of their sugar signature.

PubMed

Kanold, Julia M; Guichard, Nathalie; Immel, Françoise; Plasseraud, Laurent; Corneillat, Marion; Alcaraz, Gérard; Brümmer, Franz; Marin, Frédéric

2015-05-01

Calcified structures of sea urchins are biocomposite materials that comprise a minor fraction of organic macromolecules, such as proteins, glycoproteins and polysaccharides. These macromolecules are thought to collectively regulate mineral deposition during the process of calcification. When occluded, they modify the properties of the mineral. In the present study, the organic matrices (both soluble and insoluble in acetic acid) of spines and tests from the Mediterranean black sea urchin Arbacia lixula were extracted and characterized, in order to determine whether they exhibit similar biochemical signatures. Bulk characterizations were performed by mono-dimensional SDS/PAGE, FT-IR spectroscopy, and an in vitro crystallization assay. We concentrated our efforts on characterization of the sugar moieties. To this end, we determined the monosaccharide content of the soluble and insoluble organic matrices of A. lixula spines and tests by HPAE-PAD, together with their respective lectin-binding profiles via enzyme-linked lectin assay. Finally, we performed in situ localization of N-acetyl glucosamine-containing saccharides on spines and tests using gold-conjugated wheatgerm agglutinin. Our data show that the test and spine matrices exhibit different biochemical signatures with regard to their saccharidic fraction, suggesting that future studies should analyse the regulation of mineral deposition by the matrix in these two mineralized structures in detail. This study re-emphasizes the importance of non-protein moieties, i.e. sugars, in calcium carbonate systems, and highlights the need to clearly identify their function in the biomineralization process. © 2015 FEBS.

Kinematic state estimation and motion planning for stochastic nonholonomic systems using the exponential map.

PubMed

Park, Wooram; Liu, Yan; Zhou, Yu; Moses, Matthew; Chirikjian, Gregory S

2008-04-11

A nonholonomic system subjected to external noise from the environment, or internal noise in its own actuators, will evolve in a stochastic manner described by an ensemble of trajectories. This ensemble of trajectories is equivalent to the solution of a Fokker-Planck equation that typically evolves on a Lie group. If the most likely state of such a system is to be estimated, and plans for subsequent motions from the current state are to be made so as to move the system to a desired state with high probability, then modeling how the probability density of the system evolves is critical. Methods for solving Fokker-Planck equations that evolve on Lie groups then become important. Such equations can be solved using the operational properties of group Fourier transforms in which irreducible unitary representation (IUR) matrices play a critical role. Therefore, we develop a simple approach for the numerical approximation of all the IUR matrices for two of the groups of most interest in robotics: the rotation group in three-dimensional space, SO(3), and the Euclidean motion group of the plane, SE(2). This approach uses the exponential mapping from the Lie algebras of these groups, and takes advantage of the sparse nature of the Lie algebra representation matrices. Other techniques for density estimation on groups are also explored. The computed densities are applied in the context of probabilistic path planning for kinematic cart in the plane and flexible needle steering in three-dimensional space. In these examples the injection of artificial noise into the computational models (rather than noise in the actual physical systems) serves as a tool to search the configuration spaces and plan paths. Finally, we illustrate how density estimation problems arise in the characterization of physical noise in orientational sensors such as gyroscopes.

Kalman filters for assimilating near-surface observations into the Richards equation - Part 1: Retrieving state profiles with linear and nonlinear numerical schemes

NASA Astrophysics Data System (ADS)

Chirico, G. B.; Medina, H.; Romano, N.

2014-07-01

This paper examines the potential of different algorithms, based on the Kalman filtering approach, for assimilating near-surface observations into a one-dimensional Richards equation governing soil water flow in soil. Our specific objectives are: (i) to compare the efficiency of different Kalman filter algorithms in retrieving matric pressure head profiles when they are implemented with different numerical schemes of the Richards equation; (ii) to evaluate the performance of these algorithms when nonlinearities arise from the nonlinearity of the observation equation, i.e. when surface soil water content observations are assimilated to retrieve matric pressure head values. The study is based on a synthetic simulation of an evaporation process from a homogeneous soil column. Our first objective is achieved by implementing a Standard Kalman Filter (SKF) algorithm with both an explicit finite difference scheme (EX) and a Crank-Nicolson (CN) linear finite difference scheme of the Richards equation. The Unscented (UKF) and Ensemble Kalman Filters (EnKF) are applied to handle the nonlinearity of a backward Euler finite difference scheme. To accomplish the second objective, an analogous framework is applied, with the exception of replacing SKF with the Extended Kalman Filter (EKF) in combination with a CN numerical scheme, so as to handle the nonlinearity of the observation equation. While the EX scheme is computationally too inefficient to be implemented in an operational assimilation scheme, the retrieval algorithm implemented with a CN scheme is found to be computationally more feasible and accurate than those implemented with the backward Euler scheme, at least for the examined one-dimensional problem. The UKF appears to be as feasible as the EnKF when one has to handle nonlinear numerical schemes or additional nonlinearities arising from the observation equation, at least for systems of small dimensionality as the one examined in this study.

Large-scale 3-D EM modelling with a Block Low-Rank multifrontal direct solver

NASA Astrophysics Data System (ADS)

Shantsev, Daniil V.; Jaysaval, Piyoosh; de la Kethulle de Ryhove, Sébastien; Amestoy, Patrick R.; Buttari, Alfredo; L'Excellent, Jean-Yves; Mary, Theo

2017-06-01

We put forward the idea of using a Block Low-Rank (BLR) multifrontal direct solver to efficiently solve the linear systems of equations arising from a finite-difference discretization of the frequency-domain Maxwell equations for 3-D electromagnetic (EM) problems. The solver uses a low-rank representation for the off-diagonal blocks of the intermediate dense matrices arising in the multifrontal method to reduce the computational load. A numerical threshold, the so-called BLR threshold, controlling the accuracy of low-rank representations was optimized by balancing errors in the computed EM fields against savings in floating point operations (flops). Simulations were carried out over large-scale 3-D resistivity models representing typical scenarios for marine controlled-source EM surveys, and in particular the SEG SEAM model which contains an irregular salt body. The flop count, size of factor matrices and elapsed run time for matrix factorization are reduced dramatically by using BLR representations and can go down to, respectively, 10, 30 and 40 per cent of their full-rank values for our largest system with N = 20.6 million unknowns. The reductions are almost independent of the number of MPI tasks and threads at least up to 90 × 10 = 900 cores. The BLR savings increase for larger systems, which reduces the factorization flop complexity from O(N2) for the full-rank solver to O(Nm) with m = 1.4-1.6. The BLR savings are significantly larger for deep-water environments that exclude the highly resistive air layer from the computational domain. A study in a scenario where simulations are required at multiple source locations shows that the BLR solver can become competitive in comparison to iterative solvers as an engine for 3-D controlled-source electromagnetic Gauss-Newton inversion that requires forward modelling for a few thousand right-hand sides.

Texture zeros and hierarchical masses from flavour (mis)alignment

NASA Astrophysics Data System (ADS)

Hollik, W. G.; Saldana-Salazar, U. J.

2018-03-01

We introduce an unconventional interpretation of the fermion mass matrix elements. As the full rotational freedom of the gauge-kinetic terms renders a set of infinite bases called weak bases, basis-dependent structures as mass matrices are unphysical. Matrix invariants, on the other hand, provide a set of basis-independent objects which are of more relevance. We employ one of these invariants to give a new parametrisation of the mass matrices. By virtue of it, one gains control over its implicit implications on several mass matrix structures. The key element is the trace invariant which resembles the equation of a hypersphere with a radius equal to the Frobenius norm of the mass matrix. With the concepts of alignment or misalignment we can identify texture zeros with certain alignments whereas Froggatt-Nielsen structures in the matrix elements are governed by misalignment. This method allows further insights of traditional approaches to the underlying flavour geometry.

Uncovering the spatial structure of mobility networks

NASA Astrophysics Data System (ADS)

Louail, Thomas; Lenormand, Maxime; Picornell, Miguel; García Cantú, Oliva; Herranz, Ricardo; Frias-Martinez, Enrique; Ramasco, José J.; Barthelemy, Marc

2015-01-01

The extraction of a clear and simple footprint of the structure of large, weighted and directed networks is a general problem that has relevance for many applications. An important example is seen in origin-destination matrices, which contain the complete information on commuting flows, but are difficult to analyze and compare. We propose here a versatile method, which extracts a coarse-grained signature of mobility networks, under the form of a 2 × 2 matrix that separates the flows into four categories. We apply this method to origin-destination matrices extracted from mobile phone data recorded in 31 Spanish cities. We show that these cities essentially differ by their proportion of two types of flows: integrated (between residential and employment hotspots) and random flows, whose importance increases with city size. Finally, the method allows the determination of categories of networks, and in the mobility case, the classification of cities according to their commuting structure.

Small angle neutron and X-ray studies of carbon structures with metal atoms

NASA Astrophysics Data System (ADS)

Lebedev, V. T.; Szhogina, A. A.; Bairamukov, V. Yu

2017-05-01

Encapsulation of metal atoms inside carbon single-wall cages or within multi-layer cells has been realized using molecular precursors and high temperature processes transforming them into desirable structures. Endohedral fullerenols Fe@C60(OH)X with 3d-metal (iron) have been studied by SANS in aqueous solutions where they form stable globular clusters with radii R C ∼ 10-12 nm and aggregation numbers N C ∼ 104. This self-assembly is a crucial feature of paramagnetic fullerenols as perspective contrast agents for Magneto-Resonance Imaging in medicine. Cellular carbon-metal structures have been created by the pyrolysis of diphthalocyanines of lanthanides and actinides. It was established that these ultra porous matrices consist of globular cells of molecular precursor size (∼ 1 nm) which are aggregated into superstructures. This provides retain of metal atoms inside matrices which may serve for safety storage of spent fuel of nuclear power plants.

Layered Metal Nanoparticle Structures on Electrodes for Sensing, Switchable Controlled Uptake/Release, and Photo-electrochemical Applications.

PubMed

Tel-Vered, Ran; Kahn, Jason S; Willner, Itamar

2016-01-06

Layered metal nanoparticle (NP) assemblies provide highly porous and conductive composites of unique electrical and optical (plasmonic) properties. Two methods to construct layered metal NP matrices are described, and these include the layer-by-layer deposition of NPs, or the electropolymerization of monolayer-functionalized NPs, specifically thioaniline-modified metal NPs. The layered NP composites are used as sensing matrices through the use of electrochemistry or surface plasmon resonance (SPR) as transduction signals. The crosslinking of the metal NP composites with molecular receptors, or the imprinting of molecular recognition sites into the electropolymerized NP matrices lead to selective and chiroselective sensing interfaces. Furthermore, the electrosynthesis of redox-active, imprinted, bis-aniline bridged Au NP composites yields electrochemically triggered "sponges" for the switchable uptake and release of electron-acceptor substrates, and results in conductive surfaces of electrochemically controlled wettability. Also, photosensitizer-relay-crosslinked Au NP composites, or electrochemically polymerized layered semiconductor quantum dot/metal NP matrices on electrodes, are demonstrated as functional nanostructures for photoelectrochemical applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Monitoring the progression of calcium and protein solubilisation as affected by calcium chelators during small-scale manufacture of casein-based food matrices.

PubMed

McIntyre, Irene; O'Sullivan, Michael; O'Riordan, Dolores

2017-12-15

Calcium and protein solubilisation during small-scale manufacture of semi-solid casein-based food matrices was investigated and found to be very different in the presence or absence of calcium chelating salts. Calcium concentrations in the dispersed phase increased and calcium-ion activity (A Ca ++ ) decreased during manufacture of the matrices containing calcium chelating salts; with ∼23% of total calcium solubilised by the end of manufacture. In the absence of calcium chelating salts, these concentrations were significantly lower at equivalent processing times and remained unchanged as did A Ca ++ , throughout manufacture. The protein content of the dispersed phase was low (≤3% of total protein), but was significantly higher for matrices containing calcium chelating salts. This study elucidates the critical role of calcium chelating salts in modulating casein hydration and dispersion and gives an indication of the levels of soluble calcium and protein required to allow matrix formation during manufacture of casein-based food structures e.g. processed and analogue cheese. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tensor discriminant color space for face recognition.

PubMed

Wang, Su-Jing; Yang, Jian; Zhang, Na; Zhou, Chun-Guang

2011-09-01

Recent research efforts reveal that color may provide useful information for face recognition. For different visual tasks, the choice of a color space is generally different. How can a color space be sought for the specific face recognition problem? To address this problem, this paper represents a color image as a third-order tensor and presents the tensor discriminant color space (TDCS) model. The model can keep the underlying spatial structure of color images. With the definition of n-mode between-class scatter matrices and within-class scatter matrices, TDCS constructs an iterative procedure to obtain one color space transformation matrix and two discriminant projection matrices by maximizing the ratio of these two scatter matrices. The experiments are conducted on two color face databases, AR and Georgia Tech face databases, and the results show that both the performance and the efficiency of the proposed method are better than those of the state-of-the-art color image discriminant model, which involve one color space transformation matrix and one discriminant projection matrix, specifically in a complicated face database with various pose variations.

Influence of matching solubility parameter of polymer matrix and CNT on electrical conductivity of CNT/rubber composite

PubMed Central

Ata, Seisuke; Mizuno, Takaaki; Nishizawa, Ayumi; Subramaniam, Chandramouli; Futaba, Don N.; Hata, Kenji

2014-01-01

We report a general approach to fabricate elastomeric composites possessing high electrical conductivity for applications ranging from wireless charging interfaces to stretchable electronics. By using arbitrary nine kinds of rubbers as matrices, we experimentally demonstrate that the matching the solubility parameter of CNTs and the rubber matrix is important to achieve higher electrical conductivity in CNT/rubber composite, resulting in continuous conductive pathways leading to electrical conductivities as high as 15 S/cm with 10 vol% CNT in fluorinated rubber. Further, using thermodynamic considerations, we demonstrate an approach to mix CNTs to arbitrary rubber matrices regardless of solubility parameter of matrices by adding small amounts of fluorinated rubber as a polymeric-compatibilizer of CNTs. We thereby achieved electrical conductivities ranging from 1.2 to 13.8 S/cm (10 vol% CNTs) using nine varieties of rubber matrices differing in chemical structures and physical properties. Finally, we investigated the components of solubility parameter of CNT by using Hansen solubility parameters, these findings may useful for controlling solubility parameter of CNTs. PMID:25434701

Lyapunov exponents for one-dimensional aperiodic photonic bandgap structures

NASA Astrophysics Data System (ADS)

Kissel, Glen J.

2011-10-01

Existing in the "gray area" between perfectly periodic and purely randomized photonic bandgap structures are the socalled aperoidic structures whose layers are chosen according to some deterministic rule. We consider here a onedimensional photonic bandgap structure, a quarter-wave stack, with the layer thickness of one of the bilayers subject to being either thin or thick according to five deterministic sequence rules and binary random selection. To produce these aperiodic structures we examine the following sequences: Fibonacci, Thue-Morse, Period doubling, Rudin-Shapiro, as well as the triadic Cantor sequence. We model these structures numerically with a long chain (approximately 5,000,000) of transfer matrices, and then use the reliable algorithm of Wolf to calculate the (upper) Lyapunov exponent for the long product of matrices. The Lyapunov exponent is the statistically well-behaved variable used to characterize the Anderson localization effect (exponential confinement) when the layers are randomized, so its calculation allows us to more precisely compare the purely randomized structure with its aperiodic counterparts. It is found that the aperiodic photonic systems show much fine structure in their Lyapunov exponents as a function of frequency, and, in a number of cases, the exponents are quite obviously fractal.

A covariance correction that accounts for correlation estimation to improve finite-sample inference with generalized estimating equations: A study on its applicability with structured correlation matrices

PubMed Central

Westgate, Philip M.

2016-01-01

When generalized estimating equations (GEE) incorporate an unstructured working correlation matrix, the variances of regression parameter estimates can inflate due to the estimation of the correlation parameters. In previous work, an approximation for this inflation that results in a corrected version of the sandwich formula for the covariance matrix of regression parameter estimates was derived. Use of this correction for correlation structure selection also reduces the over-selection of the unstructured working correlation matrix. In this manuscript, we conduct a simulation study to demonstrate that an increase in variances of regression parameter estimates can occur when GEE incorporates structured working correlation matrices as well. Correspondingly, we show the ability of the corrected version of the sandwich formula to improve the validity of inference and correlation structure selection. We also study the relative influences of two popular corrections to a different source of bias in the empirical sandwich covariance estimator. PMID:27818539

A covariance correction that accounts for correlation estimation to improve finite-sample inference with generalized estimating equations: A study on its applicability with structured correlation matrices.

PubMed

Westgate, Philip M

2016-01-01

When generalized estimating equations (GEE) incorporate an unstructured working correlation matrix, the variances of regression parameter estimates can inflate due to the estimation of the correlation parameters. In previous work, an approximation for this inflation that results in a corrected version of the sandwich formula for the covariance matrix of regression parameter estimates was derived. Use of this correction for correlation structure selection also reduces the over-selection of the unstructured working correlation matrix. In this manuscript, we conduct a simulation study to demonstrate that an increase in variances of regression parameter estimates can occur when GEE incorporates structured working correlation matrices as well. Correspondingly, we show the ability of the corrected version of the sandwich formula to improve the validity of inference and correlation structure selection. We also study the relative influences of two popular corrections to a different source of bias in the empirical sandwich covariance estimator.

Development of a model of space station solar array

NASA Technical Reports Server (NTRS)

Bosela, Paul A.

1990-01-01

Space structures, such as the space station solar arrays, must be extremely lightweight, flexible structures. Accurate prediction of the natural frequencies and mode shapes is essential for determining the structural adequacy of components, and designing a control system. The tension preload in the blanket of photovoltaic solar collectors, and the free/free boundary conditions of a structure in space, causes serious reservations on the use of standard finite element techniques of solution. In particular, a phenomena known as grounding, or false stiffening, of the stiffness matrix occurs during rigid body rotation. The grounding phenomena is examined in detail. Numerous stiffness matrices developed by others are examined for rigid body rotation capability, and found lacking. Various techniques are used for developing new stiffness matrices from the rigorous solutions of the differential equations, including the solution of the directed force problem. A new directed force stiffness matrix developed by the author provides all the rigid body capabilities for the beam in space.

Shape control of structures with semi-definite stiffness matrices for adaptive wings

NASA Astrophysics Data System (ADS)

Austin, Fred; Van Nostrand, William C.; Rossi, Michael J.

1993-09-01

Maintaining an optimum-wing cross section during transonic cruise can dramatically reduce the shock-induced drag and can result in significant fuel savings and increased range. Our adaptive-wing concept employs actuators as truss elements of active ribs to reshape the wing cross section by deforming the structure. In our previous work, to derive the shape control- system gain matrix, we developed a procedure that requires the inverse of the stiffness matrix of the structure without the actuators. However, this method cannot be applied to designs where the actuators are required structural elements since the stiffness matrices are singular when the actuator are removed. Consequently, a new method was developed, where the order of the problem is reduced and only the inverse of a small nonsingular partition of the stiffness matrix is required to obtain the desired gain matrix. The procedure was experimentally validated by achieving desired shapes of a physical model of an aircraft-wing rib. The theory and test results are presented.

Utilizing food effects to overcome challenges in delivery of lipophilic bioactives: structural design of medical and functional foods.

PubMed

McClements, David Julian

2013-12-01

The oral bioavailability of many lipophilic bioactives, such as pharmaceuticals and nutraceuticals, is relatively low due to their poor solubility, permeability and/or chemical stability within the human gastrointestinal tract (GIT). The oral bioavailability of lipophilic bioactives can be improved by designing food matrices that control their release, solubilization, transport and absorption within the GIT. This article discusses the challenges associated with delivering lipophilic bioactive components, the impact of food composition and structure on oral bioavailability and the design of functional and medical foods for improving the oral bioavailability of lipophilic bioactives. Food-based delivery systems can be used to improve the oral bioavailability of lipophilic bioactives. There are a number of potential advantages to delivering lipophilic bioactives using functional or medical foods: greater compliance than conventional delivery forms; increased bioavailability and efficacy; and reduced variability in biological effects. However, food matrices are structurally complex multicomponent materials and research is still needed to identify optimum structures and compositions for particular bioactives.

Maple procedures for the coupling of angular momenta. IX. Wigner D-functions and rotation matrices

NASA Astrophysics Data System (ADS)

Pagaran, J.; Fritzsche, S.; Gaigalas, G.

2006-04-01

The Wigner D-functions, Dpqj(α,β,γ), are known for their frequent use in quantum mechanics. Defined as the matrix elements of the rotation operator Rˆ(α,β,γ) in R and parametrized in terms of the three Euler angles α, β, and γ, these functions arise not only in the transformation of tensor components under the rotation of the coordinates, but also as the eigenfunctions of the spherical top. In practice, however, the use of the Wigner D-functions is not always that simple, in particular, if expressions in terms of these and other functions from the theory of angular momentum need to be simplified before some computations can be carried out in detail. To facilitate the manipulation of such Racah expressions, here we present an extension to the RACAH program [S. Fritzsche, Comput. Phys. Comm. 103 (1997) 51] in which the properties and the algebraic rules of the Wigner D-functions and reduced rotation matrices are implemented. Care has been taken to combine the standard knowledge about the rotation matrices with the previously implemented rules for the Clebsch-Gordan coefficients, Wigner n-j symbols, and the spherical harmonics. Moreover, the application of the program has been illustrated below by means of three examples. Program summaryTitle of program:RACAH Catalogue identifier:ADFv_9_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADFv_9_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Catalogue identifier of previous version: ADFW, ADHW, title RACAH Journal reference of previous version(s): S. Fritzsche, Comput. Phys. Comm. 103 (1997) 51; S. Fritzsche, S. Varga, D. Geschke, B. Fricke, Comput. Phys. Comm. 111 (1998) 167; S. Fritzsche, T. Inghoff, M. Tomaselli, Comput. Phys. Comm. 153 (2003) 424. Does the new version supersede the previous one: Yes, in addition to the spherical harmonics and recoupling coefficients, the program now supports also the occurrence of the Wigner rotation matrices in the algebraic expressions to be evaluated. Licensing provisions:None Computer for which the program is designed and others on which it is operable: All computers with a license for the computer algebra package Maple [Maple is a registered trademark of Waterloo Maple Inc.] Installations:University of Kassel (Germany) Operating systems under which the program has been tested: Linux 8.2+ Program language used:MAPLE, Release 8 and 9 Memory required to execute with typical data:10-50 MB No. of lines in distributed program, including test data, etc.:52 653 No. of bytes in distributed program, including test data, etc.:1 195 346 Distribution format:tar.gzip Nature of the physical problem: The Wigner D-functions and (reduced) rotation matrices occur very frequently in physical applications. They are known not only as the (infinite) representation of the rotation group but also to obey a number of integral and summation rules, including those for their orthogonality and completeness. Instead of the direct computation of these matrices, therefore, one first often wishes to find algebraic simplifications before the computations can be carried out in practice. Reasons for new version: The RACAH program has been found an efficient tool during recent years, in order to evaluate and simplify expressions from Racah's algebra. Apart from the Wigner n-j symbols ( j=3,6,9) and spherical harmonics, we now extended the code to allow for Wigner rotation matrices. This extension will support the study of those quantum processes especially where different axis of quantization occurs in course of the theoretical deviations. Summary of revisions: In a revised version of the RACAH program [S. Fritzsche, Comput. Phys. Comm. 103 (1997) 51; S. Fritzsche, T. Inghoff, M. Tomaselli, Comput. Phys. Comm. 153 (2003) 424], we now also support the occurrence of the Wigner D-functions and reduced rotation matrices. By following our previous design, the (algebraic) properties of these rotation matrices as well as a number of summation and integration rules are implemented to facilitate the algebraic simplification of expressions from the theories of angular momentum and the spherical tensor operators. Restrictions onto the complexity of the problem: The definition as well as the properties of the rotation matrices, as used in our implementation, are based mainly on the book of Varshalovich et al. [D.A. Varshalovich, A.N. Moskalev, V.K. Khersonskii, Quantum Theory of Angular Momentum, World Scientific, Singapore, 1988], Chapter 4. From this monograph, most of the relations involving the Wigner D-functions and rotation matrices are taken into account although, in practice, only a rather selected set was needed to be implemented explicitly owing to the symmetries of these functions. In the integration over the rotation matrices, products of up to three Wigner D-functions or reduced matrices (with the same angular arguments) are recognized and simplified properly; for the integration over a solid angle, however, the domain of integration must be specified for the Euler angles α and γ. This restriction arose because MAPLE does not generate a constant of integration when the limits in the integral are omitted. For any integration over the angle β the range of the integration, if omitted, is always taken from 0 to π. Unusual features of the program: The RACAH program is designed for interactive use that allows a quick and algebraic evaluation of (complex) expression from Racah's algebra. It is based on a number of well-defined data structures that are now extended to incorporate the Wigner rotation matrices. For these matrices, the transformation properties, sum rules, recursion relations, as well as a variety of special function expansions have been added to the previous functionality of the RACAH program. Moreover, the knowledge about the orthogonality as well as the completeness of the Wigner D-functions is also implemented. Typical running time:All the examples presented in Section 4 take only a few seconds on a 1.5 GHz Pentium Pro computer.

Using molecular dynamics simulations and finite element method to study the mechanical properties of nanotube reinforced polyethylene and polyketone

NASA Astrophysics Data System (ADS)

Rouhi, S.; Alizadeh, Y.; Ansari, R.; Aryayi, M.

2015-09-01

Molecular dynamics simulations are used to study the mechanical behavior of single-walled carbon nanotube reinforced composites. Polyethylene and polyketone are selected as the polymer matrices. The effects of nanotube atomic structure and diameter on the mechanical properties of polymer matrix nanocomposites are investigated. It is shown that although adding nanotube to the polymer matrix raises the longitudinal elastic modulus significantly, the transverse tensile and shear moduli do not experience important change. As the previous finite element models could not be used for polymer matrices with the atom types other than carbon, molecular dynamics simulations are used to propose a finite element model which can be used for any polymer matrices. It is shown that this model can predict Young’s modulus with an acceptable accuracy.

Molecular t-matrices for Low-Energy Electron Diffraction (TMOL v1.1)

NASA Astrophysics Data System (ADS)

Blanco-Rey, Maria; de Andres, Pedro; Held, Georg; King, David A.

2004-08-01

We describe a FORTRAN-90 program that computes scattering t-matrices for a molecule. These can be used in a Low-Energy Electron Diffraction program to solve the molecular structural problem very efficiently. The intramolecular multiple scattering is computed within a Dyson-like approach, using free space Green propagators in a basis of spherical waves. The advantage of this approach is related to exploiting the chemical identity of the molecule, and to the simplicity to translate and rotate these t-matrices without performing a new multiple-scattering calculation for each configuration. FORTRAN-90 routines for rotating the resulting t-matrices using Wigner matrices are also provided. Program summaryTitle of program: TMOL Catalogue number: ADUF Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUF Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland. Computers: Alpha ev6-21264 (700 MHz) and Pentium-IV. Operating systems: Digital UNIX V5.0 and Linux (Red Hat 8.0). Programming language: FORTRAN-90/95 (Compaq True64 compiler, and Intel Fortran Compiler 7.0 for Linux). High-speed storage required for the test run: minimum 64 Mbytes, it can grow to more depending on the system considered. Disk storage required: None. No. of bits in a word: 64 and 32. No. of lines in distributed program, including test data etc.: 5404 No. of bytes in distributed program, including test data etc.: 59 856 Distribution format: tar.gz Nature of problem: We describe the FORTRAN-90 program TMOL (v1.1) for the computation of non-diagonal scattering t-matrices for molecules or any other poly-atomic sub-unit of surface structures. These matrices can be used in an standard Low-Energy Electron Diffraction program, such as LEED90 or CLEED. Method of solution: A general non-diagonal t-matrix is assumed for the atoms or more general scatterers forming the molecule. The molecular t-matrix is solved adding the possible intramolecular multiple scattering events using Green's propagator formalism. The resulting t-matrix is referred to the mass centre of the molecule and can be easily translated with these propagators and rotated applying Wigner matrices. Typical running time: Calculating the t-matrix for a single energy takes a few seconds. Time depends on the maximum angular momentum quantum number, lmax, and the number of scatterers in the molecule, N. Running time scales as lmax6 and N3. References: [1] S. Andersson, J.B. Pendry, J. Phys. C: Solid St. Phys. 13 (1980) 3547. [2] A. Gonis, W.H. Butler, Multiple Scattering in Solids, Springer-Verlag, Berlin/New York, 2000.

Rapid iterative reanalysis for automated design

NASA Technical Reports Server (NTRS)

Bhatia, K. G.

1973-01-01

A method for iterative reanalysis in automated structural design is presented for a finite-element analysis using the direct stiffness approach. A basic feature of the method is that the generalized stiffness and inertia matrices are expressed as functions of structural design parameters, and these generalized matrices are expanded in Taylor series about the initial design. Only the linear terms are retained in the expansions. The method is approximate because it uses static condensation, modal reduction, and the linear Taylor series expansions. The exact linear representation of the expansions of the generalized matrices is also described and a basis for the present method is established. Results of applications of the present method to the recalculation of the natural frequencies of two simple platelike structural models are presented and compared with results obtained by using a commonly applied analysis procedure used as a reference. In general, the results are in good agreement. A comparison of the computer times required for the use of the present method and the reference method indicated that the present method required substantially less time for reanalysis. Although the results presented are for relatively small-order problems, the present method will become more efficient relative to the reference method as the problem size increases. An extension of the present method to static reanalysis is described, ana a basis for unifying the static and dynamic reanalysis procedures is presented.

Structural and spectroscopic characterization of DMF complexes with nitrogen, carbon dioxide, ammonia and water. Infrared matrix isolation and theoretical studies

NASA Astrophysics Data System (ADS)

Sałdyka, Magdalena; Mielke, Zofia; Haupa, Karolina

2018-02-01

An infrared spectroscopic and MP2/6-311++G(2d,2p) study of the complexes between N,N-dimethylformamide (DMF) and nitrogen, carbon dioxide, water, ammonia trapped in solid argon matrices is reported. The 1:1 molecular complexes have been identified in the DMF/B/Ar matrices (B = N2, CO, H2O, NH3); their structures were determined by comparison of the spectra with the results of calculations. The analysis of the experimental and theoretical data indicate that the DMF-N2, CO complexes present in the matrices are stabilized by (C=)O⋯N and (C=)O⋯C van der Waals interactions. In turn, in the DMF-H2O, NH3 complexes the (C=)O⋯H(OH) and (C=)O⋯H(NH2) hydrogen bonding is present in which the carbonyl group of DMF acts as a proton acceptor. In all systems studied the C-H⋯X (X = N, C, O) bonding is a second intermolecular force stabilizing the planar complexes. Some spectral features indicate that for DMF-H2O, DMF-NH3 systems the nonplanar structures with the C=O⋯H interaction are also present. The study demonstrated the strong sensitivity of the CH stretching wavenumber to an involvement of the C-H and/or C=O groups of DMF in an intermolecular interaction.

Optical Properties of Metal-Dielectric Structures Based on Photon-Crystal Opal Matrices

NASA Astrophysics Data System (ADS)

Vanin, A. I.; Lukin, A. E.; Romanov, S. G.; Solovyev, V. G.; Khanin, S. D.; Yanikov, M. V.

2018-04-01

Optical properties of novel metal-dielectric nanocomposite materials based on opal matrices have been investigated. The position of optical resonances of nanocomposites, obtained by embedding of silver into the opal matrix by the electrothermodiffusion method, is explained by the Bragg diffraction, and an asymmetric form of resonance curves is attributed to the Fano resonance. An anomalous transmission and absorption of light by hybrid plasmon-photonic layered heterostructures, which is apparently associated with excitation of surface plasmon-polaritons, propagating along "metal-dielectric" interfaces, was revealed.

Matrices for Sensors from Inorganic, Organic, and Biological Nanocomposites

PubMed Central

Nicolini, Claudio; Sivozhelezov, Victor; Bavastrello, Valter; Bezzerra, Tercio; Scudieri, Dora; Spera, Rosanna; Pechkova, Eugenia

2011-01-01

Matrices and sensors resulting from inorganic, organic and biological nanocomposites are presented in this overview. The term nanocomposite designates a solid combination of a matrix and of nanodimensional phases differing in properties from the matrix due to dissimilarities in structure and chemistry. The nanoocomposites chosen for a wide variety of health and environment sensors consist of Anodic Porous Allumina and P450scc, Carbon nanotubes and Conductive Polymers, Langmuir Blodgett Films of Lipases, Laccases, Cytochromes and Rhodopsins, Three-dimensional Nanoporous Materials and Nucleic Acid Programmable Protein Arrays. PMID:28824154

Oligo p-Phenylenevinylene Derivatives as Electron Transfer Matrices for UV-MALDI

NASA Astrophysics Data System (ADS)

Castellanos-García, Laura J.; Agudelo, Brian Castro; Rosales, Hernando F.; Cely, Melissa; Ochoa-Puentes, Christian; Blanco-Tirado, Cristian; Sierra, Cesar A.; Combariza, Marianny Y.

2017-12-01

Phenylenevinylene oligomers (PVs) have outstanding photophysical characteristics for applications in the growing field of organic electronics. Yet, PVs are also versatile molecules, the optical and physicochemical properties of which can be tuned by manipulation of their structure. We report the synthesis, photophysical, and MS characterization of eight PV derivatives with potential value as electron transfer (ET) matrices for UV-MALDI. UV-vis analysis show the presence of strong characteristic absorption bands in the UV region and molar absorptivities at 355 nm similar or higher than those of traditional proton (CHCA) and ET (DCTB) MALDI matrices. Most of the PVs exhibit non-radiative quantum yields (φ) above 0.5, indicating favorable thermal decay. Ionization potential values (IP) for PVs, calculated by the Electron Propagator Theory (EPT), range from 6.88 to 7.96 eV, making these oligomers good candidates as matrices for ET ionization. LDI analysis of PVs shows only the presence of radical cations (M+.) in positive ion mode and absence of clusters, adducts, or protonated species; in addition, M+. threshold energies for PVs are lower than for DCTB. We also tested the performance of four selected PVs as ET MALDI matrices for analytes ranging from porphyrins and phthalocyanines to polyaromatic compounds. Two of the four PVs show S/N enhancement of 1961% to 304% in comparison to LDI, and laser energy thresholds from 0.17 μJ to 0.47 μJ compared to 0.58 μJ for DCTB. The use of PV matrices also results in lower LODs (low fmol range) whereas LDI LODs range from pmol to nmol. [Figure not available: see fulltext.

Using Structural Equation Modeling To Fit Models Incorporating Principal Components.

ERIC Educational Resources Information Center

Dolan, Conor; Bechger, Timo; Molenaar, Peter

1999-01-01

Considers models incorporating principal components from the perspectives of structural-equation modeling. These models include the following: (1) the principal-component analysis of patterned matrices; (2) multiple analysis of variance based on principal components; and (3) multigroup principal-components analysis. Discusses fitting these models…

Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the "On-the-Fly" Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD).

PubMed

Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S

2014-06-10

We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good agreement with experiments. Spectroscopic features are computed using a unified velocity/flux autocorrelation function and include vibrational fundamentals and combination bands. These agree well with experiments and other theories.

Towards comprehensive structural motif mining for better fold annotation in the "twilight zone" of sequence dissimilarity

PubMed Central

Jia, Yi; Huan, Jun; Buhr, Vincent; Zhang, Jintao; Carayannopoulos, Leonidas N

2009-01-01

Background Automatic identification of structure fingerprints from a group of diverse protein structures is challenging, especially for proteins whose divergent amino acid sequences may fall into the "twilight-" or "midnight-" zones where pair-wise sequence identities to known sequences fall below 25% and sequence-based functional annotations often fail. Results Here we report a novel graph database mining method and demonstrate its application to protein structure pattern identification and structure classification. The biologic motivation of our study is to recognize common structure patterns in "immunoevasins", proteins mediating virus evasion of host immune defense. Our experimental study, using both viral and non-viral proteins, demonstrates the efficiency and efficacy of the proposed method. Conclusion We present a theoretic framework, offer a practical software implementation for incorporating prior domain knowledge, such as substitution matrices as studied here, and devise an efficient algorithm to identify approximate matched frequent subgraphs. By doing so, we significantly expanded the analytical power of sophisticated data mining algorithms in dealing with large volume of complicated and noisy protein structure data. And without loss of generality, choice of appropriate compatibility matrices allows our method to be easily employed in domains where subgraph labels have some uncertainty. PMID:19208148

Partitioning sparse matrices with eigenvectors of graphs

NASA Technical Reports Server (NTRS)

Pothen, Alex; Simon, Horst D.; Liou, Kang-Pu

1990-01-01

The problem of computing a small vertex separator in a graph arises in the context of computing a good ordering for the parallel factorization of sparse, symmetric matrices. An algebraic approach for computing vertex separators is considered in this paper. It is shown that lower bounds on separator sizes can be obtained in terms of the eigenvalues of the Laplacian matrix associated with a graph. The Laplacian eigenvectors of grid graphs can be computed from Kronecker products involving the eigenvectors of path graphs, and these eigenvectors can be used to compute good separators in grid graphs. A heuristic algorithm is designed to compute a vertex separator in a general graph by first computing an edge separator in the graph from an eigenvector of the Laplacian matrix, and then using a maximum matching in a subgraph to compute the vertex separator. Results on the quality of the separators computed by the spectral algorithm are presented, and these are compared with separators obtained from other algorithms for computing separators. Finally, the time required to compute the Laplacian eigenvector is reported, and the accuracy with which the eigenvector must be computed to obtain good separators is considered. The spectral algorithm has the advantage that it can be implemented on a medium-size multiprocessor in a straightforward manner.

Damping Enhancement of Composite Panels by Inclusion of Shunted Piezoelectric Patches: A Wave-Based Modelling Approach.

PubMed

Chronopoulos, Dimitrios; Collet, Manuel; Ichchou, Mohamed

2015-02-17

The waves propagating within complex smart structures are hereby computed by employing a wave and finite element method. The structures can be of arbitrary layering and of complex geometric characteristics as long as they exhibit two-dimensional periodicity. The piezoelectric coupling phenomena are considered within the finite element formulation. The mass, stiffness and piezoelectric stiffness matrices of the modelled segment can be extracted using a conventional finite element code. The post-processing of these matrices involves the formulation of an eigenproblem whose solutions provide the phase velocities for each wave propagating within the structure and for any chosen direction of propagation. The model is then modified in order to account for a shunted piezoelectric patch connected to the composite structure. The impact of the energy dissipation induced by the shunted circuit on the total damping loss factor of the composite panel is then computed. The influence of the additional mass and stiffness provided by the attached piezoelectric devices on the wave propagation characteristics of the structure is also investigated.

Damping Enhancement of Composite Panels by Inclusion of Shunted Piezoelectric Patches: A Wave-Based Modelling Approach

PubMed Central

Chronopoulos, Dimitrios; Collet, Manuel; Ichchou, Mohamed; Shah, Tahir

2015-01-01

The waves propagating within complex smart structures are hereby computed by employing a wave and finite element method. The structures can be of arbitrary layering and of complex geometric characteristics as long as they exhibit two-dimensional periodicity. The piezoelectric coupling phenomena are considered within the finite element formulation. The mass, stiffness and piezoelectric stiffness matrices of the modelled segment can be extracted using a conventional finite element code. The post-processing of these matrices involves the formulation of an eigenproblem whose solutions provide the phase velocities for each wave propagating within the structure and for any chosen direction of propagation. The model is then modified in order to account for a shunted piezoelectric patch connected to the composite structure. The impact of the energy dissipation induced by the shunted circuit on the total damping loss factor of the composite panel is then computed. The influence of the additional mass and stiffness provided by the attached piezoelectric devices on the wave propagation characteristics of the structure is also investigated. PMID:28787972

Very High Frequency Epr: Instrument and Applications

NASA Astrophysics Data System (ADS)

Wang, Wei

Most Electron Paramagnetic Resonance (EPR, also known as ESR or EMR) experiments are performed at conventional 9 GHz or 35 GHz frequency. But there are numerous situations in which a large increase in the microwave frequency (and/or magnetic field) will result in substantial increase in the information content in EPR spectra. This has motivated us to construct a very high frequency (VHF, 95 GHz) EPR spectrometer at Illinois EPR Research Center. Many advantages of VHF EPR are demonstrated through examples in Chapter 1. The spectrometer and some unique aspects of the instrument are described and documented in Chapter 2. Chapter 3 reports use of the VHF EPR technique to study the structure/spectral relationship of a homologous series of thiophenes, which may be constituents of coal. Two successful methods to generate the cation radicals of these organic sulfur compounds are found. The g matrices (tensors) of the thiophenic radicals are obtained for the first time. The small differences between anisotropic components of the g matrices can be unambiguously resolved. Correlations of the experimentally measured g matrices with the molecular and electronic structures are reported. The g shifts correlate linearly with lambda of their Huckel molecular orbitals; the largest g components are proportional to the pi spin densities on sulfur. In addition, the small proton hyperfine interactions of dibenzothiophene (DBT) are observed for the first time by continuous wave VHF EPR. A multifrequency approach, including auxiliary 2-4 GHz pulsed measurement, has shown that a single set of spin Hamiltonian parameters describes the spin system of DBT over a microwave frequency span of 3 to 95 GHz. These newly available, detailed, and accurate data provide a valuable opportunity to test, and perhaps to improve, the existing theoretical models for predictions on g matrices of organic radicals. Finally, Chapter 4 reports trial calculations of g matrices by several molecular orbital methods.

Quantitative structure property relationships for the adsorption of pharmaceuticals onto activated carbon.

PubMed

Dickenson, E R V; Drewes, J E

2010-01-01

Isotherms were determined for the adsorption of five pharmaceutical residues, primidone, carbamazepine, ibuprofen, naproxen and diclofenac, to Calgon Filtrasorb 300 powdered activated carbon (PAC). The sorption behavior was examined in ultra-pure and wastewater effluent organic matter (EfOM) matrices, where more sorption was observed in the ultra-pure water for PAC doses greater than 10 mg/L suggesting the presence of EfOM hinders the sorption of the pharmaceuticals to the PAC. Adsorption behaviors were described by the Freundlich isotherm model. Quantitative structure property relationships (QSPRs) in the form of polyparameter linear solvation energy relationships were developed for simulating the Freundlich adsorption capacity in both ultra-pure and EfOM matrices. The significant 3D-based descriptors for the QSPRs were the molar volume, polarizability and hydrogen-bond donor parameters.

Projected quasiparticle theory for molecular electronic structure

NASA Astrophysics Data System (ADS)

Scuseria, Gustavo E.; Jiménez-Hoyos, Carlos A.; Henderson, Thomas M.; Samanta, Kousik; Ellis, Jason K.

2011-09-01

We derive and implement symmetry-projected Hartree-Fock-Bogoliubov (HFB) equations and apply them to the molecular electronic structure problem. All symmetries (particle number, spin, spatial, and complex conjugation) are deliberately broken and restored in a self-consistent variation-after-projection approach. We show that the resulting method yields a comprehensive black-box treatment of static correlations with effective one-electron (mean-field) computational cost. The ensuing wave function is of multireference character and permeates the entire Hilbert space of the problem. The energy expression is different from regular HFB theory but remains a functional of an independent quasiparticle density matrix. All reduced density matrices are expressible as an integration of transition density matrices over a gauge grid. We present several proof-of-principle examples demonstrating the compelling power of projected quasiparticle theory for quantum chemistry.

Graph theory approach to the eigenvalue problem of large space structures

NASA Technical Reports Server (NTRS)

Reddy, A. S. S. R.; Bainum, P. M.

1981-01-01

Graph theory is used to obtain numerical solutions to eigenvalue problems of large space structures (LSS) characterized by a state vector of large dimensions. The LSS are considered as large, flexible systems requiring both orientation and surface shape control. Graphic interpretation of the determinant of a matrix is employed to reduce a higher dimensional matrix into combinations of smaller dimensional sub-matrices. The reduction is implemented by means of a Boolean equivalent of the original matrices formulated to obtain smaller dimensional equivalents of the original numerical matrix. Computation time becomes less and more accurate solutions are possible. An example is provided in the form of a free-free square plate. Linearized system equations and numerical values of a stiffness matrix are presented, featuring a state vector with 16 components.

[Morphology of collagen matrices for tissue engineering (biocompatibility, biodegradation, tissue response)].

PubMed

Shekhter, A B; Guller, A E; Istranov, L P; Istranova, E V; Butnaru, D V; Vinarov, A Z; Zakharkina, O L; Kurkov, A V; Kantimerov, D F; Antonov, E N; Marisov, L V; Glybochko, P V

2015-01-01

to perform a comparative morphological study of biocompatibility, biodegradation, and tissue response to implantation of collagen matrices (scaffolds) for tissue engineering in urology and other areas of medicine. Nine matrix types, such as porous materials reconstructed from collagen solution; a collagen sponge-vicryl mesh composite; decellularized and freeze-dried bovine, equine, and fish dermis; small intestinal submucosa, decellularized bovine dura mater; and decellularized human femoral artery, were implanted subcutaneously in 225 rats. The tissues at the implantation site were investigated for a period of 5 to 90 days. Classical histology and nonlinear optical microscopy (NLOM) were applied. The investigations showed no rejection of all the collagen materials. The period of matrix bioresorption varied from 10 days for collagen sponges to 2 months for decellularized and freeze-dried vessels and vicryl meshes. Collagen was prone to macrophage resorption and enzymatic lysis, being replaced by granulation tissue and then fibrous tissue, followed by its involution. NLOM allowed the investigators to study the number, density, interposition, and spatial organization of collagen structures in the matrices and adjacent tissues, and their change over time during implantation. The performed investigation could recommend three matrices: hybrid collagen/vicryl composite; decellularized bovine dermis; and decellularized porcine small intestinal submucosa, which are most adequate for tissue engineering in urology. These and other collagen matrices may be used in different areas of regenerative medicine.

Individual differences in false memory from misinformation: cognitive factors.

PubMed

Zhu, Bi; Chen, Chuansheng; Loftus, Elizabeth F; Lin, Chongde; He, Qinghua; Chen, Chunhui; Li, He; Xue, Gui; Lu, Zhonglin; Dong, Qi

2010-07-01

This research investigated the cognitive correlates of false memories that are induced by the misinformation paradigm. A large sample of Chinese college students (N=436) participated in a misinformation procedure and also took a battery of cognitive tests. Results revealed sizable and systematic individual differences in false memory arising from exposure to misinformation. False memories were significantly and negatively correlated with measures of intelligence (measured with Raven's Advanced Progressive Matrices and Wechsler Adult Intelligence Scale), perception (Motor-Free Visual Perception Test, Change Blindness, and Tone Discrimination), memory (Wechsler Memory Scales and 2-back Working Memory tasks), and face judgement (Face Recognition and Facial Expression Recognition). These findings suggest that people with relatively low intelligence and poor perceptual abilities might be more susceptible to the misinformation effect.

Existence and stability, and discrete BB and rank conditions, for general mixed-hybrid finite elements in elasticity

NASA Technical Reports Server (NTRS)

Xue, W.-M.; Atluri, S. N.

1985-01-01

In this paper, all possible forms of mixed-hybrid finite element methods that are based on multi-field variational principles are examined as to the conditions for existence, stability, and uniqueness of their solutions. The reasons as to why certain 'simplified hybrid-mixed methods' in general, and the so-called 'simplified hybrid-displacement method' in particular (based on the so-called simplified variational principles), become unstable, are discussed. A comprehensive discussion of the 'discrete' BB-conditions, and the rank conditions, of the matrices arising in mixed-hybrid methods, is given. Some recent studies aimed at the assurance of such rank conditions, and the related problem of the avoidance of spurious kinematic modes, are presented.

Importance Sampling of Word Patterns in DNA and Protein Sequences

PubMed Central

Chan, Hock Peng; Chen, Louis H.Y.

2010-01-01

Abstract Monte Carlo methods can provide accurate p-value estimates of word counting test statistics and are easy to implement. They are especially attractive when an asymptotic theory is absent or when either the search sequence or the word pattern is too short for the application of asymptotic formulae. Naive direct Monte Carlo is undesirable for the estimation of small probabilities because the associated rare events of interest are seldom generated. We propose instead efficient importance sampling algorithms that use controlled insertion of the desired word patterns on randomly generated sequences. The implementation is illustrated on word patterns of biological interest: palindromes and inverted repeats, patterns arising from position-specific weight matrices (PSWMs), and co-occurrences of pairs of motifs. PMID:21128856

Incomplete Sparse Approximate Inverses for Parallel Preconditioning

DOE PAGES

Anzt, Hartwig; Huckle, Thomas K.; Bräckle, Jürgen; ...

2017-10-28

In this study, we propose a new preconditioning method that can be seen as a generalization of block-Jacobi methods, or as a simplification of the sparse approximate inverse (SAI) preconditioners. The “Incomplete Sparse Approximate Inverses” (ISAI) is in particular efficient in the solution of sparse triangular linear systems of equations. Those arise, for example, in the context of incomplete factorization preconditioning. ISAI preconditioners can be generated via an algorithm providing fine-grained parallelism, which makes them attractive for hardware with a high concurrency level. Finally, in a study covering a large number of matrices, we identify the ISAI preconditioner as anmore » attractive alternative to exact triangular solves in the context of incomplete factorization preconditioning.« less

Application of Contraction Mappings to the Control of Nonlinear Systems. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Killingsworth, W. R., Jr.

1972-01-01

The theoretical and applied aspects of successive approximation techniques are considered for the determination of controls for nonlinear dynamical systems. Particular emphasis is placed upon the methods of contraction mappings and modified contraction mappings. It is shown that application of the Pontryagin principle to the optimal nonlinear regulator problem results in necessary conditions for optimality in the form of a two point boundary value problem (TPBVP). The TPBVP is represented by an operator equation and functional analytic results on the iterative solution of operator equations are applied. The general convergence theorems are translated and applied to those operators arising from the optimal regulation of nonlinear systems. It is shown that simply structured matrices and similarity transformations may be used to facilitate the calculation of the matrix Green functions and the evaluation of the convergence criteria. A controllability theory based on the integral representation of TPBVP's, the implicit function theorem, and contraction mappings is developed for nonlinear dynamical systems. Contraction mappings are theoretically and practically applied to a nonlinear control problem with bounded input control and the Lipschitz norm is used to prove convergence for the nondifferentiable operator. A dynamic model representing community drug usage is developed and the contraction mappings method is used to study the optimal regulation of the nonlinear system.

Efficient block preconditioned eigensolvers for linear response time-dependent density functional theory

NASA Astrophysics Data System (ADS)

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue; Govind, Niranjan; Yang, Chao

2017-12-01

We present two efficient iterative algorithms for solving the linear response eigenvalue problem arising from the time dependent density functional theory. Although the matrix to be diagonalized is nonsymmetric, it has a special structure that can be exploited to save both memory and floating point operations. In particular, the nonsymmetric eigenvalue problem can be transformed into an eigenvalue problem that involves the product of two matrices M and K. We show that, because MK is self-adjoint with respect to the inner product induced by the matrix K, this product eigenvalue problem can be solved efficiently by a modified Davidson algorithm and a modified locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm that make use of the K-inner product. The solution of the product eigenvalue problem yields one component of the eigenvector associated with the original eigenvalue problem. We show that the other component of the eigenvector can be easily recovered in an inexpensive postprocessing procedure. As a result, the algorithms we present here become more efficient than existing methods that try to approximate both components of the eigenvectors simultaneously. In particular, our numerical experiments demonstrate that the new algorithms presented here consistently outperform the existing state-of-the-art Davidson type solvers by a factor of two in both solution time and storage.

Mapping the Geometric Evolution of Protein Folding Motor.

PubMed

Jerath, Gaurav; Hazam, Prakash Kishore; Shekhar, Shashi; Ramakrishnan, Vibin

2016-01-01

Polypeptide chain has an invariant main-chain and a variant side-chain sequence. How the side-chain sequence determines fold in terms of its chemical constitution has been scrutinized extensively and verified periodically. However, a focussed investigation on the directive effect of side-chain geometry may provide important insights supplementing existing algorithms in mapping the geometrical evolution of protein chains and its structural preferences. Geometrically, folding of protein structure may be envisaged as the evolution of its geometric variables: ϕ, and ψ dihedral angles of polypeptide main-chain directed by χ1, and χ2 of side chain. In this work, protein molecule is metaphorically modelled as a machine with 4 rotors ϕ, ψ, χ1 and χ2, with its evolution to the functional fold is directed by combinations of its rotor directions. We observe that differential rotor motions lead to different secondary structure formations and the combinatorial pattern is unique and consistent for particular secondary structure type. Further, we found that combination of rotor geometries of each amino acid is unique which partly explains how different amino acid sequence combinations have unique structural evolution and functional adaptation. Quantification of these amino acid rotor preferences, resulted in the generation of 3 substitution matrices, which later on plugged in the BLAST tool, for evaluating their efficiency in aligning sequences. We have employed BLOSUM62 and PAM30 as standard for primary evaluation. Generation of substitution matrices is a logical extension of the conceptual framework we attempted to build during the development of this work. Optimization of matrices following the conventional routines and possible application with biologically relevant data sets are beyond the scope of this manuscript, though it is a part of the larger project design.

The Robustness of LISREL Estimates in Structural Equation Models with Categorical Variables.

ERIC Educational Resources Information Center

Ethington, Corinna A.

1987-01-01

This study examined the effect of type of correlation matrix on the robustness of LISREL maximum likelihood and unweighted least squares structural parameter estimates for models with categorical variables. The analysis of mixed matrices produced estimates that closely approximated the model parameters except where dichotomous variables were…

Investigating the Structure of the WJ-III Cognitive at School Age

ERIC Educational Resources Information Center

Dombrowski, Stefan C.

2013-01-01

During its development, the Woodcock-Johnson, Third Edition Cognitive (WJ-III Cognitive; McGrew & Woodcock, 2001) was never subjected to structural analysis using exploratory and higher order factor analyses. Instead, confirmatory factor analyses were conducted on separate sets of WJ-III correlation matrices, yielding a seven-factor model…

Hybrid aerogel-derived Sn-Ni alloy immobilized within porous carbon/graphene dual matrices for high-performance lithium storage.

PubMed

Zhang, Hao; Zhang, Mengru; Zhang, Meiling; Zhang, Lin; Zhang, Anping; Zhou, Yiming; Wu, Ping; Tang, Yawen

2017-09-01

Nanoporous networks of tin-based alloys immobilized within carbon matrices possess unique structural and compositional superiorities toward lithium-storage, and are expected to manifest improved strain-accommodation and charge-transport capabilities and thus desirable anodic performance for advanced lithium-ion batteries (LIBs). Herein, a facile and scalable hybrid aerogel-derived thermal-autoreduction route has been developed for the construction of nanoporous network of SnNi alloy immobilized within carbon/graphene dual matrices (SnNi@C/G network). When applied as an anode material for LIBs, the SnNi@C/G network manifests desirable lithium-storage performances in terms of specific capacities, cycle life, and rate capability. The facile aerogel-derived route and desirable Li-storage performance of the SnNi@C/G network facilitate its practical application as a high-capacity, long-life, and high-rate anode material for advanced LIBs. Copyright © 2017 Elsevier Inc. All rights reserved.

Cell-mediated fibre recruitment drives extracellular matrix mechanosensing in engineered fibrillar microenvironments

NASA Astrophysics Data System (ADS)

Baker, Brendon M.; Trappmann, Britta; Wang, William Y.; Sakar, Mahmut S.; Kim, Iris L.; Shenoy, Vivek B.; Burdick, Jason A.; Chen, Christopher S.

2015-12-01

To investigate how cells sense stiffness in settings structurally similar to native extracellular matrices, we designed a synthetic fibrous material with tunable mechanics and user-defined architecture. In contrast to flat hydrogel surfaces, these fibrous materials recapitulated cell-matrix interactions observed with collagen matrices including stellate cell morphologies, cell-mediated realignment of fibres, and bulk contraction of the material. Increasing the stiffness of flat hydrogel surfaces induced mesenchymal stem cell spreading and proliferation; however, increasing fibre stiffness instead suppressed spreading and proliferation for certain network architectures. Lower fibre stiffness permitted active cellular forces to recruit nearby fibres, dynamically increasing ligand density at the cell surface and promoting the formation of focal adhesions and related signalling. These studies demonstrate a departure from the well-described relationship between material stiffness and spreading established with hydrogel surfaces, and introduce fibre recruitment as a previously undescribed mechanism by which cells probe and respond to mechanics in fibrillar matrices.

Antimicrobial azobenzene compounds and their potential use in biomaterials

NASA Astrophysics Data System (ADS)

Sessa, L.; Concilio, S.; Iannelli, P.; De Santis, F.; Porta, A.; Piotto, S.

2016-04-01

We recently synthesized a class of active compounds with azobenzene structure [1] and lowest in silico toxicity values. The antimicrobial activity of these molecules and their thermal stability are very promising and indicate that they may have interesting and therapeutically significant applications. This work aims to develop new materials with antibacterial and antifungal activity inserting different percentages of synthetic antimicrobial azo compounds in commercial polymer matrices. We realized thin films using solvent casting and melt compounding techniques. The obtained materials retained the proprieties of the pure matrices. This means that azo dye dissolved in the matrix does not influence the thermal behavior and the morphology of the material. Tested films exhibited the capability to inhibit biofilms formation of S. aureus and C. albicans. Spectrophotometric investigation of the azo compound released from the polymer matrices confirmed that the realized materials might be interesting for biomedical tools, antibacterial surfaces, and films for active packaging.

A multiparallel bioreactor for the cultivation of mammalian cells in a 3D-ceramic matrix.

PubMed

Goralczyk, Vicky; Driemel, Gregor; Bischof, Andreas; Peter, Andrea; Berthold, Almuth; Kroh, Lothar; Blessing, Lucienne; Schubert, Helmut; King, Rudibert

2010-01-01

For adherently growing cells, cultivation is limited by the provided growth surface. Excellent surface-to-volume ratios are found in highly porous matrices, which have to face the challenge of nutrient supply inside the matrices' caverns. Therefore, perfusion strategies are recommended which often have to deal with the need of developing an encompassing bioreactor periphery. We present a modular bioreactor system based on a porous ceramic matrix that enables the supply of cells with oxygen and nutrients by perfusion. The present version of the reactor system focuses on simple testing of various inoculation and operation modes. Moreover, it can be used to efficiently test different foam structures. Protocols are given to set-up the system together with handling procedures for long-time cultivation of a CHO cell line. Experimental results confirm vital growth of cells inside the matrices' caverns.

Both solubility and chemical stability of curcumin are enhanced by solid dispersion in cellulose derivative matrices.

PubMed

Li, Bin; Konecke, Stephanie; Wegiel, Lindsay A; Taylor, Lynne S; Edgar, Kevin J

2013-10-15

Amorphous solid dispersions (ASD) of curcumin (Cur) in cellulose derivative matrices, hydroxypropylmethylcellulose acetate succinate (HPMCAS), carboxymethylcellulose acetate butyrate (CMCAB), and cellulose acetate adipate propionate (CAAdP) were prepared in order to investigate the structure-property relationship and identify polymer properties necessary to effectively increase Cur aqueous solution concentration. XRD results indicated that all investigated solid dispersions were amorphous, even at a 9:1 Cur:polymer ratio. Both stability against crystallization and Cur solution concentration from these ASDs were significantly higher than those from physical mixtures and crystalline Cur. Remarkably, curcumin was also stabilized against chemical degradation in solution. Chemical stabilization was polymer-dependent, with stabilization in CAAdP>CMCAB>HPMCAS>PVP, while matrices enhanced solution concentration as PVP>HPMCAS>CMCAB≈CAAdP. HPMCAS/Cur dispersions have useful combinations of pH-triggered release profile, chemical stabilization, and strong enhancement of Cur solution concentration. Copyright © 2013 Elsevier Ltd. All rights reserved.

A transfer matrix approach to vibration localization in mistuned blade assemblies

NASA Technical Reports Server (NTRS)

Ottarson, Gisli; Pierre, Chritophe

1993-01-01

A study of mode localization in mistuned bladed disks is performed using transfer matrices. The transfer matrix approach yields the free response of a general, mono-coupled, perfectly cyclic assembly in closed form. A mistuned structure is represented by random transfer matrices, and the expansion of these matrices in terms of the small mistuning parameter leads to the definition of a measure of sensitivity to mistuning. An approximation of the localization factor, the spatially averaged rate of exponential attenuation per blade-disk sector, is obtained through perturbation techniques in the limits of high and low sensitivity. The methodology is applied to a common model of a bladed disk and the results verified by Monte Carlo simulations. The easily calculated sensitivity measure may prove to be a valuable design tool due to its system-independent quantification of mistuning effects such as mode localization.

Novel and simple alternative to create nanofibrillar matrices of interest for tissue engineering.

PubMed

Sohier, Jérôme; Corre, Pierre; Perret, Christophe; Pilet, Paul; Weiss, Pierre

2014-04-01

Synthetic analogs to natural extracellular matrix (ECM) at the nanometer level are of great potential for regenerative medicine. This study introduces a novel and simple method to produce polymer nanofibers and evaluates the properties of the resulting structures, as well as their suitability to support cells and their potential interest for bone and vascular applications. The devised approach diffracts a polymer solution by means of a spraying apparatus and of an airstream as sole driving force. The resulting nanofibers were produced in an effective fashion and a factorial design allowed isolating the processing parameters that control nanofiber size and distribution. The nanofibrillar matrices revealed to be of very high porosity and were effectively colonized by human bone marrow mesenchymal cells, while allowing ECM production and osteoblastic differentiation. In vivo, the matrices provided support for new bone formation and provided a good patency as small diameter vessel grafts.

Profiling and quantitative evaluation of three Nickel-Coated magnetic matrices for purification of recombinant proteins: lelpful hints for the optimized nanomagnetisable matrix preparation

PubMed Central

2011-01-01

Background Several materials are available in the market that work on the principle of protein magnetic fishing by their histidine (His) tags. Little information is available on their performance and it is often quoted that greatly improved purification of histidine-tagged proteins from crude extracts could be achieved. While some commercial magnetic matrices could be used successfully for purification of several His-tagged proteins, there are some which have been proved to operate just for a few extent of His-tagged proteins. Here, we address quantitative evaluation of three commercially available Nickel nanomagnetic beads for purification of two His-tagged proteins expressed in Escherichia coli and present helpful hints for optimized purification of such proteins and preparation of nanomagnetisable matrices. Results Marked differences in the performance of nanomagnetic matrices, principally on the basis of their specific binding capacity, recovery profile, the amount of imidazole needed for protein elution and the extent of target protein loss and purity were obtained. Based on the aforesaid criteria, one of these materials featured the best purification results (SiMAG/N-NTA/Nickel) for both proteins at the concentration of 4 mg/ml, while the other two (SiMAC-Nickel and SiMAG/CS-NTA/Nickel) did not work well with respect to specific binding capacity and recovery profile. Conclusions Taken together, functionality of different types of nanomagnetic matrices vary considerably. This variability may not only be dependent upon the structure and surface chemistry of the matrix which in turn determine the affinity of interaction, but, is also influenced to a lesser extent by the physical properties of the protein itself. Although the results of the present study may not be fully applied for all nanomagnetic matrices, but provide a framework which could be used to profiling and quantitative evaluation of other magnetisable matrices and also provide helpful hints for those researchers facing same challenge. PMID:21824404

Differential heat stability of amphenicols characterized by structural degradation, mass spectrometry and antimicrobial activity.

PubMed

Franje, Catherine A; Chang, Shao-Kuang; Shyu, Ching-Lin; Davis, Jennifer L; Lee, Yan-Wen; Lee, Ren-Jye; Chang, Chao-Chin; Chou, Chi-Chung

2010-12-01

Heat stability of amphenicols and the relationship between structural degradation and antimicrobial activity after heating has not been well investigated. Florfenicol (FF), thiamphenicol (TAP), and chloramphenicol (CAP) were heated at 100 degrees C in water, salt water, soybean sauce and chicken meat for up to 2h. Degradation and antimicrobial activity of the compounds was evaluated using capillary electrophoresis (CE) with UV-DAD spectrometry, minimum inhibitory concentration (MIC) assay, and gas chromatography with electron impact ionization mass spectrometry (GC-EI-MS). Heat stability of amphenicols in matrices was ranked as water> or =salt water>soybean sauce>meat, suggesting that heat degradation of amphenicols was accelerated in soybean sauce and was not protected in meat. Heat stability by drug and matrices was ranked as FF>TAP=CAP in water, FF=TAP>CAP in salt water, TAP> or =FF=CAP in soybean sauce, and TAP> or =FF=CAP in meat, indicating differential heat stability of amphenicols among the 3 drugs and in different matrices. In accordance with the less than 20% degradation, the MIC against Escherichia coli and Staphylococcus aureus did not change after 2h heating in water. A 5-min heating of amphenicols in water by microwave oven generated comparable percentage degradation to boiling in water bath for 30 min to 1h. Both CE and GC-MS analysis showed that heating of FF produced TAP but not FF amine as one of its breakdown products. In conclusion, despite close similarity in structure; amphenicols exhibited differential behavior toward heating degradation in solutions and protein matrices. Although higher degradations of amphenicols were observed in soybean sauce and meat, heating treatment may generate product with antimicrobial activity (FF to TAP), therefore, heating of amphenicol residues in food cannot always be assumed safe. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Inertial Mass from Spin Nonlinearity

NASA Astrophysics Data System (ADS)

Cohen, Marcus

The inertial mass of a Fermion shows up as chiral cross-coupling in its Dirac system. No scalar term can invariantly couple left and right chirality fields; the Dirac matrices must be spin tensors of mixed chirality. We show how such tensor couplings could arise from nonlinear mixing of four spinor fields, two representing the local electron fields and two inertial spinor fields sourced in the distant masses. We thus give a model that implements Mach's principle. Following Mendel Sachs,1 we let the inertial spinors factor the moving spacetime tetrads qα(x) and bar {q}α (x) that appear in the Dirac operator. The inertial spinors do more than set the spacetime "stage;" they are players in the chiral dynamics. Specifically, we show how the massive Dirac system arises as the envelope modulation equations coupling left and right chirality electron fields on a Friedmann universe via nonlinear "spin gratings" with the inertial spinor fields. These gratings implement Penrose's "mass-scatterings," which keep the null zig-zags of the bispinor wave function confined to a timelike world tube. Local perturbations to the inertial spinor fields appear in the Dirac system as Abelian and non-Abelian vector potentials.

Population Genetic Structure of Listeria monocytogenes Strains as Determined by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing

PubMed Central

Henri, Clémentine; Félix, Benjamin; Guillier, Laurent; Leekitcharoenphon, Pimlapas; Michelon, Damien; Mariet, Jean-François; Aarestrup, Frank M.; Mistou, Michel-Yves; Hendriksen, René S.

2016-01-01

ABSTRACT Listeria monocytogenes is a ubiquitous bacterium that may cause the foodborne illness listeriosis. Only a small amount of data about the population genetic structure of strains isolated from food is available. This study aimed to provide an accurate view of the L. monocytogenes food strain population in France. From 1999 to 2014, 1,894 L. monocytogenes strains were isolated from food at the French National Reference Laboratory for L. monocytogenes and classified according to the five risk food matrices defined by the European Food Safety Authority (EFSA). A total of 396 strains were selected on the basis of different pulsed-field gel electrophoresis (PFGE) clusters, serotypes, and strain origins and typed by multilocus sequence typing (MLST), and the MLST results were supplemented with MLST data available from Institut Pasteur, representing human and additional food strains from France. The distribution of sequence types (STs) was compared between food and clinical strains on a panel of 675 strains. High congruence between PFGE and MLST was found. Out of 73 PFGE clusters, the two most prevalent corresponded to ST9 and ST121. Using original statistical analysis, we demonstrated that (i) there was not a clear association between ST9 and ST121 and the food matrices, (ii) serotype IIc, ST8, and ST4 were associated with meat products, and (iii) ST13 was associated with dairy products. Of the two major STs, ST121 was the ST that included the fewest clinical strains, which might indicate lower virulence. This observation may be directly relevant for refining risk analysis models for the better management of food safety. IMPORTANCE This study showed a very useful backward compatibility between PFGE and MLST for surveillance. The results enabled better understanding of the population structure of L. monocytogenes strains isolated from food and management of the health risks associated with L. monocytogenes food strains. Moreover, this work provided an accurate view of L. monocytogenes strain populations associated with specific food matrices. We clearly showed that some STs were associated with food matrices, such as meat, meat products, and dairy products. We opened the way to source attribution modeling in order to quantify the relative importance of the main food matrices. PMID:27235443

Application of headspace and direct immersion solid-phase microextraction in the analysis of organothiophosphates related to the Chemical Weapons Convention from water and complex matrices.

PubMed

Althoff, Marc André; Bertsch, Andreas; Metzulat, Manfred; Klapötke, Thomas M; Karaghiosoff, Konstantin L

2017-11-01

The successful application of headspace (HS) and direct immersion (DI) solid phase microextraction (SPME) for the unambiguous identification and characterization of a series of toxic thiophosphate esters, such as Amiton (I), from aqueous phases and complex matrices (e.g. grass and foliage) has been demonstrated. A Thermo Scientific gas chromatograph (GC) - tandem mass spectrometer (MS/MS) system with a TriPlus RSH® autosampler and a SPME tool was used to investigate the effect of different parameters that influence the extraction efficiency: e.g. pH of the sample matrix and extraction temperature. The developed methods were employed for the detection of several Amiton derivatives (Schedule II of the CWC) that are structurally closely related to each other; some of which are new and have not been reported in literature previously. In addition, a novel DI SPME method from complex matrices for the analysis of organophosphates related to the CWC was developed. The studies clearly show that DI SPME for complex matrices is superior to HS extraction and can potentially be applied to other related compounds controlled under the CWC. Copyright © 2017. Published by Elsevier B.V.

Products of random matrices from fixed trace and induced Ginibre ensembles

NASA Astrophysics Data System (ADS)

Akemann, Gernot; Cikovic, Milan

2018-05-01

We investigate the microcanonical version of the complex induced Ginibre ensemble, by introducing a fixed trace constraint for its second moment. Like for the canonical Ginibre ensemble, its complex eigenvalues can be interpreted as a two-dimensional Coulomb gas, which are now subject to a constraint and a modified, collective confining potential. Despite the lack of determinantal structure in this fixed trace ensemble, we compute all its density correlation functions at finite matrix size and compare to a fixed trace ensemble of normal matrices, representing a different Coulomb gas. Our main tool of investigation is the Laplace transform, that maps back the fixed trace to the induced Ginibre ensemble. Products of random matrices have been used to study the Lyapunov and stability exponents for chaotic dynamical systems, where the latter are based on the complex eigenvalues of the product matrix. Because little is known about the universality of the eigenvalue distribution of such product matrices, we then study the product of m induced Ginibre matrices with a fixed trace constraint—which are clearly non-Gaussian—and M  ‑  m such Ginibre matrices without constraint. Using an m-fold inverse Laplace transform, we obtain a concise result for the spectral density of such a mixed product matrix at finite matrix size, for arbitrary fixed m and M. Very recently local and global universality was proven by the authors and their coworker for a more general, single elliptic fixed trace ensemble in the bulk of the spectrum. Here, we argue that the spectral density of mixed products is in the same universality class as the product of M independent induced Ginibre ensembles.

Z-sinapinic acid: the change of the stereochemistry of cinnamic acids as rational synthesis of a new matrix for carbohydrate MALDI-MS analysis.

PubMed

Salum, María L; Itovich, Lucia M; Erra-Balsells, Rosa

2013-11-01

Successful application of matrix-assisted laser desorption/ionization (MALDI) MS started with the introduction of efficient matrices such as cinnamic acid derivatives (i.e. 3,5-dimethoxy-4-hydroxycinnamic acid, SA; α-cyano-4-hydroxycinnamic acid). Since the empirical founding of these matrices, other commercial available cinnamic acids with different nature and location of substituents at benzene ring were attempted. Rational design and synthesis of new cinnamic acids have been recently described too. Because the presence of a rigid double bond in its molecule structure, cinnamic acids can exist as two different geometric isomers, the E-form and Z-form. Commercial available cinnamic acids currently used as matrices are the geometric isomers trans or E (E-cinnamic and trans-cinnamic acids). As a new rational design of MALDI matrices, Z-cinnamic acids were synthesized, and their properties as matrices were studied. Their performance was compared with that of the corresponding E-isomer and classical crystalline matrices (3,5-dihydroxybenzoic acid; norharmane) in the analysis of neutral/sulfated carbohydrates. Herein, we demonstrate the outstanding performance for Z-SA. Sulfated oligosaccharides were detected in negative ion mode, and the dissociation of sulfate groups was almost suppressed. Additionally, to better understand the quite different performance of each geometric isomer as matrix, the physical and morphological properties as well as the photochemical stability in solid state were studied. The influence of the E/Z photoisomerization of the matrix during MALDI was evaluated. Finally, molecular modeling (density functional theory study) of the optimized geometry and stereochemistry of E-cinnamic and Z-cinnamic acids revealed some factors governing the analyte-matrix interaction. Copyright © 2013 John Wiley & Sons, Ltd.

Application of H-matrices method to the calculation of the stress field in a viscoelastic medium

NASA Astrophysics Data System (ADS)

Ohtani, M.; Hirahara, K.

2017-12-01

In SW Japan, the Philippine Sea plate subducts from the south and the large earthquakes around M (Magnitude) 8 repeatedly occur at the plate boundary along the Nankai Trough, called as Nankai/Tonankai earthquakes. Near the rupture area of these earthquakes, the active volcanoes lines in the Kyushu region SW Japan, such as Sakurajima volcano. There are also distributed in the Tokai-Kanto region SE Japan, such as Mt. Fuji. The eruption of Mt. Fuji in 1707, called as Hoei eruption, have occurred 49 days after the one of the series of Nankai/Tonankai earthquakes, 1707 Hoei earthquake (M8.4). It suggests that the stress field due to the earthquake sometimes helps the volcanoes to erupt. When we consider the stress change due to the earthquake, the effect of viscoelastic deformation of the crust will be important. FEM is always used for modeling such inelastic effect. However, it requires the high computational cost of O(N3), where N is the number of discretized cells of the inelastic medium. Recently, a new method based on BIEM is proposed by Barbot and Fialko (2010). In their method, calculation of the stress field due to the inelastic strain is replaced to solve the inhomogeneous Navier's equation with equivalent body forces of the inelastic strain. Then, using the stress-strain greenfunction in an elastic medium, we can take into account the inelastic effect. In this study, we employ their method to evaluate the stress change at the active volcanoes around the Nankai/Tonankai earthquakes. Their method requires the computational cost and memory storage of O(N2). We try to reduce the computational amount and the memory by applying the fast computation method of H-matrices method. With H-matrices method, a dense matrix is divided into hierarchical structure of submatrices, and each submatrix is approximated to be low rank. When we divide the viscoelastic medium into N = 8,640 or 69,120 uniform cuboid cells and apply the H-matrices method, the required storage memory for the matrices of stress-strain greenfunction are reduced to 0.17 times or 0.05 times of those for the uncompressed original matrices with enough accuracy. In this study, using this method, we show the time development of the stress change at the volcanoes around the Nankai/Tonankai earthquakes, assuming the simple viscos structure.

Structure and Electrochemistry of Copper Fluoride Nanocomposites Utilizing Mixed Conducting Matrices

DTIC Science & Technology

2007-01-01

similar to the conversion reaction of the metal fluoride. Attractive materials such as V2O5 , MoS2, and MoO3-δ can be utilized. Examples of metal...fluorides enabled by these MCM matrices are nanocomposites of FeF3 ( V2O5 ),2 BiF3 (MoS2),15 and as discussed herein, CuF2 (MoO3). In all cases, the...filled dry box using Whatman GF/D glass fiber separators saturated with 1M LiPF6 in 1:1 vol/vol ethylene carbonate:dimethyl carbonate elec- trolyte

Regularization of the Perturbed Spatial Restricted Three-Body Problem by L-Transformations

NASA Astrophysics Data System (ADS)

Poleshchikov, S. M.

2018-03-01

Equations of motion for the perturbed circular restricted three-body problem have been regularized in canonical variables in a moving coordinate system. Two different L-matrices of the fourth order are used in the regularization. Conditions for generalized symplecticity of the constructed transform have been checked. In the unperturbed case, the regular equations have a polynomial structure. The regular equations have been numerically integrated using the Runge-Kutta-Fehlberg method. The results of numerical experiments are given for the Earth-Moon system parameters taking into account the perturbation of the Sun for different L-matrices.

Analysis of the structure of poly-3-hydroxybutyrate ultrathin fibers modified with iron (III) complex with tetraphenylporphyrin

NASA Astrophysics Data System (ADS)

Olkhov, A. A.; Karpova, S. G.; Lobanov, A. V.; Tyubaeva, P. M.; Artemov, N. S.; Iordansky, A. L.

2017-12-01

In the treatment of many infectious diseases and cancer, transdermal systems based on solid polymer matrices or gels containing functional substances with antiseptic (antibacterial) properties are often used. One of the most promising types of matrices with antiseptic properties are the ones of nano- and microfiber-bonded cloth obtained by electrospinning based on biopolymer poly(3-hydroxybutyrate). The present work investigates the effects of iron (III) complex with tetraphenylporphyrin and the influence on the geometry, crystalline order and molecular dynamics in the intercrystalline (amorphous phase) of ultrathin PHB fibers.

Boundary formulations for sensitivity analysis without matrix derivatives

NASA Technical Reports Server (NTRS)

Kane, J. H.; Guru Prasad, K.

1993-01-01

A new hybrid approach to continuum structural shape sensitivity analysis employing boundary element analysis (BEA) is presented. The approach uses iterative reanalysis to obviate the need to factor perturbed matrices in the determination of surface displacement and traction sensitivities via a univariate perturbation/finite difference (UPFD) step. The UPFD approach makes it possible to immediately reuse existing subroutines for computation of BEA matrix coefficients in the design sensitivity analysis process. The reanalysis technique computes economical response of univariately perturbed models without factoring perturbed matrices. The approach provides substantial computational economy without the burden of a large-scale reprogramming effort.

Infrared spectroscopy of isoprene in noble gas matrices

NASA Astrophysics Data System (ADS)

Ito, Fumiyuki

2018-06-01

In this study, the infrared absorption spectra of 2-methyl-1,3-butadiene (isoprene) in noble gas matrices (Ar, Kr, and Xe) have been reported. The vibrational structure observed at cryogenic temperature, in combination with anharmonic vibrational calculations using density functional theory, helped in unambiguously assigning the fundamental modes of isoprene unresolved in the previous gas phase measurements, which would be of basic importance in the remote sensing of this molecule. A careful comparison with the most recent gas phase study [Brauer et al., Atmos. Meas. Tech. 7 (2014) 3839-3847.] led us to alternative assignments of the weak bands.

Deep level defects in semiconductors. Final technical report 1 Jul 78-30 Jun 80

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sundaram, S.; Sharma, R.R.

1980-07-01

Using Racah's irreducible tensor operator formalism, a generalized and more refined treatment of the d-electron matrices for transition metal defects in crystals has been given. The resulting Coulomb and exchange interaction matrices have been used to calculate the electronic structures of GaAs:(2+)Cr(2+) and GaAs:Cr(3+) and interpret the optical data on MgF2:Co(2+) and MgF2:Mn(2+). The significance of the new theory is explained. From the photoluminescence and optical absorption data, the crystal field parameters have been derived.

The electronic structure of VO in its ground and electronically excited states: A combined matrix isolation and quantum chemical (MRCI) study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hübner, Olaf; Hornung, Julius; Himmel, Hans-Jörg, E-mail: hans-jorg.himmel@aci.uni-heidelberg.de

2015-07-14

The electronic ground and excited states of the vanadium monoxide (VO) molecule were studied in detail. Electronic absorption spectra for the molecule isolated in Ne matrices complement the previous gas-phase spectra. A thorough quantum chemical (multi-reference configuration interaction) study essentially confirms the assignment and characterization of the electronic excitations observed for VO in the gas-phase and in Ne matrices and allows the clarification of open issues. It provides a complete overview over the electronically excited states up to about 3 eV of this archetypical compound.

Sructure and dynamics of fluids in micropous and mesoporous earth and engineered materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cole, David R; Mamontov, Eugene; Rother, Gernot

2009-01-01

The behavior of liquids in confined geometries (pores, fractures) typically differs, due to the effects of large internal surfaces and geometri-cal confinement, from their bulk behavior in many ways. Phase transitions (i.e., freezing and capillary condensation), sorption and wetting, and dy-namical properties, including diffusion and relaxation, may be modified, with the strongest changes observed for pores ranging in size from <2 nm to 50 nm the micro- and mesoporous regimes. Important factors influ-encing the structure and dynamics of confined liquids include the average pore size and pore size distribution, the degree of pore interconnection, and the character of the liquid-surfacemore » interaction. While confinement of liq-uids in hydrophobic matrices, such as carbon nanotubes, or near the sur-faces of mixed character, such as many proteins, has also been an area of rapidly growing interest, the confining matrices of interest to earth and ma-terials sciences usually contain oxide structural units and thus are hydro-philic. The pore size distribution and the degree of porosity and inter-connection vary greatly amongst porous matrices. Vycor, xerogels, aerogels, and rocks possess irregular porous structures, whereas mesopor-ous silicas (e.g., SBA-15, MCM-41, MCM-48), zeolites, and layered sys-tems, for instance clays, have high degrees of internal order. The pore type and size may be tailored by means of adjusting the synthesis regimen. In clays, the interlayer distance may depend on the level of hydration. Al-though studied less frequently, matrices such as artificial opals and chry-sotile asbestos represent other interesting examples of ordered porous structures. The properties of neutrons make them an ideal probe for com-paring the properties of bulk fluids with those in confined geometries. In this chapter, we provide a brief review of research performed on liquids confined in materials of interest to the earth and material sciences (silicas, aluminas, zeolites, clays, rocks, etc.), emphasizing those neutron scattering techniques which assess both structural modification and dynamical behav-ior. Quantitative understanding of the complex solid-fluid interactions under different thermodynamic situations will impact both the design of bet-ter substrates for technological applications (e.g., chromatography, fluid capture, storage and release, and heterogeneous catalysis) as well as our fundamental understanding of processes encountered in the environment (i.e., fluid and waste mitigation, carbon sequestration, etc.).« less

NON-TRADITIONAL RESPONSES TO PHARMACEUTICALS IN AQUATIC ECOSYSTEMS

EPA Science Inventory

Quantitation of human and veterinary pharmaceuticals in environmental matrices has resulted in pharmaceuticals in the environment receiving unprecedented attention from the scientific community. Aquatic hazard assessments often use quantitative structure activity relationships an...

Meta-Analytic Structural Equation Modeling: A Two-Stage Approach

ERIC Educational Resources Information Center

Cheung, Mike W. L.; Chan, Wai

2005-01-01

To synthesize studies that use structural equation modeling (SEM), researchers usually use Pearson correlations (univariate r), Fisher z scores (univariate z), or generalized least squares (GLS) to combine the correlation matrices. The pooled correlation matrix is then analyzed by the use of SEM. Questionable inferences may occur for these ad hoc…

The Robustness of LISREL Estimates in Structural Equation Models with Categorical Variables.

ERIC Educational Resources Information Center

Ethington, Corinna A.

This study examined the effect of type of correlation matrix on the robustness of LISREL maximum likelihood and unweighted least squares structural parameter estimates for models with categorical manifest variables. Two types of correlation matrices were analyzed; one containing Pearson product-moment correlations and one containing tetrachoric,…

Colonization of bone matrices by cellular components

NASA Astrophysics Data System (ADS)

Shchelkunova, E. I.; Voropaeva, A. A.; Korel, A. V.; Mayer, D. A.; Podorognaya, V. T.; Kirilova, I. A.

2017-09-01

Practical surgery, traumatology, orthopedics, and oncology require bioengineered constructs suitable for replacement of large-area bone defects. Only rigid/elastic matrix containing recipient's bone cells capable of mitosis, differentiation, and synthesizing extracellular matrix that supports cell viability can comply with these requirements. Therefore, the development of the techniques to produce structural and functional substitutes, whose three-dimensional structure corresponds to the recipient's damaged tissues, is the main objective of tissue engineering. This is achieved by developing tissue-engineering constructs represented by cells placed on the matrices. Low effectiveness of carrier matrix colonization with cells and their uneven distribution is one of the major problems in cell culture on various matrixes. In vitro studies of the interactions between cells and material, as well as the development of new techniques for scaffold colonization by cellular components are required to solve this problem.

Study of modal coupling procedures for the shuttle: A matrix method for damping synthesis

NASA Technical Reports Server (NTRS)

Hasselman, T. K.

1972-01-01

The damping method was applied successfully to real structures as well as analytical models. It depends on the ability to determine an appropriate modal damping matrix for each substructure. In the past, modal damping matrices were assumed diagonal for lack of being able to determine the coupling terms which are significant in the general case of nonproportional damping. This problem was overcome by formulating the damped equations of motion as a linear perturbation of the undamped equations for light structural damping. Damped modes are defined as complex vectors derived from the complex frequency response vectors of each substructure and are obtained directly from sinusoidal vibration tests. The damped modes are used to compute first order approximations to the modal damping matrices. The perturbation approach avoids ever having to solve a complex eigenvalue problem.

Extrusion induced low-order starch matrices: Enzymic hydrolysis and structure.

PubMed

Zhang, Bin; Dhital, Sushil; Flanagan, Bernadine M; Luckman, Paul; Halley, Peter J; Gidley, Michael J

2015-12-10

Waxy, normal and highwaymen maize starches were extruded with water as sole plasticizer to achieve low-order starch matrices. Of the three starches, we found that only high-amylose extrudate showed lower digestion rate/extent than starches cooked in excess water. The ordered structure of high-amylose starches in cooked and extruded forms was similar, as judged by NMR, XRD and DSC techniques, but enzyme resistance was much greater for extruded forms. Size exclusion chromatography suggested that longer chains were involved in enzyme resistance. We propose that the local molecular density of packing of amylose chains can control the digestion kinetics rather than just crystallinity, with the principle being that density sufficient to either prevent/limit binding and/or slow down catalysis can be achieved by dense amorphous packing. Copyright © 2015 Elsevier Ltd. All rights reserved.

An exact formulation of the time-ordered exponential using path-sums

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giscard, P.-L., E-mail: p.giscard1@physics.ox.ac.uk; Lui, K.; Thwaite, S. J.

2015-05-15

We present the path-sum formulation for the time-ordered exponential of a time-dependent matrix. The path-sum formulation gives the time-ordered exponential as a branched continued fraction of finite depth and breadth. The terms of the path-sum have an elementary interpretation as self-avoiding walks and self-avoiding polygons on a graph. Our result is based on a representation of the time-ordered exponential as the inverse of an operator, the mapping of this inverse to sums of walks on a graphs, and the algebraic structure of sets of walks. We give examples demonstrating our approach. We establish a super-exponential decay bound for the magnitudemore » of the entries of the time-ordered exponential of sparse matrices. We give explicit results for matrices with commonly encountered sparse structures.« less

Matrix-assisted laser desorption/ionization mass spectrometric analysis of aliphatic biodegradable photoluminescent polymers using new ionic liquid matrices.

PubMed

Serrano, Carlos A; Zhang, Yi; Yang, Jian; Schug, Kevin A

2011-05-15

In this study, two novel ionic liquid matrices (ILMs), N,N-diisopropylethylammonium 3-oxocoumarate and N,N-diisopropylethylammonium dihydroxymonooxoacetophenoate, were tested for the structural elucidation of recently developed aliphatic biodegradable polymers by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The polymers, formed by a condensation reaction of three components, citric acid, octane diol, and an amino acid, are fluorescent, but the exact mechanism behind their luminescent properties has not been fully elucidated. In the original studies, which introduced the polymer class (J. Yang et al., Proc. Natl. Acad. Sci. USA 2009, 106, 10086-10091), a hyper-conjugated cyclic structure was proposed as the source for the photoluminescent behavior. With the use of the two new ILMs, we present evidence that supports the presence of the proposed cyclization product. In addition, the new ILMs, when compared with a previously established ILM, N,N-diisopropylethylammonium α-cyano-3-hydroxycinnimate, provided similar signal intensities and maintained similar spectral profiles. This research also established that the new ILMs provided good spot-to-spot reproducibility and high ionization efficiency compared with corresponding crystalline matrix preparations. Many polymer features revealed through the use of the ILMs could not be observed with crystalline matrices. Ultimately, the new ILMs highlighted the composition of the synthetic polymers, as well as the loss of water that was expected for the formation of the proposed cyclic structure on the polymer backbone. Copyright © 2011 John Wiley & Sons, Ltd.

An Innovative Sensing Approach Using Carbon Nanotube-Based Composites for Structural Health Monitoring of Concrete Structures

NASA Astrophysics Data System (ADS)

Dwivedi, Vatsal

This thesis presents some work on two quite disparate kinds of dynamical systems described by Hamiltonian dynamics. The first part describes a computation of gauge anomalies and their macroscopic effects in a semiclassical picture. The geometric (symplectic) formulation of classical mechanics is used to describe the dynamics of Weyl fermions in even spacetime dimensions, the only quantum input to the symplectic form being the Berry curvature that encodes the spin-momentum locking. The (semi-)classical equations of motion are used in a kinetic theory setup to compute the gauge and singlet currents, whose conservation laws reproduce the nonabelian gauge and singlet anomalies. Anomalous contributions to the hydrodynamic currents for a gas of Weyl fermions at a finite temperature and chemical potential are also calculated, and are in agreement with similar results in literature which were obtained using thermodynamic and/or quantum field theoretical arguments. The second part describes a generalized transfer matrix formalism for noninteracting tight-binding models. The formalism is used to study the bulk and edge spectra, both of which are encoded in the spectrum of the transfer matrices, for some of the common tight-binding models for noninteracting electronic topological phases of matter. The topological invariants associated with the boundary states are interpreted as winding numbers for windings around noncontractible loops on a Riemann sheet constructed using the algebraic structure of the transfer matrices, as well as with a Maslov index on a symplectic group manifold, which is the space of transfer matrices.

In Situ Evaluation of Calcium Phosphate Nucleation Kinetics and Pathways during Intra- and Extrafibrillar Mineralization of Collagen Matrices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Doyoon; Lee, Byeongdu; Thomopoulos, Stavros

Calcium phosphate (CaP) nanocrystals nucleate and grow in intrafibrillar and/or extrafibrillar spaces of collagen fibrils during the mineralization of bones and teeth. Little is known about the early stages of CaP nucleation and distribution in fibrillar matrices, despite their significant influence on the physical and chemical structures of tissue-level constructs. Using in situ small angle X-ray scattering (SAXS), we examined the nucleation and growth of CaP within collagen matrices and elucidated how a nucleation inhibitor, polyaspartic acid (pAsp), governs mineralization kinetics and pathways at multiple length scales. In situ SAXS analysis clearly revealed that nucleation sites, kinetically-controlled by the nucleationmore » inhibitor, determined the pathways of CaP morphological transformation. Mineralization with pAsp led to intrafibrillar CaP plates with a spatial distribution gradient through the depth of the matrix. Mineralization without pAsp led initially to spherical aggregates of CaP in the entire extrafibrillar spaces. With time, the spherical aggregates transformed into plates at the outermost surface of the collagen matrix, preventing intrafibrillar mineralization inside. The results illuminate mineral nucleation kinetics and real-time nanoparticle distributions within organic matrices in solutions containing body fluid components. Because the macroscale mechanical properties of collagen matrices depend on their mineral content, phase, and arrangement at the nanoscale, this study contributes to better design and fabrication of biomaterials for regenerative medicine.« less

Dense tissue-like collagen matrices formed in cell-free conditions.

PubMed

Mosser, Gervaise; Anglo, Anny; Helary, Christophe; Bouligand, Yves; Giraud-Guille, Marie-Madeleine

2006-01-01

A new protocol was developed to produce dense organized collagen matrices hierarchically ordered on a large scale. It consists of a two stage process: (1) the organization of a collagen solution and (2) the stabilization of the organizations by a sol-gel transition that leads to the formation of collagen fibrils. This new protocol relies on the continuous injection of an acid-soluble collagen solution into glass microchambers. It leads to extended concentration gradients of collagen, ranging from 5 to 1000 mg/ml. The self-organization of collagen solutions into a wide array of spatial organizations was investigated. The final matrices obtained by this procedure varied in concentration, structure and density. Changes in the liquid state of the samples were followed by polarized light microscopy, and the final stabilized gel states obtained after fibrillogenesis were analyzed by both light and electron microscopy. Typical organizations extended homogeneously by up to three centimetres in one direction and several hundreds of micrometers in other directions. Fibrillogenesis of collagen solutions of high and low concentrations led to fibrils spatially arranged as has been described in bone and derm, respectively. Moreover, a relationship was revealed between the collagen concentration and the aggregation of and rotational angles between lateral fibrils. These results constitute a strong base from which to further develop highly enriched collagen matrices that could lead to substitutes that mimic connective tissues. The matrices thus obtained may also be good candidates for the study of the three-dimensional migration of cells.

Optics and Symbolic Computing

DTIC Science & Technology

1987-03-01

applicatior for AI are in variation of classification parameters for knowledge acquisition ( changing of classes into which objects are placed), and...computation. The well-structured data formats of vectors, matrices, etc. used in numeric computing give way to data structures that can change their shapes...by "flexible data structures. The semantic meanings of objects are readily changed by adding and deleting the variable lists of attributes. Another

The spatial structure of chronic morbidity: evidence from UK census returns.

PubMed

Dutey-Magni, Peter F; Moon, Graham

2016-08-24

Disease prevalence models have been widely used to estimate health, lifestyle and disability characteristics for small geographical units when other data are not available. Yet, knowledge is often lacking about how to make informed decisions around the specification of such models, especially regarding spatial assumptions placed on their covariance structure. This paper is concerned with understanding processes of spatial dependency in unexplained variation in chronic morbidity. 2011 UK census data on limiting long-term illness (LLTI) is used to look at the spatial structure in chronic morbidity across England and Wales. The variance and spatial clustering of the odds of LLTI across local authority districts (LADs) and middle layer super output areas are measured across 40 demographic cross-classifications. A series of adjacency matrices based on distance, contiguity and migration flows are tested to examine the spatial structure in LLTI. Odds are then modelled using a logistic mixed model to examine the association with district-level covariates and their predictive power. The odds of chronic illness are more dispersed than local age characteristics, mortality, hospitalisation rates and chance alone would suggest. Of all adjacency matrices, the three-nearest neighbour method is identified as the best fitting. Migration flows can also be used to construct spatial weights matrices which uncover non-negligible autocorrelation. Once the most important characteristics observable at the LAD-level are taken into account, substantial spatial autocorrelation remains which can be modelled explicitly to improve disease prevalence predictions. Systematic investigation of spatial structures and dependency is important to develop model-based estimation tools in chronic disease mapping. Spatial structures reflecting migration interactions are easy to develop and capture autocorrelation in LLTI. Patterns of spatial dependency in the geographical distribution of LLTI are not comparable across ethnic groups. Ethnic stratification of local health information is needed and there is potential to further address complexity in prevalence models by improving access to disaggregated data.

Towards the Rational Design of Ionic Liquid Matrices for Secondary Ion Mass Spectrometry: Role of the Anion

NASA Astrophysics Data System (ADS)

Dertinger, Jennifer J.; Walker, Amy V.

2013-08-01

The role of the ionic liquid (IL) anion structure on analyte signal enhancements has been systematically investigated in secondary ion mass spectrometry (SIMS) using a variety of samples, including lipids, sterols, polymers, and peptides. Twenty-four ILs were synthesized. The 12 matrix acids were cinnamic acid derivatives. Two bases were employed: 1-methylimidazole and tripropylamine. Three matrices, methylimmidazolium o-coumarate, tripropylammonium o-coumarate, and tripropylammonium 3,4,5-trimethoxycinnamate, were "universal" matrices enhancing all analytes tested. The pKa of the matrix acid does not appear to have a strong effect on analyte ion intensities. Rather, it is observed that a single hydroxyl group on the anion aromatic ring leads to significantly increased molecular ion intensities. No analyte signal enhancements were observed for -CH3, -CF3 and -OCH3 groups present on the aromatic ring. The position of the -OH group on the aromatic ring also alters molecular ion intensity enhancements. As well as the chemical identity and position of substituents, the number of moieties on the aromatic ring may affect the analyte signal enhancements observed. These observations suggest that the activation of the IL anion aromatic ring is important for optimizing analyte signal intensities. The implications for SIMS imaging of complex structures, such as biological samples, are discussed.

A machine-learned computational functional genomics-based approach to drug classification.

PubMed

Lötsch, Jörn; Ultsch, Alfred

2016-12-01

The public accessibility of "big data" about the molecular targets of drugs and the biological functions of genes allows novel data science-based approaches to pharmacology that link drugs directly with their effects on pathophysiologic processes. This provides a phenotypic path to drug discovery and repurposing. This paper compares the performance of a functional genomics-based criterion to the traditional drug target-based classification. Knowledge discovery in the DrugBank and Gene Ontology databases allowed the construction of a "drug target versus biological process" matrix as a combination of "drug versus genes" and "genes versus biological processes" matrices. As a canonical example, such matrices were constructed for classical analgesic drugs. These matrices were projected onto a toroid grid of 50 × 82 artificial neurons using a self-organizing map (SOM). The distance, respectively, cluster structure of the high-dimensional feature space of the matrices was visualized on top of this SOM using a U-matrix. The cluster structure emerging on the U-matrix provided a correct classification of the analgesics into two main classes of opioid and non-opioid analgesics. The classification was flawless with both the functional genomics and the traditional target-based criterion. The functional genomics approach inherently included the drugs' modulatory effects on biological processes. The main pharmacological actions known from pharmacological science were captures, e.g., actions on lipid signaling for non-opioid analgesics that comprised many NSAIDs and actions on neuronal signal transmission for opioid analgesics. Using machine-learned techniques for computational drug classification in a comparative assessment, a functional genomics-based criterion was found to be similarly suitable for drug classification as the traditional target-based criterion. This supports a utility of functional genomics-based approaches to computational system pharmacology for drug discovery and repurposing.

Optical properties of graphene-based materials in transparent polymer matrices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bayrak, Osman; Demirci, Emrah, E-mail: E.Demirci@lboro.ac.uk; Silberschmidt, Vadim V.

2016-08-22

Different aspects of graphene-based materials (GBMs) and GBM-nanocomposites have been investigated due to their intriguing features; one of these features is their transparency. Transparency of GBMs has been of an interest to scientists and engineers mainly with regard to electronic devices. In this study, optical transmittance of structural, purpose-made nanocomposites reinforced with GBMs was analyzed to lay a foundation for optical microstructural characterization of nanocomposites in future studies. Two main types of GBM reinforcements were studied, graphene oxide (GO) and graphite nanoplates (GNPs). The nanocomposites investigated are GO/poly(vinyl alcohol), GO/sodium alginate, and GNP/epoxy with different volume fractions of GBMs. Togethermore » with UV-visible spectrophotometry, image-processing-assisted micro and macro photography were used to assess the transparency of GBMs embedded in the matrices. The micro and macro photography methods developed were proven to be an alternative way of measuring light transmittance of semi-transparent materials. It was found that there existed a linear relationship between light absorbance and a volume fraction of GBMs embedded in the same type of polymer matrices, provided that the nanocomposites of interest had the same thicknesses. This suggests that the GBM dispersion characteristics in the same type of polymer are similar and any possible change in crystal structure of polymer due to different volumetric contents of GBM does not have an effect on light transmittance of the matrices. The study also showed that the same types of GBMs could display different optical properties in different matrix materials. The results of this study will help to develop practical microstructural characterization techniques for GBM-based nanocomposites.« less

Biochemical Composition and Assembly of Biosilica-associated Insoluble Organic Matrices from the Diatom Thalassiosira pseudonana*

PubMed Central

Kotzsch, Alexander; Pawolski, Damian; Milentyev, Alexander; Shevchenko, Anna; Scheffel, André; Poulsen, Nicole; Shevchenko, Andrej; Kröger, Nils

2016-01-01

The nano- and micropatterned biosilica cell walls of diatoms are remarkable examples of biological morphogenesis and possess highly interesting material properties. Only recently has it been demonstrated that biosilica-associated organic structures with specific nanopatterns (termed insoluble organic matrices) are general components of diatom biosilica. The model diatom Thalassiosira pseudonana contains three types of insoluble organic matrices: chitin meshworks, organic microrings, and organic microplates, the latter being described in the present study for the first time. To date, little is known about the molecular composition, intracellular assembly, and biological functions of organic matrices. Here we have performed structural and functional analyses of the organic microrings and organic microplates from T. pseudonana. Proteomics analysis yielded seven proteins of unknown function (termed SiMat proteins) together with five known silica biomineralization proteins (four cingulins and one silaffin). The location of SiMat1-GFP in the insoluble organic microrings and the similarity of tyrosine- and lysine-rich functional domains identifies this protein as a new member of the cingulin protein family. Mass spectrometric analysis indicates that most of the lysine residues of cingulins and the other insoluble organic matrix proteins are post-translationally modified by short polyamine groups, which are known to enhance the silica formation activity of proteins. Studies with recombinant cingulins (rCinY2 and rCinW2) demonstrate that acidic conditions (pH 5.5) trigger the assembly of mixed cingulin aggregates that have silica formation activity. Our results suggest an important role for cingulins in the biogenesis of organic microrings and support the hypothesis that this type of insoluble organic matrix functions in biosilica morphogenesis. PMID:26710847

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.

Compression-induced structural and mechanical changes of fibrin-collagen composites.

PubMed

Kim, O V; Litvinov, R I; Chen, J; Chen, D Z; Weisel, J W; Alber, M S

2017-07-01

Fibrin and collagen as well as their combinations play an important biological role in tissue regeneration and are widely employed in surgery as fleeces or sealants and in bioengineering as tissue scaffolds. Earlier studies demonstrated that fibrin-collagen composite networks displayed improved tensile mechanical properties compared to the isolated protein matrices. Unlike previous studies, here unconfined compression was applied to a fibrin-collagen filamentous polymer composite matrix to study its structural and mechanical responses to compressive deformation. Combining collagen with fibrin resulted in formation of a composite hydrogel exhibiting synergistic mechanical properties compared to the isolated fibrin and collagen matrices. Specifically, the composite matrix revealed a one order of magnitude increase in the shear storage modulus at compressive strains>0.8 in response to compression compared to the mechanical features of individual components. These material enhancements were attributed to the observed structural alterations, such as network density changes, an increase in connectivity along with criss-crossing, and bundling of fibers. In addition, the compressed composite collagen/fibrin networks revealed a non-linear transformation of their viscoelastic properties with softening and stiffening regimes. These transitions were shown to depend on protein concentrations. Namely, a decrease in protein content drastically affected the mechanical response of the networks to compression by shifting the onset of stiffening to higher degrees of compression. Since both natural and artificially composed extracellular matrices experience compression in various (patho)physiological conditions, our results provide new insights into the structural biomechanics of the polymeric composite matrix that can help to create fibrin-collagen sealants, sponges, and tissue scaffolds with tunable and predictable mechanical properties. Copyright © 2016 Elsevier B.V. All rights reserved.

Simple One-Pot Syntheses and Characterizations of Free Fluoride- and Bifluoride-Containing Polymers Soluble in Non-Aqueous Solvents

PubMed Central

Steinle, Dominik; Friedrich, Laura; Bevilacqua, Nico; von Hauff, Elizabeth; Gschwind, Fabienne

2016-01-01

One of the problems that arise with bifluoride- or fluoride-containing compounds is their poor solubility in non-aqueous solvents. We report herein a facile one-pot synthesis and the chemical analysis of fluoride/bifluoride-containing polymers, which are soluble in MeCN. Different polymers, such as Polyvinylacetate or Polyethylene imine and saccharides, such as maltodextrin, were complexed with ammonium (bi)fluoride using hydrogen bonds to form the desired (bi)fluoride-containing compounds. The newly formed hydrogen bonding (bi)fluoride-doped polymer matrices were analyzed using infrared and nuclear magnetic resonance spectroscopies, and X-ray diffraction. The promising materials also underwent impedance spectroscopy, conductivity measurements and preliminary tests as electrolytes for room temperature fluoride ion batteries along with an analysis of their performance. PMID:28774092

Connecting Fermion Masses and Mixings to BSM Physics - Quarks

NASA Astrophysics Data System (ADS)

Goldman, Terrence; Stephenson, Gerard J., Jr.

2015-10-01

The ``democratic'' mass matrix with BSM physics assumptions has been studied without success. We invert the process and use the ``democratic'' mass matrix plus a parametrization of all possible BSM corrections to analyze the implications of the observed masses and CKM weak interaction current mixing for the BSM parameter values for the up-quarks and down-quarks. We observe that the small mixing of the so-called ``third generation'' is directly related to the large mass gap from the two lighter generations. Conversely, the relatively large value of the Cabibbo angle arises because the mass matrices in the light sub-sector (block diagonalized from the full three channel problem) are neither diagonal nor degenerate and differ significantly between the up and down cases. Alt email:t.goldman@gmail.com

A Class of Population Covariance Matrices in the Bootstrap Approach to Covariance Structure Analysis

ERIC Educational Resources Information Center

Yuan, Ke-Hai; Hayashi, Kentaro; Yanagihara, Hirokazu

2007-01-01

Model evaluation in covariance structure analysis is critical before the results can be trusted. Due to finite sample sizes and unknown distributions of real data, existing conclusions regarding a particular statistic may not be applicable in practice. The bootstrap procedure automatically takes care of the unknown distribution and, for a given…

A Two-Stage Approach to Synthesizing Covariance Matrices in Meta-Analytic Structural Equation Modeling

ERIC Educational Resources Information Center

Cheung, Mike W. L.; Chan, Wai

2009-01-01

Structural equation modeling (SEM) is widely used as a statistical framework to test complex models in behavioral and social sciences. When the number of publications increases, there is a need to systematically synthesize them. Methodology of synthesizing findings in the context of SEM is known as meta-analytic SEM (MASEM). Although correlation…

Meta-Analytic Methods of Pooling Correlation Matrices for Structural Equation Modeling under Different Patterns of Missing Data

ERIC Educational Resources Information Center

Furlow, Carolyn F.; Beretvas, S. Natasha

2005-01-01

Three methods of synthesizing correlations for meta-analytic structural equation modeling (SEM) under different degrees and mechanisms of missingness were compared for the estimation of correlation and SEM parameters and goodness-of-fit indices by using Monte Carlo simulation techniques. A revised generalized least squares (GLS) method for…

Dispersions of Carbon nanotubes in Polymer Matrices

NASA Technical Reports Server (NTRS)

Wise, Kristopher Eric (Inventor); Park, Cheol (Inventor); Siochi, Emilie J. (Inventor); Harrison, Joycelyn S. (Inventor); Lillehei, Peter T. (Inventor); Lowther, Sharon E. (Inventor)

2010-01-01

Dispersions of carbon nanotubes exhibiting long term stability are based on a polymer matrix having moieties therein which are capable of a donor-acceptor complexation with carbon nanotubes. The carbon nanotubes are introduced into the polymer matrix and separated therein by standard means. Nanocomposites produced from these dispersions are useful in the fabrication of structures, e.g., lightweight aerospace structures.

A unified statistical approach to non-negative matrix factorization and probabilistic latent semantic indexing

PubMed Central

Wang, Guoli; Ebrahimi, Nader

2014-01-01

Non-negative matrix factorization (NMF) is a powerful machine learning method for decomposing a high-dimensional nonnegative matrix V into the product of two nonnegative matrices, W and H, such that V ∼ W H. It has been shown to have a parts-based, sparse representation of the data. NMF has been successfully applied in a variety of areas such as natural language processing, neuroscience, information retrieval, image processing, speech recognition and computational biology for the analysis and interpretation of large-scale data. There has also been simultaneous development of a related statistical latent class modeling approach, namely, probabilistic latent semantic indexing (PLSI), for analyzing and interpreting co-occurrence count data arising in natural language processing. In this paper, we present a generalized statistical approach to NMF and PLSI based on Renyi's divergence between two non-negative matrices, stemming from the Poisson likelihood. Our approach unifies various competing models and provides a unique theoretical framework for these methods. We propose a unified algorithm for NMF and provide a rigorous proof of monotonicity of multiplicative updates for W and H. In addition, we generalize the relationship between NMF and PLSI within this framework. We demonstrate the applicability and utility of our approach as well as its superior performance relative to existing methods using real-life and simulated document clustering data. PMID:25821345

A unified statistical approach to non-negative matrix factorization and probabilistic latent semantic indexing.

PubMed

Devarajan, Karthik; Wang, Guoli; Ebrahimi, Nader

2015-04-01

Non-negative matrix factorization (NMF) is a powerful machine learning method for decomposing a high-dimensional nonnegative matrix V into the product of two nonnegative matrices, W and H , such that V ∼ W H . It has been shown to have a parts-based, sparse representation of the data. NMF has been successfully applied in a variety of areas such as natural language processing, neuroscience, information retrieval, image processing, speech recognition and computational biology for the analysis and interpretation of large-scale data. There has also been simultaneous development of a related statistical latent class modeling approach, namely, probabilistic latent semantic indexing (PLSI), for analyzing and interpreting co-occurrence count data arising in natural language processing. In this paper, we present a generalized statistical approach to NMF and PLSI based on Renyi's divergence between two non-negative matrices, stemming from the Poisson likelihood. Our approach unifies various competing models and provides a unique theoretical framework for these methods. We propose a unified algorithm for NMF and provide a rigorous proof of monotonicity of multiplicative updates for W and H . In addition, we generalize the relationship between NMF and PLSI within this framework. We demonstrate the applicability and utility of our approach as well as its superior performance relative to existing methods using real-life and simulated document clustering data.

Hematopoietic-to-mesenchymal transition of adipose tissue macrophages is regulated by integrin β1 and fabricated fibrin matrices

PubMed Central

Majka, Susan M.; Kohrt, Wendy M.; Miller, Heidi L.; Sullivan, Timothy M.; Klemm, Dwight J.

2017-01-01

ABSTRACT Some bona fide adult adipocytes arise de novo from a bone marrow-derived myeloid lineage. These studies further demonstrate that adipose tissue stroma contains a resident population of myeloid cells capable of adipocyte and multilineage mesenchymal differentiation. These resident myeloid cells lack hematopoietic markers and express mesenchymal and progenitor cell markers. Because bone marrow mesenchymal progenitor cells have not been shown to enter the circulation, we hypothesized that myeloid cells acquire mesenchymal differentiation capacity in adipose tissue. We fabricated a 3-dimensional fibrin matrix culture system to define the adipose differentiation potential of adipose tissue-resident myeloid subpopulations, including macrophages, granulocytes and dendritic cells. Our data show that multilineage mesenchymal potential was limited to adipose tissue macrophages, characterized by the acquisition of adipocyte, osteoblast, chondrocyte and skeletal muscle myocyte phenotypes. Fibrin hydrogel matrices stimulated macrophage loss of hematopoietic cell lineage determinants and the expression of mesenchymal and progenitor cell markers, including integrin β1. Ablation of integrin β1 in macrophages inhibited adipocyte specification. Therefore, some bona fide adipocytes are specifically derived from adipose tissue-resident macrophages via an integrin β1-dependent hematopoietic-to-mesenchymal transition, whereby they become capable of multipotent mesenchymal differentiation. The requirement for integrin β1 highlights this molecule as a potential target for controlling the production of marrow-derived adipocytes and their contribution to adipose tissue development and function. PMID:28441086

An iterative ensemble quasi-linear data assimilation approach for integrated reservoir monitoring

NASA Astrophysics Data System (ADS)

Li, J. Y.; Kitanidis, P. K.

2013-12-01

Reservoir forecasting and management are increasingly relying on an integrated reservoir monitoring approach, which involves data assimilation to calibrate the complex process of multi-phase flow and transport in the porous medium. The numbers of unknowns and measurements arising in such joint inversion problems are usually very large. The ensemble Kalman filter and other ensemble-based techniques are popular because they circumvent the computational barriers of computing Jacobian matrices and covariance matrices explicitly and allow nonlinear error propagation. These algorithms are very useful but their performance is not well understood and it is not clear how many realizations are needed for satisfactory results. In this presentation we introduce an iterative ensemble quasi-linear data assimilation approach for integrated reservoir monitoring. It is intended for problems for which the posterior or conditional probability density function is not too different from a Gaussian, despite nonlinearity in the state transition and observation equations. The algorithm generates realizations that have the potential to adequately represent the conditional probability density function (pdf). Theoretical analysis sheds light on the conditions under which this algorithm should work well and explains why some applications require very few realizations while others require many. This algorithm is compared with the classical ensemble Kalman filter (Evensen, 2003) and with Gu and Oliver's (2007) iterative ensemble Kalman filter on a synthetic problem of monitoring a reservoir using wellbore pressure and flux data.

LASERS IN MEDICINE: Structure of matrices for the transformation of laser radiation by biofractals

NASA Astrophysics Data System (ADS)

Angel'skii, O. V.; Ushenko, A. G.; Arkhelyuk, A. D.; Ermolenko, S. B.; Burkovets, D. N.

1999-12-01

The changes in the state of polarisation of laser radiation transformed by biofractal objects are examined. The orientational angular structure of the matrix elements of the operator representing the optical properties of biofractals with different morphological structures (mineralised collagen fibres and myosin bundles) is investigated. An optical model for the description of fractal laser fields under the conditions of single light scattering is proposed.

Advanced thermoplastic resins, phase 2

NASA Technical Reports Server (NTRS)

Brown, A. M.; Hill, S. G.; Falcone, A.

1991-01-01

High temperature structural resins are required for use on advanced aerospace vehicles as adhesives and composite matrices. NASA-Langley developed polyimide resins were evaluated as high temperature structural adhesives for metal to metal bonding and as composite matrices. Adhesive tapes were prepared on glass scrim fabric from solutions of polyamide acids of the semicrystalline polyimide LARC-CPI, developed at the NASA-Langley Research Center. Using 6Al-4V titanium adherends, high lap shear bond strengths were obtained at ambient temperature (45.2 MPa, 6550 psi) and acceptable strengths were obtained at elevated temperature (14.0 MPa, 2030 psi) using the Pasa-Jell 107 conversion coating on the titanium and a bonding pressure of 1.38 MPa (200 psi). Average zero degree composite tensile and compressive strengths of 1290 MPa (187 ksi) and 883 MPa (128 ksi) respectively were obtained at ambient temperature with unsized AS-4 carbon fiber reinforcement.

Acoustooptic linear algebra processors - Architectures, algorithms, and applications

NASA Technical Reports Server (NTRS)

Casasent, D.

1984-01-01

Architectures, algorithms, and applications for systolic processors are described with attention to the realization of parallel algorithms on various optical systolic array processors. Systolic processors for matrices with special structure and matrices of general structure, and the realization of matrix-vector, matrix-matrix, and triple-matrix products and such architectures are described. Parallel algorithms for direct and indirect solutions to systems of linear algebraic equations and their implementation on optical systolic processors are detailed with attention to the pipelining and flow of data and operations. Parallel algorithms and their optical realization for LU and QR matrix decomposition are specifically detailed. These represent the fundamental operations necessary in the implementation of least squares, eigenvalue, and SVD solutions. Specific applications (e.g., the solution of partial differential equations, adaptive noise cancellation, and optimal control) are described to typify the use of matrix processors in modern advanced signal processing.

A uniform object-oriented solution to the eigenvalue problem for real symmetric and Hermitian matrices

NASA Astrophysics Data System (ADS)

Castro, María Eugenia; Díaz, Javier; Muñoz-Caro, Camelia; Niño, Alfonso

2011-09-01

We present a system of classes, SHMatrix, to deal in a unified way with the computation of eigenvalues and eigenvectors in real symmetric and Hermitian matrices. Thus, two descendant classes, one for the real symmetric and other for the Hermitian cases, override the abstract methods defined in a base class. The use of the inheritance relationship and polymorphism allows handling objects of any descendant class using a single reference of the base class. The system of classes is intended to be the core element of more sophisticated methods to deal with large eigenvalue problems, as those arising in the variational treatment of realistic quantum mechanical problems. The present system of classes allows computing a subset of all the possible eigenvalues and, optionally, the corresponding eigenvectors. Comparison with well established solutions for analogous eigenvalue problems, as those included in LAPACK, shows that the present solution is competitive against them. Program summaryProgram title: SHMatrix Catalogue identifier: AEHZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2616 No. of bytes in distributed program, including test data, etc.: 127 312 Distribution format: tar.gz Programming language: Standard ANSI C++. Computer: PCs and workstations. Operating system: Linux, Windows. Classification: 4.8. Nature of problem: The treatment of problems involving eigensystems is a central topic in the quantum mechanical field. Here, the use of the variational approach leads to the computation of eigenvalues and eigenvectors of real symmetric and Hermitian Hamiltonian matrices. Realistic models with several degrees of freedom leads to large (sometimes very large) matrices. Different techniques, such as divide and conquer, can be used to factorize the matrices in order to apply a parallel computing approach. However, it is still interesting to have a core procedure able to tackle the computation of eigenvalues and eigenvectors once the matrix has been factorized to pieces of enough small size. Several available software packages, such as LAPACK, tackled this problem under the traditional imperative programming paradigm. In order to ease the modelling of complex quantum mechanical models it could be interesting to apply an object-oriented approach to the treatment of the eigenproblem. This approach offers the advantage of a single, uniform treatment for the real symmetric and Hermitian cases. Solution method: To reach the above goals, we have developed a system of classes: SHMatrix. SHMatrix is composed by an abstract base class and two descendant classes, one for real symmetric matrices and the other for the Hermitian case. The object-oriented characteristics of inheritance and polymorphism allows handling both cases using a single reference of the base class. The basic computing strategy applied in SHMatrix allows computing subsets of eigenvalues and (optionally) eigenvectors. The tests performed show that SHMatrix is competitive, and more efficient for large matrices, than the equivalent routines of the LAPACK package. Running time: The examples included in the distribution take only a couple of seconds to run.

On a Poisson homogeneous space of bilinear forms with a Poisson-Lie action

NASA Astrophysics Data System (ADS)

Chekhov, L. O.; Mazzocco, M.

2017-12-01

Let \\mathscr A be the space of bilinear forms on C^N with defining matrices A endowed with a quadratic Poisson structure of reflection equation type. The paper begins with a short description of previous studies of the structure, and then this structure is extended to systems of bilinear forms whose dynamics is governed by the natural action A\\mapsto B ABT} of the {GL}_N Poisson-Lie group on \\mathscr A. A classification is given of all possible quadratic brackets on (B, A)\\in {GL}_N× \\mathscr A preserving the Poisson property of the action, thus endowing \\mathscr A with the structure of a Poisson homogeneous space. Besides the product Poisson structure on {GL}_N× \\mathscr A, there are two other (mutually dual) structures, which (unlike the product Poisson structure) admit reductions by the Dirac procedure to a space of bilinear forms with block upper triangular defining matrices. Further generalisations of this construction are considered, to triples (B,C, A)\\in {GL}_N× {GL}_N× \\mathscr A with the Poisson action A\\mapsto B ACT}, and it is shown that \\mathscr A then acquires the structure of a Poisson symmetric space. Generalisations to chains of transformations and to the quantum and quantum affine algebras are investigated, as well as the relations between constructions of Poisson symmetric spaces and the Poisson groupoid. Bibliography: 30 titles.

Water relations and photosynthesis in the cryptoendolithic microbial habitat of hot and cold deserts

NASA Technical Reports Server (NTRS)

Palmer, R. J. Jr; Friedmann, E. I.

1990-01-01

Two cryptoendolithic microbial communities, lichens in the Ross Desert of Antarctica and cyanobacteria in the Negev Desert, inhabit porous sandstone rocks of similar physical structure. Both rock types adsorb water vapor by physical mechanisms unrelated to biological processes. Yet the two microbial communities respond differently to water stress: cryptoendolithic lichens begin to photosynthesize at a matric water potential of -46.4 megaPascals (MPa) [70% relative humidity (RH) at 8 degrees C], resembling thallose desert lichens. Cryptoendolithic cyanobacteria, like other prokaryotes, photosynthesize only at very high matric water potentials [> -6.9 MPa, 90% RH at 20 degrees C].

Matrices of radiation-protective composites using bismuth oxide

NASA Astrophysics Data System (ADS)

Yashkina, S. Yu; Doroganov, V. A.; Trepalina, Yu N.; Loktionov, V. A.; Evtushenko, E. I.

2018-03-01

The article presents the results of investigations of radiation-protective composites with two types of matrices based on chamotte and aluminous binders. The synthesis of binders was carried out according to the principles of the production of ceramic concrete based on the artificial ceramic binders (ACB). Bismuth oxide was selected as filler. Basic physical and mechanical, as well as radiation-protective characteristics, of composites with different ratios of ACB and Bi2O3 were shown. It was found out that binder of high-alumina chamotte can be used as an optimal matrix base. Composites on its basis have higher structural and radiation-protective properties.

Phase Transitions of KIO3 Ferroelectrics in Al2O3-Based Nanoporous Matrices

NASA Astrophysics Data System (ADS)

Milinskii, A. Yu.; Baryshnikov, S. V.

2018-03-01

Temperature dependences of the linear permittivity ɛ' and the third harmonic amplitude γ3ω of composites prepared by introducing ferroelectrics KIO3 into matrices of porous aluminum oxide Al2O3 with pore sizes of 240 nm were studied. It is found that the IV → III and III → II structural transition temperatures of potassium iodide in Al2O3 pores decrease by 5 K and 24 K, respectively, with respect to bulk KIO3. The measurements of the dielectric properties do not reveal V → IV and II → I phase transitions in the composite samples.

An inexpensive and fast method for infiltration coating of complex geometry matrices for ISOL production target applications

NASA Astrophysics Data System (ADS)

Kawai, Y.; Alton, G. D.; Bilheux, J.-C.

2005-12-01

An inexpensive, fast, and close to universal infiltration coating technique has been developed for fabricating fast diffusion-release ISOL targets. Targets are fabricated by deposition of finely divided (∼1 μm) compound materials in a paint-slurry onto highly permeable, complex structure reticulated-vitreous-carbon-foam (RVCF) matrices, followed by thermal heat treatment. In this article, we describe the coating method and present information on the physical integrity, uniformity of deposition, and matrix adherence of SiC, HfC and UC2 targets, destined for on-line use as targets at the Holifield Radioactive Ion Beam Facility (HRIBF).

Emerin modulates spatial organization of chromosome territories in cells on softer matrices

PubMed Central

Pradhan, Roopali; Ranade, Devika

2018-01-01

Abstract Cells perceive and relay external mechanical forces into the nucleus through the nuclear envelope. Here we examined the effect of lowering substrate stiffness as a paradigm to address the impact of altered mechanical forces on nuclear structure-function relationships. RNA sequencing of cells on softer matrices revealed significant transcriptional imbalances, predominantly in chromatin associated processes and transcriptional deregulation of human Chromosome 1. Furthermore, 3-Dimensional fluorescence in situ hybridization (3D-FISH) analyses showed a significant mislocalization of Chromosome 1 and 19 Territories (CT) into the nuclear interior, consistent with their transcriptional deregulation. However, CT18 with relatively lower transcriptional dysregulation, also mislocalized into the nuclear interior. Furthermore, nuclear Lamins that regulate chromosome positioning, were mislocalized into the nuclear interior in response to lowered matrix stiffness. Notably, Lamin B2 overexpression retained CT18 near the nuclear periphery in cells on softer matrices. While, cells on softer matrices also activated emerin phosphorylation at a novel Tyr99 residue, the inhibition of which in a phospho-deficient mutant (emerinY99F), selectively retained chromosome 18 and 19 but not chromosome 1 territories at their conserved nuclear locations. Taken together, emerin functions as a key mechanosensor, that modulates the spatial organization of chromosome territories in the interphase nucleus. PMID:29684168

Photoinduced transformations of indole and 3-formylindole monomers isolated in low-temperature matrices

NASA Astrophysics Data System (ADS)

Reva, Igor; Lapinski, Leszek; Lopes Jesus, A. J.; Nowak, Maciej J.

2017-11-01

Photochemical transformations were studied for monomers of indole and 3-formylindole isolated in low-temperature noble-gas matrices. Upon UV (λ > 270 nm) irradiation of indole trapped in argon and neon matrices, the initial 1H-form of the compound converted into the 3H-tautomer. Alongside this photoinduced hydrogen-atom transfer, an indolyl radical was also generated by photodetachment of the hydrogen atom from the N1-H bond. Excitation of 3-formylindole isolated in an argon matrix with UV (λ > 335 nm) light led to interconversion between the two conformers of the 1H-tautomer, differing from each other in the orientation of the formyl group (cis or trans). Parallel to this conformational phototransformation, the 3H-form of the compound was generated in the 1H → 3H phototautomeric conversion. The photoproducts emerging upon UV irradiation of indole and 3-formylindole were identified by comparison of their infrared spectra with the spectra calculated for candidate structures.

RuO2 pH Sensor with Super-Glue-Inspired Reference Electrode

PubMed Central

Wajrak, Magdalena; Alameh, Kamal

2017-01-01

A pH-sensitive RuO2 electrode coated in a commercial cyanoacrylate adhesive typically exhibits very low pH sensitivity, and could be paired with a RuO2 working electrode as a differential type pH sensor. However, such sensors display poor performance in real sample matrices. A pH sensor employing a RuO2 pH-sensitive working electrode and a SiO2-PVB junction-modified RuO2 reference electrode is developed as an alternative high-performance solution. This sensor exhibits a performance similar to that of a commercial glass pH sensor in some common sample matrices, particularly, an excellent pH sensitivity of 55.7 mV/pH, a hysteresis as low as 2.7 mV, and a drift below 2.2 mV/h. The developed sensor structure opens the way towards the development of a simple, cost effective, and robust pH sensor for pH analysis in various sample matrices. PMID:28878182

RuO₂ pH Sensor with Super-Glue-Inspired Reference Electrode.

PubMed

Lonsdale, Wade; Wajrak, Magdalena; Alameh, Kamal

2017-09-06

A pH-sensitive RuO₂ electrode coated in a commercial cyanoacrylate adhesive typically exhibits very low pH sensitivity, and could be paired with a RuO₂ working electrode as a differential type pH sensor. However, such sensors display poor performance in real sample matrices. A pH sensor employing a RuO₂ pH-sensitive working electrode and a SiO₂-PVB junction-modified RuO₂ reference electrode is developed as an alternative high-performance solution. This sensor exhibits a performance similar to that of a commercial glass pH sensor in some common sample matrices, particularly, an excellent pH sensitivity of 55.7 mV/pH, a hysteresis as low as 2.7 mV, and a drift below 2.2 mV/h. The developed sensor structure opens the way towards the development of a simple, cost effective, and robust pH sensor for pH analysis in various sample matrices.

Optimal Frequency-Domain System Realization with Weighting

NASA Technical Reports Server (NTRS)

Juang, Jer-Nan; Maghami, Peiman G.

1999-01-01

Several approaches are presented to identify an experimental system model directly from frequency response data. The formulation uses a matrix-fraction description as the model structure. Frequency weighting such as exponential weighting is introduced to solve a weighted least-squares problem to obtain the coefficient matrices for the matrix-fraction description. A multi-variable state-space model can then be formed using the coefficient matrices of the matrix-fraction description. Three different approaches are introduced to fine-tune the model using nonlinear programming methods to minimize the desired cost function. The first method uses an eigenvalue assignment technique to reassign a subset of system poles to improve the identified model. The second method deals with the model in the real Schur or modal form, reassigns a subset of system poles, and adjusts the columns (rows) of the input (output) influence matrix using a nonlinear optimizer. The third method also optimizes a subset of poles, but the input and output influence matrices are refined at every optimization step through least-squares procedures.

The molecular and electronic structure of s-tetrazine in the ground and first excited state: A theoretical investigation

NASA Astrophysics Data System (ADS)

Schütz, Martin; Hutter, Jürg; Lüthi, Hans Peter

1995-10-01

The ground- and first excited state of s-tetrazine arising from a π*←n excitation (1Ag,1B3u) have been studied using the complete active space (CASSCF) and the second order multiconfiguration perturbation theory (CASPT2) ab initio methods. The focus of this study is on the effect of the electronic excitation on the molecular structure and on those electronic properties which are important to model the solvatochromatic behavior of the molecule in polymer matrices as used in permanent hole burning experiments. Since the accurate computation of excited state molecular properties represents a major challenge for today's numerical quantum chemistry, some technical aspects are also considered. The present study shows that the change in geometry upon electronic excitation is small. This is in partial contradiction with the experimental studies which however disagree among themselves [see K. K. Innes, I. G. Ross, and W. R. Moomaw, J. Mol. Spectrosc. 132, 492 (1988), and R. E. Smalley, L. Wharton, and D. H. Levi, ibid. 66, 375 (1977)]. This study also confirms that the first excited state equilibrium structure is of D2h symmetry. In an earlier theoretical study it was found that the D2h symmetry structure may represent a saddle point rather than a minimum on the excited state potential surface [see A. C. Scheiner and H. F. Schaefer III, J. Chem. Phys. 87, 3539 (1987)]. In the first excited state, we observe an increase of the mean polarizability of s-tetrazine along with an enhanced anisotropy. The change in the polarizability is almost exclusively in the ``in-plane'' components of the tensor; the polarizability in the vertical direction is nearly unchanged. This observation questions recent experimental results reported for this molecule [see S. Heitz, D. Weidnauer, and A. Hese, J. Chem. Phys. 95, 7952 (1991)].

An Analysis of the Max-Min Texture Measure.

DTIC Science & Technology

1982-01-01

PANC 33 D2 Confusion Matrices for Scene A, IR 34 D3 Confusion Matrices for Scene B, PANC 35 D4 Confusion Matrices for Scene B, IR 36 D5 Confusion...Matrices for Scene C, PANC 37 D6 Confusion Matrices for Scene C, IR 38 D7 Confusion Matrices for Scene E, PANC 39 D8 Confusion Matrices for Scene E, IR 40...D9 Confusion Matrices for Scene H, PANC 41 DIO Confusion Matrices for Scene H, JR 42 3 .D 10CnuinMtie o cn ,IR4 AN ANALYSIS OF THE MAX-MIN TEXTURE

Continuous production of controlled release dosage forms based on hot-melt extruded gum arabic: Formulation development, in vitro characterization and evaluation of potential application fields.

PubMed

Kipping, Thomas; Rein, Hubert

2016-01-30

Controlled release matrices based on gum arabic are prepared by applying a continuous hot-melt extrusion technology: the pre-mixture consisting of gum arabic and the incorporated API is plasticized by a co-rotating twin-screw extruder, an intermediate strand is formed by a round nozzle. Single dosed matrices are prepared by cutting the semi elastic strand with a rotary fly cutter. Paracetamol and phenazone are used as model drug substances. High drug loadings up to 70% can be realized. Matrices are characterized concerning their crystalline structure, in vitro dissolution, disintegration time and various physical parameters including glass transition temperature (Tg). Release characteristic behavior is mainly influenced by erosion of the matrices. At higher drug loadings also diffusion based transport gain importance. The solubility of the API shows an influence on the erosion rate of the matrix and should therefore be considered during formulation development. Tg is mainly influenced by the solubility of the API in the surrounding matrix. High soluble phenazone shows a decrease, whereas paracetamol addition has nearly no influence on the Tg of the polymeric system. Activation energy (EA) of the glass transition is determined via dynamic mechanical analysis. The addition of APIs leads to a reduction of EA indicating an increased molecular movement at Tg region compared to placebo extrudates. X-ray diffraction is used to determine the crystalline state of the extruded matrices and interaction between matrix and incorporated APIs. The production of thin layer matrices is an interesting option to provide a fast drug delivery to the oral cavity. High mechanical strength combined with fast disintegration times can be a great advantage for the development of oro-dispersible tablets. A great benefit of the evaluated processing technology is the simple adaption of the final dose by varying either the cutting length or the diameter of the nozzle resulting in a cost-effective production of single dosed matrices without modification of the base formula. Copyright © 2015 Elsevier B.V. All rights reserved.

Texture analysis of aeromagnetic data for enhancing geologic features using co-occurrence matrices in Elallaqi area, South Eastern Desert of Egypt

NASA Astrophysics Data System (ADS)

Eldosouky, Ahmed M.; Elkhateeb, Sayed O.

2018-06-01

Enhancement of aeromagnetic data for qualitative purposes depends on the variations of texture and amplitude to outline various geologic features within the data. The texture of aeromagnetic data consists continuity of adjacent anomalies, size, and pattern. Variations in geology, or particularly rock magnetization, in a study area cause fluctuations in texture. In the present study, the anomalous features of Elallaqi area were extracted from aeromagnetic data. In order to delineate textures from the aeromagnetic data, the Red, Green, and Blue Co-occurrence Matrices (RGBCM) were applied to the reduced to the pole (RTP) grid of Elallaqi district in the South Eastern Desert of Egypt. The RGBCM are fashioned of sets of spatial analytical parameters that transform magnetic data into texture forms. Six texture features (parameters), i.e. Correlation, Contrast, Entropy, Homogeneity, Second Moment, and Variance, of RGB Co-occurrence Matrices (RGBCM) are used for analyzing the texture of the RTP grid in this study. These six RGBCM texture characteristics were mixed into a single image using principal component analysis. The calculated texture images present geologic characteristics and structures with much greater sidelong resolution than the original RTP grid. The estimated texture images enabled us to distinguish multiple geologic regions and structures within Elallaqi area including geologic terranes, lithologic boundaries, cracks, and faults. The faults of RGBCM maps were more represented than those of magnetic derivatives providing enhancement of the fine structures of Elallaqi area like the NE direction which scattered WNW metavolcanics and metasediments trending in the northwestern division of Elallaqi area.

Kinematic state estimation and motion planning for stochastic nonholonomic systems using the exponential map

PubMed Central

Park, Wooram; Liu, Yan; Zhou, Yu; Moses, Matthew; Chirikjian, Gregory S.

2010-01-01

SUMMARY A nonholonomic system subjected to external noise from the environment, or internal noise in its own actuators, will evolve in a stochastic manner described by an ensemble of trajectories. This ensemble of trajectories is equivalent to the solution of a Fokker–Planck equation that typically evolves on a Lie group. If the most likely state of such a system is to be estimated, and plans for subsequent motions from the current state are to be made so as to move the system to a desired state with high probability, then modeling how the probability density of the system evolves is critical. Methods for solving Fokker-Planck equations that evolve on Lie groups then become important. Such equations can be solved using the operational properties of group Fourier transforms in which irreducible unitary representation (IUR) matrices play a critical role. Therefore, we develop a simple approach for the numerical approximation of all the IUR matrices for two of the groups of most interest in robotics: the rotation group in three-dimensional space, SO(3), and the Euclidean motion group of the plane, SE(2). This approach uses the exponential mapping from the Lie algebras of these groups, and takes advantage of the sparse nature of the Lie algebra representation matrices. Other techniques for density estimation on groups are also explored. The computed densities are applied in the context of probabilistic path planning for kinematic cart in the plane and flexible needle steering in three-dimensional space. In these examples the injection of artificial noise into the computational models (rather than noise in the actual physical systems) serves as a tool to search the configuration spaces and plan paths. Finally, we illustrate how density estimation problems arise in the characterization of physical noise in orientational sensors such as gyroscopes. PMID:20454468

Fermion Universality Manifesting Itself in the Dirac Component of Neutrino Mass Matrix

NASA Astrophysics Data System (ADS)

Krolikowski, Wojciech

2002-02-01

An effective texture is presented for six Majorana conventional neutrinos (three active and three sterile), based on a 6× 6 neutrino mixing matrix whose 3× 3 active--active component arises from the popular bimaximal mixing matrix of active neutrinos ν e, ν μ , ν τ by three small rotations in the 14, 25, 36 planes of ν 1 , ν 2 , ν 3 and ν 4 , ν5, ν 6 neutrino mass states. The Dirac component (i.e. , 3 × 3 active-sterile component) of the resulting 6 × 6 neutrino mass matrix is conjectured to get a structure similar to the charged-lepton and quark 3 × 3 mass matrices, after the bimaximal mixing, specific for neutrinos, is transformed out unitarily from the neutrino mass matrix. The charged-lepton and quark mass matrices are taken in a universal form constructed previously by the author with a conside- rable phenomenological success. Then, for the option of m21 ≃ m22 ≃ m23 ≫ m24 ≃ m25 ≃ m26 ≃ 0, the proposed texture predicts oscillations of solar ν e's with Δ m2sol ≡ Δ m221 ˜ (1.1 to 1.2) × 10-5 eV2, not inconsistent with the LMA solar solution, if the SuperKamiokande value Δ m2atm ≡ Δ m232 ˜ (3 to 3.5) × 10-3eV2 for oscillations of atmospheric ν μ 's is taken as an input. Here, sin2 2θ sol ˜ 1 and sin2 2 θ atm ˜ 1. The texture predicts also an LSND effect with sin2 2θ LSND (1.4 to 1.9)× 10-11 (eV/m1)4 and Δ m2LSND ≡ Δ m225 ˜ m21 + (1.1 to 1.2) 10-5 eV}2. Unfortunately, the Chooz experiment imposes on the LSND effect (in our texture) a very small upper bound sin2 2θ LSND ≲ 1.3 × 10-3, which corresponds to the lower limit m1 ≳ (1.0 to 1.1)× 10-2 eV.

Certification and verification for Northrup model NSC-01-0732 fresnel lens concentrating solar collector

NASA Technical Reports Server (NTRS)

1979-01-01

Structural analysis and certification of the collector system is presented. System verification against the interim performance criteria is presented and indicated by matrices. The verification discussion, analysis, and test results are also given.

Webs on surfaces, rings of invariants, and clusters.

PubMed

Fomin, Sergey; Pylyavskyy, Pavlo

2014-07-08

We construct and study cluster algebra structures in rings of invariants of the special linear group action on collections of 3D vectors, covectors, and matrices. The construction uses Kuperberg's calculus of webs on marked surfaces with boundary.

Elaboration et caracterisation de nanocomposites polyethylene/montmorillonite

NASA Astrophysics Data System (ADS)

Stoeffler, Karen

This research project consists in preparing polyethylene/montmorillonite nanocomposites for film packaging applications. Montmorillonite is a natural clay with an exceptional aspect ratio. In recent years, its incorporation in polymer matrices has attracted great interest. The pioneer work from Toyota on polyamide-6/montmorillonite composites has shown that it was possible to disperse the clay at a nanometric scale. Such a structure, so-called exfoliated, leads to a significant increase in mechanical, barrier and fire retardant properties, even at low volumetric fractions of clay. This allows a valorization of the polymeric material at moderate cost. Due to its high polarity, montmorilloite exfoliation in polymeric matrices is problematic. In the particular case of polyolefin matrices, the platelets dispersion remains limited: most frequently, the composites obtained exhibit conventional structures (microcomposites) or intercalated structures. To solve this problem, two techniques are commonly employed: the surface treatment of the clay, which allows the expansion of the interfoliar gallery while increasing the affinity between the clay and the polymer, and the use of a polar compatibilizing agent (grafted polyolefin). The first part of this thesis deals with the preparation and the characterization of highly thermally stable organophilic montmorillonites. Commercial organophilic montmorillonites are treated with quaternary ammonium intercalating agents. However, those intercalating agents present a poor thermal stability and are susceptible to decompose upon processing, thus affecting the clay dispersion and the final properties of the nanocomposites. In this work, it was proposed to modify the clay with alkyl pyridinium, alkyl imidazolium and alkyl phosphonium intercalating agents, which are more stable than ammonium based cations. Organophilic montmorillonites with enhanced thermal stabilites compared to commercial organoclays (+20°C to +70°C) were prepared. The effect of the chemical structure of the intercalating agent on the capacity of the organoclay to be dispersed in polyethylene matrices was analyzed. In addition, the influence of the dispersion on the thermal stability of the nanocomposites prepared is discussed. In a second part, the effect of the compatibilizing agent characteristics on the quality of the clay dispersion in polyethylene/montmorillonite nanocomposites was analyzed. The mechanical properties and the oxygen permeability of the nanocomposites were evaluated and related to the level of clay delamination and to the strength of the polymer/clay interface, which was evaluated through surface tension measurements.

A new look at the simultaneous analysis and design of structures

NASA Technical Reports Server (NTRS)

Striz, Alfred G.

1994-01-01

The minimum weight optimization of structural systems, subject to strength and displacement constraints as well as size side constraints, was investigated by the Simultaneous ANalysis and Design (SAND) approach. As an optimizer, the code NPSOL was used which is based on a sequential quadratic programming (SQP) algorithm. The structures were modeled by the finite element method. The finite element related input to NPSOL was automatically generated from the input decks of such standard FEM/optimization codes as NASTRAN or ASTROS, with the stiffness matrices, at present, extracted from the FEM code ANALYZE. In order to avoid ill-conditioned matrices that can be encountered when the global stiffness equations are used as additional nonlinear equality constraints in the SAND approach (with the displacements as additional variables), the matrix displacement method was applied. In this approach, the element stiffness equations are used as constraints instead of the global stiffness equations, in conjunction with the nodal force equilibrium equations. This approach adds the element forces as variables to the system. Since, for complex structures and the associated large and very sparce matrices, the execution times of the optimization code became excessive due to the large number of required constraint gradient evaluations, the Kreisselmeier-Steinhauser function approach was used to decrease the computational effort by reducing the nonlinear equality constraint system to essentially a single combined constraint equation. As the linear equality and inequality constraints require much less computational effort to evaluate, they were kept in their previous form to limit the complexity of the KS function evaluation. To date, the standard three-bar, ten-bar, and 72-bar trusses have been tested. For the standard SAND approach, correct results were obtained for all three trusses although convergence became slower for the 72-bar truss. When the matrix displacement method was used, correct results were still obtained, but the execution times became excessive due to the large number of constraint gradient evaluations required. Using the KS function, the computational effort dropped, but the optimization seemed to become less robust. The investigation of this phenomenon is continuing. As an alternate approach, the code MINOS for the optimization of sparse matrices can be applied to the problem in lieu of the Kreisselmeier-Steinhauser function. This investigation is underway.

Photonic structures based on hybrid nanocomposites

NASA Astrophysics Data System (ADS)

Husaini, Saima

In this thesis, photonic structures embedded with two types of nanomaterials, (i) quantum dots and (ii) metal nanoparticles are studied. Both of these exhibit optical and electronic properties different from their bulk counterpart due to their nanoscale physical structure. By integrating these nanomaterials into photonic structures, in which the electromagnetic field can be confined and controlled via modification of geometry and composition, we can enhance their linear and nonlinear optical properties to realize functional photonic structures. Before embedding quantum dots into photonic structures, we study the effect of various host matrices and fabrication techniques on the optical properties of the colloidal quantum dots. The two host matrices of interest are SU8 and PMMA. It is shown that the emission properties of the quantum dots are significantly altered in these host matrices (especially SU8) and this is attributed to a high rate of nonradiative quenching of the dots. Furthermore, the effects of fabrication techniques on the optical properties of quantum dots are also investigated. Finally a microdisk resonator embedded with quantum dots is fabricated using soft lithography and luminescence from the quantum dots in the disk is observed. We investigate the absorption and effective index properties of silver nanocomposite films. It is shown that by varying the fill factor of the metal nanoparticles and fabrication parameters such as heating time, we can manipulate the optical properties of the metal nanocomposite. Optimizing these parameters, a silver nanocomposite film with a 7% fill factor is prepared. A one-dimensional photonic crystal consisting of alternating layers of the silver nanocomposite and a polymer (Polymethyl methacrylate) is fabricated using spin coating and its linear and nonlinear optical properties are investigated. Using reflectivity measurements we demonstrate that the one-dimensional silver-nanocomposite-dielectric photonic crystal exhibits a 200% enhancement of the reflection band which is attributed to the interplay between the plasmon resonance of the silver nanoparticles and the Bloch modes of the photonic crystal. Nonlinear optical studies on this one-dimensional silver-nanocomposite-dielectric structure using z-scan measurements are conducted. These measurements indicate a three-fold enhancement in the nonlinear absorption coefficient when compared to a single film of comparable metal composite thickness.

Efficient block preconditioned eigensolvers for linear response time-dependent density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue

Within this paper, we present two efficient iterative algorithms for solving the linear response eigenvalue problem arising from the time dependent density functional theory. Although the matrix to be diagonalized is nonsymmetric, it has a special structure that can be exploited to save both memory and floating point operations. In particular, the nonsymmetric eigenvalue problem can be transformed into an eigenvalue problem that involves the product of two matrices M and K. We show that, because MK is self-adjoint with respect to the inner product induced by the matrix K, this product eigenvalue problem can be solved efficiently by amore » modified Davidson algorithm and a modified locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm that make use of the K-inner product. Additionally, the solution of the product eigenvalue problem yields one component of the eigenvector associated with the original eigenvalue problem. We show that the other component of the eigenvector can be easily recovered in an inexpensive postprocessing procedure. As a result, the algorithms we present here become more efficient than existing methods that try to approximate both components of the eigenvectors simultaneously. In particular, our numerical experiments demonstrate that the new algorithms presented here consistently outperform the existing state-of-the-art Davidson type solvers by a factor of two in both solution time and storage.« less

Efficient block preconditioned eigensolvers for linear response time-dependent density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue

In this article, we present two efficient iterative algorithms for solving the linear response eigenvalue problem arising from the time dependent density functional theory. Although the matrix to be diagonalized is nonsymmetric, it has a special structure that can be exploited to save both memory and floating point operations. In particular, the nonsymmetric eigenvalue problem can be transformed into an eigenvalue problem that involves the product of two matrices M and K. We show that, because MK is self-adjoint with respect to the inner product induced by the matrix K, this product eigenvalue problem can be solved efficiently by amore » modified Davidson algorithm and a modified locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm that make use of the K-inner product. The solution of the product eigenvalue problem yields one component of the eigenvector associated with the original eigenvalue problem. We show that the other component of the eigenvector can be easily recovered in an inexpensive postprocessing procedure. As a result, the algorithms we present here become more efficient than existing methods that try to approximate both components of the eigenvectors simultaneously. In particular, our numerical experiments demonstrate that the new algorithms presented here consistently outperform the existing state-of-the-art Davidson type solvers by a factor of two in both solution time and storage.« less

Folding- and Dynamics-Based Electrochemical DNA Sensors.

PubMed

Lai, Rebecca Y

2017-01-01

A number of electrochemical DNA sensors based on the target-induced change in the conformation and/or flexibility of surface-bound oligonucleotides have been developed in recent years. These sensors, which are often termed E-DNA sensors, are comprised of an oligonucleotide probe modified with a redox label (e.g., methylene blue) at one terminus and attached to a gold electrode via a thiol-gold bond at the other. Binding of the target to the DNA probe changes its structure and dynamics, which, in turn, influences the efficiency of electron transfer to the interrogating electrode. Since electrochemically active contaminants are less common, these sensors are resistant to false-positive signals arising from the nonspecific adsorption of contaminants and perform well even when employed directly in serum, whole blood, and other realistically complex sample matrices. Moreover, because all of the sensor components are chemisorbed to the electrode, the E-DNA sensors are essentially label-free and readily reusable. To date, these sensors have achieved state-of-the-art sensitivity, while offering the unprecedented selectivity, reusability, and the operational convenience of direct electrochemical detection. This chapter reviews the recent advances in the development of both "signal-off" and "signal-on" E-DNA sensors. Critical aspects that dictate the stability and performance of these sensors are also addressed so as to provide a realistic overview of this oligonucleotide detection platform. © 2017 Elsevier Inc. All rights reserved.

A review of designer anabolic steroids in equine sports.

PubMed

Waller, Christopher C; McLeod, Malcolm D

2017-09-01

In recent years, the potential for anabolic steroid abuse in equine sports has increased due to the growing availability of designer steroids. These compounds are readily accessible online in 'dietary' or 'nutritional' supplements and contain steroidal compounds which have never been tested or approved as veterinary agents. They typically have unusual structures or substitution and as a result may pass undetected through current anti-doping screening protocols, making them a significant concern for the integrity of the industry. Despite considerable focus in human sports, until recently there has been limited investigation into these compounds in equine systems. To effectively respond to the threat of designer steroids, a detailed understanding of their metabolism is needed to identify markers and metabolites arising from their misuse. A summary of the literature detailing the metabolism of these compounds in equine systems is presented with an aim to identify metabolites suitable for incorporation into screening protocols by anti-doping laboratories. The future of equine anti-doping research is likely to be guided by the incorporation of alternate testing matrices into routine screening, the improvement of in vitro technologies that can mimic in vivo equine metabolism, and the improvement of instrumentation or analytical methods that allow for the development of untargeted screening, and metabolomics approaches for use in anti-doping screening protocols. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Application of high-resolution, two-dimensional 1H and 13C nuclear magnetic resonance techniques to the characterization of lipid oxidation products in autoxidized linoleoyl/linolenoylglycerols.

PubMed

Silwood, C J; Grootveld, M

1999-07-01

Subjection of polyunsaturated fatty acid (PUFA)-rich culinary oils to standard frying episodes generates a range of lipid oxidation products (LOP), including saturated and alpha,beta-unsaturated aldehydes which arise from the thermally induced fragmentation of conjugated hydroperoxydiene precursors. Since such LOP are damaging to human health, we have employed high-resolution, two-dimensional 1H-1H relayed coherence transfer, 1H-1H total correlation, 1H-13C heteronuclear multiple quantum correlation, and 1H-1H J-resolved nuclear magnetic resonance (NMR) spectroscopic techniques to further elucidate the molecular structures of these components present in (i) a model linoleoylglycerol compound (1,3-dilinolein) allowed to autoxidize at ambient temperature and (ii) PUFA-rich culinary oils subjected to repeated frying episodes. The above techniques readily facilitate the resolution of selected vinylic and aldehydic resonances of LOP which appear as complex overlapping patterns in conventional one-dimensional spectra, particularly when employed in combination with solvent-induced spectral shift modifications. Hence, much useful multi-component information regarding the identity and/or classification of glycerol-bound conjugated hydroperoxydiene and hydroxydiene adducts, and saturated and alpha,beta-unsaturated aldehydes, present in autoxidized PUFA matrices is provided by these NMR methods. Such molecular information is of much value to researchers investigating the deleterious health effects of LOP available in the diet.

Hydrophilic interaction chromatography coupled matrix assisted laser desorption/ionization mass spectrometry for molecular analysis of organic compounds in medicines, tea, and coffee.

PubMed

Wang, Ren-Qi; Bao, Kai; Croué, Jean-Philippe; Ng, Siu Choon

2013-11-21

Natural occurring organic compounds from food, natural organic matter, as well as metabolic products have received intense attention in current chemical and biological studies. Examination of unknown compounds in complex sample matrices is hampered by the limited choices for data readout and molecular elucidation. Herein, we report a generic method of hydrophilic interaction chromatography (HILIC) coupled with matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) for the rapid characterization of ingredients in pharmaceutical compounds, tea, and coffee. The analytes were first fractionated using a cationic HILIC column prior to MALDI-MS analyses. It was found that the retention times of a compound arising from different samples were consistent under the same conditions. Accordingly, molecules can be readily characterized by both the mass and chromatographic retention time. The retention behaviors of acidic and basic compounds on the cationic HILIC column were found to be significantly influenced by the pH of mobile phases, whereas neutral compounds depicted a constant retention time at different pH. The general HILIC-MALDI-MS method is feasible for fast screening of naturally occurring organic compounds. A series of homologs can be determined if they have the same retention behavior. Their structural features can be elucidated by considering their mass differences and hydrophilic properties as determined by HILIC chromatogram.

Efficient block preconditioned eigensolvers for linear response time-dependent density functional theory

DOE PAGES

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue; ...

2017-12-01

In this article, we present two efficient iterative algorithms for solving the linear response eigenvalue problem arising from the time dependent density functional theory. Although the matrix to be diagonalized is nonsymmetric, it has a special structure that can be exploited to save both memory and floating point operations. In particular, the nonsymmetric eigenvalue problem can be transformed into an eigenvalue problem that involves the product of two matrices M and K. We show that, because MK is self-adjoint with respect to the inner product induced by the matrix K, this product eigenvalue problem can be solved efficiently by amore » modified Davidson algorithm and a modified locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm that make use of the K-inner product. The solution of the product eigenvalue problem yields one component of the eigenvector associated with the original eigenvalue problem. We show that the other component of the eigenvector can be easily recovered in an inexpensive postprocessing procedure. As a result, the algorithms we present here become more efficient than existing methods that try to approximate both components of the eigenvectors simultaneously. In particular, our numerical experiments demonstrate that the new algorithms presented here consistently outperform the existing state-of-the-art Davidson type solvers by a factor of two in both solution time and storage.« less

Efficient block preconditioned eigensolvers for linear response time-dependent density functional theory

DOE PAGES

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue; ...

2017-08-24

Within this paper, we present two efficient iterative algorithms for solving the linear response eigenvalue problem arising from the time dependent density functional theory. Although the matrix to be diagonalized is nonsymmetric, it has a special structure that can be exploited to save both memory and floating point operations. In particular, the nonsymmetric eigenvalue problem can be transformed into an eigenvalue problem that involves the product of two matrices M and K. We show that, because MK is self-adjoint with respect to the inner product induced by the matrix K, this product eigenvalue problem can be solved efficiently by amore » modified Davidson algorithm and a modified locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm that make use of the K-inner product. Additionally, the solution of the product eigenvalue problem yields one component of the eigenvector associated with the original eigenvalue problem. We show that the other component of the eigenvector can be easily recovered in an inexpensive postprocessing procedure. As a result, the algorithms we present here become more efficient than existing methods that try to approximate both components of the eigenvectors simultaneously. In particular, our numerical experiments demonstrate that the new algorithms presented here consistently outperform the existing state-of-the-art Davidson type solvers by a factor of two in both solution time and storage.« less

CYTODIFFERENTIATION DURING SPERMIOGENESIS IN LUMBRICUS TERRESTRIS

PubMed Central

Anderson, W. A.; Weissman, A.; Ellis, R. A.

1967-01-01

The structural changes during spermiogenesis were studied on developing spermatids in seminal vesicles and receptacles of Lumbricus terrestris fixed in glutaraldehyde-osmium tetroxide and embedded in Epon-Araldite. The centriole plays a prominent role in the morphogenesis and organization of the microtubules of the manchette and flagellum. Microtubules arising from the centriole extend anteriorly to encase the developing middle piece, the nucleus, and the acrosome. The manchette not only provides a supporting framework for the cell during elongation, but also may provide the motive force for the elimination of both nucleoplasm and cytoplasm. The manchette participates in segregation and elimination of the nuclear vesicle that contains the nonchromatin nucleoplasm. Compartmentalization and conservation may also be a function of the manchette since those elements which remain within the framework of microtubules are retained, while all the cytoplasm outside the manchette is discarded. At maturation, the endoplasmic reticulum plays a key role in dismantling the manchette and reducing the cytoplasm external to it. During the early stages of middle-piece formation, six ovoid mitochondria aggregate at the posterior pole of the spermatid nucleus. Concurrent with manchette formation, the mitochondria are compressed laterally into elongate wedge-shaped components, and their outer limiting membranes fuse to form an hexagonal framework that surrounds the dense intramitochondrial matrices. Dense glycogen granules are arranged linearly between the peripheral flagellar tubules and the outer membrane of the mature sperm tail. PMID:10976199

A 3D in vitro model to explore the inter-conversion between epithelial and mesenchymal states during EMT and its reversion.

PubMed

Bidarra, S J; Oliveira, P; Rocha, S; Saraiva, D P; Oliveira, C; Barrias, C C

2016-06-03

Epithelial-to-mesenchymal transitions (EMT) are strongly implicated in cancer dissemination. Intermediate states, arising from inter-conversion between epithelial (E) and mesenchymal (M) states, are characterized by phenotypic heterogeneity combining E and M features and increased plasticity. Hybrid EMT states are highly relevant in metastatic contexts, but have been largely neglected, partially due to the lack of physiologically-relevant 3D platforms to study them. Here we propose a new in vitro model, combining mammary E cells with a bioengineered 3D matrix, to explore phenotypic and functional properties of cells in transition between E and M states. Optimized alginate-based 3D matrices provided adequate 3D microenvironments, where normal epithelial morphogenesis was recapitulated, with formation of acini-like structures, similar to those found in native mammary tissue. TGFβ1-driven EMT in 3D could be successfully promoted, generating M-like cells. TGFβ1 removal resulted in phenotypic switching to an intermediate state (RE cells), a hybrid cell population expressing both E and M markers at gene/protein levels. RE cells exhibited increased proliferative/clonogenic activity, as compared to M cells, being able to form large colonies containing cells with front-back polarity, suggesting a more aggressive phenotype. Our 3D model provides a powerful tool to investigate the role of the microenvironment on metastable EMT stages.

An improved semi-implicit method for structural dynamics analysis

NASA Technical Reports Server (NTRS)

Park, K. C.

1982-01-01

A semi-implicit algorithm is presented for direct time integration of the structural dynamics equations. The algorithm avoids the factoring of the implicit difference solution matrix and mitigates the unacceptable accuracy losses which plagued previous semi-implicit algorithms. This substantial accuracy improvement is achieved by augmenting the solution matrix with two simple diagonal matrices of the order of the integration truncation error.

Chemically Active, Porous 3D-Printed Thermoplastic Composites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Evans, Kent A.; Kennedy, Zachary C.; Arey, Bruce W.

Metal-organic frameworks (MOFs) exhibit exceptional properties and are widely investigated because of their structural and functional versatility relevant to catalysis, separations, and sensing applications. However, their commercial or large-scale application is often limited by their powder forms. To address this, we report the production of MOF-thermoplastic polymer composites accessed via a standard 3D printer. MOFs (Zeolitic imidazolate framework; ZIF-8) were successfully incorporated homogeneously into both poly(lactic acid) (PLA) and thermoplastic polyurethane (TPU) matrices, extruded into filaments, and utilized for on-demand access to 3D structures by fused-deposition modeling. Printed rigid PLA-MOF composites displayed good structural integrity, high surface area ((SA)avg =more » 531 m2 g-1) and hierarchical pore features. Flexible TPU-MOF composites (SAavg = 706 m2 g-1) were achieved by employing a sacrificial fluoropolymer readily removed post-printing. Critically, embedded particles in the plastic matrices retain their ability to participate in chemical interactions characteristic of the parent MOF. The fabrication strategies can be extended to other MOFs and illustrate the potential of 3D printing to create unique porous and high surface area chemically-active structures.« less

Damage location and quantification of a pretensioned concrete beam using stochastic subspace identification

NASA Astrophysics Data System (ADS)

Cancelli, Alessandro; Micheli, Laura; Laflamme, Simon; Alipour, Alice; Sritharan, Sri; Ubertini, Filippo

2017-04-01

Stochastic subspace identification (SSID) is a first-order linear system identification technique enabling modal analysis through the time domain. Research in the field of structural health monitoring has demonstrated that SSID can be used to successfully retrieve modal properties, including modal damping ratios, using output-only measurements. In this paper, the utilization of SSID for indirectly retrieving structures' stiffness matrix was investigated, through the study of a simply supported reinforced concrete beam subjected to dynamic loads. Hence, by introducing a physical model of the structure, a second-order identification method is achieved. The reconstruction is based on system condensation methods, which enables calculation of reduced order stiffness, damping, and mass matrices for the structural system. The methods compute the reduced order matrices directly from the modal properties, obtained through the use of SSID. Lastly, the reduced properties of the system are used to reconstruct the stiffness matrix of the beam. The proposed approach is first verified through numerical simulations and then validated using experimental data obtained from a full-scale reinforced concrete beam that experienced progressive damage. Results show that the SSID technique can be used to diagnose, locate, and quantify damage through the reconstruction of the stiffness matrix.

Spatio-Temporal EEG Models for Brain Interfaces

PubMed Central

Gonzalez-Navarro, P.; Moghadamfalahi, M.; Akcakaya, M.; Erdogmus, D.

2016-01-01

Multichannel electroencephalography (EEG) is widely used in non-invasive brain computer interfaces (BCIs) for user intent inference. EEG can be assumed to be a Gaussian process with unknown mean and autocovariance, and the estimation of parameters is required for BCI inference. However, the relatively high dimensionality of the EEG feature vectors with respect to the number of labeled observations lead to rank deficient covariance matrix estimates. In this manuscript, to overcome ill-conditioned covariance estimation, we propose a structure for the covariance matrices of the multichannel EEG signals. Specifically, we assume that these covariances can be modeled as a Kronecker product of temporal and spatial covariances. Our results over the experimental data collected from the users of a letter-by-letter typing BCI show that with less number of parameter estimations, the system can achieve higher classification accuracies compared to a method that uses full unstructured covariance estimation. Moreover, in order to illustrate that the proposed Kronecker product structure could enable shortening the BCI calibration data collection sessions, using Cramer-Rao bound analysis on simulated data, we demonstrate that a model with structured covariance matrices will achieve the same estimation error as a model with no covariance structure using fewer labeled EEG observations. PMID:27713590

Optimum structural design with static aeroelastic constraints

NASA Technical Reports Server (NTRS)

Bowman, Keith B; Grandhi, Ramana V.; Eastep, F. E.

1989-01-01

The static aeroelastic performance characteristics, divergence velocity, control effectiveness and lift effectiveness are considered in obtaining an optimum weight structure. A typical swept wing structure is used with upper and lower skins, spar and rib thicknesses, and spar cap and vertical post cross-sectional areas as the design parameters. Incompressible aerodynamic strip theory is used to derive the constraint formulations, and aerodynamic load matrices. A Sequential Unconstrained Minimization Technique (SUMT) algorithm is used to optimize the wing structure to meet the desired performance constraints.

Characterizing protein conformations by correlation analysis of coarse-grained contact matrices.

PubMed

Lindsay, Richard J; Siess, Jan; Lohry, David P; McGee, Trevor S; Ritchie, Jordan S; Johnson, Quentin R; Shen, Tongye

2018-01-14

We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

Generalized Eigenvalues for pairs on heritian matrices

NASA Technical Reports Server (NTRS)

Rublein, George

1988-01-01

A study was made of certain special cases of a generalized eigenvalue problem. Let A and B be nxn matrics. One may construct a certain polynomial, P(A,B, lambda) which specializes to the characteristic polynomial of B when A equals I. In particular, when B is hermitian, that characteristic polynomial, P(I,B, lambda) has real roots, and one can ask: are the roots of P(A,B, lambda) real when B is hermitian. We consider the case where A is positive definite and show that when N equals 3, the roots are indeed real. The basic tools needed in the proof are Shur's theorem on majorization for eigenvalues of hermitian matrices and the interlacing theorem for the eigenvalues of a positive definite hermitian matrix and one of its principal (n-1)x(n-1) minors. The method of proof first reduces the general problem to one where the diagonal of B has a certain structure: either diag (B) = diag (1,1,1) or diag (1,1,-1), or else the 2 x 2 principal minors of B are all 1. According as B has one of these three structures, we use an appropriate method to replace A by a positive diagonal matrix. Since it can be easily verified that P(D,B, lambda) has real roots, the result follows. For other configurations of B, a scaling and a continuity argument are used to prove the result in general.

Characterizing protein conformations by correlation analysis of coarse-grained contact matrices

NASA Astrophysics Data System (ADS)

Lindsay, Richard J.; Siess, Jan; Lohry, David P.; McGee, Trevor S.; Ritchie, Jordan S.; Johnson, Quentin R.; Shen, Tongye

2018-01-01

We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

Effects of Pressure-shift Freezing on the Structural and Physical Properties of Gelatin Hydrogel Matrices

PubMed Central

Kim, Byeongsoo; Gil, Hyung Bae; Min, Sang-Gi; Lee, Si-Kyung; Choi, Mi-Jung

2014-01-01

This study investigates the effects of the gelatin concentration (10-40%, w/v), freezing temperatures (from -20℃ to -50℃) and freezing methods on the structural and physical properties of gelatin matrices. To freeze gelatin, the pressure-shift freezing (PSF) is being applied at 0.1 (under atmospheric control), 50 and 100 MPa, respectively. The freezing point of gelatin solutions decrease with increasing gelatin concentrations, from -0.2℃ (10% gelatin) to -6.7℃ (40% gelatin), while the extent of supercooling did not show any specific trends. The rheological properties of the gelatin indicate that both the storage (G') and loss (G") moduli were steady in the strain amplitude range of 0.1-10%. To characterize gelatin matrices formed by the various freezing methods, the ice crystal sizes which were being determined by the scanning electron microscopy (SEM) are affected by the gelatin concentrations. The ice crystal sizes are affected by gelatin concentrations and freezing temperature, while the size distributions of ice crystals depend on the freezing methods. Smaller ice crystals are being formed with PSF rather than under the atmospheric control where the freezing temperature is above -40℃. Thus, the results of this study indicate that the PSF processing at a very low freezing temperature (-50℃) offers a potential advantage over commercial atmospheric freezing points for the formation of small ice crystals. PMID:26760743

Peculiar spectral statistics of ensembles of trees and star-like graphs

NASA Astrophysics Data System (ADS)

Kovaleva, V.; Maximov, Yu; Nechaev, S.; Valba, O.

2017-07-01

In this paper we investigate the eigenvalue statistics of exponentially weighted ensembles of full binary trees and p-branching star graphs. We show that spectral densities of corresponding adjacency matrices demonstrate peculiar ultrametric structure inherent to sparse systems. In particular, the tails of the distribution for binary trees share the ‘Lifshitz singularity’ emerging in the one-dimensional localization, while the spectral statistics of p-branching star-like graphs is less universal, being strongly dependent on p. The hierarchical structure of spectra of adjacency matrices is interpreted as sets of resonance frequencies, that emerge in ensembles of fully branched tree-like systems, known as dendrimers. However, the relaxational spectrum is not determined by the cluster topology, but has rather the number-theoretic origin, reflecting the peculiarities of the rare-event statistics typical for one-dimensional systems with a quenched structural disorder. The similarity of spectral densities of an individual dendrimer and of an ensemble of linear chains with exponential distribution in lengths, demonstrates that dendrimers could be served as simple disorder-less toy models of one-dimensional systems with quenched disorder.

Peculiar spectral statistics of ensembles of trees and star-like graphs

DOE PAGES

Kovaleva, V.; Maximov, Yu; Nechaev, S.; ...

2017-07-11

In this paper we investigate the eigenvalue statistics of exponentially weighted ensembles of full binary trees and p-branching star graphs. We show that spectral densities of corresponding adjacency matrices demonstrate peculiar ultrametric structure inherent to sparse systems. In particular, the tails of the distribution for binary trees share the \\Lifshitz singularity" emerging in the onedimensional localization, while the spectral statistics of p-branching star-like graphs is less universal, being strongly dependent on p. The hierarchical structure of spectra of adjacency matrices is interpreted as sets of resonance frequencies, that emerge in ensembles of fully branched tree-like systems, known as dendrimers. However,more » the relaxational spectrum is not determined by the cluster topology, but has rather the number-theoretic origin, re ecting the peculiarities of the rare-event statistics typical for one-dimensional systems with a quenched structural disorder. The similarity of spectral densities of an individual dendrimer and of ensemble of linear chains with exponential distribution in lengths, demonstrates that dendrimers could be served as simple disorder-less toy models of one-dimensional systems with quenched disorder.« less

Distributed parameter modeling of repeated truss structures

NASA Technical Reports Server (NTRS)

Wang, Han-Ching

1994-01-01

A new approach to find homogeneous models for beam-like repeated flexible structures is proposed which conceptually involves two steps. The first step involves the approximation of 3-D non-homogeneous model by a 1-D periodic beam model. The structure is modeled as a 3-D non-homogeneous continuum. The displacement field is approximated by Taylor series expansion. Then, the cross sectional mass and stiffness matrices are obtained by energy equivalence using their additive properties. Due to the repeated nature of the flexible bodies, the mass, and stiffness matrices are also periodic. This procedure is systematic and requires less dynamics detail. The first step involves the homogenization from a 1-D periodic beam model to a 1-D homogeneous beam model. The periodic beam model is homogenized into an equivalent homogeneous beam model using the additive property of compliance along the generic axis. The major departure from previous approaches in literature is using compliance instead of stiffness in homogenization. An obvious justification is that the stiffness is additive at each cross section but not along the generic axis. The homogenized model preserves many properties of the original periodic model.

Solvation structures of water in trihexyltetradecylphosphonium-orthoborate ionic liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yong-Lei, E-mail: wangyonl@gmail.com; System and Component Design, Department of Machine Design, KTH Royal Institute of Technology, SE-100 44 Stockholm; Sarman, Sten

2016-08-14

Atomistic molecular dynamics simulations have been performed to investigate effective interactions of isolated water molecules dispersed in trihexyltetradecylphosphonium-orthoborate ionic liquids (ILs). The intrinsic free energy changes in solvating one water molecule from gas phase into bulk IL matrices were estimated as a function of temperature, and thereafter, the calculations of potential of mean force between two dispersed water molecules within different IL matrices were performed using umbrella sampling simulations. The systematic analyses of local ionic microstructures, orientational preferences, probability and spatial distributions of dispersed water molecules around neighboring ionic species indicate their preferential coordinations to central polar segments in orthoboratemore » anions. The effective interactions between two dispersed water molecules are partially or totally screened as their separation distance increases due to interference of ionic species in between. These computational results connect microscopic anionic structures with macroscopically and experimentally observed difficulty in completely removing water from synthesized IL samples and suggest that the introduction of hydrophobic groups to central polar segments and the formation of conjugated ionic structures in orthoborate anions can effectively reduce residual water content in the corresponding IL samples.« less

Peculiar spectral statistics of ensembles of trees and star-like graphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kovaleva, V.; Maximov, Yu; Nechaev, S.

In this paper we investigate the eigenvalue statistics of exponentially weighted ensembles of full binary trees and p-branching star graphs. We show that spectral densities of corresponding adjacency matrices demonstrate peculiar ultrametric structure inherent to sparse systems. In particular, the tails of the distribution for binary trees share the \\Lifshitz singularity" emerging in the onedimensional localization, while the spectral statistics of p-branching star-like graphs is less universal, being strongly dependent on p. The hierarchical structure of spectra of adjacency matrices is interpreted as sets of resonance frequencies, that emerge in ensembles of fully branched tree-like systems, known as dendrimers. However,more » the relaxational spectrum is not determined by the cluster topology, but has rather the number-theoretic origin, re ecting the peculiarities of the rare-event statistics typical for one-dimensional systems with a quenched structural disorder. The similarity of spectral densities of an individual dendrimer and of ensemble of linear chains with exponential distribution in lengths, demonstrates that dendrimers could be served as simple disorder-less toy models of one-dimensional systems with quenched disorder.« less

Fungible Correlation Matrices: A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for Monte Carlo Research.

PubMed

Waller, Niels G

2016-01-01

For a fixed set of standardized regression coefficients and a fixed coefficient of determination (R-squared), an infinite number of predictor correlation matrices will satisfy the implied quadratic form. I call such matrices fungible correlation matrices. In this article, I describe an algorithm for generating positive definite (PD), positive semidefinite (PSD), or indefinite (ID) fungible correlation matrices that have a random or fixed smallest eigenvalue. The underlying equations of this algorithm are reviewed from both algebraic and geometric perspectives. Two simulation studies illustrate that fungible correlation matrices can be profitably used in Monte Carlo research. The first study uses PD fungible correlation matrices to compare penalized regression algorithms. The second study uses ID fungible correlation matrices to compare matrix-smoothing algorithms. R code for generating fungible correlation matrices is presented in the supplemental materials.

Structural Features of Algebraic Quantum Notations

ERIC Educational Resources Information Center

Gire, Elizabeth; Price, Edward

2015-01-01

The formalism of quantum mechanics includes a rich collection of representations for describing quantum systems, including functions, graphs, matrices, histograms of probabilities, and Dirac notation. The varied features of these representations affect how computations are performed. For example, identifying probabilities of measurement outcomes…

The power law and dynamic rheology in food analysis

USDA-ARS?s Scientific Manuscript database

Protein networks impart functional and structural characteristics to food, and should be examined to gain an understanding of properties of the product. Food matrices are investigated nondestructively by small amplitude oscillatory shear analysis, which provides information on viscoelasticity, incl...

Lorentz quantum mechanics

NASA Astrophysics Data System (ADS)

Zhang, Qi; Wu, Biao

2018-01-01

We present a theoretical framework for the dynamics of bosonic Bogoliubov quasiparticles. We call it Lorentz quantum mechanics because the dynamics is a continuous complex Lorentz transformation in complex Minkowski space. In contrast, in usual quantum mechanics, the dynamics is the unitary transformation in Hilbert space. In our Lorentz quantum mechanics, three types of state exist: space-like, light-like and time-like. Fundamental aspects are explored in parallel to the usual quantum mechanics, such as a matrix form of a Lorentz transformation, and the construction of Pauli-like matrices for spinors. We also investigate the adiabatic evolution in these mechanics, as well as the associated Berry curvature and Chern number. Three typical physical systems, where bosonic Bogoliubov quasi-particles and their Lorentz quantum dynamics can arise, are presented. They are a one-dimensional fermion gas, Bose-Einstein condensate (or superfluid), and one-dimensional antiferromagnet.

Multigrid method for stability problems

NASA Technical Reports Server (NTRS)

Ta'asan, Shlomo

1988-01-01

The problem of calculating the stability of steady state solutions of differential equations is addressed. Leading eigenvalues of large matrices that arise from discretization are calculated, and an efficient multigrid method for solving these problems is presented. The resulting grid functions are used as initial approximations for appropriate eigenvalue problems. The method employs local relaxation on all levels together with a global change on the coarsest level only, which is designed to separate the different eigenfunctions as well as to update their corresponding eigenvalues. Coarsening is done using the FAS formulation in a nonstandard way in which the right-hand side of the coarse grid equations involves unknown parameters to be solved on the coarse grid. This leads to a new multigrid method for calculating the eigenvalues of symmetric problems. Numerical experiments with a model problem are presented which demonstrate the effectiveness of the method.

Protein structure similarity from Principle Component Correlation analysis.

PubMed

Zhou, Xiaobo; Chou, James; Wong, Stephen T C

2006-01-25

Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD) in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities. We measure structural similarity between proteins by correlating the principle components of their secondary structure interaction matrix. In our approach, the Principle Component Correlation (PCC) analysis, a symmetric interaction matrix for a protein structure is constructed with relationship parameters between secondary elements that can take the form of distance, orientation, or other relevant structural invariants. When using a distance-based construction in the presence or absence of encoded N to C terminal sense, there are strong correlations between the principle components of interaction matrices of structurally or topologically similar proteins. The PCC method is extensively tested for protein structures that belong to the same topological class but are significantly different by RMSD measure. The PCC analysis can also differentiate proteins having similar shapes but different topological arrangements. Additionally, we demonstrate that when using two independently defined interaction matrices, comparison of their maximum eigenvalues can be highly effective in clustering structurally or topologically similar proteins. We believe that the PCC analysis of interaction matrix is highly flexible in adopting various structural parameters for protein structure comparison.

Porous Aluminum Oxide and Magnesium Oxide Films Using Organic Hydrogels as Structure Matrices

PubMed Central

Chen, Zimei

2018-01-01

We describe the synthesis of mesoporous Al2O3 and MgO layers on silicon wafer substrates by using poly(dimethylacrylamide) hydrogels as porogenic matrices. Hydrogel films are prepared by spreading the polymer through spin-coating, followed by photo-cross-linking and anchoring to the substrate surface. The metal oxides are obtained by swelling the hydrogels in the respective metal nitrate solutions and subsequent thermal conversion. Combustion of the hydrogel results in mesoporous metal oxide layers with thicknesses in the μm range and high specific surface areas up to 558 m2∙g−1. Materials are characterized by SEM, FIB ablation, EDX, and Kr physisorption porosimetry. PMID:29565802

Complexity of Kronecker Operations on Sparse Matrices with Applications to the Solution of Markov Models

NASA Technical Reports Server (NTRS)

Buchholz, Peter; Ciardo, Gianfranco; Donatelli, Susanna; Kemper, Peter

1997-01-01

We present a systematic discussion of algorithms to multiply a vector by a matrix expressed as the Kronecker product of sparse matrices, extending previous work in a unified notational framework. Then, we use our results to define new algorithms for the solution of large structured Markov models. In addition to a comprehensive overview of existing approaches, we give new results with respect to: (1) managing certain types of state-dependent behavior without incurring extra cost; (2) supporting both Jacobi-style and Gauss-Seidel-style methods by appropriate multiplication algorithms; (3) speeding up algorithms that consider probability vectors of size equal to the "actual" state space instead of the "potential" state space.

Buckling of Fiber Reinforced Composite Plates with Nanofiber Reinforced Matrices

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Murthy, Pappu L. N.

2010-01-01

Anisotropic composite plates were evaluated with nanofiber reinforced matrices (NFRM). The nanofiber reinforcement volumes ratio in the matrix was 0.01. The plate dimensions were 20 by 10 by 1.0 in. (508 by 254 by 25.4 mm). Seven different loading condition cases were evaluated: three for uniaxial loading, three for pairs of combined loading, and one with three combined loadings. The anisotropy arose from the unidirectional plates having been at 30 from the structural axis. The anisotropy had a full 6 by 6 rigidities matrix which were satisfied and solved by a Galerkin buckling algorithm. The buckling results showed that the NFRM plates buckled at about twice those with conventional matrix.

An Evaluation of the Organizational Structure of Air Force Emergency Operations Centers Using Social Network Analysis and Design Structure Matrices

DTIC Science & Technology

2013-03-01

areas that are most frequently needed 4 in a national response” (FEMA, 2008). Finally, during emergencies, individual Unit Control Centers ( UCCs ...stand up, as a means to supporting the response. Typically, the UCCs provide information or resources as required through communication from the...EOC. Currently there is no defined staffing or organizational structure for the UCC , each unit is responsible for adequately staffing the UCCs as

Molecular Toxicology of Chromatin

DTIC Science & Technology

1992-01-01

towards the DNA analogs used as coenzymes suggests that the maximal activation by spermine , that depends on coDNA, may involve DNA structures which...evidence for the participation of spermine in an ADPRT-mediated regulatory system that can modify DNA structures , it seems plausible to assume tnat ADPRT may...DNA-dependent manner. The binding properties of spermine -, polylysine- and p olyarginine-Sepharose 4B affinity matrices were also determined. The

Hierarchic Agglomerative Clustering Methods for Automatic Document Classification.

ERIC Educational Resources Information Center

Griffiths, Alan; And Others

1984-01-01

Considers classifications produced by application of single linkage, complete linkage, group average, and word clustering methods to Keen and Cranfield document test collections, and studies structure of hierarchies produced, extent to which methods distort input similarity matrices during classification generation, and retrieval effectiveness…

QUANTIFICATION OF FLUOROTELOMER-BASED CHEMICALS IN MAMMALIAN MATRICES BY MONITORING PERFLUOROALKYL CHAIN FRAGMENTS WITH GC/MS

EPA Science Inventory

Perfluorocarboxylic acids (PFCAs), namely perfluorooctanoic acid (PFOA) and perfluorononanoic acid (PFNA), have been identified as persistent, bioaccurnulative and potentially toxic compounds. The structural analog, 8-2 fluorotelomer alcohol (8-2 FTOH) is considered the probable ...

GC/HRSIR as a Complementary Technique to GC/ECNIMS

EPA Science Inventory

Gas chromatography/electron capture negative ion mass spectrometry (GC/ECNIMS) is a highly selective and sensitive technique for the analysis of appropriate analytes in complex matrices. Its major drawback is often the lack of fragmentation indicative of structure that can be use...

Polymorph-dependent titanium dioxide nanoparticle dissolution in acidic and alkali digestions

EPA Science Inventory

Multiple polymorphs (anatase, brookite and rutile) of titanium dioxide nanoparticles (TiO2-NPs) with variable structures were quantified in environmental matrices via microwave-based hydrofluoric (HF) and nitric (HNO3) mixed acid digestion and muffle furnace (MF)-based potassium ...

Green electrospun pantothenic acid/silk fibroin composite nanofibers: fabrication, characterization and biological activity.

PubMed

Fan, Linpeng; Cai, Zengxiao; Zhang, Kuihua; Han, Feng; Li, Jingliang; He, Chuanglong; Mo, Xiumei; Wang, Xungai; Wang, Hongsheng

2014-05-01

Silk fibroin (SF) from Bombyx mori has many established excellent properties and has found various applications in the biomedical field. However, some abilities or capacities of SF still need improving to meet the need for using practically. Indeed, diverse SF-based composite biomaterials have been developed. Here we report the feasibility of fabricating pantothenic acid (vitamin B5, VB5)-reinforcing SF nanofibrous matrices for biomedical applications through green electrospinning. Results demonstrated the successful loading of D-pantothenic acid hemicalcium salt (VB5-hs) into resulting composite nanofibers. The introduction of VB5-hs did not alter the smooth ribbon-like morphology and the silk I structure of SF, but significantly decreased the mean width of SF fibers. SF conformation transformed into β-sheet from random coil when composite nanofibrous matrices were exposed to 75% (v/v) ethanol vapor. Furthermore, nanofibers still remained good morphology after being soaked in water environment for five days. Interestingly, as-prepared composite nanofibrous matrices supported a higher level of cell viability, especially in a long culture period and significantly assisted skin cells to survive under oxidative stress compared with pure SF nanofibrous matrices. These findings provide a basis for further extending the application of SF in the biomedical field, especially in the personal skin-care field. Copyright © 2013 Elsevier B.V. All rights reserved.

Microstrip Butler matrix design and realization for 7 T MRI.

PubMed

Yazdanbakhsh, Pedram; Solbach, Klaus

2011-07-01

This article presents the design and realization of 8 × 8 and 16 × 16 Butler matrices for 7 T MRI systems. With the focus on low insertion loss and high amplitude/phase accuracy, the microstrip line integration technology (microwave-integrated circuit) was chosen for the realization. Laminate material of high permittivity (ε(r) = 11) and large thickness (h = 3.2 mm) is shown to allow the best trade-off of circuit board size versus insertion loss, saving circuit area by extensive folding of branch-line coupler topology and meandering phase shifter and connecting strip lines and reducing mutual coupling of neighboring strip lines by shield structures between strip lines. With this approach, 8 × 8 Butler matrices were produced in single boards of 310 mm × 530 mm, whereas the 16 × 16 Butler matrices combined two submatrices of 8 × 8 with two smaller boards. Insertion loss was found at 0.73 and 1.1 dB for an 8 × 8 matrix and 16 × 16 matrix, respectively. Measured amplitude and phase errors are shown to represent highly pure mode excitation with unwanted modes suppressed by 40 and 35 dB, respectively. Both types of matrices were implemented with a 7 T MRI system and 8- and 16-element coil arrays for RF mode shimming experiments and operated successfully with 8 kW of RF power. Copyright © 2011 Wiley-Liss, Inc.

Solution of the determinantal assignment problem using the Grassmann matrices

NASA Astrophysics Data System (ADS)

Karcanias, Nicos; Leventides, John

2016-02-01

The paper provides a direct solution to the determinantal assignment problem (DAP) which unifies all frequency assignment problems of the linear control theory. The current approach is based on the solvability of the exterior equation ? where ? is an n -dimensional vector space over ? which is an integral part of the solution of DAP. New criteria for existence of solution and their computation based on the properties of structured matrices are referred to as Grassmann matrices. The solvability of this exterior equation is referred to as decomposability of ?, and it is in turn characterised by the set of quadratic Plücker relations (QPRs) describing the Grassmann variety of the corresponding projective space. Alternative new tests for decomposability of the multi-vector ? are given in terms of the rank properties of the Grassmann matrix, ? of the vector ?, which is constructed by the coordinates of ?. It is shown that the exterior equation is solvable (? is decomposable), if and only if ? where ?; the solution space for a decomposable ?, is the space ?. This provides an alternative linear algebra characterisation of the decomposability problem and of the Grassmann variety to that defined by the QPRs. Further properties of the Grassmann matrices are explored by defining the Hodge-Grassmann matrix as the dual of the Grassmann matrix. The connections of the Hodge-Grassmann matrix to the solution of exterior equations are examined, and an alternative new characterisation of decomposability is given in terms of the dimension of its image space. The framework based on the Grassmann matrices provides the means for the development of a new computational method for the solutions of the exact DAP (when such solutions exist), as well as computing approximate solutions, when exact solutions do not exist.

Salmonella serovars and their distribution in Nigerian commercial chicken layer farms

PubMed Central

Fagbamila, Idowu Oluwabunmi; Barco, Lisa; Mancin, Marzia; Kwaga, Jacob; Ngulukun, Sati Samuel; Zavagnin, Paola; Lettini, Antonia Anna; Lorenzetto, Monica; Abdu, Paul Ayuba; Kabir, Junaidu; Umoh, Jarlath; Ricci, Antonia; Muhammad, Maryam

2017-01-01

Commercial poultry farms (n° 523), located in all the six regions of Nigeria were sampled with a view to generate baseline information about the distribution of Salmonella serovars in this country. Five different matrices (litter, dust, faeces, feed and water) were collected from each visited farm. Salmonella was isolated from at least one of the five matrices in 228 farms, with a farm prevalence of 43.6% (CI95[39.7–48.3%]). Altogether, 370 of 2615 samples collected (14.1%, CI95[12.8; 15.5%]) contained Salmonella. Considering the number of positive farms and the number of positive samples, it was evident that for the majority of the sampled farms, few samples were positive for Salmonella. With regard to the matrices, there was no difference in Salmonella prevalence among the five matrices considered. Of the 370 isolates serotyped, eighty-two different serotypes were identified and Salmonella Kentucky was identified as having the highest isolation rate in all the matrices sampled (16.2%), followed by S. Poona and S. Elisabethville. S. Kentucky was distributed across the country, whereas the other less frequent serovars had a more circumscribed diffusion. This is one of few comprehensive studies on the occurrence and distribution of Salmonella in commercial chicken layer farms from all the six regions of Nigeria. The relatively high prevalence rate documented in this study may be attributed to the generally poor infrastructure and low biosecurity measures in controlling stray animals, rodents and humans. Data collected could be valuable for instituting effective intervention strategies for Salmonella control in Nigeria and also in other developing countries with a similar poultry industry structure, with the final aim of reducing Salmonella spread in animals and ultimately in humans. PMID:28278292

Salmonella serovars and their distribution in Nigerian commercial chicken layer farms.

PubMed

Fagbamila, Idowu Oluwabunmi; Barco, Lisa; Mancin, Marzia; Kwaga, Jacob; Ngulukun, Sati Samuel; Zavagnin, Paola; Lettini, Antonia Anna; Lorenzetto, Monica; Abdu, Paul Ayuba; Kabir, Junaidu; Umoh, Jarlath; Ricci, Antonia; Muhammad, Maryam

2017-01-01

Commercial poultry farms (n° 523), located in all the six regions of Nigeria were sampled with a view to generate baseline information about the distribution of Salmonella serovars in this country. Five different matrices (litter, dust, faeces, feed and water) were collected from each visited farm. Salmonella was isolated from at least one of the five matrices in 228 farms, with a farm prevalence of 43.6% (CI95[39.7-48.3%]). Altogether, 370 of 2615 samples collected (14.1%, CI95[12.8; 15.5%]) contained Salmonella. Considering the number of positive farms and the number of positive samples, it was evident that for the majority of the sampled farms, few samples were positive for Salmonella. With regard to the matrices, there was no difference in Salmonella prevalence among the five matrices considered. Of the 370 isolates serotyped, eighty-two different serotypes were identified and Salmonella Kentucky was identified as having the highest isolation rate in all the matrices sampled (16.2%), followed by S. Poona and S. Elisabethville. S. Kentucky was distributed across the country, whereas the other less frequent serovars had a more circumscribed diffusion. This is one of few comprehensive studies on the occurrence and distribution of Salmonella in commercial chicken layer farms from all the six regions of Nigeria. The relatively high prevalence rate documented in this study may be attributed to the generally poor infrastructure and low biosecurity measures in controlling stray animals, rodents and humans. Data collected could be valuable for instituting effective intervention strategies for Salmonella control in Nigeria and also in other developing countries with a similar poultry industry structure, with the final aim of reducing Salmonella spread in animals and ultimately in humans.

Sun protection enhancement of titanium dioxide crystals by the use of carnauba wax nanoparticles: the synergistic interaction between organic and inorganic sunscreens at nanoscale.

PubMed

Villalobos-Hernández, J R; Müller-Goymann, C C

2006-09-28

Carnauba wax is partially composed of cinnamates. The rational combination of cinnamates and titanium dioxide has shown a synergistic effect to improve the sun protection factor (SPF) of cosmetic preparations. However, the mechanism of this interaction has not been fully understood. In this study, an ethanolic extract of the carnauba wax and an ethanolic solution of a typical cinnamate derivative, ethylcinnamate, were prepared and their UV absorption and SPF either alone or in the presence of titanium dioxide were compared. The titanium dioxide crystals and the cinnamates solutions were also distributed into a matrix composed of saturated fatty acids to emulate the structure of the crystallized carnauba wax. SPF, differential scanning calorimetry (DSC) and X-ray studies of these matrices were performed. Additionally, carnauba wax nanosuspensions containing titanium dioxide either in the lipid phase or in the aqueous phase were prepared to evaluate their SPFs and their physical structure. Strong UV absorption was observed in diluted suspensions of titanium dioxide after the addition of cinnamates. The saturated fatty acid matrices probably favored the adsorption of the cinnamates at the surface of titanium dioxide crystals, which was reflected by an increase in the SPF. No modification of the crystal structure of the fatty acid matrices was observed after the addition of cinnamates or titanium dioxide. The distribution of the titanium dioxide inside the lipid phase of the nanosuspensions was more effective to reach higher SPFs than that at the aqueous phase. The close contact between the carnauba wax and the titanium dioxide crystals after the high-pressure homogenization process was confirmed by transmission electron microscopy (TEM).

New trends in the analytical determination of emerging contaminants and their transformation products in environmental waters.

PubMed

Agüera, Ana; Martínez Bueno, María Jesús; Fernández-Alba, Amadeo R

2013-06-01

Since the so-called emerging contaminants were established as a new group of pollutants of environmental concern, a great effort has been devoted to the knowledge of their distribution, fate and effects in the environment. After more than 20 years of work, a significant improvement in knowledge about these contaminants has been achieved, but there is still a large gap of information on the growing number of new potential contaminants that are appearing and especially of their unpredictable transformation products. Although the environmental problem arising from emerging contaminants must be addressed from an interdisciplinary point of view, it is obvious that analytical chemistry plays an important role as the first step of the study, as it allows establishing the presence of chemicals in the environment, estimate their concentration levels, identify sources and determine their degradation pathways. These tasks involve serious difficulties requiring different analytical solutions adjusted to purpose. Thus, the complexity of the matrices requires highly selective analytical methods; the large number and variety of compounds potentially present in the samples demands the application of wide scope methods; the low concentrations at which these contaminants are present in the samples require a high detection sensitivity, and high demands on the confirmation and high structural information are needed for the characterisation of unknowns. New developments on analytical instrumentation have been applied to solve these difficulties. Furthermore and not less important has been the development of new specific software packages intended for data acquisition and, in particular, for post-run analysis. Thus, the use of sophisticated software tools has allowed successful screening analysis, determining several hundreds of analytes, and assisted in the structural elucidation of unknown compounds in a timely manner.

Dynamic Stabilization of Expressed Proteins in Engineered Diatom Biosilica Matrices.

PubMed

Xiong, Yijia; Ford, Nicole R; Hecht, Karen A; Roesijadi, Guritno; Squier, Thomas C

2016-05-18

Self-assembly of recombinant proteins within the biosilica of living diatoms represents a means to construct functional materials in a reproducible and scalable manner that will enable applications that harness the inherent specificities of proteins to sense and respond to environmental cues. Here we describe the use of a silaffin-derived lysine-rich 39-amino-acid targeting sequence (Sil3T8) that directs a single chain fragment variable (scFv) antibody or an enhanced green fluorescent protein (EGFP) to assemble within the biosilica frustule, resulting in abundance of >200 000 proteins per frustule. Using either a fluorescent ligand bound to the scFv or the intrinsic fluorescence of EGFP, we monitored protein conformational dynamics, accessibility to external quenchers, binding affinity, and conformational stability. Like proteins in solution, proteins within isolated frustules undergo isotropic rotational motion, but with 2-fold increases in rotational correlation times that are indicative of weak macromolecular associations within the biosilica. Solvent accessibilities and high-affinity (pM) binding are comparable to those in solution. In contrast to solution conditions, scFv antibodies within the biosilica matrix retain their binding affinity in the presence of chaotropic agents (i.e., 8 M urea). Together, these results argue that dramatic increases in protein conformational stability within the biosilica matrices arise through molecular crowding, acting to retain native protein folds and associated functionality with the potential to allow the utility of engineered proteins under a range of harsh environmental conditions associated with environmental sensing and industrial catalytic transformations.

A Tensor-Train accelerated solver for integral equations in complex geometries

NASA Astrophysics Data System (ADS)

Corona, Eduardo; Rahimian, Abtin; Zorin, Denis

2017-04-01

We present a framework using the Quantized Tensor Train (QTT) decomposition to accurately and efficiently solve volume and boundary integral equations in three dimensions. We describe how the QTT decomposition can be used as a hierarchical compression and inversion scheme for matrices arising from the discretization of integral equations. For a broad range of problems, computational and storage costs of the inversion scheme are extremely modest O (log ⁡ N) and once the inverse is computed, it can be applied in O (Nlog ⁡ N) . We analyze the QTT ranks for hierarchically low rank matrices and discuss its relationship to commonly used hierarchical compression techniques such as FMM and HSS. We prove that the QTT ranks are bounded for translation-invariant systems and argue that this behavior extends to non-translation invariant volume and boundary integrals. For volume integrals, the QTT decomposition provides an efficient direct solver requiring significantly less memory compared to other fast direct solvers. We present results demonstrating the remarkable performance of the QTT-based solver when applied to both translation and non-translation invariant volume integrals in 3D. For boundary integral equations, we demonstrate that using a QTT decomposition to construct preconditioners for a Krylov subspace method leads to an efficient and robust solver with a small memory footprint. We test the QTT preconditioners in the iterative solution of an exterior elliptic boundary value problem (Laplace) formulated as a boundary integral equation in complex, multiply connected geometries.

Matrix factorization-based data fusion for the prediction of lncRNA-disease associations.

PubMed

Fu, Guangyuan; Wang, Jun; Domeniconi, Carlotta; Yu, Guoxian

2018-05-01

Long non-coding RNAs (lncRNAs) play crucial roles in complex disease diagnosis, prognosis, prevention and treatment, but only a small portion of lncRNA-disease associations have been experimentally verified. Various computational models have been proposed to identify lncRNA-disease associations by integrating heterogeneous data sources. However, existing models generally ignore the intrinsic structure of data sources or treat them as equally relevant, while they may not be. To accurately identify lncRNA-disease associations, we propose a Matrix Factorization based LncRNA-Disease Association prediction model (MFLDA in short). MFLDA decomposes data matrices of heterogeneous data sources into low-rank matrices via matrix tri-factorization to explore and exploit their intrinsic and shared structure. MFLDA can select and integrate the data sources by assigning different weights to them. An iterative solution is further introduced to simultaneously optimize the weights and low-rank matrices. Next, MFLDA uses the optimized low-rank matrices to reconstruct the lncRNA-disease association matrix and thus to identify potential associations. In 5-fold cross validation experiments to identify verified lncRNA-disease associations, MFLDA achieves an area under the receiver operating characteristic curve (AUC) of 0.7408, at least 3% higher than those given by state-of-the-art data fusion based computational models. An empirical study on identifying masked lncRNA-disease associations again shows that MFLDA can identify potential associations more accurately than competing models. A case study on identifying lncRNAs associated with breast, lung and stomach cancers show that 38 out of 45 (84%) associations predicted by MFLDA are supported by recent biomedical literature and further proves the capability of MFLDA in identifying novel lncRNA-disease associations. MFLDA is a general data fusion framework, and as such it can be adopted to predict associations between other biological entities. The source code for MFLDA is available at: http://mlda.swu.edu.cn/codes.php? name = MFLDA. gxyu@swu.edu.cn. Supplementary data are available at Bioinformatics online.

Adaptive framework to better characterize errors of apriori fluxes and observational residuals in a Bayesian setup for the urban flux inversions.

NASA Astrophysics Data System (ADS)

Ghosh, S.; Lopez-Coto, I.; Prasad, K.; Karion, A.; Mueller, K.; Gourdji, S.; Martin, C.; Whetstone, J. R.

2017-12-01

The National Institute of Standards and Technology (NIST) supports the North-East Corridor Baltimore Washington (NEC-B/W) project and Indianapolis Flux Experiment (INFLUX) aiming to quantify sources of Greenhouse Gas (GHG) emissions as well as their uncertainties. These projects employ different flux estimation methods including top-down inversion approaches. The traditional Bayesian inversion method estimates emission distributions by updating prior information using atmospheric observations of Green House Gases (GHG) coupled to an atmospheric and dispersion model. The magnitude of the update is dependent upon the observed enhancement along with the assumed errors such as those associated with prior information and the atmospheric transport and dispersion model. These errors are specified within the inversion covariance matrices. The assumed structure and magnitude of the specified errors can have large impact on the emission estimates from the inversion. The main objective of this work is to build a data-adaptive model for these covariances matrices. We construct a synthetic data experiment using a Kalman Filter inversion framework (Lopez et al., 2017) employing different configurations of transport and dispersion model and an assumed prior. Unlike previous traditional Bayesian approaches, we estimate posterior emissions using regularized sample covariance matrices associated with prior errors to investigate whether the structure of the matrices help to better recover our hypothetical true emissions. To incorporate transport model error, we use ensemble of transport models combined with space-time analytical covariance to construct a covariance that accounts for errors in space and time. A Kalman Filter is then run using these covariances along with Maximum Likelihood Estimates (MLE) of the involved parameters. Preliminary results indicate that specifying sptio-temporally varying errors in the error covariances can improve the flux estimates and uncertainties. We also demonstrate that differences between the modeled and observed meteorology can be used to predict uncertainties associated with atmospheric transport and dispersion modeling which can help improve the skill of an inversion at urban scales.

In-situ Micro-structural Studies of Gas Hydrate Formation in Sedimentary Matrices

NASA Astrophysics Data System (ADS)

Kuhs, Werner F.; Chaouachi, Marwen; Falenty, Andrzej; Sell, Kathleen; Schwarz, Jens-Oliver; Wolf, Martin; Enzmann, Frieder; Kersten, Michael; Haberthür, David

2015-04-01

The formation process of gas hydrates in sedimentary matrices is of crucial importance for the physical and transport properties of the resulting aggregates. This process has never been observed in-situ with sub-micron resolution. Here, we report on synchrotron-based micro-tomographic studies by which the nucleation and growth processes of gas hydrate were observed in different sedimentary matrices (natural quartz, glass beds with different surface properties, with and without admixtures of kaolinite and montmorillonite) at varying water saturation. The nucleation sites can be easily identified and the growth pattern is clearly established. In under-saturated sediments the nucleation starts at the water-gas interface and proceeds from there to form predominantly isometric single crystals of 10-20μm size. Using a newly developed synchrotron-based method we have determined the crystallite size distributions (CSD) of the gas hydrate in the sedimentary matrix confirming in a quantitative and statistically relevant manner the impressions from the tomographic reconstructions. It is noteworthy that the CSDs from synthetic hydrates are distinctly smaller than those of natural gas hydrates [1], which suggest that coarsening processes take place in the sedimentary matrix after the initial hydrate formation. Understanding the processes of formation and coarsening may eventually permit the determination of the age of gas hydrates in sedimentary matrices [2], which are largely unknown at present. Furthermore, the full micro-structural picture and its evolution will enable quantitative digital rock physics modeling to reveal poroelastic properties and in this way to support the exploration and exploitation of gas hydrate resources in the future. [1] Klapp S.A., Hemes S., Klein H., Bohrmann G., McDonald I., Kuhs W.F. Grain size measurements of natural gas hydrates. Marine Geology 2010; 274(1-4):85-94. [2] Klapp S.A., Klein H, Kuhs W.F. First determination of gas hydrate crystallite size distribution using high-energy synchrotron radiation. Geophys.Res.Letters, 2007 ; 34 : L13608, DOI:10.1029/2006GL029134

Molecular Packing, Hydrogen Bonding, and Fast Dynamics in Lysozyme/Trehalose/Glycerol and Trehalose/Glycerol Glasses at Low Hydration.

PubMed

Lerbret, Adrien; Affouard, Frédéric

2017-10-12

Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast (∼picosecond-nanosecond, ps-ns) and small-amplitude (∼Å) motions of proteins, which govern their stability in freeze-dried sugar mixtures. To determine how they interact with proteins and sugars in glassy matrices and, thereby, modulate their fast dynamics, we performed molecular dynamics (MD) simulations of lysozyme/trehalose/glycerol (LTG) and trehalose/glycerol (TG) mixtures at low glycerol and water concentrations. Upon addition of glycerol and/or water, the glass transition temperature, T g , of LTG and TG mixtures decreases, the molecular packing of glasses is improved, and the mean-square displacements (MSDs) of lysozyme and trehalose either decrease or increase, depending on the time scale and on the temperature considered. A detailed analysis of the hydrogen bonds (HBs) formed between species reveals that water and glycerol may antiplasticize the fast dynamics of lysozyme and trehalose by increasing the total number and/or the strength of the HBs they form in glassy matrices.

Mullite fiber reinforced reaction bonded Si3N4 composites

NASA Technical Reports Server (NTRS)

Saleh, T.; Sayir, A.; Lightfoot, A.; Haggerty, J.

1996-01-01

Fracture toughnesses of brittle ceramic materials have been improved by introducing reinforcements and carefully tailored interface layers. Silicon carbide and Si3N4 have been emphasized as matrices of structural composites intended for high temperature service because they combine excellent mechanical, chemical, thermal and physical properties. Both matrices have been successfully toughened with SiC fibers, whiskers and particles for ceramic matrix composite (CMC) parts made by sintering, hot pressing or reaction forming processes. These SiC reinforced CMCs have exhibited significantly improved toughnesses at low and intermediate temperature levels, as well as retention of properties at high temperatures for selected exposures; however, they are vulnerable to attack from elevated temperature dry and wet oxidizing atmospheres after the matrix has cracked. Property degradation results from oxidation of interface layers and/or reinforcements. The problem is particularly acute for small diameter (-20 tim) polymer derived SiC fibers used for weavable toes. This research explored opportunities for reinforcing Si3N4 matrices with fibers having improved environmental stability; the findings should also be applicable to SiC matrix CMCs.

Dia-Interacting Protein (DIP) Imposes Migratory Plasticity in mDia2-Dependent Tumor Cells in Three-Dimensional Matrices

PubMed Central

Wyse, Meghan M.; Lei, Jun; Nestor-Kalinoski, Andrea L.; Eisenmann, Kathryn M.

2012-01-01

Tumor cells rely upon membrane pliancy to escape primary lesions and invade secondary metastatic sites. This process relies upon localized assembly and disassembly cycles of F-actin that support and underlie the plasma membrane. Dynamic actin generates both spear-like and bleb structures respectively characterizing mesenchymal and amoeboid motility programs utilized by metastatic cells in three-dimensional matrices. The molecular mechanism and physiological trigger(s) driving membrane plasticity are poorly understood. mDia formins are F-actin assembly factors directing membrane pliancy in motile cells. mDia2 is functionally coupled with its binding partner DIP, regulating cortical actin and inducing membrane blebbing in amoeboid cells. Here we show that mDia2 and DIP co-tether to nascent blebs and this linkage is required for bleb formation. DIP controls mesenchymal/amoeboid cell interconvertability, while CXCL12 induces assembly of mDia2:DIP complexes to bleb cortices in 3D matrices. These results demonstrate how DIP-directed mDia2-dependent F-actin dynamics regulate morphological plasticity in motile cancer cells. PMID:23024796

Project Solo; Newsletter Number Twenty.

ERIC Educational Resources Information Center

Pittsburgh Univ., PA. Project Solo.

Three Project Solo modules are presented. They are designed to teach the concepts of elementary matrix operation, matrix multiplication, and finite-state automata. Together with the module on communication matrices from Newsletter #17 they form a well motivated but structured path to expertise in this area. (JY)

Mechanisms of deterioration of nutrients. [improved quality of freeze-dried foods

NASA Technical Reports Server (NTRS)

Karel, M.; Flink, J. M.

1978-01-01

Methods for improving the quality of freeze-dried foods were investigated. Areas discussed include: (1) microstructure of freeze-dried systems, (2) structural changes in freeze-dried systems, (3) artificial food matrices, and (4) osmotic preconcentration to yield improved freeze-dried products.

Modeling visual problem solving as analogical reasoning.

PubMed

Lovett, Andrew; Forbus, Kenneth

2017-01-01

We present a computational model of visual problem solving, designed to solve problems from the Raven's Progressive Matrices intelligence test. The model builds on the claim that analogical reasoning lies at the heart of visual problem solving, and intelligence more broadly. Images are compared via structure mapping, aligning the common relational structure in 2 images to identify commonalities and differences. These commonalities or differences can themselves be reified and used as the input for future comparisons. When images fail to align, the model dynamically rerepresents them to facilitate the comparison. In our analysis, we find that the model matches adult human performance on the Standard Progressive Matrices test, and that problems which are difficult for the model are also difficult for people. Furthermore, we show that model operations involving abstraction and rerepresentation are particularly difficult for people, suggesting that these operations may be critical for performing visual problem solving, and reasoning more generally, at the highest level. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Bioaccessibility of four calcium sources in different whey-based dairy matrices assessed by in vitro digestion.

PubMed

Lorieau, Lucie; Le Roux, Linda; Gaucheron, Frédéric; Ligneul, Amandine; Hazart, Etienne; Dupont, Didier; Floury, Juliane

2018-04-15

Numerous calcium sources are available to enrich food, but their behavior during digestion is still unknown. This study focused on the influence of the gastro-intestinal pH, the food structure and the calcium source on the bioaccessibility of the nutrient. Four calcium sources were studied: calcium carbonate, calcium citrate malate, calcium phosphate and calcium bisglycinate. These were added to dairy matrices, containing cream and whey proteins, of different forms (liquid or gel). The kinetics of solubility and ionic calcium concentration during in vitro digestion were studied, as function of gastro-intestinal pH. All calcium sources were almost fully soluble in the gastric compartment, and then became insoluble in the intestinal phase. The level of calcium insolubilisation in the intestinal phase was not significantly influenced by the matrix structure (liquid or gel), but was more dependent on the calcium source, this effect leading to different final calcium bioaccessibility from 36% to 20%. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sintering Process and Mechanical Property of MWCNTs/HDPE Bulk Composite.

PubMed

Ming-Wen, Wang; Tze-Chi, Hsu; Jie-Ren, Zheng

2009-08-01

Studies have proved that increasing polymer matrices by carbon nanotubes to form structural reinforcement and electrical conductivity have significantly improved mechanical and electrical properties at very low carbon nanotubes loading. In other words, increasing polymer matrices by carbon nanotubes to form structural reinforcement can reduce friction coefficient and enhance anti-wear property. However, producing traditional MWCNTs in polymeric materix is an extremely complicated process. Using melt-mixing process or in situ polymerization leads to better dispersion effect on composite materials. In this study, therefore, to simplify MWCNTs /HDPE composite process and increase dispersion, powder was used directly to replace pellet to mix and sinter with MWCNTs. The composite bulks with 0, 0.5, 1, 2 and 4% nanotube content by weight was analyzed under SEM to observe nanotubes dispersion. At this rate, a MWCNTs/HDPE composite bulk with uniformly dispersed MWCNTs was achieved, and through the wear bench (Pin-on-Disk), the wear experiment has accomplished. Accordingly, the result suggests the sintered MWCNTs/HDPE composites amplify the hardness and wear-resist property.

The Incremental Multiresolution Matrix Factorization Algorithm

PubMed Central

Ithapu, Vamsi K.; Kondor, Risi; Johnson, Sterling C.; Singh, Vikas

2017-01-01

Multiresolution analysis and matrix factorization are foundational tools in computer vision. In this work, we study the interface between these two distinct topics and obtain techniques to uncover hierarchical block structure in symmetric matrices – an important aspect in the success of many vision problems. Our new algorithm, the incremental multiresolution matrix factorization, uncovers such structure one feature at a time, and hence scales well to large matrices. We describe how this multiscale analysis goes much farther than what a direct “global” factorization of the data can identify. We evaluate the efficacy of the resulting factorizations for relative leveraging within regression tasks using medical imaging data. We also use the factorization on representations learned by popular deep networks, providing evidence of their ability to infer semantic relationships even when they are not explicitly trained to do so. We show that this algorithm can be used as an exploratory tool to improve the network architecture, and within numerous other settings in vision. PMID:29416293

Covariance Partition Priors: A Bayesian Approach to Simultaneous Covariance Estimation for Longitudinal Data.

PubMed

Gaskins, J T; Daniels, M J

2016-01-02

The estimation of the covariance matrix is a key concern in the analysis of longitudinal data. When data consists of multiple groups, it is often assumed the covariance matrices are either equal across groups or are completely distinct. We seek methodology to allow borrowing of strength across potentially similar groups to improve estimation. To that end, we introduce a covariance partition prior which proposes a partition of the groups at each measurement time. Groups in the same set of the partition share dependence parameters for the distribution of the current measurement given the preceding ones, and the sequence of partitions is modeled as a Markov chain to encourage similar structure at nearby measurement times. This approach additionally encourages a lower-dimensional structure of the covariance matrices by shrinking the parameters of the Cholesky decomposition toward zero. We demonstrate the performance of our model through two simulation studies and the analysis of data from a depression study. This article includes Supplementary Material available online.

CMV matrices in random matrix theory and integrable systems: a survey

NASA Astrophysics Data System (ADS)

Nenciu, Irina

2006-07-01

We present a survey of recent results concerning a remarkable class of unitary matrices, the CMV matrices. We are particularly interested in the role they play in the theory of random matrices and integrable systems. Throughout the paper we also emphasize the analogies and connections to Jacobi matrices.

Polarization-dependent diffraction in all-dielectric, twisted-band structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kardaś, Tomasz M.; Jagodnicka, Anna; Wasylczyk, Piotr, E-mail: pwasylcz@fuw.edu.pl

2015-11-23

We propose a concept for light polarization management: polarization-dependent diffraction in all-dielectric microstructures. Numerical simulations of light propagation show that with an appropriately configured array of twisted bands, such structures may exhibit zero birefringence and at the same time diffract two circular polarizations with different efficiencies. Non-birefringent structures as thin as 3 μm have a significant difference in diffraction efficiency for left- and right-hand circular polarizations. We identify the structural parameters of such twisted-band matrices for optimum performance as circular polarizers.

Basal Cell Carcinoma With Matrical Differentiation: Clinicopathologic, Immunohistochemical, and Molecular Biological Study of 22 Cases.

PubMed

Kyrpychova, Liubov; Carr, Richard A; Martinek, Petr; Vanecek, Tomas; Perret, Raul; Chottová-Dvořáková, Magdalena; Zamecnik, Michal; Hadravsky, Ladislav; Michal, Michal; Kazakov, Dmitry V

2017-06-01

Basal cell carcinoma (BCC) with matrical differentiation is a fairly rare neoplasm, with about 30 cases documented mainly as isolated case reports. We studied a series of this neoplasm, including cases with an atypical matrical component, a hitherto unreported feature. Lesions coded as BCC with matrical differentiation were reviewed; 22 cases were included. Immunohistochemical studies were performed using antibodies against BerEp4, β-catenin, and epithelial membrane antigen (EMA). Molecular genetic studies using Ion AmpliSeq Cancer Hotspot Panel v2 by massively parallel sequencing on Ion Torrent PGM were performed in 2 cases with an atypical matrical component (1 was previously subjected to microdissection to sample the matrical and BCC areas separately). There were 13 male and 9 female patients, ranging in age from 41 to 89 years. Microscopically, all lesions manifested at least 2 components, a BCC area (follicular germinative differentiation) and areas with matrical differentiation. A BCC component dominated in 14 cases, whereas a matrical component dominated in 4 cases. Matrical differentiation was recognized as matrical/supramatrical cells (n=21), shadow cells (n=21), bright red trichohyaline granules (n=18), and blue-gray corneocytes (n=18). In 2 cases, matrical areas manifested cytologic atypia, and a third case exhibited an infiltrative growth pattern, with the tumor metastasizing to a lymph node. BerEP4 labeled the follicular germinative cells, whereas it was markedly reduced or negative in matrical areas. The reverse pattern was seen with β-catenin. EMA was negative in BCC areas but stained a proportion of matrical/supramatrical cells. Genetic studies revealed mutations of the following genes: CTNNB1, KIT, CDKN2A, TP53, SMAD4, ERBB4, and PTCH1, with some differences between the matrical and BCC components. It is concluded that matrical differentiation in BCC in most cases occurs as multiple foci. Rare neoplasms manifest atypia in the matrical areas. Immunohistochemical analysis for BerEP4, EMA, and β-catenin can be helpful in limited biopsy specimens. From a molecular biological prospective, BCC and matrical components appear to share some of the gene mutations but have differences in others, but this observation must be validated in a large series.

Porous Structure Design of Polymeric Membranes for Gas Separation

DOE PAGES

Zhang, Jinshui; Schott, Jennifer Ann; Mahurin, Shannon Mark; ...

2017-04-04

High-performance polymeric membranes for gas separation are of interest for molecular-level separations in industrial-scale chemical, energy and environmental processes. To overcome the inherent trade-off relationship between permeability and selectivity, the creation of permanent microporosity in polymeric matrices is highly desirable because the porous structures can provide a high fractional free volume to facilitate gas transport through the dense layer. In this feature article, recent developments in the formation of porous polymeric membranes and potential strategies for pore structure design are reviewed.

Comparative Proteomic Analyses of Human Adipose Extracellular Matrices Decellularized Using Alternative Procedures.

PubMed

Thomas-Porch, Caasy; Li, Jie; Zanata, Fabiana; Martin, Elizabeth C; Pashos, Nicholas; Genemaras, Kaylynn; Poche, J Nicholas; Totaro, Nicholas P; Bratton, Melyssa R; Gaupp, Dina; Frazier, Trivia; Wu, Xiying; Ferreira, Lydia Masako; Tian, Weidong; Wang, Guangdi; Bunnell, Bruce A; Flynn, Lauren; Hayes, Daniel; Gimble, Jeffrey M

2018-04-25

Decellularized human adipose tissue has potential clinical utility as a processed biological scaffold for soft tissue cosmesis, grafting and reconstruction. Adipose tissue decellularization has been accomplished using enzymatic-, detergent-, and/or solvent-based methods. To examine the hypothesis that distinct decellularization processes may yield scaffolds with differing compositions, the current study employed mass spectrometry to compare the proteomes of human adipose-derived matrices generated through three independent methods combining enzymatic-, detergent-, and/or solvent-based steps. In addition to protein content, bioscaffolds were evaluated for DNA depletion, ECM composition, and physical structure using optical density, histochemical staining, and scanning electron microscopy (SEM). Mass spectrometry (MS) based proteomic analyses identified 25 proteins (having at least two peptide sequences detected) in the scaffolds generated with an enzymatic approach, 143 with the detergent approach, and 102 with the solvent approach, as compared to 155 detected in unprocessed native human fat. Immunohistochemical detection confirmed the presence of the structural proteins actin, collagen type VI, fibrillin, laminin, and vimentin. Subsequent in vivo analysis of the predominantly enzymatic- and detergent-based decellularized scaffolds following subcutaneous implantation in GFP + transgenic mice demonstrated that the matrices generated with both approaches supported the ingrowth of host-derived adipocyte progenitors and vasculature in a time dependent manner. Together, these results determine that decellularization methods influence the protein composition of adipose tissue-derived bioscaffolds. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

Progress report 3 of cooperative program for design, fabrication, and testing of high modulus composite helicopter shafting

NASA Technical Reports Server (NTRS)

Wright, C. C.; Baker, D. J.

1980-01-01

This report describes the third phase of work, the objective of which was to overcome the excessive brittleness of the previously developed UH-1 helicopter tail rotor drive shaft design which demonstrated a shaft train weight savings of 53.1% over the current 2024-T3 aluminum shaft train. A materials impact program demonstrated exceptionally noteworthy performance of two woven constructions containing E-glass and PRD 49-III (designation later changed to KEVLAR 49) fibers in an epoxy resin matrix. Thermoplastic matrices and PRD 49-III fiber provided impact resistance at low weight which was superior to composites having the same fiber in a thermoset resin matrix. A design, fabrication, and test program showed that shaft impact resistance could be improved over the previously developed graphite composite design at a cost in shaft train rate savings. The shaft train weight savings of the most impact tolerant construction was 4.0% over the current aluminum shaft train. Alternating plies of graphite and glass appear to provide substantially greater tube impact durability than that provided by hybridization of the two fibers into one tape wound to a ply design equivalent in strength and stiffness to that of the alternating ply design. Recommendations were made to continue research work to exploit the potential for more impact-durable structures through the use of KEVLAR 49 fiber, woven structures, thermoplastic matrices and THORNEL 50-S/KEVLAR 49 blends with thermoset matrices.

Automatic face naming by learning discriminative affinity matrices from weakly labeled images.

PubMed

Xiao, Shijie; Xu, Dong; Wu, Jianxin

2015-10-01

Given a collection of images, where each image contains several faces and is associated with a few names in the corresponding caption, the goal of face naming is to infer the correct name for each face. In this paper, we propose two new methods to effectively solve this problem by learning two discriminative affinity matrices from these weakly labeled images. We first propose a new method called regularized low-rank representation by effectively utilizing weakly supervised information to learn a low-rank reconstruction coefficient matrix while exploring multiple subspace structures of the data. Specifically, by introducing a specially designed regularizer to the low-rank representation method, we penalize the corresponding reconstruction coefficients related to the situations where a face is reconstructed by using face images from other subjects or by using itself. With the inferred reconstruction coefficient matrix, a discriminative affinity matrix can be obtained. Moreover, we also develop a new distance metric learning method called ambiguously supervised structural metric learning by using weakly supervised information to seek a discriminative distance metric. Hence, another discriminative affinity matrix can be obtained using the similarity matrix (i.e., the kernel matrix) based on the Mahalanobis distances of the data. Observing that these two affinity matrices contain complementary information, we further combine them to obtain a fused affinity matrix, based on which we develop a new iterative scheme to infer the name of each face. Comprehensive experiments demonstrate the effectiveness of our approach.

A Comparison of Pseudo-Maximum Likelihood and Asymptotically Distribution-Free Dynamic Factor Analysis Parameter Estimation in Fitting Covariance Structure Models to Block-Toeplitz Matrices Representing Single-Subject Multivariate Time-Series.

ERIC Educational Resources Information Center

Molenaar, Peter C. M.; Nesselroade, John R.

1998-01-01

Pseudo-Maximum Likelihood (p-ML) and Asymptotically Distribution Free (ADF) estimation methods for estimating dynamic factor model parameters within a covariance structure framework were compared through a Monte Carlo simulation. Both methods appear to give consistent model parameter estimates, but only ADF gives standard errors and chi-square…

Chemically Active, Porous 3D-Printed Thermoplastic Composites.

PubMed

Evans, Kent A; Kennedy, Zachary C; Arey, Bruce W; Christ, Josef F; Schaef, Herbert T; Nune, Satish K; Erikson, Rebecca L

2018-05-02

Metal-organic frameworks (MOFs) exhibit exceptional properties and are widely investigated because of their structural and functional versatility relevant to catalysis, separations, and sensing applications. However, their commercial or large-scale application is often limited by their powder forms which make integration into devices challenging. Here, we report the production of MOF-thermoplastic polymer composites in well-defined and customizable forms and with complex internal structural features accessed via a standard three-dimensional (3D) printer. MOFs (zeolitic imidazolate framework; ZIF-8) were incorporated homogeneously into both poly(lactic acid) (PLA) and thermoplastic polyurethane (TPU) matrices at high loadings (up to 50% by mass), extruded into filaments, and utilized for on-demand access to 3D structures by fused deposition modeling. Printed, rigid PLA/MOF composites display a large surface area (SA avg = 531 m 2 g -1 ) and hierarchical pore features, whereas flexible TPU/MOF composites achieve a high surface area (SA avg = 706 m 2 g -1 ) by employing a simple method developed to expose obstructed micropores postprinting. Critically, embedded particles in the plastic matrices retain their ability to participate in chemical interactions characteristic of the parent framework. The fabrication strategies were extended to other MOFs and illustrate the potential of 3D printing to create unique porous and high surface area chemically active structures.

High pressure effects on the structural functionality of condensed globular-protein matrices.

PubMed

Savadkoohi, Sobhan; Kasapis, Stefan

2016-07-01

High pressure technology is the outcome of consumer demand for better quality control of processed foods. There is great potential to apply HPP to condensed systems of globular proteins for the generation of industry-relevant biomaterials with advanced techno- and biofunctionality. To this end, research demonstrates that application of high hydrostatic pressure generates a coherent structure and preserves the native conformation in condensed globular proteins, which is an entirely unexpected but interesting outcome on both scientific and technological grounds. In microbiological challenge tests, high pressure at conventional commercial conditions, demonstrated to effectively reduce the concentration of typical Gram negative or Gram positive foodborne pathogens, and proteolytic enzymes in high-solid protein samples. This may have industrial significance in relation to the formulation and stabilisation of "functional food" products as well as in protein ingredients and concentrates by replacing spray dried powders with condensed HPP-treated pastes that maintain structure and bioactivity. Fundamental concepts and structural functionality of condensed matrices of globular proteins are the primary interest in this mini-review, which may lead to opportunities for industrial exploitation, but earlier work on low-solid systems is also summarised presently to put recent developments in context of this rapidly growing field. Copyright © 2016. Published by Elsevier B.V.

Development of damage probability matrices based on Greek earthquake damage data

NASA Astrophysics Data System (ADS)

Eleftheriadou, Anastasia K.; Karabinis, Athanasios I.

2011-03-01

A comprehensive study is presented for empirical seismic vulnerability assessment of typical structural types, representative of the building stock of Southern Europe, based on a large set of damage statistics. The observational database was obtained from post-earthquake surveys carried out in the area struck by the September 7, 1999 Athens earthquake. After analysis of the collected observational data, a unified damage database has been created which comprises 180,945 damaged buildings from/after the near-field area of the earthquake. The damaged buildings are classified in specific structural types, according to the materials, seismic codes and construction techniques in Southern Europe. The seismic demand is described in terms of both the regional macroseismic intensity and the ratio α g/ a o, where α g is the maximum peak ground acceleration (PGA) of the earthquake event and a o is the unique value PGA that characterizes each municipality shown on the Greek hazard map. The relative and cumulative frequencies of the different damage states for each structural type and each intensity level are computed in terms of damage ratio. Damage probability matrices (DPMs) and vulnerability curves are obtained for specific structural types. A comparison analysis is fulfilled between the produced and the existing vulnerability models.

A Brief Historical Introduction to Matrices and Their Applications

ERIC Educational Resources Information Center

Debnath, L.

2014-01-01

This paper deals with the ancient origin of matrices, and the system of linear equations. Included are algebraic properties of matrices, determinants, linear transformations, and Cramer's Rule for solving the system of algebraic equations. Special attention is given to some special matrices, including matrices in graph theory and electrical…

A structure preserving Lanczos algorithm for computing the optical absorption spectrum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shao, Meiyue; Jornada, Felipe H. da; Lin, Lin

2016-11-16

We present a new structure preserving Lanczos algorithm for approximating the optical absorption spectrum in the context of solving full Bethe-Salpeter equation without Tamm-Dancoff approximation. The new algorithm is based on a structure preserving Lanczos procedure, which exploits the special block structure of Bethe-Salpeter Hamiltonian matrices. A recently developed technique of generalized averaged Gauss quadrature is incorporated to accelerate the convergence. We also establish the connection between our structure preserving Lanczos procedure with several existing Lanczos procedures developed in different contexts. Numerical examples are presented to demonstrate the effectiveness of our Lanczos algorithm.

Effects of nitrogenous substituent groups on the benzene dication

NASA Astrophysics Data System (ADS)

Forgy, C. C.; Schlimgen, A. W.; Mazziotti, D. A.

2018-05-01

The benzene dication possesses a pentagonal-pyramidal structure with a hexacoordinated carbon. In contrast, halogenated benzene dications retain a similar structure to their parent molecules. In this work, we report on theoretical studies of the structures of the dications of benzene with nitrogenous substituents. We find that the nitrobenzene dication favours a near ideal pentagonal-pyramidal structure, while the aniline dication favours a flat, hexagonal structure. Reduced-density-matrices methods give predictions in agreement with available ab initio calculations and experiment. These results are also compared with those from the Hartree-Fock method and density functional theory.

Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells

PubMed Central

Nasir, Arshan; Kim, Kyung Mo; Caetano-Anollés, Gustavo

2017-01-01

Untangling the origin and evolution of viruses remains a challenging proposition. We recently studied the global distribution of protein domain structures in thousands of completely sequenced viral and cellular proteomes with comparative genomics, phylogenomics, and multidimensional scaling methods. A tree of life describing the evolution of proteomes revealed viruses emerging from the base of the tree as a fourth supergroup of life. A tree of domains indicated an early origin of modern viral lineages from ancient cells that co-existed with the cellular ancestors. However, it was recently argued that the rooting of our trees and the basal placement of viruses was artifactually induced by small genome (proteome) size. Here we show that these claims arise from misunderstanding and misinterpretations of cladistic methodology. Trees are reconstructed unrooted, and thus, their topologies cannot be distorted a posteriori by the rooting methodology. Tracing proteome size in trees and multidimensional views of evolutionary relationships as well as tests of leaf stability and exclusion/inclusion of taxa demonstrated that the smallest proteomes were neither attracted toward the root nor caused any topological distortions of the trees. Simulations confirmed that taxa clustering patterns were independent of proteome size and were determined by the presence of known evolutionary relatives in data matrices, highlighting the need for broader taxon sampling in phylogeny reconstruction. Instead, phylogenetic tracings of proteome size revealed a slowdown in innovation of the structural domain vocabulary and four regimes of allometric scaling that reflected a Heaps law. These regimes explained increasing economies of scale in the evolutionary growth and accretion of kernel proteome repertoires of viruses and cellular organisms that resemble growth of human languages with limited vocabulary sizes. Results reconcile dynamic and static views of domain frequency distributions that are consistent with the axiom of spatiotemporal continuity that is tenet of evolutionary thinking. PMID:28690608

MODFLOW–USG version 1: An unstructured grid version of MODFLOW for simulating groundwater flow and tightly coupled processes using a control volume finite-difference formulation

USGS Publications Warehouse

Panday, Sorab; Langevin, Christian D.; Niswonger, Richard G.; Ibaraki, Motomu; Hughes, Joseph D.

2013-01-01

A new version of MODFLOW, called MODFLOW–USG (for UnStructured Grid), was developed to support a wide variety of structured and unstructured grid types, including nested grids and grids based on prismatic triangles, rectangles, hexagons, and other cell shapes. Flexibility in grid design can be used to focus resolution along rivers and around wells, for example, or to subdiscretize individual layers to better represent hydrostratigraphic units. MODFLOW–USG is based on an underlying control volume finite difference (CVFD) formulation in which a cell can be connected to an arbitrary number of adjacent cells. To improve accuracy of the CVFD formulation for irregular grid-cell geometries or nested grids, a generalized Ghost Node Correction (GNC) Package was developed, which uses interpolated heads in the flow calculation between adjacent connected cells. MODFLOW–USG includes a Groundwater Flow (GWF) Process, based on the GWF Process in MODFLOW–2005, as well as a new Connected Linear Network (CLN) Process to simulate the effects of multi-node wells, karst conduits, and tile drains, for example. The CLN Process is tightly coupled with the GWF Process in that the equations from both processes are formulated into one matrix equation and solved simultaneously. This robustness results from using an unstructured grid with unstructured matrix storage and solution schemes. MODFLOW–USG also contains an optional Newton-Raphson formulation, based on the formulation in MODFLOW–NWT, for improving solution convergence and avoiding problems with the drying and rewetting of cells. Because the existing MODFLOW solvers were developed for structured and symmetric matrices, they were replaced with a new Sparse Matrix Solver (SMS) Package developed specifically for MODFLOW–USG. The SMS Package provides several methods for resolving nonlinearities and multiple symmetric and asymmetric linear solution schemes to solve the matrix arising from the flow equations and the Newton-Raphson formulation, respectively.

Polyphenylquinoxalines Via Aromatic Nucleophilic Displacement

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M.; Connell, John W.

1991-01-01

Process for synthesis of polyphenylquinoxalines (PPQ's) involves nucleophilic displacement reactions of di(hydroxyphenyl) quinoxaline monomers with activated aromatic dihalides. New process costs less than other processes for synthesis of PPQ's. Facilitates synthesis of PPQ's of new and varied molecular structures. Useful as adhesives, coatings, films, membranes, and matrices for composites.

The Infinitesimal Jackknife with Exploratory Factor Analysis

ERIC Educational Resources Information Center

Zhang, Guangjian; Preacher, Kristopher J.; Jennrich, Robert I.

2012-01-01

The infinitesimal jackknife, a nonparametric method for estimating standard errors, has been used to obtain standard error estimates in covariance structure analysis. In this article, we adapt it for obtaining standard errors for rotated factor loadings and factor correlations in exploratory factor analysis with sample correlation matrices. Both…

SAXS Combined with UV-vis Spectroscopy and QELS: Accurate Characterization of Silver Sols Synthesized in Polymer Matrices.

PubMed

Bulavin, Leonid; Kutsevol, Nataliya; Chumachenko, Vasyl; Soloviov, Dmytro; Kuklin, Alexander; Marynin, Andrii

2016-12-01

The present work demonstrates a validation of small-angle X-ray scattering (SAXS) combining with ultra violet and visible (UV-vis) spectroscopy and quasi-elastic light scattering (QELS) analysis for characterization of silver sols synthesized in polymer matrices. Polymer matrix internal structure and polymer chemical nature actually controlled the sol size characteristics. It was shown that for precise analysis of nanoparticle size distribution these techniques should be used simultaneously. All applied methods were in good agreement for the characterization of size distribution of small particles (less than 60 nm) in the sols. Some deviations of the theoretical curves from the experimental ones were observed. The most probable cause is that nanoparticles were not entirely spherical in form.

Symmetries in geometrical optics: theory

NASA Astrophysics Data System (ADS)

Szilagyi, M.; Mui, P. H.

1995-12-01

A study of light and charged-particle optical systems with inversion, reflection, rotation, translation, and/or glide symmetries is presented. The constraints imposed by the various symmetries on the first-order properties of a lens are investigated. In particular, the mathematical structures of the deflection vectors and the transfer matrices are described for various symmetrical systems. In the course of studying the translation and the glide symmetries, a simple technique for characterizing a general system of N identical components in series (or cascade) is also developed, based on the linear algebra theory of factoring matrices into Jordan canonical forms. Applications of these results are presented in a follow-up paper [J. Opt. Soc. Am. 12, XXXX (1995)]. Copyright (c) 1995 Optical Society of America

A Theorem on the Rank of a Product of Matrices with Illustration of Its Use in Goodness of Fit Testing.

PubMed

Satorra, Albert; Neudecker, Heinz

2015-12-01

This paper develops a theorem that facilitates computing the degrees of freedom of Wald-type chi-square tests for moment restrictions when there is rank deficiency of key matrices involved in the definition of the test. An if and only if (iff) condition is developed for a simple rule of difference of ranks to be used when computing the desired degrees of freedom of the test. The theorem is developed exploiting basics tools of matrix algebra. The theorem is shown to play a key role in proving the asymptotic chi-squaredness of a goodness of fit test in moment structure analysis, and in finding the degrees of freedom of this chi-square statistic.

Design of dissipative low-authority controllers using an eigensystem assignment technique

NASA Technical Reports Server (NTRS)

Maghami, P. G.; Gupta, S.; Joshi, S. M.

1992-01-01

A novel method for the design of dissipative, low-authority controllers has been developed. The method uses a sequential approach along with eigensystem assignment to compute rate and position gain matrices that assign a number of closed-loop poles of the system to desired locations. Because the feedback gain matrices are symmetric and nonnegative definite, the closed-loop stability is always guaranteed regardless of the model order or parameter inaccuracies. The resulting (nominal) closed-loop system can have specified damping ratios for m modes, which makes the plant amenable to high-authority controller design, using methods such as LQG/LTR or H-infinity. A numerical example is worked out for a flexible structure in order to demonstrate the proposed technique.

Correlations of RMT characteristic polynomials and integrability: Hermitean matrices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osipov, Vladimir Al., E-mail: Vladimir.Osipov@uni-due.d; Kanzieper, Eugene, E-mail: Eugene.Kanzieper@hit.ac.i; Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100

Integrable theory is formulated for correlation functions of characteristic polynomials associated with invariant non-Gaussian ensembles of Hermitean random matrices. By embedding the correlation functions of interest into a more general theory of {tau} functions, we (i) identify a zoo of hierarchical relations satisfied by {tau} functions in an abstract infinite-dimensional space and (ii) present a technology to translate these relations into hierarchically structured nonlinear differential equations describing the correlation functions of characteristic polynomials in the physical, spectral space. Implications of this formalism for fermionic, bosonic, and supersymmetric variations of zero-dimensional replica field theories are discussed at length. A particular emphasismore » is placed on the phenomenon of fermionic-bosonic factorisation of random-matrix-theory correlation functions.« less

Miscellaneous methods for measuring matric or water potential

USGS Publications Warehouse

Scanlon, Bridget R.; Andraski, Brian J.; Bilskie, Jim; Dane, Jacob H.; Topp, G. Clarke

2002-01-01

A variety of techniques to measure matric potential or water potential in the laboratory and in the field are described in this section. The techniques described herein require equilibration of some medium whose matric or water potential can be determined from previous calibration or can be measured directly. Under equilibrium conditions the matric or water potential of the medium is equal to that of the soil. The techniques can be divided into: (i) those that measure matric potential and (ii) those that measure water potential (sum of matric and osmotic potentials). Matric potential is determined when the sensor matrix is in direct contact with the soil, so salts are free to diffuse in or out of the sensor matrix, and the equilibrium measurement therefore reflects matric forces acting on the water. Water potential is determined when the sensor is separated from the soil by a vapor gap, so salts are not free to move in or out of the sensor, and the equilibrium measurement reflects the sum of the matric and osmotic forces acting on the water.Seven different techniques are described in this section. Those that measure matric potential include (i) heat dissipation sensors, (ii) electrical resistance sensors, (iii) frequency domain and time domain sensors, and (iv) electro-optical switches. A method that can be used to measure matric potential or water potential is the (v) filter paper method. Techniques that measure water potential include (vi) the Dew Point Potentiameter (Decagon Devices, Inc., Pullman, WA1) (water activity meter) and (vii) vapor equilibration.The first four techniques are electronically based methods for measuring matric potential. Heat dissipation sensors and electrical resistance sensors infer matric potential from previously determined calibration relations between sensor heat dissipation or electrical resistance and matric potential. Frequency-domain and timedomain matric potential sensors measure water content, which is related to matric potential of the sensor through calibration. Electro-optical switches measure changes in light transmission through thin, nylon filters as they absorb or desorb water in response to changes in matric potential. Heat dissipation sensors and electrical resistance sensors are used primarily in the field to provide information on matric potential. Frequency domain matric potential sensors are new and have not been widely used. Time domain matric potential sensors and electro-optical switches are new and have not been commercialized. For the fifth technique, filter paper is used as the standard matrix. The filter paper technique measures matric potential when the filter paper is in direct contact with soil or water potential when separated from soil by a vapor gap. The Dew Point Potentiameter calculates water potential from the measured dew point and sample temperature. The vapor equilibration technique involves equilibration of soil samples with salt solutions of known osmotic potential. The filter paper, Dew Point Potentiameter, and vapor equilibration techniques are generally used in the laboratory to measure water potential of disturbed field samples or to measure water potential for water retention functions.

Characterization of internal structure of hydrated agar and gelatin matrices by cryo-SEM.

PubMed

Rahbani, Janane; Behzad, Ali R; Khashab, Niveen M; Al-Ghoul, Mazen

2013-02-01

There has been a considerable interest in recent years in developing polymer gel matrices for many important applications such as 2DE for quantization and separation of a variety of proteins and drug delivery system to control the release of active agents. However, a well-defined knowledge of the ultrastructures of the gels has been elusive. In this study, we report the characterization of two different polymers used in 2DE: Gelatin, a naturally occurring polymer derived from collagen (protein) and agar, a polymer of polysaccharide (sugar) origin. Low-temperature SEM is used to examine the internal structure of these gels in their frozen natural hydrated states. Results of this study show that both polymers have an array of hollow cells that resembles honeycomb structures. While agar pores are almost circular, the corresponding Gaussian curve is very broad exhibiting a range of radii from nearly 370 to 700 nm. Gelatin pores are smaller and more homogeneous reflecting a narrower distribution from nearly 320 to 650 nm. Overall, these ultrastructural findings could be used to correlate with functions of the polymers. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Filtered gradient reconstruction algorithm for compressive spectral imaging

NASA Astrophysics Data System (ADS)

Mejia, Yuri; Arguello, Henry

2017-04-01

Compressive sensing matrices are traditionally based on random Gaussian and Bernoulli entries. Nevertheless, they are subject to physical constraints, and their structure unusually follows a dense matrix distribution, such as the case of the matrix related to compressive spectral imaging (CSI). The CSI matrix represents the integration of coded and shifted versions of the spectral bands. A spectral image can be recovered from CSI measurements by using iterative algorithms for linear inverse problems that minimize an objective function including a quadratic error term combined with a sparsity regularization term. However, current algorithms are slow because they do not exploit the structure and sparse characteristics of the CSI matrices. A gradient-based CSI reconstruction algorithm, which introduces a filtering step in each iteration of a conventional CSI reconstruction algorithm that yields improved image quality, is proposed. Motivated by the structure of the CSI matrix, Φ, this algorithm modifies the iterative solution such that it is forced to converge to a filtered version of the residual ΦTy, where y is the compressive measurement vector. We show that the filtered-based algorithm converges to better quality performance results than the unfiltered version. Simulation results highlight the relative performance gain over the existing iterative algorithms.

When fast and slow interfaces grow together: Connection to the half-space problem of the Kardar-Parisi-Zhang class

NASA Astrophysics Data System (ADS)

Ito, Yasufumi; Takeuchi, Kazumasa A.

2018-04-01

We study height fluctuations of interfaces in the (1 +1 ) -dimensional Kardar-Parisi-Zhang (KPZ) class, growing at different speeds in the left half and the right half of space. Carrying out simulations of the discrete polynuclear growth model with two different growth rates, combined with the standard setting for the droplet, flat, and stationary geometries, we find that the fluctuation properties at and near the boundary are described by the KPZ half-space problem developed in the theoretical literature. In particular, in the droplet case, the distribution at the boundary is given by the largest-eigenvalue distribution of random matrices in the Gaussian symplectic ensemble, often called the GSE Tracy-Widom distribution. We also characterize crossover from the full-space statistics to the half-space one, which arises when the difference between the two growth speeds is small.

A Gibbs sampler for motif detection in phylogenetically close sequences

NASA Astrophysics Data System (ADS)

Siddharthan, Rahul; van Nimwegen, Erik; Siggia, Eric

2004-03-01

Genes are regulated by transcription factors that bind to DNA upstream of genes and recognize short conserved ``motifs'' in a random intergenic ``background''. Motif-finders such as the Gibbs sampler compare the probability of these short sequences being represented by ``weight matrices'' to the probability of their arising from the background ``null model'', and explore this space (analogous to a free-energy landscape). But closely related species may show conservation not because of functional sites but simply because they have not had sufficient time to diverge, so conventional methods will fail. We introduce a new Gibbs sampler algorithm that accounts for common ancestry when searching for motifs, while requiring minimal ``prior'' assumptions on the number and types of motifs, assessing the significance of detected motifs by ``tracking'' clusters that stay together. We apply this scheme to motif detection in sporulation-cycle genes in the yeast S. cerevisiae, using recent sequences of other closely-related Saccharomyces species.

Self-assembly behavior of poly(fluorenyl styrene)-block-poly(2-vinyl pyridine) and their blends with single wall carbon nanotubes (SWCNT)

NASA Astrophysics Data System (ADS)

Mezzenga, Raffaele; Li, Chaoxu; Hsu, Jung-Ching; Chen, Wen-Chang; Sugiyama, Kenji; Hirao, Akira

2010-03-01

We describe a supramolecular strategy to disperse carbon nanotubes in block copolymer matrices. To achieve the desired functions and morphologies, comb-type architectures in which one and two fluorene units attached on the styrene ring of polystyrene-block-poly(2-vinyl pyridine) were studied. Depending on the pendant fluorene units, the block ratio, the casting solvent and thermal annealing history, multiple morphologies were found. The phase diagram, compared to PS-b-P2VP, was interpreted in terms of the conformational asymmetry arising from grafting of fluorene units of variable lengths. Hydrogen bonds between COOH-SWCNT and P2VP favor miscibility of SWCNT within P2VP domains and the blending of these two components is reflected both on the final morphologies and on the electron conductivity of the blends.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hurd, J.R.

The active-passive shuffler installed and certified a few years ago in Los Alamos National Laboratory`s plutonium facility has now been calibrated for different matrices to measure Waste Isolation Pilot Plant (WIPP)-destined transuranic (TRU)-waste. Little or no data presently exist for these types of measurements in plant environments where there may be sudden large changes in the neutron background radiation which causes distortions in the results. Measurements and analyses of twenty-two 55-gallon drums, consisting of mixtures of varying quantities of uranium and plutonium, have been recently completed at the plutonium facility. The calibration and measurement techniques, including the method used tomore » separate out the plutonium component, will be presented and discussed. Particular attention will be directed to those problems identified as arising from the plant environment. The results of studies to quantify the distortion effects in the data will be presented. Various solution scenarios will be indicated, along with those adopted here.« less

Online Updating of Statistical Inference in the Big Data Setting.

PubMed

Schifano, Elizabeth D; Wu, Jing; Wang, Chun; Yan, Jun; Chen, Ming-Hui

2016-01-01

We present statistical methods for big data arising from online analytical processing, where large amounts of data arrive in streams and require fast analysis without storage/access to the historical data. In particular, we develop iterative estimating algorithms and statistical inferences for linear models and estimating equations that update as new data arrive. These algorithms are computationally efficient, minimally storage-intensive, and allow for possible rank deficiencies in the subset design matrices due to rare-event covariates. Within the linear model setting, the proposed online-updating framework leads to predictive residual tests that can be used to assess the goodness-of-fit of the hypothesized model. We also propose a new online-updating estimator under the estimating equation setting. Theoretical properties of the goodness-of-fit tests and proposed estimators are examined in detail. In simulation studies and real data applications, our estimator compares favorably with competing approaches under the estimating equation setting.

Numerical stability in problems of linear algebra.

NASA Technical Reports Server (NTRS)

Babuska, I.

1972-01-01

Mathematical problems are introduced as mappings from the space of input data to that of the desired output information. Then a numerical process is defined as a prescribed recurrence of elementary operations creating the mapping of the underlying mathematical problem. The ratio of the error committed by executing the operations of the numerical process (the roundoff errors) to the error introduced by perturbations of the input data (initial error) gives rise to the concept of lambda-stability. As examples, several processes are analyzed from this point of view, including, especially, old and new processes for solving systems of linear algebraic equations with tridiagonal matrices. In particular, it is shown how such a priori information can be utilized as, for instance, a knowledge of the row sums of the matrix. Information of this type is frequently available where the system arises in connection with the numerical solution of differential equations.

Space of symmetry matrices with elements 0, ±1 and complete geometric description; its properties and application.

PubMed

Stróż, Kazimierz

2011-09-01

A fixed set, that is the set of all lattice metrics corresponding to the arithmetic holohedry of a primitive lattice, is a natural tool for keeping track of the symmetry changes that may occur in a deformable lattice [Ericksen (1979). Arch. Rat. Mech. Anal. 72, 1-13; Michel (1995). Symmetry and Structural Properties of Condensed Matter, edited by T. Lulek, W. Florek & S. Walcerz. Singapore: Academic Press; Pitteri & Zanzotto (1996). Acta Cryst. A52, 830-838; and references quoted therein]. For practical applications it is desirable to limit the infinite number of arithmetic holohedries, and simplify their classification and construction of the fixed sets. A space of 480 matrices with cyclic consecutive powers, determinant 1, elements from {0, ±1} and geometric description were analyzed and offered as the framework for dealing with the symmetry of reduced lattices. This matrix space covers all arithmetic holohedries of primitive lattice descriptions related to the three shortest lattice translations in direct or reciprocal spaces, and corresponds to the unique list of 39 fixed points with integer coordinates in six-dimensional space of lattice metrics. Matrices are presented by the introduced dual symbol, which sheds some light on the lattice and its symmetry-related properties, without further digging into matrices. By the orthogonal lattice distortion the lattice group-subgroup relations are easily predicted. It was proven and exemplified that new symbols enable classification of lattice groups on an absolute basis, without metric considerations. In contrast to long established but sophisticated methods for assessing the metric symmetry of a lattice, simple filtering of the symmetry operations from the predefined set is proposed. It is concluded that the space of symmetry matrices with elements from {0, ±1} is the natural environment of lattice symmetries related to the reduced cells and that complete geometric characterization of matrices in the arithmetic holohedry provides a useful tool for solving practical lattice-related problems, especially in the context of lattice deformation. © 2011 International Union of Crystallography

Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

PubMed

Ivanciuc, Ovidiu

2013-06-01

Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance.

GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition

PubMed Central

2011-01-01

Background Calculation of the root mean square deviation (RMSD) between the atomic coordinates of two optimally superposed structures is a basic component of structural comparison techniques. We describe a quaternion based method, GPU-Q-J, that is stable with single precision calculations and suitable for graphics processor units (GPUs). The application was implemented on an ATI 4770 graphics card in C/C++ and Brook+ in Linux where it was 260 to 760 times faster than existing unoptimized CPU methods. Source code is available from the Compbio website http://software.compbio.washington.edu/misc/downloads/st_gpu_fit/ or from the author LHH. Findings The Nutritious Rice for the World Project (NRW) on World Community Grid predicted de novo, the structures of over 62,000 small proteins and protein domains returning a total of 10 billion candidate structures. Clustering ensembles of structures on this scale requires calculation of large similarity matrices consisting of RMSDs between each pair of structures in the set. As a real-world test, we calculated the matrices for 6 different ensembles from NRW. The GPU method was 260 times faster that the fastest existing CPU based method and over 500 times faster than the method that had been previously used. Conclusions GPU-Q-J is a significant advance over previous CPU methods. It relieves a major bottleneck in the clustering of large numbers of structures for NRW. It also has applications in structure comparison methods that involve multiple superposition and RMSD determination steps, particularly when such methods are applied on a proteome and genome wide scale. PMID:21453553

Genetic code, hamming distance and stochastic matrices.

PubMed

He, Matthew X; Petoukhov, Sergei V; Ricci, Paolo E

2004-09-01

In this paper we use the Gray code representation of the genetic code C=00, U=10, G=11 and A=01 (C pairs with G, A pairs with U) to generate a sequence of genetic code-based matrices. In connection with these code-based matrices, we use the Hamming distance to generate a sequence of numerical matrices. We then further investigate the properties of the numerical matrices and show that they are doubly stochastic and symmetric. We determine the frequency distributions of the Hamming distances, building blocks of the matrices, decomposition and iterations of matrices. We present an explicit decomposition formula for the genetic code-based matrix in terms of permutation matrices, which provides a hypercube representation of the genetic code. It is also observed that there is a Hamiltonian cycle in a genetic code-based hypercube.

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

PubMed Central

Dršata, Tomáš; Pérez, Alberto; Orozco, Modesto; Morozov, Alexandre V.; Šponer, Jiřĺ; Lankaš, Filip

2013-01-01

The Dickerson–Drew dodecamer (DD) d-[CGCGAATTCGCG]2 is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6–2.4-µs-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states. The nonlocal stiffness matrices for a rigid-base mechanical model of DD are reported for the first time, suggesting salient stiffness features of the central A-tract. The Riemann distance and Kullback–Leibler divergence are used for stiffness matrix comparison. The basic structural parameters converge very well within 300 ns, convergence of the BI/BII populations and stiffness matrices is less sharp. Our work presents new findings about the DD structural dynamics, mechanical properties, and the coupling between basepair and backbone configurations, including their statistical reliability. The results may also be useful for optimizing future force fields for DNA. PMID:23976886

Impact of an autologous oxygenating matrix culture system on rat islet transplantation outcome.

PubMed

Schaschkow, A; Mura, C; Bietiger, W; Peronet, C; Langlois, A; Bodin, F; Dissaux, C; Bruant-Rodier, C; Pinget, M; Jeandidier, N; Juszczak, M T; Sigrist, S; Maillard, E

2015-06-01

Disruption of the pancreatic islet environment combined with the decrease in oxygen supply that occurs during isolation leads to poor islet survival. The aim of this study was to validate the benefit of using a plasma-based scaffold supplemented with perfluorodecalin to improve islet transplantation outcome. Rat islets were cultured in three conditions: i) control group, ii) plasma based-matrix (P-matrix), and iii) P-matrix supplemented with emulsified perfluorodecalin. After 24 h culture, matrix/cell contacts (Integrinβ1, p-FAK/FAK, p-Akt/Akt), survival (caspase 3, TUNEL, FDA/PI), function, and HIF-1α translocation were assessed. Afterwards, P-matrices were dissolved and the islets were intraportally transplanted. Graft function was monitored for 31 days with glycaemia and C-peptide follow up. Inflammation was assessed by histology (macrophage and granulocyte staining) and thrombin/anti-thrombin complex measurement. Islet survival correlated with an increase in integrin, FAK, and Akt activation in P-matrices and function was maintained. Perfluorodecalin supplementation decreased translocation of HIF-1α in the nucleus and post-transplantation islet structure was better preserved in P-matrices, but a quicker activation of IBMIR resulted in early loss of graft function. "Oxygenating" P-matrices provided a real benefit to islet survival and resistance in vivo. However, intraportal transplantation is not suitable for this kind of culture due to IBMIR; thus, alternative sites must be explored. Copyright © 2015 Elsevier Ltd. All rights reserved.

Zirconium phosphatidylcholine-based nanocapsules as an in vivo degradable drug delivery system of MAP30, a momordica anti-HIV protein.

PubMed

Caizhen, Guo; Yan, Gao; Ronron, Chang; Lirong, Yang; Panpan, Chu; Xuemei, Hu; Yuanbiao, Qiao; Qingshan, Li

2015-04-10

An essential in vivo drug delivery system of a momordica anti-HIV protein, MAP30, was developed through encapsulating in chemically synthesized matrices of zirconium egg- and soy-phosphatidylcholines, abbreviated to Zr/EPC and Zr/SPC, respectively. Matrices were characterized by transmission electron microscopy and powder X-ray diffractometry studies. Zr/EPC granule at an approximate diameter of 69.43±7.78 nm was a less efficient encapsulator than the granule of Zr/SPC. Interlayer spacing of the matrices encapsulating MAP30 increased from 8.8 and 9.7 Å to 7.4 and 7.9 nm, respectively. In vivo kinetics on degradation and protein release was performed by analyzing the serum sampling of intravenously injected SPF chickens. The first order and biphasic variations were obtained for in vivo kinetics using equilibrium dialysis. Antimicrobial and anti-HIV assays yielded greatly decreased MIC50 and EC50 values of nanoformulated MAP30. An acute toxicity of MAP30 encapsulated in Zr/EPC occurred at a single intravenous dose above 14.24 mg/kg bw in NIH/KM/ICR mice. The folding of MAP30 from Zr/EPC sustained in vivo chickens for more than 8 days in high performance liquid chromatography assays. These matrices could protect MAP30 efficiently with strong structure retention, lowered toxicity and prolonged in vivo life. Copyright © 2015 Elsevier B.V. All rights reserved.

Building Enterprise Transition Plans Through the Development of Collapsing Design Structure Matrices

DTIC Science & Technology

2015-09-17

processes from the earliest input to the final output to evaluate where change is needed to reduce costs, reduce waste, and improve the flow of information...from) integrating a large complex enterprise? • How should firms/enterprises evaluate systems prior to integration? What are some valid taxonomies

Parameter Accuracy in Meta-Analyses of Factor Structures

ERIC Educational Resources Information Center

Gnambs, Timo; Staufenbiel, Thomas

2016-01-01

Two new methods for the meta-analysis of factor loadings are introduced and evaluated by Monte Carlo simulations. The direct method pools each factor loading individually, whereas the indirect method synthesizes correlation matrices reproduced from factor loadings. The results of the two simulations demonstrated that the accuracy of…

Discovering Authorities and Hubs in Different Topological Web Graph Structures.

ERIC Educational Resources Information Center

Meghabghab, George

2002-01-01

Discussion of citation analysis on the Web considers Web hyperlinks as a source to analyze citations. Topics include basic graph theory applied to Web pages, including matrices, linear algebra, and Web topology; and hubs and authorities, including a search technique called HITS (Hyperlink Induced Topic Search). (Author/LRW)

New England wildlife: management forested habitats

Treesearch

Richard M. DeGraaf; Mariko Yamasaki; William B. Leak; John W. Lanier

1992-01-01

Presents silvicultural treatments for six major cover-type groups in New England to produce stand conditions that provide habitat opportunities for a wide range of wildlife species. Includes matrices for species occurrence and utilization by forested and nonforested habitats, habitat breadth and size class, and structural habitat features for the 338 wildlife species...

On Dynamics of Spinning Structures

NASA Technical Reports Server (NTRS)

Gupta, K. K.; Ibrahim, A.

2012-01-01

This paper provides details of developments pertaining to vibration analysis of gyroscopic systems, that involves a finite element structural discretization followed by the solution of the resulting matrix eigenvalue problem by a progressive, accelerated simultaneous iteration technique. Thus Coriolis, centrifugal and geometrical stiffness matrices are derived for shell and line elements, followed by the eigensolution details as well as solution of representative problems that demonstrates the efficacy of the currently developed numerical procedures and tools.

DCTune Perceptual Optimization of Compressed Dental X-Rays

NASA Technical Reports Server (NTRS)

Watson, Andrew B.; Null, Cynthia H. (Technical Monitor)

1996-01-01

In current dental practice, x-rays of completed dental work are often sent to the insurer for verification. It is faster and cheaper to transmit instead digital scans of the x-rays. Further economies result if the images are sent in compressed form. DCTune is a technology for optimizing DCT (digital communication technology) quantization matrices to yield maximum perceptual quality for a given bit-rate, or minimum bit-rate for a given perceptual quality. Perceptual optimization of DCT color quantization matrices. In addition, the technology provides a means of setting the perceptual quality of compressed imagery in a systematic way. The purpose of this research was, with respect to dental x-rays, 1) to verify the advantage of DCTune over standard JPEG (Joint Photographic Experts Group), 2) to verify the quality control feature of DCTune, and 3) to discover regularities in the optimized matrices of a set of images. We optimized matrices for a total of 20 images at two resolutions (150 and 300 dpi) and four bit-rates (0.25, 0.5, 0.75, 1.0 bits/pixel), and examined structural regularities in the resulting matrices. We also conducted psychophysical studies (1) to discover the DCTune quality level at which the images became 'visually lossless,' and (2) to rate the relative quality of DCTune and standard JPEG images at various bitrates. Results include: (1) At both resolutions, DCTune quality is a linear function of bit-rate. (2) DCTune quantization matrices for all images at all bitrates and resolutions are modeled well by an inverse Gaussian, with parameters of amplitude and width. (3) As bit-rate is varied, optimal values of both amplitude and width covary in an approximately linear fashion. (4) Both amplitude and width vary in systematic and orderly fashion with either bit-rate or DCTune quality; simple mathematical functions serve to describe these relationships. (5) In going from 150 to 300 dpi, amplitude parameters are substantially lower and widths larger at corresponding bit-rates or qualities. (6) Visually lossless compression occurs at a DCTune quality value of about 1. (7) At 0.25 bits/pixel, comparative ratings give DCTune a substantial advantage over standard JPEG. As visually lossless bit-rates are approached, this advantage of necessity diminishes. We have concluded that DCTune optimized quantization matrices provide better visual quality than standard JPEG. Meaningful quality levels may be specified by means of the DCTune metric. Optimized matrices are very similar across the class of dental x-rays, suggesting the possibility of a 'class-optimal' matrix. DCTune technology appears to provide some value in the context of compressed dental x-rays.

Predicting the ethanol potential of wheat straw using near-infrared spectroscopy and chemometrics: The challenge of inherently intercorrelated response functions

DOE PAGES

Rinnan, Asmund; Bruun, Sander; Lindedam, Jane; ...

2017-02-07

Here, the combination of NIR spectroscopy and chemometrics is a powerful correlation method for predicting the chemical constituents in biological matrices, such as the glucose and xylose content of straw. However, difficulties arise when it comes to predicting enzymatic glucose and xylose release potential, which is matrix dependent. Further complications are caused by xylose and glucose release potential being highly intercorrelated. This study emphasizes the importance of understanding the causal relationship between the model and the constituent of interest. It investigates the possibility of using near-infrared spectroscopy to evaluate the ethanol potential of wheat straw by analyzing more than 1000more » samples from different wheat varieties and growth conditions. During the calibration model development, the prime emphasis was to investigate the correlation structure between the two major quality traits for saccharification of wheat straw: glucose and xylose release. The large sample set enabled a versatile and robust calibration model to be developed, showing that the prediction model for xylose release is based on a causal relationship with the NIR spectral data. In contrast, the prediction of glucose release was found to be highly dependent on the intercorrelation with xylose release. If this correlation is broken, the model performance breaks down. A simple method was devised for avoiding this breakdown and can be applied to any large dataset for investigating the causality or lack of causality of a prediction model.« less

Predicting the ethanol potential of wheat straw using near-infrared spectroscopy and chemometrics: The challenge of inherently intercorrelated response functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rinnan, Asmund; Bruun, Sander; Lindedam, Jane

Here, the combination of NIR spectroscopy and chemometrics is a powerful correlation method for predicting the chemical constituents in biological matrices, such as the glucose and xylose content of straw. However, difficulties arise when it comes to predicting enzymatic glucose and xylose release potential, which is matrix dependent. Further complications are caused by xylose and glucose release potential being highly intercorrelated. This study emphasizes the importance of understanding the causal relationship between the model and the constituent of interest. It investigates the possibility of using near-infrared spectroscopy to evaluate the ethanol potential of wheat straw by analyzing more than 1000more » samples from different wheat varieties and growth conditions. During the calibration model development, the prime emphasis was to investigate the correlation structure between the two major quality traits for saccharification of wheat straw: glucose and xylose release. The large sample set enabled a versatile and robust calibration model to be developed, showing that the prediction model for xylose release is based on a causal relationship with the NIR spectral data. In contrast, the prediction of glucose release was found to be highly dependent on the intercorrelation with xylose release. If this correlation is broken, the model performance breaks down. A simple method was devised for avoiding this breakdown and can be applied to any large dataset for investigating the causality or lack of causality of a prediction model.« less

Algebraic multigrid methods applied to problems in computational structural mechanics

NASA Technical Reports Server (NTRS)

Mccormick, Steve; Ruge, John

1989-01-01

The development of algebraic multigrid (AMG) methods and their application to certain problems in structural mechanics are described with emphasis on two- and three-dimensional linear elasticity equations and the 'jacket problems' (three-dimensional beam structures). Various possible extensions of AMG are also described. The basic idea of AMG is to develop the discretization sequence based on the target matrix and not the differential equation. Therefore, the matrix is analyzed for certain dependencies that permit the proper construction of coarser matrices and attendant transfer operators. In this manner, AMG appears to be adaptable to structural analysis applications.

Matrix Perturbation Techniques in Structural Dynamics

NASA Technical Reports Server (NTRS)

Caughey, T. K.

1973-01-01

Matrix perturbation are developed techniques which can be used in the dynamical analysis of structures where the range of numerical values in the matrices extreme or where the nature of the damping matrix requires that complex valued eigenvalues and eigenvectors be used. The techniques can be advantageously used in a variety of fields such as earthquake engineering, ocean engineering, aerospace engineering and other fields concerned with the dynamical analysis of large complex structures or systems of second order differential equations. A number of simple examples are included to illustrate the techniques.

Computationally Efficient Modeling and Simulation of Large Scale Systems

NASA Technical Reports Server (NTRS)

Jain, Jitesh (Inventor); Koh, Cheng-Kok (Inventor); Balakrishnan, Vankataramanan (Inventor); Cauley, Stephen F (Inventor); Li, Hong (Inventor)

2014-01-01

A system for simulating operation of a VLSI interconnect structure having capacitive and inductive coupling between nodes thereof, including a processor, and a memory, the processor configured to perform obtaining a matrix X and a matrix Y containing different combinations of passive circuit element values for the interconnect structure, the element values for each matrix including inductance L and inverse capacitance P, obtaining an adjacency matrix A associated with the interconnect structure, storing the matrices X, Y, and A in the memory, and performing numerical integration to solve first and second equations.

Triangles with Integer Dimensions

ERIC Educational Resources Information Center

Gilbertson, Nicholas J.; Rogers, Kimberly Cervello

2016-01-01

Interesting and engaging mathematics problems can come from anywhere. Sometimes great problems arise from interesting contexts. At other times, interesting problems arise from asking "what if" questions while appreciating the structure and beauty of mathematics. The intriguing problem described in this article resulted from the second…

Simultaneous structural and control optimization via linear quadratic regulator eigenstructure assignment

NASA Technical Reports Server (NTRS)

Becus, G. A.; Lui, C. Y.; Venkayya, V. B.; Tischler, V. A.

1987-01-01

A method for simultaneous structural and control design of large flexible space structures (LFSS) to reduce vibration generated by disturbances is presented. Desired natural frequencies and damping ratios for the closed loop system are achieved by using a combination of linear quadratic regulator (LQR) synthesis and numerical optimization techniques. The state and control weighing matrices (Q and R) are expressed in terms of structural parameters such as mass and stiffness. The design parameters are selected by numerical optimization so as to minimize the weight of the structure and to achieve the desired closed-loop eigenvalues. An illustrative example of the design of a two bar truss is presented.

Effect of diisocyanate linkers on the degradation characteristics of copolyester urethanes as potential drug carrier matrices.

PubMed

Mathew, Simi; Baudis, Stefan; Neffe, Axel T; Behl, Marc; Wischke, Christian; Lendlein, Andreas

2015-09-01

In this study, the effect of three aliphatic diisocyanate linkers, L-lysine diisocyanate ethyl ester (LDI), hexamethylene diisocyanate (HDI), and racemic 2,2,4-/2,4,4-trimethyl hexamethylene diisocyanate (TMDI), on the degradation of oligo[(rac-lactide)-co-glycolide] (64:36 mol%) based polyester urethanes (PEU) was examined. Samples were characterized for their molecular weight, mass loss, water uptake, sequence structure, and thermal and mechanical properties. Compared to non-segmented PLGA, the PEU showed higher water uptake and generally degraded faster. Interestingly, the rate of degradation was not directly correlating with the hydrophilicity of the diisocyanate moieties; instead, competing intra-/intermolecular hydrogen bonds in between urethane moieties appear to substantially decrease the rate of degradation for LDI-derived PEU. By comparing microparticles (μm) and films (mm) as matrices of different dimensions, it was shown that autocatalysis remains a contributor to degradation of the larger-sized PEU matrices as it is typical for non-segmented lactide/glycolide copolymers. The shown capacity of lactide/glycolide-based multiblock copolymers to degrade faster than PLGA and exhibit improved elastic properties could be of interest for medical implants and drug release systems. Copyright © 2015 Elsevier B.V. All rights reserved.

Application of Semi-Definite Programming for Many-Fermion Systems

NASA Astrophysics Data System (ADS)

Zhao, Zhengji; Braams, Bastiaan; Fukuda, Mituhiro; Overton, Michael

2003-03-01

The ground state energy and other important observables of a many-fermion system with one- and two-body interactions only can all be obtained from the first order and second order Reduced Density Matrices (RDM's) of the system. Using these density matrices and a family of associated representability conditions one may obtain an approximation method for electronic structure theory that is in the mathematical form of Semi-Definite Programming (SDP): minimize a linear matrix functional over a space of positive semidefinite matrices subject to linear constraints. The representability conditions are some known necessary conditions, starting with the well-known P, Q, and G conditions [Claude Garrod and Jerome K. Percus, Reducation of the N-Particle Variational Problem, J. Math. Phys. 5 (1964) 1756-1776]. The RDM method with SDP has great potential advantages over the wave function method when the particle number N is large. The dimension of the full configuration space increases exponentially with N, but in RDM method with SDP the dimension of the objective matrix (which includes RDM's) increases only polynomially with N. We will report on the effect of adding the generalized three-index conditions proposed in [R. M. Erdahl, Representability, Int. J. Quantum Chem. 13 (1978) 697-718].

Mechanical critical phenomena and the elastic response of fiber networks

NASA Astrophysics Data System (ADS)

Mackintosh, Fred

The mechanics of cells and tissues are largely governed by scaffolds of filamentous proteins that make up the cytoskeleton, as well as extracellular matrices. Evidence is emerging that such networks can exhibit rich mechanical phase behavior. A classic example of a mechanical phase transition was identified by Maxwell for macroscopic engineering structures: networks of struts or springs exhibit a continuous, second-order phase transition at the isostatic point, where the number of constraints imposed by connectivity just equals the number of mechanical degrees of freedom. We present recent theoretical predictions and experimental evidence for mechanical phase transitions in in both synthetic and biopolymer networks. We show, in particular, excellent quantitative agreement between the mechanics of collagen matrices and the predictions of a strain-controlled phase transition in sub-isostatic networks.

Photoluminescence properties of arsenic and boron doped Si3N4 nanocrystal embedded in SiN x O y matrix

NASA Astrophysics Data System (ADS)

Puglia, Denise; Sombrio, Guilherme; dos Reis, Roberto; Boudinov, Henri

2018-03-01

Photoluminescence emission of Si3N4 nanocrystals embedded in SiN x O y matrices was investigated. Nanocrystals were grown by annealing of silicon oxynitride films deposited by sputtering, passivated in forming gas atmosphere and implanted with boron and arsenic. Emission energy was tuned from green to ultraviolet by changing the composition of SiN x O y matrices. Structural characterization of the nanocrystals was performed by Transmission Electron Microscopy. Photoluminescence at room and low temperatures was analyzed and the results suggest that light emission originates in the interface between the nanocrystals and the matrix. The highest photoluminescence intensity at room temperature was achieved by arsenic doped silicon oxynitride films deposited with an excess of nitrogen.

Symmetries at ultrahigh energies and searches for neutrino oscillations

NASA Astrophysics Data System (ADS)

Papageorgiu, E.

1995-02-01

Motivated by the possibility that new (gauge) symmetries which are broken at the grand- (string-) unification scale give rise to texture zeros in the fermion mass matrices which are at the origin of the hierarchy of masses and mixings we explore the effect of such zeros on the neutrino spectrum of SUSY-GUT models. We find that the quadratic-seesaw spectrum on which most expectations are focused is neither the only nor the most interesting possibility. Cases of strong νμ- ντ or νe- ντ mixing are present for a specific texture structure of the Yukawa matrices and experimental evidence can thus throw some light on the latter. In contrast if the quadratic-seesaw scenario should be confirmed very little could be said about the symmetries of the Yukawa sector.

A performance study of sparse Cholesky factorization on INTEL iPSC/860

NASA Technical Reports Server (NTRS)

Zubair, M.; Ghose, M.

1992-01-01

The problem of Cholesky factorization of a sparse matrix has been very well investigated on sequential machines. A number of efficient codes exist for factorizing large unstructured sparse matrices. However, there is a lack of such efficient codes on parallel machines in general, and distributed machines in particular. Some of the issues that are critical to the implementation of sparse Cholesky factorization on a distributed memory parallel machine are ordering, partitioning and mapping, load balancing, and ordering of various tasks within a processor. Here, we focus on the effect of various partitioning schemes on the performance of sparse Cholesky factorization on the Intel iPSC/860. Also, a new partitioning heuristic for structured as well as unstructured sparse matrices is proposed, and its performance is compared with other schemes.