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.

Numerical solution of quadratic matrix equations for free vibration analysis of structures

NASA Technical Reports Server (NTRS)

Gupta, K. K.

1975-01-01

This paper is concerned with the efficient and accurate solution of the eigenvalue problem represented by quadratic matrix equations. Such matrix forms are obtained in connection with the free vibration analysis of structures, discretized by finite 'dynamic' elements, resulting in frequency-dependent stiffness and inertia matrices. The paper presents a new numerical solution procedure of the quadratic matrix equations, based on a combined Sturm sequence and inverse iteration technique enabling economical and accurate determination of a few required eigenvalues and associated vectors. An alternative procedure based on a simultaneous iteration procedure is also described when only the first few modes are the usual requirement. The employment of finite dynamic elements in conjunction with the presently developed eigenvalue routines results in a most significant economy in the dynamic analysis of structures.

Interacting quasi-band model for electronic states in compound semiconductor alloys: Zincblende structure

NASA Astrophysics Data System (ADS)

Shinozuka, Yuzo; Oda, Masato

2015-09-01

The interacting quasi-band model proposed for electronic states in simple alloys is extended for compound semiconductor alloys with general lattice structures containing several atoms per unit cell. Using a tight-binding model, a variational electronic wave function for quasi-Bloch states yields a non-Hermitian Hamiltonian matrix characterized by matrix elements of constituent crystals and concentration of constituents. Solving secular equations for each k-state yields the alloy’s energy spectrum for any type of randomness and arbitrary concentration. The theory is used to address III-V (II-VI) alloys with a zincblende lattice with crystal band structures well represented by the sp3s* model. Using the resulting 15 × 15 matrix, the concentration dependence of valence and conduction bands is calculated in a unified scheme for typical alloys: Al1-xGaxAs, GaAs1-xPx, and GaSb1-xPx. Results agree well with experiments and are discussed with respect to the concentration dependence, direct-indirect gap transition, and band-gap-bowing origin.

Fundamental Studies of Low Velocity Impact Resistance of Graphite Fiber Reinforced Polymer Matrix Composites. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Bowles, K. J.

1985-01-01

A study was conducted to relate the impact resistance of graphite fiber reinforced composites with matrix properties through gaining an understanding of the basic mechanics involved in the deformation and fracture process, and the effect of the polymer matrix structure on these mechanisms. It was found that the resin matrix structure influences the composite impact resistance in at least two ways. The integration of flexibilizers into the polymer chain structure tends to reduce the T sub g and the mechanical properties of the polymer. The reduction in the mechanical properties of the matrix does not enhance the composite impact resistance because it allows matrix controlled failure to initiate impact damage. It was found that when the instrumented dropweight impact tester is used as a means for assessing resin toughness, the resin toughness is enhanced by the ability of the clamped specimen to deflect enough to produce sufficient membrane action to support a significant amount of the load. The results of this study indicate that crossplied composite impact resistance is very much dependent on the matrix mechanical properties.

Effects of Adiabatic Heating on the High Strain Rate Deformation of Polymer Matrix Composites

NASA Technical Reports Server (NTRS)

Sorini, Chris; Chattopadhyay, Aditi; Goldberg, Robert K.

2017-01-01

Polymer matrix composites (PMCs) are increasingly being used in aerospace structures that are expected to experience complex dynamic loading conditions throughout their lifetime. As such, a detailed understanding of the high strain rate behavior of the constituents, particularly the strain rate, temperature, and pressure dependent polymer matrix, is paramount. In this paper, preliminary efforts in modeling experimentally observed temperature rises due to plastic deformation in PMCs subjected to dynamic loading are presented. To this end, an existing isothermal viscoplastic polymer constitutive formulation is extended to model adiabatic conditions by incorporating temperature dependent elastic properties and modifying the components of the inelastic strain rate tensor to explicitly depend on temperature. It is demonstrated that the modified polymer constitutive model is capable of capturing strain rate and temperature dependent yield as well as thermal softening associated with the conversion of plastic work to heat at high rates of strain. The modified constitutive model is then embedded within a strength of materials based micromechanics framework to investigate the manifestation of matrix thermal softening, due to the conversion of plastic work to heat, on the high strain rate response of a T700Epon 862 (T700E862) unidirectional composite. Adiabatic model predictions for high strain rate composite longitudinal tensile, transverse tensile, and in-plane shear loading are presented. Results show a substantial deviation from isothermal conditions; significant thermal softening is observed for matrix dominated deformation modes (transverse tension and in-plane shear), highlighting the importance of accounting for the conversion of plastic work to heat in the polymer matrix in the high strain rate analysis of PMC structures.

Characterizing the Joint Effect of Diverse Test-Statistic Correlation Structures and Effect Size on False Discovery Rates in a Multiple-Comparison Study of Many Outcome Measures

NASA Technical Reports Server (NTRS)

Feiveson, Alan H.; Ploutz-Snyder, Robert; Fiedler, James

2011-01-01

In their 2009 Annals of Statistics paper, Gavrilov, Benjamini, and Sarkar report the results of a simulation assessing the robustness of their adaptive step-down procedure (GBS) for controlling the false discovery rate (FDR) when normally distributed test statistics are serially correlated. In this study we extend the investigation to the case of multiple comparisons involving correlated non-central t-statistics, in particular when several treatments or time periods are being compared to a control in a repeated-measures design with many dependent outcome measures. In addition, we consider several dependence structures other than serial correlation and illustrate how the FDR depends on the interaction between effect size and the type of correlation structure as indexed by Foerstner s distance metric from an identity. The relationship between the correlation matrix R of the original dependent variables and R, the correlation matrix of associated t-statistics is also studied. In general R depends not only on R, but also on sample size and the signed effect sizes for the multiple comparisons.

Luminescence properties of femtosecond-laser-activated silver oxide nanoparticles embedded in a biopolymer matrix

NASA Astrophysics Data System (ADS)

Gleitsmann, T.; Bernhardt, T. M.; Wöste, L.

2006-01-01

Strong visible luminescence is observed from silver clusters generated by femtosecond-laser-induced reduction of silver oxide nanoparticles embedded in a polymeric gelatin matrix. Light emission from the femtosecond-laser-activated matrix areas considerably exceeds the luminescence intensity of similarly activated bare silver oxide nanoparticle films. Optical spectroscopy of the activated polymer films supports the assignment of the emissive properties to the formation of small silver clusters under focused femtosecond-laser irradiation. The size of the photogenerated clusters is found to sensitively depend on the laser exposure time, eventually leading to the formation of areas of metallic silver in the biopolymer matrix. In this case, luminescence can still be observed in the periphery of the metallic silver structures, emphasizing the importance of the organic matrix for the stabilization of the luminescent nanocluster structures at the metal matrix interface.

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.

Intrinsically disordered proteins drive enamel formation via an evolutionarily conserved self-assembly motif.

PubMed

Wald, Tomas; Spoutil, Frantisek; Osickova, Adriana; Prochazkova, Michaela; Benada, Oldrich; Kasparek, Petr; Bumba, Ladislav; Klein, Ophir D; Sedlacek, Radislav; Sebo, Peter; Prochazka, Jan; Osicka, Radim

2017-02-28

The formation of mineralized tissues is governed by extracellular matrix proteins that assemble into a 3D organic matrix directing the deposition of hydroxyapatite. Although the formation of bones and dentin depends on the self-assembly of type I collagen via the Gly-X-Y motif, the molecular mechanism by which enamel matrix proteins (EMPs) assemble into the organic matrix remains poorly understood. Here we identified a Y/F-x-x-Y/L/F-x-Y/F motif, evolutionarily conserved from the first tetrapods to man, that is crucial for higher order structure self-assembly of the key intrinsically disordered EMPs, ameloblastin and amelogenin. Using targeted mutations in mice and high-resolution imaging, we show that impairment of ameloblastin self-assembly causes disorganization of the enamel organic matrix and yields enamel with disordered hydroxyapatite crystallites. These findings define a paradigm for the molecular mechanism by which the EMPs self-assemble into supramolecular structures and demonstrate that this process is crucial for organization of the organic matrix and formation of properly structured enamel.

On the damping capacity of cast irons

NASA Astrophysics Data System (ADS)

Golovin, S. A.

2012-07-01

The treatment of experimental data on the amplitude-dependent internal friction (ADIF) in terms of various theoretical models has revealed a staged character and the main mechanisms of the processes of energy dissipation in graphite with increasing amplitude of vibrations upon cyclic loading. It is shown that the level of the damping capacity of lamellar cast iron depends on the relationship between the elastic and strength characteristics of graphite and the matrix phase. In cast irons with a rigid matrix structure (pearlite, martensite), the energy dissipation is determined by the volume fraction and morphology of the initial graphite phase. In cast irons with a softer metallic phase (ferrite), the contact interaction of graphite inclusions with the matrix and the properties of the matrix introduce additional sources of high damping.

Development of a Genetic Algorithm to Automate Clustering of a Dependency Structure Matrix

NASA Technical Reports Server (NTRS)

Rogers, James L.; Korte, John J.; Bilardo, Vincent J.

2006-01-01

Much technology assessment and organization design data exists in Microsoft Excel spreadsheets. Tools are needed to put this data into a form that can be used by design managers to make design decisions. One need is to cluster data that is highly coupled. Tools such as the Dependency Structure Matrix (DSM) and a Genetic Algorithm (GA) can be of great benefit. However, no tool currently combines the DSM and a GA to solve the clustering problem. This paper describes a new software tool that interfaces a GA written as an Excel macro with a DSM in spreadsheet format. The results of several test cases are included to demonstrate how well this new tool works.

Sparse matrix-vector multiplication on network-on-chip

NASA Astrophysics Data System (ADS)

Sun, C.-C.; Götze, J.; Jheng, H.-Y.; Ruan, S.-J.

2010-12-01

In this paper, we present an idea for performing matrix-vector multiplication by using Network-on-Chip (NoC) architecture. In traditional IC design on-chip communications have been designed with dedicated point-to-point interconnections. Therefore, regular local data transfer is the major concept of many parallel implementations. However, when dealing with the parallel implementation of sparse matrix-vector multiplication (SMVM), which is the main step of all iterative algorithms for solving systems of linear equation, the required data transfers depend on the sparsity structure of the matrix and can be extremely irregular. Using the NoC architecture makes it possible to deal with arbitrary structure of the data transfers; i.e. with the irregular structure of the sparse matrices. So far, we have already implemented the proposed SMVM-NoC architecture with the size 4×4 and 5×5 in IEEE 754 single float point precision using FPGA.

Imaging Carbon Nanotubes in High Performance Polymer Composites via Magnetic Force Microscope

NASA Technical Reports Server (NTRS)

Lillehei, Peter T.; Park, Cheol; Rouse, Jason H.; Siochi, Emilie J.; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

Application of carbon nanotubes as reinforcement in structural composites is dependent on the efficient dispersion of the nanotubes in a high performance polymer matrix. The characterization of such dispersion is limited by the lack of available tools to visualize the quality of the matrix/carbon nanotube interaction. The work reported herein demonstrates the use of magnetic force microscopy (MFM) as a promising technique for characterizing the dispersion of nanotubes in a high performance polymer matrix.

The structure of myristoylated Mason-Pfizer monkey virus matrix protein and the role of phosphatidylinositol-(4,5)-bisphosphate in its membrane binding.

PubMed

Prchal, Jan; Srb, Pavel; Hunter, Eric; Ruml, Tomáš; Hrabal, Richard

2012-10-26

We determined the solution structure of myristoylated Mason-Pfizer monkey virus matrix protein by NMR spectroscopy. The myristoyl group is buried inside the protein and causes a slight reorientation of the helices. This reorientation leads to the creation of a binding site for phosphatidylinositols. The interaction between the matrix protein and phosphatidylinositols carrying C(8) fatty acid chains was monitored by observation of concentration-dependent chemical shift changes of the affected amino acid residues, a saturation transfer difference experiment and changes in (31)P chemical shifts. No differences in the binding mode or affinity were observed with differently phosphorylated phosphatidylinositols. The structure of the matrix protein-phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P(2)] complex was then calculated with HADDOCK software based on the intermolecular nuclear Overhauser enhancement contacts between the ligand and the matrix protein obtained from a (13)C-filtered/(13)C-edited nuclear Overhauser enhancement spectroscopy experiment. PI(4,5)P(2) binding was not strong enough for triggering of the myristoyl-switch. The structural changes of the myristoylated matrix protein were also found to result in a drop in the oligomerization capacity of the protein. Copyright © 2012. Published by Elsevier Ltd.

Analytic tools for investigating the structure of network reliability measures with regard to observation correlations

NASA Astrophysics Data System (ADS)

Prószyński, W.; Kwaśniak, M.

2018-03-01

A global measure of observation correlations in a network is proposed, together with the auxiliary indices related to non-diagonal elements of the correlation matrix. Based on the above global measure, a specific representation of the correlation matrix is presented, being the result of rigorously proven theorem formulated within the present research. According to the theorem, each positive definite correlation matrix can be expressed by a scale factor and a so-called internal weight matrix. Such a representation made it possible to investigate the structure of the basic reliability measures with regard to observation correlations. Numerical examples carried out for two test networks illustrate the structure of those measures that proved to be dependent on global correlation index. Also, the levels of global correlation are proposed. It is shown that one can readily find an approximate value of the global correlation index, and hence the correlation level, for the expected values of auxiliary indices being the only knowledge about a correlation matrix of interest. The paper is an extended continuation of the previous study of authors that was confined to the elementary case termed uniform correlation. The extension covers arbitrary correlation matrices and a structure of correlation effect.

Modeling the Role of Bulk and Surface Characteristics of Carbon Fiber on Thermal Conductance across the Carbon Fiber/Matrix Interface (Postprint)

DTIC Science & Technology

2015-11-09

Osguthorpe, D. J.; Wolff, J.; Genest, M.; Hagler, A. T. Structure and Energetics of Ligand Binding to Proteins: Escherichia Coli Dihydrofolate...available at DOI: 10.1021/acsami.5b08591 14. ABSTRACT (Maximum 200 words) The rapid heating of carbon-fiber-reinforced polymer matrix composites leads ...polymer matrix composites leads to complex thermophysical interactions which not only are dependent on the thermal properties of the constituents and

Structure and function of yeast glutaredoxin 2 depend on postranslational processing and are related to subcellular distribution.

PubMed

Porras, Pablo; McDonagh, Brian; Pedrajas, Jose Rafael; Bárcena, J Antonio; Padilla, C Alicia

2010-04-01

We have previously shown that glutaredoxin 2 (Grx2) from Saccharomyces cerevisiae localizes at 3 different subcellular compartments, cytosol, mitochondrial matrix and outer membrane, as the result of different postranslational processing of one single gene. Having set the mechanism responsible for this remarkable phenomenon, we have now aimed at defining whether this diversity of subcellular localizations correlates with differences in structure and function of the Grx2 isoforms. We have determined the N-terminal sequence of the soluble mitochondrial matrix Grx2 by mass spectrometry and have determined the exact cleavage site by Mitochondrial Processing Peptidase (MPP). As a consequence of this cleavage, the mitochondrial matrix Grx2 isoform possesses a basic tetrapeptide extension at the N-terminus compared to the cytosolic form. A functional relationship to this structural difference is that mitochondrial Grx2 displays a markedly higher activity in the catalysis of GSSG reduction by the mitochondrial dithiol dihydrolipoamide. We have prepared Grx2 mutants affected on key residues inside the presequence to direct the protein to one single cellular compartment; either the cytosol, the mitochondrial membrane or the matrix and have analyzed their functional phenotypes. Strains expressing Grx2 only in the cytosol are equally sensitive to H(2)O(2) as strains lacking the gene, whereas those expressing Grx2 exclusively in the mitochondrial matrix are more resistant. Mutations on key basic residues drastically affect the cellular fate of the protein, showing that evolutionary diversification of Grx2 structural and functional properties are strictly dependent on the sequence of the targeting signal peptide. Copyright 2009 Elsevier B.V. All rights reserved.

Toxoplasma gondii infection shifts dendritic cells into an amoeboid rapid migration mode encompassing podosome dissolution, secretion of TIMP-1, and reduced proteolysis of extracellular matrix.

PubMed

Ólafsson, Einar B; Varas-Godoy, Manuel; Barragan, Antonio

2018-03-01

Dendritic cells (DCs) infected by Toxoplasma gondii rapidly acquire a hypermigratory phenotype that promotes systemic parasite dissemination by a "Trojan horse" mechanism in mice. Recent paradigms of leukocyte migration have identified the amoeboid migration mode of DCs as particularly suited for rapid locomotion in extracellular matrix and tissues. Here, we have developed a microscopy-based high-throughput approach to assess motility and matrix degradation by Toxoplasma-challenged murine and human DCs. DCs challenged with T. gondii exhibited dependency on metalloproteinase activity for hypermotility and transmigration but, strikingly, also dramatically reduced pericellular proteolysis. Toxoplasma-challenged DCs up-regulated expression and secretion of tissue inhibitor of metalloproteinases-1 (TIMP-1) and their supernatants impaired matrix degradation by naïve DCs and by-stander DCs dose dependently. Gene silencing of TIMP-1 by short hairpin RNA restored matrix degradation activity in Toxoplasma-infected DCs. Additionally, dissolution of podosome structures in parasitised DCs coincided with abrogated matrix degradation. Toxoplasma lysates inhibited pericellular proteolysis in a MyD88-dependent fashion whereas abrogated proteolysis persevered in Toxoplasma-infected MyD88-deficient DCs. This indicated that both TLR/MyD88-dependent and TLR/MyD88-independent signalling pathways mediated podosome dissolution and the abrogated matrix degradation. We report that increased TIMP-1 secretion and cytoskeletal rearrangements encompassing podosome dissolution are features of Toxoplasma-induced hypermigration of DCs with an impact on matrix degradation. Jointly, the data highlight how an obligate intracellular parasite orchestrates key regulatory cellular processes consistent with non-proteolytic amoeboid migration of the vehicle cells that facilitate its dissemination. © 2017 John Wiley & Sons Ltd.

Dynamic Jahn-Teller effect: Calculation of fine structure spectrum, isotope shift and Zeeman behavior at deep center Ni2+ in CdS

NASA Astrophysics Data System (ADS)

Schoepp, Juergen

The internal transition of the deep center Ni2+ in II to IV semiconductor cadmium sulfide is examined with reference to crystal field theory. An algorithm was developed for calculation, in a basis fitted to trigonal symmetry, of fine structure operator matrix which is made of the sum of operators from spin trajectory coupling, trigonal field and electron phonon coupling. The dependence of energy level on the mass was calculated in order to examine the isotropy effect at Ni2+ transition. The mass dependence of phonon energy was estimated in an atomic cluster by using a valence force model from Keating for elastic energy. The Zeeman behavior of Ni2+ transition was examined for magnetic fields; the Zeeman operator was added to the fine structure operator and the resulting matrix was diagonalized. It is noticed that calculations are quantitatively and qualitatively in agreement with experiments.

Individual movement behavior, matrix heterogeneity, and the dynamics of spatially structured populations.

PubMed

Revilla, Eloy; Wiegand, Thorsten

2008-12-09

The dynamics of spatially structured populations is characterized by within- and between-patch processes. The available theory describes the latter with simple distance-dependent functions that depend on landscape properties such as interpatch distance or patch size. Despite its potential role, we lack a good mechanistic understanding of how the movement of individuals between patches affects the dynamics of these populations. We used the theoretical framework provided by movement ecology to make a direct representation of the processes determining how individuals connect local populations in a spatially structured population of Iberian lynx. Interpatch processes depended on the heterogeneity of the matrix where patches are embedded and the parameters defining individual movement behavior. They were also very sensitive to the dynamic demographic variables limiting the time moving, the within-patch dynamics of available settlement sites (both spatiotemporally heterogeneous) and the response of individuals to the perceived risk while moving. These context-dependent dynamic factors are an inherent part of the movement process, producing connectivities and dispersal kernels whose variability is affected by other demographic processes. Mechanistic representations of interpatch movements, such as the one provided by the movement-ecology framework, permit the dynamic interaction of birth-death processes and individual movement behavior, thus improving our understanding of stochastic spatially structured populations.

Matrix coatings based on anodic alumina with carbon nanostructures in the pores

NASA Astrophysics Data System (ADS)

Gorokh, G. G.; Pashechko, M. I.; Borc, J. T.; Lozovenko, A. A.; Kashko, I. A.; Latos, A. I.

2018-03-01

The nanoporous anodic alumina matrixes thickness of 1.5 mm and pore sizes of 45, 90 and 145 nm were formed on Si substrates. The tubular carbon nanostructures were synthesized into the matrixes pores by pyrolysis of fluid hydrocarbon xylene with 1% ferrocene. The structure and composition of the matrix coatings were examined by scanning electron microscopy, Auger analysis and Raman spectroscopy. The carbon nanostructures completely filled the pores of templates and uniformly covered the tops. The structure of carbon nanostructures corresponded to the structure of multiwall carbon nanotubes. Investigations of mechanical and tribological properties of nanostructured oxide-carbon composite performed by scratching and nanoindentation showed nonlinear dependencies of the frictional force, penetration depth of the cantilever, hardness and plane strain modulus on the load. It was found that the microhardness of the samples increases with reduced of alumina pore diameter, and the penetration depth of the cantilever into the film grows with carbon nanostructures size. The results showed the high mechanical strength of nanostructured oxide-carbon composite.

Tendon exhibits complex poroelastic behavior at the nanoscale as revealed by high-frequency AFM-based rheology.

PubMed

Connizzo, Brianne K; Grodzinsky, Alan J

2017-03-21

Tendons transmit load from muscle to bone by utilizing their unique static and viscoelastic tensile properties. These properties are highly dependent on the composition and structure of the tissue matrix, including the collagen I hierarchy, proteoglycans, and water. While the role of matrix constituents in the tensile response has been studied, their role in compression, particularly in matrix pressurization via regulation of fluid flow, is not well understood. Injured or diseased tendons and tendon regions that naturally experience compression are known to have alterations in glycosaminoglycan content, which could modulate fluid flow and ultimately mechanical function. While recent theoretical studies have predicted tendon mechanics using poroelastic theory, no experimental data have directly demonstrated such behavior. In this study, we use high-bandwidth AFM-based rheology to determine the dynamic response of tendons to compressive loading at the nanoscale and to determine the presence of poroelastic behavior. Tendons are found to have significant characteristic dynamic relaxation behavior occurring at both low and high frequencies. Classic poroelastic behavior is observed, although we hypothesize that the full dynamic response is caused by a combination of flow-dependent poroelasticity as well as flow-independent viscoelasticity. Tendons also demonstrate regional dependence in their dynamic response, particularly near the junction of tendon and bone, suggesting that the structural and compositional heterogeneity in tendon may be responsible for regional poroelastic behavior. Overall, these experiments provide the foundation for understanding fluid-flow-dependent poroelastic mechanics of tendon, and the methodology is valuable for assessing changes in tendon matrix compressive behavior at the nanoscale. Copyright © 2017 Elsevier Ltd. All rights reserved.

Role of segregation and precipitates on interfacial strengthening mechanisms in metal matrix composites when subjected to thermo-mechanical processing

NASA Astrophysics Data System (ADS)

Myriounis, Dimitrios

Metal Matrix ceramic-reinforced composites are rapidly becoming strong candidates as structural materials for many high temperatures and aerospace applications. Metal matrix composites combine the ductile properties of the matrix with a brittle phase of the reinforcement, leading to high stiffness and strength with a reduction in structural weight. The main objective of using a metal matrix composite system is to increase service temperature or improve specific mechanical properties of structural components by replacing existing superalloys.The satisfactory performance of metal matrix composites depends critically on their integrity, the heart of which is the quality of the matrix-reinforcement interface. The nature of the interface depends on the processing of the metal matrix composite component. At the micro-level the development of local stress concentration gradients around the ceramic reinforcement, as the metal matrix attempts to deform during processing, can be very different to the nominal conditions and play a crucial role in important microstructural events such as segregation and precipitation at the matrix-reinforcement interface. These events dominate the cohesive strength and subsequent mechanical properties of the interface.At present the relationship between the strength properties of metal matrix composites and the details of the thermo-mechanical forming processes is not well understood.The purpose of the study is to investigate several strengthening mechanisms and the effect of thermo-mechanical processing of SiCp reinforced A359 aluminium alloy composites on the particle-matrix interface and the overall mechanical properties of the material. From experiments performed on composite materials subjected to various thermo-mechanical conditions and by observation using SEM microanalysis and mechanical testing, data were obtained, summarised and mathematically/statistically analysed upon their significance.The Al/SiCp composites studied, processed in specific thermo-mechanical conditions in order to attain higher values of interfacial fracture strength, due to precipitation hardening and segregation mechanisms, also exhibited enhanced bulk mechanical and fracture resistant properties.An analytical model to predict the interfacial fracture strength in the presence of material segregation was also developed during this research effort. Its validity was determined based on the data gathered from the experiments.The tailoring of the properties due to the microstructural modification of the composites was examined in relation to the experimental measurements obtained, which define the macroscopical behaviour of the material.

Analytic structure of the S-matrix for singular quantum mechanics

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

Camblong, Horacio E.; Epele, Luis N.; Fanchiotti, Huner

2015-06-15

The analytic structure of the S-matrix of singular quantum mechanics is examined within a multichannel framework, with primary focus on its dependence with respect to a parameter (Ω) that determines the boundary conditions. Specifically, a characterization is given in terms of salient mathematical and physical properties governing its behavior. These properties involve unitarity and associated current-conserving Wronskian relations, time-reversal invariance, and Blaschke factorization. The approach leads to an interpretation of effective nonunitary solutions in singular quantum mechanics and their determination from the unitary family.

Micromechanics Fatigue Damage Analysis Modeling for Fabric Reinforced Ceramic Matrix Composites

NASA Technical Reports Server (NTRS)

Min, J. B.; Xue, D.; Shi, Y.

2013-01-01

A micromechanics analysis modeling method was developed to analyze the damage progression and fatigue failure of fabric reinforced composite structures, especially for the brittle ceramic matrix material composites. A repeating unit cell concept of fabric reinforced composites was used to represent the global composite structure. The thermal and mechanical properties of the repeating unit cell were considered as the same as those of the global composite structure. The three-phase micromechanics, the shear-lag, and the continuum fracture mechanics models were integrated with a statistical model in the repeating unit cell to predict the progressive damages and fatigue life of the composite structures. The global structure failure was defined as the loss of loading capability of the repeating unit cell, which depends on the stiffness reduction due to material slice failures and nonlinear material properties in the repeating unit cell. The present methodology is demonstrated with the analysis results evaluated through the experimental test performed with carbon fiber reinforced silicon carbide matrix plain weave composite specimens.

Magnetic Properties and Phase Composition of Metamaterials Based on an Opal Matrix with 3 d-Transition Metal Particles

NASA Astrophysics Data System (ADS)

Rinkevich, A. B.; Korolev, A. V.; Samoilovich, M. I.; Perov, D. V.; Nemytova, O. V.

2018-02-01

The magnetic properties of metamaterials based on an opal matrix with transition-metal (iron, nickel, cobalt) particles have been studied. Magnetization curves and magnetic hysteresis loops have been measured and the dependences of real and imaginary parts of magnetization have been determined using the dynamic ac susceptibility measuring procedure. Structural studies of metamaterials have been performed. The saturation magnetization and coercive force of the studied metamaterials have been found to depend weakly on the temperature. The temperature dependence of magnetic susceptibility at a temperature above 30 K can be described adequately by Curie-Weiss law and, at lower temperature, deviates from the law.

The mesangial matrix in the normal and sclerotic glomerulus.

PubMed

Rosenblum, N D

1994-02-01

Mesangial sclerosis is a final common pathway to glomerular destruction in a variety of glomerular diseases. The expression of several classes of extracellular matrix (ECM) molecules has been defined in the normal and diseased mesangial matrix (MM). However, the manner in which these ECM components determine the three dimensional structure and function of the MM remains to be defined. Structural studies of the MM suggest that its constituent molecules are regionally organized into subcompartments with different three dimensional structures. The diversity of matrix molecules expressed within the MM as well as the organization of these components in nonrenal ECM's, such as the cornea, provides further support for this organizational model. The study of the cornea has also revealed that novel short chain collagenous proteins partially determine the three dimensional structure of the matrix. Recently, a novel collagen, type VIII collagen, has been described in mesangial cells and in the intact glomerulus. It is hypothesized that type VIII collagen is expressed both as a polymer and as a monomer within the glomerulus, and depending on its conformation, may serve unique functions. In the chronically diseased MM, normal MM components are overexpressed and fibrillar collagens are expressed de novo in a delayed fashion. Enhanced proteoglycan expression, observed early in disease, may determine increased volume of the mesangium. This, in turn, may stimulate the production of fibrillar collagens by mesangial cells resulting in a fibrillar noncompliant mesangial matrix.

Size-dependent characterization of embedded Ge nanocrystals: Structural and thermal properties

NASA Astrophysics Data System (ADS)

Araujo, L. L.; Giulian, R.; Sprouster, D. J.; Schnohr, C. S.; Llewellyn, D. J.; Kluth, P.; Cookson, D. J.; Foran, G. J.; Ridgway, M. C.

2008-09-01

A combination of conventional and synchrotron-based techniques has been used to characterize the size-dependent structural and thermal properties of Ge nanocrystals (NCs) embedded in a silica (a-SiO2) matrix. Ge NC size distributions with four different diameters ranging from 4.0 to 9.0 nm were produced by ion implantation and thermal annealing as characterized with small-angle x-ray scattering and transmission electron microscopy. The NCs were well represented by the superposition of bulklike crystalline and amorphous environments, suggesting the formation of an amorphous layer separating the crystalline NC core and the a-SiO2 matrix. The amorphous fraction was quantified with x-ray-absorption near-edge spectroscopy and increased as the NC diameter decreased, consistent with the increase in surface-to-volume ratio. The structural parameters of the first three nearest-neighbor shells were determined with extended x-ray-absorption fine-structure (EXAFS) spectroscopy and evolved linearly with inverse NC diameter. Specifically, increases in total disorder, interatomic distance, and the asymmetry in the distribution of distances were observed as the NC size decreased, demonstrating that finite-size effects govern the structural properties of embedded Ge NCs. Temperature-dependent EXAFS measurements in the range of 15-300 K were employed to probe the mean vibrational frequency and the variation of the interatomic distance distribution (mean value, variance, and asymmetry) with temperature for all NC distributions. A clear trend of increased stiffness (higher vibrational frequency) and decreased thermal expansion with decreasing NC size was evident, confirming the close relationship between the variation of structural and thermal/vibrational properties with size for embedded Ge NCs. The increase in surface-to-volume ratio and the presence of an amorphous Ge layer separating the matrix and crystalline NC core are identified as the main factors responsible for the observed behavior, with the surrounding a-SiO2 matrix also contributing to a lesser extent. Such results are compared to previous reports and discussed in terms of the influence of the surface-to-volume ratio in objects of nanometer dimensions.

A Probabilistic Graphical Model to Detect Chromosomal Domains

NASA Astrophysics Data System (ADS)

Heermann, Dieter; Hofmann, Andreas; Weber, Eva

To understand the nature of a cell, one needs to understand the structure of its genome. For this purpose, experimental techniques such as Hi-C detecting chromosomal contacts are used to probe the three-dimensional genomic structure. These experiments yield topological information, consistently showing a hierarchical subdivision of the genome into self-interacting domains across many organisms. Current methods for detecting these domains using the Hi-C contact matrix, i.e. a doubly-stochastic matrix, are mostly based on the assumption that the domains are distinct, thus non-overlapping. For overcoming this simplification and for being able to unravel a possible nested domain structure, we developed a probabilistic graphical model that makes no a priori assumptions on the domain structure. Within this approach, the Hi-C contact matrix is analyzed using an Ising like probabilistic graphical model whose coupling constant is proportional to each lattice point (entry in the contact matrix). The results show clear boundaries between identified domains and the background. These domain boundaries are dependent on the coupling constant, so that one matrix yields several clusters of different sizes, which show the self-interaction of the genome on different scales. This work was supported by a Grant from the International Human Frontier Science Program Organization (RGP0014/2014).

Theoretical study of solvent effects on the electronic coupling matrix elements in rigidly linked donor-acceptor systems

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

Cave, R.J.; Newton, M.D.; Kumar, K.

1995-12-07

The recently developed generalized Mulliken-Hush approach for the calculation of the electronic coupling matrix element for electron-transfer processes is applied to two rigidly linked donor-bridge-acceptor systems having dimethoxyanthracene as the donor and a dicarbomethoxycyclobutene unit as the acceptor. The dependence of the electronic coupling matrix element as a function of bridge type is examined with and without solvent molecules present. For clamp-shaped bridge structures solvent can have a dramatic effect on the electronic coupling matrix element. The behavior with variation of solvent is in good agreement with that observed experimentally for these systems. 23 refs., 2 tabs.

Serum, liver, and lung levels of the major extracellular matrix components at the early stage of BCG-induced granulomatosis depending on the infection route.

PubMed

Kim, L B; Shkurupy, V A; Putyatina, A N

2015-01-01

Experiments on the model of mouse BCG-induced granulomatous showed that the content of glycosaminoglycans and proteoglycans in the extracellular matrix of the liver and lungs are changed at the early stages of inflammation (days 3 and 30 postinfection) before cell destruction in the organs begins. This is related to degradation of extracellular matrix structures. Their high content in the blood and interstitium probably contributes to the formation of granulomas, fibroblast proliferation and organ fibrosis. These processes depend on the infection route that determines different conditions for generalization of the inflammation process. Intravenous method of vaccine injection is preferable to use when designing the experiments simulating tuberculosis granulomatosis, especially for the analysis of its early stages.

A proteomic study of the arabidopsis nuclear matrix.

PubMed

Calikowski, Tomasz T; Meulia, Tea; Meier, Iris

2003-10-01

The eukaryotic nucleus has been proposed to be organized by two interdependent nucleoprotein structures, the DNA-based chromatin and the RNA-dependent nuclear matrix. The functional composition and molecular organization of the second component have not yet been resolved. Here, we describe the isolation of the nuclear matrix from the model plant Arabidopsis, its initial characterization by confocal and electron microscopy, and the identification of 36 proteins by mass spectrometry. Electron microscopy of resinless samples confirmed a structure very similar to that described for the animal nuclear matrix. Two-dimensional gel electrophoresis resolved approximately 300 protein spots. Proteins were identified in batches by ESI tandem mass spectrometry after resolution by 1D SDS-PAGE. Among the identified proteins were a number of demonstrated or predicted Arabidopsis homologs of nucleolar proteins such as IMP4, Nop56, Nop58, fibrillarins, nucleolin, as well as ribosomal components and a putative histone deacetylase. Others included homologs of eEF-1, HSP/HSC70, and DnaJ, which have also been identified in the nucleolus or nuclear matrix of human cells, as well as a number of novel proteins with unknown function. This study is the first proteomic approach towards the characterization of a higher plant nuclear matrix. It demonstrates the striking similarities both in structure and protein composition of the operationally defined nuclear matrix across kingdoms whose unicellular ancestors have separated more than one billion years ago. Copyright 2003 Wiley-Liss, Inc.

Improved Estimation and Interpretation of Correlations in Neural Circuits

PubMed Central

Yatsenko, Dimitri; Josić, Krešimir; Ecker, Alexander S.; Froudarakis, Emmanouil; Cotton, R. James; Tolias, Andreas S.

2015-01-01

Ambitious projects aim to record the activity of ever larger and denser neuronal populations in vivo. Correlations in neural activity measured in such recordings can reveal important aspects of neural circuit organization. However, estimating and interpreting large correlation matrices is statistically challenging. Estimation can be improved by regularization, i.e. by imposing a structure on the estimate. The amount of improvement depends on how closely the assumed structure represents dependencies in the data. Therefore, the selection of the most efficient correlation matrix estimator for a given neural circuit must be determined empirically. Importantly, the identity and structure of the most efficient estimator informs about the types of dominant dependencies governing the system. We sought statistically efficient estimators of neural correlation matrices in recordings from large, dense groups of cortical neurons. Using fast 3D random-access laser scanning microscopy of calcium signals, we recorded the activity of nearly every neuron in volumes 200 μm wide and 100 μm deep (150–350 cells) in mouse visual cortex. We hypothesized that in these densely sampled recordings, the correlation matrix should be best modeled as the combination of a sparse graph of pairwise partial correlations representing local interactions and a low-rank component representing common fluctuations and external inputs. Indeed, in cross-validation tests, the covariance matrix estimator with this structure consistently outperformed other regularized estimators. The sparse component of the estimate defined a graph of interactions. These interactions reflected the physical distances and orientation tuning properties of cells: The density of positive ‘excitatory’ interactions decreased rapidly with geometric distances and with differences in orientation preference whereas negative ‘inhibitory’ interactions were less selective. Because of its superior performance, this ‘sparse+latent’ estimator likely provides a more physiologically relevant representation of the functional connectivity in densely sampled recordings than the sample correlation matrix. PMID:25826696

Half a century of "the nuclear matrix".

PubMed

Pederson, T

2000-03-01

A cell fraction that would today be termed "the nuclear matrix" was first described and patented in 1948 by Russian investigators. In 1974 this fraction was rediscovered and promoted as a fundamental organizing principle of eukaryotic gene expression. Yet, convincing evidence for this functional role of the nuclear matrix has been elusive and has recently been further challenged. What do we really know about the nonchromatin elements (if any) of internal nuclear structure? Are there objective reasons (as opposed to thinly veiled disdain) to question experiments that use harsh nuclear extraction steps and precipitation-prone conditions? Are the known biophysical properties of the nucleoplasm in vivo consistent with the existence of an extensive network of anastomosing filaments coursing dendritically throughout the interchromatin space? To what extent may the genome itself contribute information for its own quarternary structure in the interphase nucleus? These questions and recent work that bears on the mystique of the nuclear matrix are addressed in this essay. The degree to which gene expression literally depends on nonchromatin nuclear structure as a facilitating organizational format remains an intriguing but unsolved issue in eukaryotic cell biology, and considerable skepticism continues to surround the nuclear matrix fraction as an accurate representation of the in vivo situation.

Controlled nucleation and growth of CdS nanoparticles in a polymer matrix.

PubMed

Di Luccio, Tiziana; Laera, Anna Maria; Tapfer, Leander; Kempter, Susanne; Kraus, Robert; Nickel, Bert

2006-06-29

In-situ synchrotron X-ray diffraction (XRD) was used to monitor the thermal decomposition (thermolysis) of Cd thiolates precursors embedded in a polymer matrix and the nucleation of CdS nanoparticles. A thiolate precursor/polymer solid foil was heated to 300 degrees C in the X-ray diffraction setup of beamline W1.1 at Hasylab, and the diffraction curves were each recorded at 10 degrees C. At temperatures above 240 degrees C, the precursor decomposition is complete and CdS nanoparticles grow within the polymer matrix forming a nanocomposite with interesting optical properties. The nanoparticle structural properties (size and crystal structure) depend on the annealing temperature. Transmission electron microscopy (TEM) and photoluminescence (PL) analyses were used to characterize the nanoparticles. A possible mechanism driving the structural transformation of the precursor is inferred from the diffraction features arising at the different temperatures.

3D cancer cell migration in a confined matrix

NASA Astrophysics Data System (ADS)

Alobaidi, Amani; Sun, Bo

Cancer cell migration is widely studied in 2D motion, which does not mimic the invasion processes in vivo. More recently, 3D cell migration studies have been performed. The ability of cancer cells to migrate within the extracellular matrix depends on the physical and biochemical features of the extracellular matrix. We present a model of cell motility in confined matrix geometry. The aim of the study is to study cancer migration in collagen matrix, as a soft tissue, to investigate their motility within the confined and surrounding collagen environment. Different collagen concentrations have been used to show the ability of these cancer cells to move through such a complex structure by measuring Cancer cell migration velocity as well as the displacement. Graduate student physics department.

Nuclear matrix - structure, function and pathogenesis.

PubMed

Wasąg, Piotr; Lenartowski, Robert

2016-12-20

The nuclear matrix (NM), or nuclear skeleton, is the non-chromatin, ribonucleoproteinaceous framework that is resistant to high ionic strength buffers, nonionic detergents, and nucleolytic enzymes. The NM fulfills a structural role in eukaryotic cells and is responsible for maintaining the shape of the nucleus and the spatial organization of chromatin. Moreover, the NM participates in several cellular processes, such as DNA replication/repair, gene expression, RNA transport, cell signaling and differentiation, cell cycle regulation, apoptosis and carcinogenesis. Short nucleotide sequences called scaffold/matrix attachment regions (S/MAR) anchor the chromatin loops to the NM proteins (NMP). The NMP composition is dynamic and depends on the cell type and differentiation stage or metabolic activity. Alterations in the NMP composition affect anchoring of the S/MARs and thus alter gene expression. This review aims to systematize information about the skeletal structure of the nucleus, with particular emphasis on the organization of the NM and its role in selected cellular processes. We also discuss several diseases that are caused by aberrant NM structure or dysfunction of individual NM elements.

Structural diversity of a collagen-binding matrix protein from the byssus of blue mussels upon refolding.

PubMed

Suhre, Michael H; Scheibel, Thomas

2014-04-01

Blue mussels firmly adhere to a variety of different substrates by the byssus, an extracorporal structure consisting of several protein threads. These threads are mainly composed of fibrillar collagens called preCols which are embedded in a proteinaceous matrix. One of the two so far identified matrix proteins is the Proximal Thread Matrix Protein 1 (PTMP1). PTMP1 comprises two von Willebrand factor type A-like domains (A1 and A2) in a special arrangement. Here, we describe the refolding of recombinant PTMP1 from inclusion bodies. PTMP1 refolded into two distinct monomeric isoforms. Both isomers exhibited alternative intramolecular disulfide bonds. One of these isomers is thermodynamically favored and presumably represents the native form of PTMP1, while the other isoform is kinetically favored but is likely non-native. Oligomerization during refolding was influenced by, but not strictly dependent on disulfide formation. The conformational stability of PTMP1 indicates an influence of intramolecular disulfides on the native state, but not on unfolding intermediates. Monomeric PTMP1 exhibited a high thermal stability, dependent on the pH of the surrounding environment. Especially under acidic conditions the disulfide bonds were critically involved in thermal stability. Copyright © 2014 Elsevier Inc. All rights reserved.

Dynamical simulation of electron transfer processes in self-assembled monolayers at metal surfaces using a density matrix approach.

PubMed

Prucker, V; Bockstedte, M; Thoss, M; Coto, P B

2018-03-28

A single-particle density matrix approach is introduced to simulate the dynamics of heterogeneous electron transfer (ET) processes at interfaces. The characterization of the systems is based on a model Hamiltonian parametrized by electronic structure calculations and a partitioning method. The method is applied to investigate ET in a series of nitrile-substituted (poly)(p-phenylene)thiolate self-assembled monolayers adsorbed at the Au(111) surface. The results show a significant dependence of the ET on the orbital symmetry of the donor state and on the molecular and electronic structure of the spacer.

Phonon vibrational frequencies of all single-wall carbon nanotubes at the lambda point: reduced matrix calculations.

PubMed

Wang, Yufang; Wu, Yanzhao; Feng, Min; Wang, Hui; Jin, Qinghua; Ding, Datong; Cao, Xuewei

2008-12-01

With a simple method-the reduced matrix method, we simplified the calculation of the phonon vibrational frequencies according to SWNTs structure and their phonon symmetric property and got the dispersion properties of all SWNTs at Gamma point in Brillouin zone, whose diameters lie between 0.6 and 2.5 nm. The calculating time is shrunk about 2-4 orders. A series of the dependent relationships between the diameters of SWNTs and the frequencies of Raman and IR active modes are given. Several fine structures including "glazed tile" structures in omega approximately d figures are found, which might predict a certain macro-quantum phenomenon of the phonons in SWNTs.

A bias correction for covariance estimators to improve inference with generalized estimating equations that use an unstructured correlation matrix.

PubMed

Westgate, Philip M

2013-07-20

Generalized estimating equations (GEEs) are routinely used for the marginal analysis of correlated data. The efficiency of GEE depends on how closely the working covariance structure resembles the true structure, and therefore accurate modeling of the working correlation of the data is important. A popular approach is the use of an unstructured working correlation matrix, as it is not as restrictive as simpler structures such as exchangeable and AR-1 and thus can theoretically improve efficiency. However, because of the potential for having to estimate a large number of correlation parameters, variances of regression parameter estimates can be larger than theoretically expected when utilizing the unstructured working correlation matrix. Therefore, standard error estimates can be negatively biased. To account for this additional finite-sample variability, we derive a bias correction that can be applied to typical estimators of the covariance matrix of parameter estimates. Via simulation and in application to a longitudinal study, we show that our proposed correction improves standard error estimation and statistical inference. Copyright © 2012 John Wiley & Sons, Ltd.

Cellular growth in plants requires regulation of cell wall biochemistry.

PubMed

Chebli, Youssef; Geitmann, Anja

2017-02-01

Cell and organ morphogenesis in plants are regulated by the chemical structure and mechanical properties of the extracellular matrix, the cell wall. The two primary load bearing components in the plant cell wall, the pectin matrix and the cellulose/xyloglucan network, are constantly remodelled to generate the morphological changes required during plant development. This remodelling is regulated by a plethora of loosening and stiffening agents such as pectin methyl-esterases, calcium ions, expansins, and glucanases. The tight spatio-temporal regulation of the activities of these agents is a sine qua non condition for proper morphogenesis at cell and tissue levels. The pectin matrix and the cellulose-xyloglucan network operate in concert and their behaviour is mutually dependent on their chemical, structural and mechanical modifications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Extracellular matrix and hormones transcriptionally regulate bovine. beta. -casein 5 prime sequences in stably transfected mouse mammary cells

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

Schmidhauser, C. Bissell, M.J.; Myers, C.A.; Casperson, G.F.

1990-12-01

Milk protein regulation involves synergistic action of lactogenic hormones and extracellular matrix (ECM). It is well established that substratum has a dramatic effect on morphology and function of mammary cells. The molecular mechanisms that regulate the ECM- and hormone-dependent gene expression, however, have not been resolved. To address this question, a subpopulation (designated CID 9) of the mouse mammary epithelial cell strain COMMA-2D has been developed in which more than 35% of the cells express {beta}-casein, form alveoli-like structures when plated onto a reconstituted basement membrane, and secrete {beta}-casein undirectionally into a lumen. These cells were stably transfected with amore » series of chloramphenicol acetyltransferase (CAT) fusion genes to study transcriptional regulation of the bovine {beta}-casein gene. The expression of CAT in these lines demonstrated a striking matrix and hormone dependency. This regulation occurered primarily at the transcriptional level and was dependent on the length of the 5{prime} flanking region of the {beta}-casein promotor. Both matrix and hormonal control of transcription occurred within at least the first 1790 base pairs upstream and/or 42 base pairs downstream of the transcriptional initiation site. The ECM effect was independent of glucocorticoid stimulation. However, prolactin was essential and hydrocortisone further increased CAT expression. Endogenous {beta}-casein expression in these lines was similar to that of the parent CID 9 cells. Our data indicate the existence of matrix-dependent elements that regulate transcription.« less

Thermal-Interaction Matrix For Resistive Test Structure

NASA Technical Reports Server (NTRS)

Buehler, Martin G.; Dhiman, Jaipal K.; Zamani, Nasser

1990-01-01

Linear mathematical model predicts increase in temperature in each segment of 15-segment resistive structure used to test electromigration. Assumption of linearity based on fact: equations that govern flow of heat are linear and coefficients in equations (heat conductivities and capacities) depend only weakly on temperature and considered constant over limited range of temperature.

Up-and-coming IMCs. [Intermetallic-Matrix Composites

NASA Technical Reports Server (NTRS)

Bowman, Randy; Noebe, Ronald

1989-01-01

While the good oxidation and environmental resistance, high melting points, and comparatively low densities of such ordered intermetallics as Ti3Al, NiAl, FeAl, and NbAl3 render them good candidates for advanced aerospace structures, their poor toughness at low temperatures and low strength at elevated temperatures have prompted the development of fiber-reinforced intermetallic-matrix composites (IMCs) with more balanced characteristics. Fabrication methods for continuous-fiber IMCs under development include the P/M 'powder cloth' method, the foil/fiber method, and thermal spraying. The ultimate success of IMCs depends on fibers truly compatible with the matrix materials.

Water in the presence of inert Lennard-Jones obstacles

NASA Astrophysics Data System (ADS)

Kurtjak, Mario; Urbic, Tomaz

2014-04-01

Water confined by the presence of a 'sea' of inert obstacles was examined. In the article, freely mobile two-dimensional Mercedes-Benz (MB) water put to a disordered, but fixed, matrix of Lennard-Jones disks was studied by the Monte Carlo computer simulations. For the MB water molecules in the matrix of Lennard-Jones disks, we explored the structures, hydrogen-bond-network formation and thermodynamics as a function of temperature and size and density of matrix particles. We found that the structure of model water is perturbed by the presence of the obstacles. Density of confined water, which was in equilibrium with the bulk water, was smaller than the density of the bulk water and the temperature dependence of the density of absorbed water did not show the density anomaly in the studied temperature range. The behaviour observed as a consequence of confinement is similar to that of increasing temperature, which can for a matrix lead to a process similar to capillary evaporation. At the same occupancy of space, smaller matrix molecules cause higher destruction effect on the absorbed water molecules than the bigger ones. We have also tested the hypothesis that at low matrix densities the obstacles induce an increased ordering and 'hydrogen bonding' of the MB model molecules, relative to pure fluid, while at high densities the obstacles reduce MB water structuring, as they prevent the fluid to form good 'hydrogen-bonding' networks. However, for the size of matrix molecules similar to that of water, we did not observe this effect.

Computing the structural influence matrix for biological systems.

PubMed

Giordano, Giulia; Cuba Samaniego, Christian; Franco, Elisa; Blanchini, Franco

2016-06-01

We consider the problem of identifying structural influences of external inputs on steady-state outputs in a biological network model. We speak of a structural influence if, upon a perturbation due to a constant input, the ensuing variation of the steady-state output value has the same sign as the input (positive influence), the opposite sign (negative influence), or is zero (perfect adaptation), for any feasible choice of the model parameters. All these signs and zeros can constitute a structural influence matrix, whose (i, j) entry indicates the sign of steady-state influence of the jth system variable on the ith variable (the output caused by an external persistent input applied to the jth variable). Each entry is structurally determinate if the sign does not depend on the choice of the parameters, but is indeterminate otherwise. In principle, determining the influence matrix requires exhaustive testing of the system steady-state behaviour in the widest range of parameter values. Here we show that, in a broad class of biological networks, the influence matrix can be evaluated with an algorithm that tests the system steady-state behaviour only at a finite number of points. This algorithm also allows us to assess the structural effect of any perturbation, such as variations of relevant parameters. Our method is applied to nontrivial models of biochemical reaction networks and population dynamics drawn from the literature, providing a parameter-free insight into the system dynamics.

Sequencing of Dust Filter Production Process Using Design Structure Matrix (DSM)

NASA Astrophysics Data System (ADS)

Sari, R. M.; Matondang, A. R.; Syahputri, K.; Anizar; Siregar, I.; Rizkya, I.; Ursula, C.

2018-01-01

Metal casting company produces machinery spare part for manufactures. One of the product produced is dust filter. Most of palm oil mill used this product. Since it is used in most of palm oil mill, company often have problems to address this product. One of problem is the disordered of production process. It carried out by the job sequencing. The important job that should be solved first, least implement, while less important job and could be completed later, implemented first. Design Structure Matrix (DSM) used to analyse and determine priorities in the production process. DSM analysis is sort of production process through dependency sequencing. The result of dependency sequences shows the sequence process according to the inter-process linkage considering before and after activities. Finally, it demonstrates their activities to the coupled activities for metal smelting, refining, grinding, cutting container castings, metal expenditure of molds, metal casting, coating processes, and manufacture of molds of sand.

Curvature and gravity actions for matrix models: II. The case of general Poisson structures

NASA Astrophysics Data System (ADS)

Blaschke, Daniel N.; Steinacker, Harold

2010-12-01

We study the geometrical meaning of higher order terms in matrix models of Yang-Mills type in the semi-classical limit, generalizing recent results (Blaschke and Steinacker 2010 Class. Quantum Grav. 27 165010 (arXiv:1003.4132)) to the case of four-dimensional spacetime geometries with general Poisson structure. Such terms are expected to arise e.g. upon quantization of the IKKT-type models. We identify terms which depend only on the intrinsic geometry and curvature, including modified versions of the Einstein-Hilbert action as well as terms which depend on the extrinsic curvature. Furthermore, a mechanism is found which implies that the effective metric G on the spacetime brane {\\cal M}\\subset \\mathds{R}^D 'almost' coincides with the induced metric g. Deviations from G = g are suppressed, and characterized by the would-be U(1) gauge field.

Polarization independent asymmetric light absorption in plasmonic nanostructure

NASA Astrophysics Data System (ADS)

Franco Rêgo, Davi; Rodriguez-Esquerre, Vitaly Felix

2017-08-01

The directional dependency of the optical coefficients, such as absorbance and reflectance, of a periodic hole plasmonic structure is numerically simulated and investigated. The tridimensional structure, which is composed of a metallic thin layer on a semiconductor matrix, is polarization independent and exhibits wide angle tolerance. It is found that the optical coefficients of the simulated structure have strong dependency to the radii of the holes due to cavity modes resonance and surface plasmon resonance. Simulations were carried out using gold and silver, varying the holes radii ranging from 40 to 70nm, as well as its depth, from 30 to 60nm of the metallic thin layer and from 100 to 200nm of the semiconductor matrix. A maximum contrast ratio of a unit was obtained. The resonant modes excited in the structure and excitation of surface plasmon polaritons in the metallic side illumination favors absorption, which explains the asymmetric behavior. We also investigate the structure's fabrication sensitivity by randomizing the generation of center of the holes in a supercell. These findings are significant for a diverse range of applications, ranging from optical integrated circuits to solar and thermovoltaics energy harvesting.

Efficient tree tensor network states (TTNS) for quantum chemistry: Generalizations of the density matrix renormalization group algorithm

NASA Astrophysics Data System (ADS)

Nakatani, Naoki; Chan, Garnet Kin-Lic

2013-04-01

We investigate tree tensor network states for quantum chemistry. Tree tensor network states represent one of the simplest generalizations of matrix product states and the density matrix renormalization group. While matrix product states encode a one-dimensional entanglement structure, tree tensor network states encode a tree entanglement structure, allowing for a more flexible description of general molecules. We describe an optimal tree tensor network state algorithm for quantum chemistry. We introduce the concept of half-renormalization which greatly improves the efficiency of the calculations. Using our efficient formulation we demonstrate the strengths and weaknesses of tree tensor network states versus matrix product states. We carry out benchmark calculations both on tree systems (hydrogen trees and π-conjugated dendrimers) as well as non-tree molecules (hydrogen chains, nitrogen dimer, and chromium dimer). In general, tree tensor network states require much fewer renormalized states to achieve the same accuracy as matrix product states. In non-tree molecules, whether this translates into a computational savings is system dependent, due to the higher prefactor and computational scaling associated with tree algorithms. In tree like molecules, tree network states are easily superior to matrix product states. As an illustration, our largest dendrimer calculation with tree tensor network states correlates 110 electrons in 110 active orbitals.

N-(1-Naphthyl) Ethylenediamine Dinitrate: A New Matrix for Negative Ion MALDI-TOF MS Analysis of Small Molecules

NASA Astrophysics Data System (ADS)

Chen, Rui; Chen, Suming; Xiong, Caiqiao; Ding, Xunlei; Wu, Chih-Che; Chang, Huan-Cheng; Xiong, Shaoxiang; Nie, Zongxiu

2012-09-01

An organic salt, N-(1-naphthyl) ethylenediamine dinitrate (NEDN), with rationally designed properties of a strong UV absorbing chromophore, hydrogen binding and nitrate anion donors, has been employed as a matrix to analyze small molecules ( m/z < 1000) such as oligosaccharides, peptides, metabolites and explosives using negative ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Compared with conventional matrixes such as α-cyano-4-hydroxycinnamic acid (CCA) and 2,5-dihydroxybenzoic acid (DHB), NEDN provides a significant improvement in detection sensitivity and yields very few matrix-associated fragment and cluster ions interfering with MS analysis. For low-molecular-weight saccharides, the lowest detection limit achieved ranges from 500 amol to 5 pmol, depending on the molecular weight and the structure of the analytes. Additionally, the mass spectra in the lower mass range ( m/z < 200) consist of only nitrate and nitric acid cluster ions, making the matrix particularly useful for structural identification of oligosaccharides by post-source decay (PSD) MALDI-MS. Such a characteristic is illustrated by using maltoheptaose as a model system. This work demonstrates that NEDN is a novel negative ion-mode matrix for MALDI-MS analysis of small molecules with nitrate anion attachment.

Fluid flow increases mineralized matrix deposition in 3D perfusion culture of marrow stromal osteoblasts in a dose-dependent manner

NASA Technical Reports Server (NTRS)

Bancroft, Gregory N.; Sikavitsas, Vassilios I.; van den Dolder, Juliette; Sheffield, Tiffany L.; Ambrose, Catherine G.; Jansen, John A.; Mikos, Antonios G.; McIntire, L. V. (Principal Investigator)

2002-01-01

Bone is a complex highly structured mechanically active 3D tissue composed of cellular and matrix elements. The true biological environment of a bone cell is thus derived from a dynamic interaction between responsively active cells experiencing mechanical forces and a continuously changing 3D matrix architecture. To investigate this phenomenon in vitro, marrow stromal osteoblasts were cultured on 3D scaffolds under flow perfusion with different rates of flow for an extended period to permit osteoblast differentiation and significant matrix production and mineralization. With all flow conditions, mineralized matrix production was dramatically increased over statically cultured constructs with the total calcium content of the cultured scaffolds increasing with increasing flow rate. Flow perfusion induced de novo tissue modeling with the formation of pore-like structures in the scaffolds and enhanced the distribution of cells and matrix throughout the scaffolds. These results represent reporting of the long-term effects of fluid flow on primary differentiating osteoblasts and indicate that fluid flow has far-reaching effects on osteoblast differentiation and phenotypic expression in vitro. Flow perfusion culture permits the generation and study of a 3D, actively modeled, mineralized matrix and can therefore be a valuable tool for both bone biology and tissue engineering.

The roles of biofilm matrix polysaccharide Psl in mucoid Pseudomonas aeruginosa biofilms.

PubMed

Ma, Luyan; Wang, Shiwei; Wang, Di; Parsek, Matthew R; Wozniak, Daniel J

2012-07-01

The opportunistic pathogen Pseudomonas aeruginosa causes life-threatening, persistent infections in patients with cystic fibrosis (CF). Persistence is attributed to the ability of these bacteria to form structured communities (biofilms). Biofilms rely on an extracellular polymeric substances matrix to maintain structure. Psl exopolysaccharide is a key matrix component of nonmucoid biofilms, yet the role of Psl in mucoid biofilms is unknown. In this report, using a variety of mutants in a mucoid P. aeruginosa background, we found that deletion of Psl-encoding genes dramatically decreased their biofilm formation ability, indicating that Psl is also a critical matrix component of mucoid biofilms. Our data also suggest that the overproduction of alginate leads to mucoid biofilms, which occupy more space, whereas Psl-dependent biofilms are densely packed. These data suggest that Psl polysaccharide may have significant contributions in biofilm persistence in patients with CF and may be helpful for designing therapies for P. aeruginosa CF infection. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Protein Immobilization Capabilities of Sucrose and Trehalose Glasses: The Effect of Protein/Sugar Concentration Unraveled by High-Field EPR.

PubMed

Malferrari, Marco; Savitsky, Anton; Lubitz, Wolfgang; Möbius, Klaus; Venturoli, Giovanni

2016-12-01

Disaccharide glasses are increasingly used to immobilize proteins at room temperature for structural/functional studies and long-term preservation. To unravel the molecular basis of protein immobilization, we studied the effect of sugar/protein concentration ratios in trehalose or sucrose matrixes, in which the bacterial photosynthetic reaction center (RC) was embedded as a model protein. The structural, dynamical, and H-bonding characteristics of the sugar-protein systems were probed by high-field W-band EPR of a matrix-dissolved nitroxide radical. We discovered that RC immobilization and thermal stabilization, being independent of the protein concentration in trehalose, occur in sucrose only at sufficiently low sugar/protein ratios. EPR reveals that only under such conditions does sucrose form a microscopically homogeneous matrix that immobilizes, via H-bonds, the nitroxide probe. We conclude that the protein immobilization capability depends critically on the propensity of the glass-forming sugar to create intermolecular H-bond networks, thus establishing long-range, homogeneous connectivity within the matrix.

Heterogeneous Polarized States in Ferroelectric Inclusions in a Ferroelectric-Dielectric Nanocomposite

NASA Astrophysics Data System (ADS)

Nechaev, V. N.; Viskovatykh, A. V.

2018-06-01

The behavior of the previously observed inhomogeneous polarized states in ferroelectric inclusions of the nanocomposite is analyzed in detail. The domain structure of ferroelectric particles depends on the temperature and nature of interaction with the dielectric matrix. The possibility of controlling the domain structure in ferroelectric particles using an external electric field is shown.

A comparison of likelihood ratio tests and Rao's score test for three separable covariance matrix structures.

PubMed

Filipiak, Katarzyna; Klein, Daniel; Roy, Anuradha

2017-01-01

The problem of testing the separability of a covariance matrix against an unstructured variance-covariance matrix is studied in the context of multivariate repeated measures data using Rao's score test (RST). The RST statistic is developed with the first component of the separable structure as a first-order autoregressive (AR(1)) correlation matrix or an unstructured (UN) covariance matrix under the assumption of multivariate normality. It is shown that the distribution of the RST statistic under the null hypothesis of any separability does not depend on the true values of the mean or the unstructured components of the separable structure. A significant advantage of the RST is that it can be performed for small samples, even smaller than the dimension of the data, where the likelihood ratio test (LRT) cannot be used, and it outperforms the standard LRT in a number of contexts. Monte Carlo simulations are then used to study the comparative behavior of the null distribution of the RST statistic, as well as that of the LRT statistic, in terms of sample size considerations, and for the estimation of the empirical percentiles. Our findings are compared with existing results where the first component of the separable structure is a compound symmetry (CS) correlation matrix. It is also shown by simulations that the empirical null distribution of the RST statistic converges faster than the empirical null distribution of the LRT statistic to the limiting χ 2 distribution. The tests are implemented on a real dataset from medical studies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The kinesin KIF9 and reggie/flotillin proteins regulate matrix degradation by macrophage podosomes

PubMed Central

Cornfine, Susanne; Himmel, Mirko; Kopp, Petra; el Azzouzi, Karim; Wiesner, Christiane; Krüger, Marcus; Rudel, Thomas; Linder, Stefan

2011-01-01

Podosomes are actin-based matrix contacts in a variety of cell types, most notably monocytic cells, and are characterized by their ability to lyse extracellular matrix material. Besides their dependence on actin regulation, podosomes are also influenced by microtubules and microtubule-dependent transport processes. Here we describe a novel role for KIF9, a previously little-characterized member of the kinesin motor family, in the regulation of podosomes in primary human macrophages. We find that small interfering RNA (siRNA)/short-hairpin RNA–induced knockdown of KIF9 significantly affects both numbers and matrix degradation of podosomes. Overexpression and microinjection experiments reveal that the unique C-terminal region of KIF9 is crucial for these effects, presumably through binding of specific interactors. Indeed, we further identify reggie-1/flotillin-2, a signaling mediator between intracellular vesicles and the cell periphery, as an interactor of the KIF9 C-terminus. Reggie-1 dynamically colocalizes with KIF9 in living cells, and, consistent with KIF9-mediated effects, siRNA-induced knockdown of reggies/flotillins significantly impairs matrix degradation by podosomes. In sum, we identify the kinesin KIF9 and reggie/flotillin proteins as novel regulators of macrophage podosomes and show that their interaction is critical for the matrix-degrading ability of these structures. PMID:21119006

Development and application of a density dependent matrix ...

EPA Pesticide Factsheets

Ranging along the Atlantic coast from US Florida to the Maritime Provinces of Canada, the Atlantic killifish (Fundulus heteroclitus) is an important and well-studied model organism for understanding the effects of pollutants and other stressors in estuarine and marine ecosystems. Matrix population models are useful tools for ecological risk assessment because they integrate effects across the life cycle, provide a linkage between endpoints observed in the individual and ecological risk to the population as a whole, and project outcomes for many generations in the future. We developed a density dependent matrix population model for Atlantic killifish by modifying a model developed for fathead minnow (Pimephales promelas) that has proved to be extremely useful, e.g. to incorporate data from laboratory studies and project effects of endocrine disrupting chemicals. We developed a size-structured model (as opposed to one that is based upon developmental stages or age class structure) so that we could readily incorporate output from a Dynamic Energy Budget (DEB) model, currently under development. Due to a lack of sufficient data to accurately define killifish responses to density dependence, we tested a number of scenarios realistic for other fish species in order to demonstrate the outcome of including this ecologically important factor. We applied the model using published data for killifish exposed to dioxin-like compounds, and compared our results to those using

The structure of the "amorphous" matrix of keratins.

PubMed

Kadir, Murat; Wang, Xinwei; Zhu, Bowen; Liu, Jing; Harland, Duane; Popescu, Crisan

2017-05-01

Various keratin fibers, particularly human hairs, were investigated by transmission electron microscopy, TEM, solid-state 1 H NMR and Transient Electro-Thermal Technique, TET. The results converge to suggest that the matrix of keratin fiber cortex, far from being amorphous, has a well-defined nano-scale grainy structure, the size of these grains being around 2-4nm. The size of the grains appears to strongly depend on the chemical treatment of the fiber, on the temperature and on the relative humidity of the environment, as well as on the physiological factors at the level of fiber production in follicle. By suggesting an organization at the nano-scale of the protein chains in these grains, likely to be Keratin Associated Proteins, the results challenge the view of matrix as a homogeneous glassy material. Moreover, they indicate the potential of further investigating the purpose of this structure that appears to reflect not only chemical treatments of keratins but also biological processes at the level of the follicle. Copyright © 2017 Elsevier Inc. All rights reserved.

Linear-scaling implementation of molecular response theory in self-consistent field electronic-structure theory.

PubMed

Coriani, Sonia; Høst, Stinne; Jansík, Branislav; Thøgersen, Lea; Olsen, Jeppe; Jørgensen, Poul; Reine, Simen; Pawłowski, Filip; Helgaker, Trygve; Sałek, Paweł

2007-04-21

A linear-scaling implementation of Hartree-Fock and Kohn-Sham self-consistent field theories for the calculation of frequency-dependent molecular response properties and excitation energies is presented, based on a nonredundant exponential parametrization of the one-electron density matrix in the atomic-orbital basis, avoiding the use of canonical orbitals. The response equations are solved iteratively, by an atomic-orbital subspace method equivalent to that of molecular-orbital theory. Important features of the subspace method are the use of paired trial vectors (to preserve the algebraic structure of the response equations), a nondiagonal preconditioner (for rapid convergence), and the generation of good initial guesses (for robust solution). As a result, the performance of the iterative method is the same as in canonical molecular-orbital theory, with five to ten iterations needed for convergence. As in traditional direct Hartree-Fock and Kohn-Sham theories, the calculations are dominated by the construction of the effective Fock/Kohn-Sham matrix, once in each iteration. Linear complexity is achieved by using sparse-matrix algebra, as illustrated in calculations of excitation energies and frequency-dependent polarizabilities of polyalanine peptides containing up to 1400 atoms.

Stage-structured transmission of phocine distemper virus in the Dutch 2002 outbreak

PubMed Central

Klepac, Petra; Pomeroy, Laura W.; Bjørnstad, Ottar N.; Kuiken, Thijs; Osterhaus, Albert D.M.E.; Rijks, Jolianne M.

2009-01-01

Heterogeneities in transmission among hosts can be very important in shaping infectious disease dynamics. In mammals with strong social organization, such heterogeneities are often structured by functional stage: juveniles, subadults and adults. We investigate the importance of such stage-related heterogeneities in shaping the 2002 phocine distemper virus (PDV) outbreak in the Dutch Wadden Sea, when more than 40 per cent of the harbour seals were killed. We do this by comparing the statistical fit of a hierarchy of models with varying transmission complexity: homogeneous versus heterogeneous mixing and density- versus frequency-dependent transmission. We use the stranding data as a proxy for incidence and use Poisson likelihoods to estimate the ‘who acquires infection from whom’ (WAIFW) matrix. Statistically, the model with strong heterogeneous mixing and density-dependent transmission was found to best describe the transmission dynamics. However, patterns of incidence support a model of frequency-dependent transmission among adults and juveniles. Based on the maximum-likelihood WAIFW matrix estimates, we use the next-generation formalism to calculate an R0 between 2 and 2.5 for the Dutch 2002 PDV epidemic. PMID:19364743

Molecular mechanisms of mechanotransduction in integrin-mediated cell-matrix adhesion

PubMed Central

Li, Zhenhai; Lee, Hyunjung; Zhu, Cheng

2016-01-01

Cell-matrix adhesion complexes are multi-protein structures linking the extracellular matrix (ECM) to the cytoskeleton. They are essential to both cell motility and function by bidirectionally sensing and transmitting mechanical and biochemical stimulations. Several types of cell-matrix adhesions have been identified and they share many key molecular components, such as integrins and actin-integrin linkers. Mechanochemical coupling between ECM molecules and the actin cytoskeleton has been observed from the single cell to the single molecule level and from immune cells to neuronal cells. However, the mechanisms underlying force regulation of integrin-mediated mechanotransduction still need to be elucidated. In this review article, we focus on integrin-mediated adhesions and discuss force regulation of cell-matrix adhesions and key adaptor molecules, three different force-dependent behaviors, and molecular mechanisms for mechanochemical coupling in force regulation. PMID:27720950

Robustness of Thirty Meter Telescope primary mirror control

NASA Astrophysics Data System (ADS)

Macmynowski, Douglas G.; Thompson, Peter M.; Shelton, Chris; Roberts, Lewis C., Jr.

2010-07-01

The primary mirror control system for the Thirty Meter Telescope (TMT) maintains the alignment of the 492 segments in the presence of both quasi-static (gravity and thermal) and dynamic disturbances due to unsteady wind loads. The latter results in a desired control bandwidth of 1Hz at high spatial frequencies. The achievable bandwidth is limited by robustness to (i) uncertain telescope structural dynamics (control-structure interaction) and (ii) small perturbations in the ill-conditioned influence matrix that relates segment edge sensor response to actuator commands. Both of these effects are considered herein using models of TMT. The former is explored through multivariable sensitivity analysis on a reduced-order Zernike-basis representation of the structural dynamics. The interaction matrix ("A-matrix") uncertainty has been analyzed theoretically elsewhere, and is examined here for realistic amplitude perturbations due to segment and sensor installation errors, and gravity and thermal induced segment motion. The primary influence of A-matrix uncertainty is on the control of "focusmode"; this is the least observable mode, measurable only through the edge-sensor (gap-dependent) sensitivity to the dihedral angle between segments. Accurately estimating focus-mode will require updating the A-matrix as a function of the measured gap. A-matrix uncertainty also results in a higher gain-margin requirement for focus-mode, and hence the A-matrix and CSI robustness need to be understood simultaneously. Based on the robustness analysis, the desired 1 Hz bandwidth is achievable in the presence of uncertainty for all except the lowest spatial-frequency response patterns of the primary mirror.

Super-resolution Doppler beam sharpening method using fast iterative adaptive approach-based spectral estimation

NASA Astrophysics Data System (ADS)

Mao, Deqing; Zhang, Yin; Zhang, Yongchao; Huang, Yulin; Yang, Jianyu

2018-01-01

Doppler beam sharpening (DBS) is a critical technology for airborne radar ground mapping in forward-squint region. In conventional DBS technology, the narrow-band Doppler filter groups formed by fast Fourier transform (FFT) method suffer from low spectral resolution and high side lobe levels. The iterative adaptive approach (IAA), based on the weighted least squares (WLS), is applied to the DBS imaging applications, forming narrower Doppler filter groups than the FFT with lower side lobe levels. Regrettably, the IAA is iterative, and requires matrix multiplication and inverse operation when forming the covariance matrix, its inverse and traversing the WLS estimate for each sampling point, resulting in a notably high computational complexity for cubic time. We propose a fast IAA (FIAA)-based super-resolution DBS imaging method, taking advantage of the rich matrix structures of the classical narrow-band filtering. First, we formulate the covariance matrix via the FFT instead of the conventional matrix multiplication operation, based on the typical Fourier structure of the steering matrix. Then, by exploiting the Gohberg-Semencul representation, the inverse of the Toeplitz covariance matrix is computed by the celebrated Levinson-Durbin (LD) and Toeplitz-vector algorithm. Finally, the FFT and fast Toeplitz-vector algorithm are further used to traverse the WLS estimates based on the data-dependent trigonometric polynomials. The method uses the Hermitian feature of the echo autocorrelation matrix R to achieve its fast solution and uses the Toeplitz structure of R to realize its fast inversion. The proposed method enjoys a lower computational complexity without performance loss compared with the conventional IAA-based super-resolution DBS imaging method. The results based on simulations and measured data verify the imaging performance and the operational efficiency.

Marsh Soil Responses to Nutrients: Belowground Structural and Organic Properties

EPA Science Inventory

Coastal marsh responses to nutrient enrichment apparently depend upon soil matrix and whether the system is primarily biogenic or minerogenic. Deteriorating organic rich marshes (Jamaica Bay, NY) receiving wastewater effluent had lower belowground biomass, organic matter, and soi...

Marsh Soil Responses to Nutrients: Belowground Structural and Organic Properties.

EPA Science Inventory

Coastal marsh responses to nutrient enrichment apparently depend upon soil matrix and whether the system is primarily biogenic or minerogenic. Deteriorating organic rich marshes (Jamaica Bay, NY) receiving wastewater effluent had lower belowground biomass, organic matter, and soi...

Structured output-feedback controller synthesis with design specifications

NASA Astrophysics Data System (ADS)

Hao, Yuqing; Duan, Zhisheng

2017-03-01

This paper considers the problem of structured output-feedback controller synthesis with finite frequency specifications. Based on the orthogonal space information of input matrix, an improved parameter-dependent Lyapunov function method is first proposed. Then, a two-stage construction method is designed, which depends on an initial centralised controller. Corresponding design conditions for three types of output-feedback controllers are presented in terms of unified representations. Moreover, heuristic algorithms are provided to explore the desirable controllers. Finally, the effectiveness of these proposed methods is illustrated via some practical examples.

Effects of freezing-induced cell-fluid-matrix interactions on the cells and extracellular matrix of engineered tissues.

PubMed

Teo, Ka Yaw; DeHoyos, Tenok O; Dutton, J Craig; Grinnell, Frederick; Han, Bumsoo

2011-08-01

The two most significant challenges for successful cryopreservation of engineered tissues (ETs) are preserving tissue functionality and controlling highly tissue-type dependent preservation outcomes. In order to address these challenges, freezing-induced cell-fluid-matrix interactions should be understood, which determine the post-thaw cell viability and extracellular matrix (ECM) microstructure. However, the current understanding of this tissue-level biophysical interaction is still limited. In this study, freezing-induced cell-fluid-matrix interactions and their impact on the cells and ECM microstructure of ETs were investigated using dermal equivalents as a model ET. The dermal equivalents were constructed by seeding human dermal fibroblasts in type I collagen matrices with varying cell seeding density and collagen concentration. While these dermal equivalents underwent an identical freeze/thaw condition, their spatiotemporal deformation during freezing, post-thaw ECM microstructure, and cellular level cryoresponse were characterized. The results showed that the extent and characteristics of freezing-induced deformation were significantly different among the experimental groups, and the ETs with denser ECM microstructure experienced a larger deformation. The magnitude of the deformation was well correlated to the post-thaw ECM structure, suggesting that the freezing-induced deformation is a good indicator of post-thaw ECM structure. A significant difference in the extent of cellular injury was also noted among the experimental groups, and it depended on the extent of freezing-induced deformation of the ETs and the initial cytoskeleton organization. These results suggest that the cells have been subjected to mechanical insult due to the freezing-induced deformation as well as thermal insult. These findings provide insight on tissue-type dependent cryopreservation outcomes, and can help to design and modify cryopreservation protocols for new types of tissues from a pre-developed cryopreservation protocol. Copyright © 2011 Elsevier Ltd. All rights reserved.

Flutter analysis using transversality theory

NASA Technical Reports Server (NTRS)

Afolabi, D.

1993-01-01

A new method of calculating flutter boundaries of undamped aeronautical structures is presented. The method is an application of the weak transversality theorem used in catastrophe theory. In the first instance, the flutter problem is cast in matrix form using a frequency domain method, leading to an eigenvalue matrix. The characteristic polynomial resulting from this matrix usually has a smooth dependence on the system's parameters. As these parameters change with operating conditions, certain critical values are reached at which flutter sets in. Our approach is to use the transversality theorem in locating such flutter boundaries using this criterion: at a flutter boundary, the characteristic polynomial does not intersect the axis of the abscissa transversally. Formulas for computing the flutter boundaries and flutter frequencies of structures with two degrees of freedom are presented, and extension to multi-degree of freedom systems is indicated. The formulas have obvious applications in, for instance, problems of panel flutter at supersonic Mach numbers.

Quantitative analysis of ultrasonic images of fibrotic liver using co-occurrence matrix based on multi-Rayleigh model

NASA Astrophysics Data System (ADS)

Isono, Hiroshi; Hirata, Shinnosuke; Hachiya, Hiroyuki

2015-07-01

In medical ultrasonic images of liver disease, a texture with a speckle pattern indicates a microscopic structure such as nodules surrounded by fibrous tissues in hepatitis or cirrhosis. We have been applying texture analysis based on a co-occurrence matrix to ultrasonic images of fibrotic liver for quantitative tissue characterization. A co-occurrence matrix consists of the probability distribution of brightness of pixel pairs specified with spatial parameters and gives new information on liver disease. Ultrasonic images of different types of fibrotic liver were simulated and the texture-feature contrast was calculated to quantify the co-occurrence matrices generated from the images. The results show that the contrast converges with a value that can be theoretically estimated using a multi-Rayleigh model of echo signal amplitude distribution. We also found that the contrast value increases as liver fibrosis progresses and fluctuates depending on the size of fibrotic structure.

A continuum deformation theory for metal-matrix composites at high temperature

NASA Technical Reports Server (NTRS)

Robinson, D. N.

1987-01-01

A continuum theory is presented for representing the high temperature, time dependent, hereditary deformation behavior of metallic composites that can be idealized as pseudohomogeneous continua with locally definable directional characteristics. Homogenization of textured materials (molecular, granular, fibrous) and applicability of continuum mechanics in structural applications depends on characteristic body dimensions, the severity of gradients (stress, temperature, etc.) in the structure and the relative size of the internal structure (cell size) of the material. The point of view taken here is that the composite is a material in its own right, with its own properties that can be measured and specified for the composite as a whole.

Activity-dependent shedding of the NMDA receptor glycine binding site by matrix metalloproteinase 3: a PUTATIVE mechanism of postsynaptic plasticity.

PubMed

Pauly, Thorsten; Ratliff, Miriam; Pietrowski, Eweline; Neugebauer, Rainer; Schlicksupp, Andrea; Kirsch, Joachim; Kuhse, Jochen

2008-07-16

Functional and structural alterations of clustered postsynaptic ligand gated ion channels in neuronal cells are thought to contribute to synaptic plasticity and memory formation in the human brain. Here, we describe a novel molecular mechanism for structural alterations of NR1 subunits of the NMDA receptor. In cultured rat spinal cord neurons, chronic NMDA receptor stimulation induces disappearance of extracellular epitopes of NMDA receptor NR1 subunits, which was prevented by inhibiting matrix metalloproteinases (MMPs). Immunoblotting revealed the digestion of solubilized NR1 subunits by MMP-3 and identified a fragment of about 60 kDa as MMPs-activity-dependent cleavage product of the NR1 subunit in cultured neurons. The expression of MMP-3 in the spinal cord culture was shown by immunoblotting and immunofluorescence microscopy. Recombinant NR1 glycine binding protein was used to identify MMP-3 cleavage sites within the extracellular S1 and S2-domains. N-terminal sequencing and site-directed mutagenesis revealed S542 and L790 as two putative major MMP-3 cleavage sites of the NR1 subunit. In conclusion, our data indicate that MMPs, and in particular MMP-3, are involved in the activity dependent alteration of NMDA receptor structure at postsynaptic membrane specializations in the CNS.

Activity-Dependent Shedding of the NMDA Receptor Glycine Binding Site by Matrix Metalloproteinase 3: A PUTATIVE Mechanism of Postsynaptic Plasticity

PubMed Central

Pietrowski, Eweline; Neugebauer, Rainer; Schlicksupp, Andrea; Kirsch, Joachim; Kuhse, Jochen

2008-01-01

Functional and structural alterations of clustered postsynaptic ligand gated ion channels in neuronal cells are thought to contribute to synaptic plasticity and memory formation in the human brain. Here, we describe a novel molecular mechanism for structural alterations of NR1 subunits of the NMDA receptor. In cultured rat spinal cord neurons, chronic NMDA receptor stimulation induces disappearance of extracellular epitopes of NMDA receptor NR1 subunits, which was prevented by inhibiting matrix metalloproteinases (MMPs). Immunoblotting revealed the digestion of solubilized NR1 subunits by MMP-3 and identified a fragment of about 60 kDa as MMPs-activity-dependent cleavage product of the NR1 subunit in cultured neurons. The expression of MMP-3 in the spinal cord culture was shown by immunoblotting and immunofluorescence microscopy. Recombinant NR1 glycine binding protein was used to identify MMP-3 cleavage sites within the extracellular S1 and S2-domains. N-terminal sequencing and site-directed mutagenesis revealed S542 and L790 as two putative major MMP-3 cleavage sites of the NR1 subunit. In conclusion, our data indicate that MMPs, and in particular MMP-3, are involved in the activity dependent alteration of NMDA receptor structure at postsynaptic membrane specializations in the CNS. PMID:18629001

TEM study of {beta} Prime precipitate interaction mechanisms with dislocations and {beta} Prime interfaces with the aluminium matrix in Al-Mg-Si alloys

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

Teichmann, Katharina; Marioara, Calin D.; Andersen, Sigmund J.

The interaction mechanisms between dislocations and semi-coherent, needle-shaped {beta} Prime precipitates in Al-Mg-Si alloys have been studied by High Resolution Transmission Electron Microscopy (HRTEM). Dislocation loops appearing as broad contrast rings around the precipitate cross-sections were identified in the Al matrix. A size dependency of the interaction mechanism was observed; the precipitates were sheared when the longest dimension of their cross-section was shorter than approximately 15 nm, and looped otherwise. A more narrow ring located between the Al matrix and bulk {beta} Prime indicates the presence of a transition interface layer. Together with the bulk {beta} Prime structure, this wasmore » further investigated by High Angle Annular Dark Field Scanning TEM (HAADF-STEM). In the bulk {beta} Prime a higher intensity could be correlated with a third of the Si-columns, as predicted from the published structure. The transition layer incorporates Si columns in the same arrangement as in bulk {beta} Prime , although it is structurally distinct from it. The Z-contrast information and arrangement of these Si-columns demonstrate that they are an extension of the Si-network known to structurally connect all the precipitate phases in the Al-Mg-Si(-Cu) system. The width of the interface layer was estimated to about 1 nm. - Highlights: Black-Right-Pointing-Pointer {beta} Prime is found to be looped at sizes larger than 15 nm (cross section diameter). Black-Right-Pointing-Pointer {beta} Prime is found to be sheared at sizes smaller than 15 nm (cross section diameter). Black-Right-Pointing-Pointer The recently determined crystal structure of {beta} Prime is confirmed by HAADF-STEM. Black-Right-Pointing-Pointer Between {beta} Prime and the Al-matrix a transition layer of about 1 nm is existent. Black-Right-Pointing-Pointer The {beta} Prime /matrix layer is structurally distinct from bulk {beta} Prime and the aluminium matrix.« less

Biofilms produced by Burkholderia cenocepacia: influence of media and solid supports on composition of matrix exopolysaccharides.

PubMed

Pellizzoni, Elena; Ravalico, Fabio; Scaini, Denis; Delneri, Ambra; Rizzo, Roberto; Cescutti, Paola

2016-02-01

Bacteria usually grow forming biofilms, which are communities of cells embedded in a self-produced dynamic polymeric matrix, characterized by a complex three-dimensional structure. The matrix holds cells together and above a surface, and eventually releases them, resulting in colonization of other surfaces. Although exopolysaccharides (EPOLs) are important components of the matrix, determination of their structure is usually performed on samples produced in non-biofilm conditions, or indirectly through genetic studies. Among the Burkholderia cepacia complex species, Burkholderia cenocepacia is an important pathogen in cystic fibrosis (CF) patients and is generally more aggressive than other species. In the present investigation, B. cenocepacia strain BTS2, a CF isolate, was grown in biofilm mode on glass slides and cellulose membranes, using five growth media, one of which mimics the nutritional content of CF sputum. The structure of the matrix EPOLs was determined by 1H-NMR spectroscopy, while visualization of the biofilms on glass slides was obtained by means of confocal laser microscopy, phase-contrast microscopy and atomic force microscopy. The results confirmed that the type of EPOLs biosynthesized depends both on the medium used and on the type of support, and showed that mucoid conditions do not always lead to significant biofilm production, while bacteria in a non-mucoid state can still form biofilm containing EPOLs.

Myc-induced anchorage of the rDNA IGS region to nucleolar matrix modulates growth-stimulated changes in higher-order rDNA architecture

PubMed Central

Shiue, Chiou-Nan; Nematollahi-Mahani, Amir; Wright, Anthony P.H.

2014-01-01

Chromatin domain organization and the compartmentalized distribution of chromosomal regions are essential for packaging of deoxyribonucleic acid (DNA) in the eukaryotic nucleus as well as regulated gene expression. Nucleoli are the most prominent morphological structures of cell nuclei and nucleolar organization is coupled to cell growth. It has been shown that nuclear scaffold/matrix attachment regions often define the base of looped chromosomal domains in vivo and that they are thereby critical for correct chromosome architecture and gene expression. Here, we show regulated organization of mammalian ribosomal ribonucleic acid genes into distinct chromatin loops by tethering to nucleolar matrix via the non-transcribed inter-genic spacer region of the ribosomal DNA (rDNA). The rDNA gene loop structures are induced specifically upon growth stimulation and are dependent on the activity of the c-Myc protein. Matrix-attached rDNA genes are hypomethylated at the promoter and are thus available for transcriptional activation. rDNA genes silenced by methylation are not recruited to the matrix. c-Myc, which has been shown to induce rDNA transcription directly, is physically associated with rDNA gene looping structures and the intergenic spacer sequence in growing cells. Such a role of Myc proteins in gene activation has not been reported previously. PMID:24609384

Myc-induced anchorage of the rDNA IGS region to nucleolar matrix modulates growth-stimulated changes in higher-order rDNA architecture.

PubMed

Shiue, Chiou-Nan; Nematollahi-Mahani, Amir; Wright, Anthony P H

2014-05-01

Chromatin domain organization and the compartmentalized distribution of chromosomal regions are essential for packaging of deoxyribonucleic acid (DNA) in the eukaryotic nucleus as well as regulated gene expression. Nucleoli are the most prominent morphological structures of cell nuclei and nucleolar organization is coupled to cell growth. It has been shown that nuclear scaffold/matrix attachment regions often define the base of looped chromosomal domains in vivo and that they are thereby critical for correct chromosome architecture and gene expression. Here, we show regulated organization of mammalian ribosomal ribonucleic acid genes into distinct chromatin loops by tethering to nucleolar matrix via the non-transcribed inter-genic spacer region of the ribosomal DNA (rDNA). The rDNA gene loop structures are induced specifically upon growth stimulation and are dependent on the activity of the c-Myc protein. Matrix-attached rDNA genes are hypomethylated at the promoter and are thus available for transcriptional activation. rDNA genes silenced by methylation are not recruited to the matrix. c-Myc, which has been shown to induce rDNA transcription directly, is physically associated with rDNA gene looping structures and the intergenic spacer sequence in growing cells. Such a role of Myc proteins in gene activation has not been reported previously. © 2014 The Author(s). Published by Oxford University Press [on behalf of Nucleic Acids Research].

A self-recalibration method based on scale-invariant registration for structured light measurement systems

NASA Astrophysics Data System (ADS)

Chen, Rui; Xu, Jing; Zhang, Song; Chen, Heping; Guan, Yong; Chen, Ken

2017-01-01

The accuracy of structured light measurement depends on delicate offline calibration. However, in some practical applications, the system is supposed to be reconfigured so frequently to track the target that an online calibration is required. To this end, this paper proposes a rapid and autonomous self-recalibration method. For the proposed method, first, the rotation matrix and the normalized translation vector are attained from the fundamental matrix; second, the scale factor is acquired based on scale-invariant registration such that the actual translation vector is obtained. Experiments have been conducted to verify the effectiveness of our proposed method and the results indicate a high degree of accuracy.

Reliability and life prediction of ceramic composite structures at elevated temperatures

NASA Technical Reports Server (NTRS)

Duffy, Stephen F.; Gyekenyesi, John P.

1994-01-01

Methods are highlighted that ascertain the structural reliability of components fabricated of composites with ceramic matrices reinforced with ceramic fibers or whiskers and subject to quasi-static load conditions at elevated temperatures. Each method focuses on a particular composite microstructure: whisker-toughened ceramics, laminated ceramic matrix composites, and fabric reinforced ceramic matrix composites. In addition, since elevated service temperatures usually involve time-dependent effects, a section dealing with reliability degradation as a function of load history has been included. A recurring theme throughout this chapter is that even though component failure is controlled by a sequence of many microfailure events, failure of ceramic composites will be modeled using macrovariables.

Age-dependence of power spectral density and fractal dimension of bone mineralized matrix in atomic force microscope topography images: potential correlates of bone tissue age and bone fragility in female femoral neck trabeculae

PubMed Central

Milovanovic, Petar; Djuric, Marija; Rakocevic, Zlatko

2012-01-01

There is an increasing interest in bone nano-structure, the ultimate goal being to reveal the basis of age-related bone fragility. In this study, power spectral density (PSD) data and fractal dimensions of the mineralized bone matrix were extracted from atomic force microscope topography images of the femoral neck trabeculae. The aim was to evaluate age-dependent differences in the mineralized matrix of human bone and to consider whether these advanced nano-descriptors might be linked to decreased bone remodeling observed by some authors and age-related decline in bone mechanical competence. The investigated bone specimens belonged to a group of young adult women (n = 5, age: 20–40 years) and a group of elderly women (n = 5, age: 70–95 years) without bone diseases. PSD graphs showed the roughness density distribution in relation to spatial frequency. In all cases, there was a fairly linear decrease in magnitude of the power spectra with increasing spatial frequencies. The PSD slope was steeper in elderly individuals (−2.374 vs. −2.066), suggesting the dominance of larger surface morphological features. Fractal dimension of the mineralized bone matrix showed a significant negative trend with advanced age, declining from 2.467 in young individuals to 2.313 in the elderly (r = 0.65, P = 0.04). Higher fractal dimension in young women reflects domination of smaller mineral grains, which is compatible with the more freshly remodeled structure. In contrast, the surface patterns in elderly individuals were indicative of older tissue age. Lower roughness and reduced structural complexity (decreased fractal dimension) of the interfibrillar bone matrix in the elderly suggest a decline in bone toughness, which explains why aged bone is more brittle and prone to fractures. PMID:22946475

Age-dependence of power spectral density and fractal dimension of bone mineralized matrix in atomic force microscope topography images: potential correlates of bone tissue age and bone fragility in female femoral neck trabeculae.

PubMed

Milovanovic, Petar; Djuric, Marija; Rakocevic, Zlatko

2012-11-01

There is an increasing interest in bone nano-structure, the ultimate goal being to reveal the basis of age-related bone fragility. In this study, power spectral density (PSD) data and fractal dimensions of the mineralized bone matrix were extracted from atomic force microscope topography images of the femoral neck trabeculae. The aim was to evaluate age-dependent differences in the mineralized matrix of human bone and to consider whether these advanced nano-descriptors might be linked to decreased bone remodeling observed by some authors and age-related decline in bone mechanical competence. The investigated bone specimens belonged to a group of young adult women (n = 5, age: 20-40 years) and a group of elderly women (n = 5, age: 70-95 years) without bone diseases. PSD graphs showed the roughness density distribution in relation to spatial frequency. In all cases, there was a fairly linear decrease in magnitude of the power spectra with increasing spatial frequencies. The PSD slope was steeper in elderly individuals (-2.374 vs. -2.066), suggesting the dominance of larger surface morphological features. Fractal dimension of the mineralized bone matrix showed a significant negative trend with advanced age, declining from 2.467 in young individuals to 2.313 in the elderly (r = 0.65, P = 0.04). Higher fractal dimension in young women reflects domination of smaller mineral grains, which is compatible with the more freshly remodeled structure. In contrast, the surface patterns in elderly individuals were indicative of older tissue age. Lower roughness and reduced structural complexity (decreased fractal dimension) of the interfibrillar bone matrix in the elderly suggest a decline in bone toughness, which explains why aged bone is more brittle and prone to fractures. © 2012 The Authors Journal of Anatomy © 2012 Anatomical Society.

The sintered microsphere matrix for bone tissue engineering: in vitro osteoconductivity studies.

PubMed

Borden, Mark; Attawia, Mohamed; Laurencin, Cato T

2002-09-05

A tissue engineering approach has been used to design three-dimensional synthetic matrices for bone repair. The osteoconductivity and degradation profile of a novel polymeric bone-graft substitute was evaluated in an in vitro setting. Using the copolymer poly(lactide-co-glycolide) [PLAGA], a sintering technique based on microsphere technology was used to fabricate three-dimensional porous scaffolds for bone regeneration. Osteoblasts and fibroblasts were seeded onto a 50:50 PLAGA scaffold. Morphologic evaluation through scanning electron microscopy demonstrated that both cell types attached and spread over the scaffold. Cells migrated through the matrix using cytoplasmic extensions to bridge the structure. Cross-sectional images indicated that cellular proliferation had penetrated into the matrix approximately 700 microm from the surface. Examination of the surfaces of cell/matrix constructs demonstrated that cellular proliferation had encompassed the pores of the matrix by 14 days of cell culture. With the aim of optimizing polymer composition and polymer molecular weight, a degradation study was conducted utilizing the matrix. The results demonstrate that degradation of the sintered matrix is dependent on molecular weight, copolymer ratio, and pore volume. From this data, it was determined that 75:25 PLAGA with an initial molecular weight of 100,000 has an optimal degradation profile. These studies show that the sintered microsphere matrix has an osteoconductive structure capable of functioning as a cellular scaffold with a degradation profile suitable for bone regeneration. Copyright 2002 Wiley Periodicals, Inc.

On the role of hydrogel structure and degradation in controlling the transport of cell-secreted matrix molecules for engineered cartilage.

PubMed

Dhote, Valentin; Skaalure, Stacey; Akalp, Umut; Roberts, Justine; Bryant, Stephanie J; Vernerey, Franck J

2013-03-01

Damage to cartilage caused by injury or disease can lead to pain and loss of mobility, diminishing one's quality of life. Because cartilage has a limited capacity for self-repair, tissue engineering strategies, such as cells encapsulated in synthetic hydrogels, are being investigated as a means to restore the damaged cartilage. However, strategies to date are suboptimal in part because designing degradable hydrogels is complicated by structural and temporal complexities of the gel and evolving tissue along multiple length scales. To address this problem, this study proposes a multi-scale mechanical model using a triphasic formulation (solid, fluid, unbound matrix molecules) based on a single chondrocyte releasing extracellular matrix molecules within a degrading hydrogel. This model describes the key players (cells, proteoglycans, collagen) of the biological system within the hydrogel encompassing different length scales. Two mechanisms are included: temporal changes of bulk properties due to hydrogel degradation, and matrix transport. Numerical results demonstrate that the temporal change of bulk properties is a decisive factor in the diffusion of unbound matrix molecules through the hydrogel. Transport of matrix molecules in the hydrogel contributes both to the development of the pericellular matrix and the extracellular matrix and is dependent on the relative size of matrix molecules and the hydrogel mesh. The numerical results also demonstrate that osmotic pressure, which leads to changes in mesh size, is a key parameter for achieving a larger diffusivity for matrix molecules in the hydrogel. The numerical model is confirmed with experimental results of matrix synthesis by chondrocytes in biodegradable poly(ethylene glycol)-based hydrogels. This model may ultimately be used to predict key hydrogel design parameters towards achieving optimal cartilage growth. Copyright © 2012 Elsevier Ltd. All rights reserved.

On the role of hydrogel structure and degradation in controlling the transport of cell-secreted matrix molecules for engineered cartilage

PubMed Central

Dhote, Valentin; Skaalure, Stacey; Akalp, Umut; Roberts, Justine; Bryant, Stephanie J.; Vernerey, Franck J.

2012-01-01

Damage to cartilage caused by injury or disease can lead to pain and loss of mobility, diminishing one’s quality of life. Because cartilage has a limited capacity for self-repair, tissue engineering strategies, such as cells encapsulated in synthetic hydrogels, are being investigated as a means to restore the damaged cartilage. However, strategies to date are suboptimal in part because designing degradable hydrogels is complicated by structural and temporal complexities of the gel and evolving tissue along multiple length scales. To address this problem, this study proposes a multi-scale mechanical model using a triphasic formulation (solid, fluid, unbound matrix molecules) based on a single chondrocyte releasing extracellular matrix molecules within a degrading hydrogel. This model describes the key players (cells, proteoglycans, collagen) of the biological system within the hydrogel encompassing different length scales. Two mechanisms are included: temporal changes of bulk properties due to hydrogel degradation, and matrix transport. Numerical results demonstrate that the temporal change of bulk properties is a decisive factor in the diffusion of unbound matrix molecules through the hydrogel. Transport of matrix molecules in the hydrogel contributes both to the development of the pericellular matrix and the extracellular matrix and is dependent on the relative size of matrix molecules and the hydrogel mesh. The numerical results also demonstrate that osmotic pressure, which leads to changes in mesh size, is a key parameter for achieving a larger diffusivity for matrix molecules in the hydrogel. The numerical model is confirmed with experimental results of matrix synthesis by chondrocytes in biodegradable poly(ethylene glycol)-based hydrogels. This model may ultimately be used to predict key hydrogel design parameters towards achieving optimal cartilage growth. PMID:23276516

A novel physical eco-hydrological model concept for preferential flow based on experimental applications.

NASA Astrophysics Data System (ADS)

Jackisch, Conrad; van Schaik, Loes; Graeff, Thomas; Zehe, Erwin

2014-05-01

Preferential flow through macropores often determines hydrological characteristics - especially regarding runoff generation and fast transport of solutes. Macropore settings may yet be very different in nature and dynamics, depending on their origin. While biogenic structures follow activity cycles (e.g. earth worms) and population conditions (e.g. roots), pedogenic and geogenic structures may depend on water stress (e.g. cracks) or large events (e.g. flushed voids between skeleton and soil pipes) or simply persist (e.g. bedrock interface). On the one hand, such dynamic site characteristics can be observed in seasonal changes in its reaction to precipitation. On the other hand, sprinkling experiments accompanied by tracers or time-lapse 3D Ground-Penetrating-Radar are suitable tools to determine infiltration patterns and macropore configuration. However, model representation of the macropore-matrix system is still problematic, because models either rely on effective parameters (assuming well-mixed state) or on explicit advection strongly simplifying or neglecting interaction with the diffusive flow domain. Motivated by the dynamic nature of macropores, we present a novel model approach for interacting diffusive and advective water, solutes and energy transport in structured soils. It solely relies on scale- and process-aware observables. A representative set of macropores (data from sprinkling experiments) determines the process model scale through 1D advective domains. These are connected to a 2D matrix domain which is defined by pedo-physical retention properties. Water is represented as particles. Diffusive flow is governed by a 2D random walk of these particles while advection may take place in the macropore domain. Macropore-matrix interaction is computed as dissipation of the advective momentum of a particle by its experienced drag from the matrix domain. Through a representation of matrix and macropores as connected diffusive and advective domains for water transport we open up double domain concepts linking porescale physics to preferential macroscale fingerprints without effective parameterisation or mixing assumptions. Moreover, solute transport, energy balance aspects and lateral heterogeneity in soil moisture distribution are intrinsically captured. In addition, macropore and matrix domain settings may change over time based on physical and stochastic observations. The representativity concept allows scaleability from plotscale to the lower mesoscale.

Robust Image Regression Based on the Extended Matrix Variate Power Exponential Distribution of Dependent Noise.

PubMed

Luo, Lei; Yang, Jian; Qian, Jianjun; Tai, Ying; Lu, Gui-Fu

2017-09-01

Dealing with partial occlusion or illumination is one of the most challenging problems in image representation and classification. In this problem, the characterization of the representation error plays a crucial role. In most current approaches, the error matrix needs to be stretched into a vector and each element is assumed to be independently corrupted. This ignores the dependence between the elements of error. In this paper, it is assumed that the error image caused by partial occlusion or illumination changes is a random matrix variate and follows the extended matrix variate power exponential distribution. This has the heavy tailed regions and can be used to describe a matrix pattern of l×m dimensional observations that are not independent. This paper reveals the essence of the proposed distribution: it actually alleviates the correlations between pixels in an error matrix E and makes E approximately Gaussian. On the basis of this distribution, we derive a Schatten p -norm-based matrix regression model with L q regularization. Alternating direction method of multipliers is applied to solve this model. To get a closed-form solution in each step of the algorithm, two singular value function thresholding operators are introduced. In addition, the extended Schatten p -norm is utilized to characterize the distance between the test samples and classes in the design of the classifier. Extensive experimental results for image reconstruction and classification with structural noise demonstrate that the proposed algorithm works much more robustly than some existing regression-based methods.

Structure and evolutionary aspects of matrix metalloproteinases: a brief overview.

PubMed

Das, Sudip; Mandal, Malay; Chakraborti, Tapati; Mandal, Amritlal; Chakraborti, Sajal

2003-11-01

The matrix metalloproteinases (MMPs) are zinc dependent endopeptidases known for their ability to cleave one or several extracellular matrix (ECM) constituents, as well as non-matrix proteins. They comprise a large family of proteinases that share common structural and functional elements and are products of different genes. All members of this family contain a signal peptide, a propeptide and a catalytic domain. The catalytic domain contains two zinc ions and at least one calcium ion coordinated to various residues. All MMPs, with the exception matrilysin, have a hemopexin/vitronectin-like domain that is connected to the catalytic domain by a hinge or linker region. The hemopexin-like domain influences tissue inhibitor of metalloproteinases (TIMP) binding, the binding of certain substrates, membrane activation, and some proteolytic activities. It has been proposed that the origin of MMPs could be traced to before the emergence of vertebrates from invertebrates. It appears conceivable that the domain assemblies occurred at an early stage of the diversification of different MMPs and that they progressed through the evolutionary process independent of one another, and perhaps parallel to each other.

Geometry of matrix product states: Metric, parallel transport, and curvature

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

Haegeman, Jutho, E-mail: jutho.haegeman@gmail.com; Verstraete, Frank; Faculty of Physics and Astronomy, University of Ghent, Krijgslaan 281 S9, 9000 Gent

2014-02-15

We study the geometric properties of the manifold of states described as (uniform) matrix product states. Due to the parameter redundancy in the matrix product state representation, matrix product states have the mathematical structure of a (principal) fiber bundle. The total space or bundle space corresponds to the parameter space, i.e., the space of tensors associated to every physical site. The base manifold is embedded in Hilbert space and can be given the structure of a Kähler manifold by inducing the Hilbert space metric. Our main interest is in the states living in the tangent space to the base manifold,more » which have recently been shown to be interesting in relation to time dependence and elementary excitations. By lifting these tangent vectors to the (tangent space) of the bundle space using a well-chosen prescription (a principal bundle connection), we can define and efficiently compute an inverse metric, and introduce differential geometric concepts such as parallel transport (related to the Levi-Civita connection) and the Riemann curvature tensor.« less

Curcumin: a potential candidate for matrix metalloproteinase inhibitors.

PubMed

Kumar, Dileep; Kumar, Manish; Saravanan, Chinnadurai; Singh, Sushil Kumar

2012-10-01

Curcumin, a natural yellow pigment of turmeric, has become focus of interest with regard to its role in regulation of matrix metalloproteinases (MMPs). MMPs are metal-dependent endopeptidases capable of degrading components of the extracellular matrix. MMPs are involved in chronic diseases such as arthritis, Alzheimer's disease, psoriasis, chronic obstructive pulmonary disease, asthma, cancer, neuropathic pain, and atherosclerosis. Curcumin regulates the expression and secretion of various MMPs. This review documents the matrix metalloproteinase inhibitory activity of curcumin on various diseases viz., cancer, arthritis, and ulcer. Finally, the steps to be taken for getting potent curcuminoids have also been discussed in the structure-activity relationship (SAR) section. From this review, readers can get answer to the question: Is curcumin a potential MMPI candidate? Numerous approaches have been taken to beget a molecule with specificity restricted to a particular MMP as well as good oral bioavailability; however, nearly all the molecules lack these criteria. Using quantitative structure-activity relationship (QSAR) modeling and virtual screening, new analogs of curcumin can be designed which will be selectively inhibiting different MMPs.

Matrix Gelatinases in Atherosclerosis and Diabetic Nephropathy: Progress and Challenges.

PubMed

Dimas, Grigorios G; Didangelos, Triantafyllos P; Grekas, Dimitrios M

2017-01-01

Matrix metalloproteinases (MMPs) are zinc-dependent proteases that degrade components of the extracellular matrix (ECM). In glomerular disease, MMPs are major regulators of ECM degradation as well as structural and functional integrity in the glomerulus. In altered matrix composition diseases, glomerular damage is due to increased degradation of kidney and vessel basement membranes (BMs) by MMPs. MMP -2 and -9 are both considered as the main enzymes that degrade collagen type-IV (coll-IV), which represents the key collagenous component of ECM and constitutes the architectural structure of vessels and glomerular BM. There is growing evidence implicating MMPs in atherosclerosis as well as in cardiovascular disease (CVD) and chronic kidney disease (CKD). Specific endogenous tissue inhibitors of MMPs (TIMPs) are also implicated in CKD, CVD and diabetic nephropathy (DN). The present review discusses the role of MMPs -2 and -9 in DN, as a leading cause of endstage renal disease and as a model of the link between progressive glomerulosclerosis and MMP expression. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Mechanical Properties of Nanostructured Materials Determined Through Molecular Modeling Techniques

NASA Technical Reports Server (NTRS)

Clancy, Thomas C.; Gates, Thomas S.

2005-01-01

The potential for gains in material properties over conventional materials has motivated an effort to develop novel nanostructured materials for aerospace applications. These novel materials typically consist of a polymer matrix reinforced with particles on the nanometer length scale. In this study, molecular modeling is used to construct fully atomistic models of a carbon nanotube embedded in an epoxy polymer matrix. Functionalization of the nanotube which consists of the introduction of direct chemical bonding between the polymer matrix and the nanotube, hence providing a load transfer mechanism, is systematically varied. The relative effectiveness of functionalization in a nanostructured material may depend on a variety of factors related to the details of the chemical bonding and the polymer structure at the nanotube-polymer interface. The objective of this modeling is to determine what influence the details of functionalization of the carbon nanotube with the polymer matrix has on the resulting mechanical properties. By considering a range of degree of functionalization, the structure-property relationships of these materials is examined and mechanical properties of these models are calculated using standard techniques.

Activity-Dependent Exocytosis of Lysosomes Regulates the Structural Plasticity of Dendritic Spines.

PubMed

Padamsey, Zahid; McGuinness, Lindsay; Bardo, Scott J; Reinhart, Marcia; Tong, Rudi; Hedegaard, Anne; Hart, Michael L; Emptage, Nigel J

2017-01-04

Lysosomes have traditionally been viewed as degradative organelles, although a growing body of evidence suggests that they can function as Ca 2+ stores. Here we examined the function of these stores in hippocampal pyramidal neurons. We found that back-propagating action potentials (bpAPs) could elicit Ca 2+ release from lysosomes in the dendrites. This Ca 2+ release triggered the fusion of lysosomes with the plasma membrane, resulting in the release of Cathepsin B. Cathepsin B increased the activity of matrix metalloproteinase 9 (MMP-9), an enzyme involved in extracellular matrix (ECM) remodelling and synaptic plasticity. Inhibition of either lysosomal Ca 2+ signaling or Cathepsin B release prevented the maintenance of dendritic spine growth induced by Hebbian activity. This impairment could be rescued by exogenous application of active MMP-9. Our findings suggest that activity-dependent exocytosis of Cathepsin B from lysosomes regulates the long-term structural plasticity of dendritic spines by triggering MMP-9 activation and ECM remodelling. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

Discontinuities in effective permeability due to fracture percolation

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

Hyman, Jeffrey De'Haven; Karra, Satish; Carey, James William

Motivated by a triaxial coreflood experiment with a sample of Utica shale where an abrupt jump in permeability was observed, possibly due to the creation of a percolating fracture network through the sample, we perform numerical simulations based on the experiment to characterize how the effective permeability of otherwise low-permeability porous media depends on fracture formation, connectivity, and the contrast between the fracture and matrix permeabilities. While a change in effective permeability due to fracture formation is expected, the dependence of its magnitude upon the contrast between the matrix permeability and fracture permeability and the fracture network structure is poorlymore » characterized. We use two different high-fidelity fracture network models to characterize how effective permeability changes as percolation occurs. The first is a dynamic two-dimensional fracture propagation model designed to mimic the laboratory settings of the experiment. The second is a static three-dimensional discrete fracture network (DFN) model, whose fracture and network statistics are based on the fractured sample of Utica shale. Once the network connects the inflow and outflow boundaries, the effective permeability increases non-linearly with network density. In most networks considered, a jump in the effective permeability was observed when the embedded fracture network percolated. We characterize how the magnitude of the jump, should it occur, depends on the contrast between the fracture and matrix permeabilities. For small contrasts between the matrix and fracture permeabilities the change is insignificant. However, for larger contrasts, there is a substantial jump whose magnitude depends non-linearly on the difference between matrix and fracture permeabilities. A power-law relationship between the size of the jump and the difference between the matrix and fracture permeabilities is observed. In conclusion, the presented results underscore the importance of fracture network topology on the upscaled properties of the porous medium in which it is embedded.« less

Discontinuities in effective permeability due to fracture percolation

DOE PAGES

Hyman, Jeffrey De'Haven; Karra, Satish; Carey, James William; ...

2018-01-31

Motivated by a triaxial coreflood experiment with a sample of Utica shale where an abrupt jump in permeability was observed, possibly due to the creation of a percolating fracture network through the sample, we perform numerical simulations based on the experiment to characterize how the effective permeability of otherwise low-permeability porous media depends on fracture formation, connectivity, and the contrast between the fracture and matrix permeabilities. While a change in effective permeability due to fracture formation is expected, the dependence of its magnitude upon the contrast between the matrix permeability and fracture permeability and the fracture network structure is poorlymore » characterized. We use two different high-fidelity fracture network models to characterize how effective permeability changes as percolation occurs. The first is a dynamic two-dimensional fracture propagation model designed to mimic the laboratory settings of the experiment. The second is a static three-dimensional discrete fracture network (DFN) model, whose fracture and network statistics are based on the fractured sample of Utica shale. Once the network connects the inflow and outflow boundaries, the effective permeability increases non-linearly with network density. In most networks considered, a jump in the effective permeability was observed when the embedded fracture network percolated. We characterize how the magnitude of the jump, should it occur, depends on the contrast between the fracture and matrix permeabilities. For small contrasts between the matrix and fracture permeabilities the change is insignificant. However, for larger contrasts, there is a substantial jump whose magnitude depends non-linearly on the difference between matrix and fracture permeabilities. A power-law relationship between the size of the jump and the difference between the matrix and fracture permeabilities is observed. In conclusion, the presented results underscore the importance of fracture network topology on the upscaled properties of the porous medium in which it is embedded.« less

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.

Impact of change of matrix crystallinity and polymorphism on ovalbumin release from lipid-based implants.

PubMed

Duque, Luisa; Körber, Martin; Bodmeier, Roland

2018-05-30

The objectives of this study were to prepare lipid-based implants by hot melt extrusion (HME) for the prolonged release of ovalbumin (OVA), and to relate protein release to crystallinity and polymorphic changes of the lipid matrix. Two lipids, glycerol tristearate and hydrogenated palm oil, with different composition and degree of crystallinity were studied. Solid OVA was dispersed within the lipid matrixes, which preserved its stability during extrusion. This was partially attributed to a protective effect of the lipidic matrix. The incorporation of OVA decreased the mechanical strength of the implants prepared with the more crystalline matrix, glycerol tristearate, whereas it remained comparable for the hydrogenated palm oil because of stronger physical and non-covalent interactions between the protein and this lipid. This was also the reason for the faster release of OVA from the glycerol tristearate matrix when compared to the hydrogenated palm oil (8 vs. 28 weeks). Curing induced and increased crystallinity, and changes in the release rate, especially for the more crystalline matrix. In this case, both an increase and a decrease in release, were observed depending on the tempering condition. Curing at higher temperatures induced a melt-mediated crystallization and solid state transformation of the glycerol tristearate matrix and led to rearrangements of the inner structure with the formation of larger pores, which accelerated the release. In contrast, changes in the hydrogenated palm oil under the same curing conditions were less noticeable leading to a more robust formulation, because of less polymorphic changes over time. This study helps to understand the effect of lipid matrix composition and crystallinity degree on the performance of protein-loaded implants, and to establish criteria for the selection of a lipid carrier depending on the release profile desired. Copyright © 2018. Published by Elsevier B.V.

The dimer interface of the membrane type 1 matrix metalloproteinase hemopexin domain: crystal structure and biological functions.

PubMed

Tochowicz, Anna; Goettig, Peter; Evans, Richard; Visse, Robert; Shitomi, Yasuyuki; Palmisano, Ralf; Ito, Noriko; Richter, Klaus; Maskos, Klaus; Franke, Daniel; Svergun, Dmitri; Nagase, Hideaki; Bode, Wolfram; Itoh, Yoshifumi

2011-03-04

Homodimerization is an essential step for membrane type 1 matrix metalloproteinase (MT1-MMP) to activate proMMP-2 and to degrade collagen on the cell surface. To uncover the molecular basis of the hemopexin (Hpx) domain-driven dimerization of MT1-MMP, a crystal structure of the Hpx domain was solved at 1.7 Å resolution. Two interactions were identified as potential biological dimer interfaces in the crystal structure, and mutagenesis studies revealed that the biological dimer possesses a symmetrical interaction where blades II and III of molecule A interact with blades III and II of molecule B. The mutations of amino acids involved in the interaction weakened the dimer interaction of Hpx domains in solution, and incorporation of these mutations into the full-length enzyme significantly inhibited dimer-dependent functions on the cell surface, including proMMP-2 activation, collagen degradation, and invasion into the three-dimensional collagen matrix, whereas dimer-independent functions, including gelatin film degradation and two-dimensional cell migration, were not affected. These results shed light on the structural basis of MT1-MMP dimerization that is crucial to promote cellular invasion.

Evidence for novel age-dependent network structures as a putative primo vascular network in the dura mater of the rat brain

PubMed Central

Lee, Ho-Sung; Kang, Dai-In; Yoon, Seung Zhoo; Ryu, Yeon Hee; Lee, Inhyung; Kim, Hoon-Gi; Lee, Byung-Cheon; Lee, Ki Bog

2015-01-01

With chromium-hematoxylin staining, we found evidence for the existence of novel age-dependent network structures in the dura mater of rat brains. Under stereomicroscopy, we noticed that chromium-hematoxylin-stained threadlike structures, which were barely observable in 1-week-old rats, were networked in specific areas of the brain, for example, the lateral lobes and the cerebella, in 4-week-old rats. In 7-week-old rats, those structures were found to have become larger and better networked. With phase contrast microscopy, we found that in 1-week-old rats, chromium-hematoxylin-stained granules were scattered in the same areas of the brain in which the network structures would later be observed in the 4- and 7-week-old rats. Such age-dependent network structures were examined by using optical and transmission electron microscopy, and the following results were obtained. The scattered granules fused into networks with increasing age. Cross-sections of the age-dependent network structures demonstrated heavily-stained basophilic substructures. Transmission electron microscopy revealed the basophilic substructures to be clusters with high electron densities consisting of nanosized particles. We report these data as evidence for the existence of age-dependent network structures in the dura mater, we discuss their putative functions of age-dependent network structures beyond the general concept of the dura mater as a supporting matrix. PMID:26330833

Optimal Tikhonov Regularization in Finite-Frequency Tomography

NASA Astrophysics Data System (ADS)

Fang, Y.; Yao, Z.; Zhou, Y.

2017-12-01

The last decade has witnessed a progressive transition in seismic tomography from ray theory to finite-frequency theory which overcomes the resolution limit of the high-frequency approximation in ray theory. In addition to approximations in wave propagation physics, a main difference between ray-theoretical tomography and finite-frequency tomography is the sparseness of the associated sensitivity matrix. It is well known that seismic tomographic problems are ill-posed and regularizations such as damping and smoothing are often applied to analyze the tradeoff between data misfit and model uncertainty. The regularizations depend on the structure of the matrix as well as noise level of the data. Cross-validation has been used to constrain data uncertainties in body-wave finite-frequency inversions when measurements at multiple frequencies are available to invert for a common structure. In this study, we explore an optimal Tikhonov regularization in surface-wave phase-velocity tomography based on minimization of an empirical Bayes risk function using theoretical training datasets. We exploit the structure of the sensitivity matrix in the framework of singular value decomposition (SVD) which also allows for the calculation of complete resolution matrix. We compare the optimal Tikhonov regularization in finite-frequency tomography with traditional tradeo-off analysis using surface wave dispersion measurements from global as well as regional studies.

Chemical/molecular structure of the dentin-enamel junction is dependent on the intratooth location.

PubMed

Xu, Changqi; Yao, Xiaomei; Walker, Mary P; Wang, Yong

2009-03-01

The dentin-enamel junction (DEJ) plays an important role in preventing crack propagation from enamel into dentin. This function stems from its complex structure and materials properties that are different from either dentin or enamel. The molecular structural differences in both mineral and organic matrix across the DEJ zone were investigated by two-dimensional confocal Raman microspectroscopic mapping/imaging technique. The intensity ratios of 1450 (CH, matrix)/960 (P-O, mineral) decreased gradually to nearly zero across the DEJ. The width of this transition zone was dependent on the intratooth location, with 12.9 +/- 3.2 microm width at occlusal positions and 6.2 +/- 1.3 microm at cervical positions. The difference in width was significant (P < 0.001). Concurrently, spectral differences in both organic and inorganic matrices across the DEJ were also noted. For example, the ratios of 1243 (amide III)/1450 (CH) within the DEJ were lower than the values in dentin; however, the ratios of 1665 (amide I)/1450 (CH) within the DEJ were higher than those values in dentin. In addition, the ratios of 1070 (carbonate)/960 (phosphate) within the dentin were lower than the values in the DEJ. Raman images indicated that the distribution of the above ratios across the DEJ zone were also different at occlusal and cervical positions. The results suggest that the intratooth-location-dependent structure of the DEJ may be related to its function. Micro-Raman spectroscopic/imaging analysis of the DEJ provides a powerful means of identifying the functional width and molecular structural differences across the DEJ.

High-Temperature Formation Phases and Crystal Structure of Hot-Pressed Thermoelectric CuGaTe2 with Chalcopyrite-Type Structure

NASA Astrophysics Data System (ADS)

Fujii, Yosuke; Kosuga, Atsuko

2017-11-01

Polycrystalline CuGaTe2 with a chalcopyrite-type structure consolidated by hot-pressing is a potential candidate as a medium-temperature thermoelectric (TE) material. However, its high-temperature formation phases have rarely been reported to date. Here, we investigated the temperature-dependent formation phases and crystal structure at 300-800 K of hot-pressed CuGaTe2. From synchrotron x-ray diffraction data and crystal structure analysis of the heating and cooling processes, it was clarified that a certain amount of impurity phases, such as Te and CuTe, precipitated from the CuGaTe2 matrix when the temperature was increased (to 500-650 K). This is the temperature range where CuGaTe2 has been reported to show high TE performance. After CuGaTe2 was heated to 800 K, such impurity phases remained, even when cooled to room temperature. They also affected the tetragonal distortion and the x-coordinate of Te in the CuGaTe2 matrix, probably due to deficiencies of Cu and Te in the matrix. Our results reveal detailed information on the formation phases of CuGaTe2 at high temperature and thus provide insight for evaluation of its high-temperature stability and transport properties.

R-Matrix Analysis of Structures in Economic Indices: from Nuclear Reactions to High-Frequency Trading

NASA Astrophysics Data System (ADS)

Firk, Frank W. K.

2014-03-01

It is shown that the R-matrix theory of nuclear reactions is a viable mathematical theory for the description of the fine, intermediate and gross structure observed in the time-dependence of economic indices in general, and the daily Dow Jones Industrial Average in particular. A Lorentzian approximation to R-matrix theory is used to analyze the complex structures observed in the Dow Jones Industrial Average on a typical trading day. Resonant structures in excited nuclei are characterized by the values of their fundamental strength function, (average total width of the states)/(average spacing between adjacent states). Here, values of the ratios (average lifetime of individual states of a given component of the daily Dow Jones Industrial Average)/(average interval between the adjacent states) are determined. The ratios for the observed fine and intermediate structure of the index are found to be essentially constant throughout the trading day. These quantitative findings are characteristic of the highly statistical nature of many-body, strongly interacting systems, typified by daily trading. It is therefore proposed that the values of these ratios, determined in the first hour-or-so of trading, be used to provide valuable information concerning the likely performance of the fine and intermediate components of the index for the remainder of the trading day.

Structural phase composition and effectiveness of gas-dynamic spraying of hybrid coatings based on AlMg2 nanocrystalline matrix reinforced with graphene-like structures and micro-size corundum

NASA Astrophysics Data System (ADS)

Aborkin, A. V.; Sobol'kov, A. V.; Elkin, A. I.; Arkhipov, V. E.

2018-01-01

The method of cold gas-dynamic spraying of mechanically synthesized powders based on a nanocrystalline AlMg2 matrix reinforced with graphene-like structures and micro-sized corundum particles was used for obtaining hybrid coatings. A feature of the formed coatings is the presence of a two-level micro- and nanocomposite structure. It was found that an increase in the content of corundum microdimensional particles in the mixture from 10 to 30% by weight contributes to an increase in the thickness of the coating obtained at the same time by a factor of 2 from 140 to 310 μm. Further increase in the content of a mixture of micron-sized corundum particles to 50% by weight leads to a decrease in the thickness of the coating formed to 40 μm. The resulting coatings correspond to a high microhardness, varying depending on the composition in the range from 1.7 GPa to 3.2 GPa. The high hardness of the coatings is due to the increase in the hardness of the matrix material due to the creation of a nanocomposite structure, which increases the strength of fixing micro-sized corundum particles therein, improving the characteristics of the heterogeneous coating as a whole.

High-Temperature Formation Phases and Crystal Structure of Hot-Pressed Thermoelectric CuGaTe2 with Chalcopyrite-Type Structure

NASA Astrophysics Data System (ADS)

Fujii, Yosuke; Kosuga, Atsuko

2018-06-01

Polycrystalline CuGaTe2 with a chalcopyrite-type structure consolidated by hot-pressing is a potential candidate as a medium-temperature thermoelectric (TE) material. However, its high-temperature formation phases have rarely been reported to date. Here, we investigated the temperature-dependent formation phases and crystal structure at 300-800 K of hot-pressed CuGaTe2. From synchrotron x-ray diffraction data and crystal structure analysis of the heating and cooling processes, it was clarified that a certain amount of impurity phases, such as Te and CuTe, precipitated from the CuGaTe2 matrix when the temperature was increased (to 500-650 K). This is the temperature range where CuGaTe2 has been reported to show high TE performance. After CuGaTe2 was heated to 800 K, such impurity phases remained, even when cooled to room temperature. They also affected the tetragonal distortion and the x-coordinate of Te in the CuGaTe2 matrix, probably due to deficiencies of Cu and Te in the matrix. Our results reveal detailed information on the formation phases of CuGaTe2 at high temperature and thus provide insight for evaluation of its high-temperature stability and transport properties.

A sparse matrix-vector multiplication based algorithm for accurate density matrix computations on systems of millions of atoms

NASA Astrophysics Data System (ADS)

Ghale, Purnima; Johnson, Harley T.

2018-06-01

We present an efficient sparse matrix-vector (SpMV) based method to compute the density matrix P from a given Hamiltonian in electronic structure computations. Our method is a hybrid approach based on Chebyshev-Jackson approximation theory and matrix purification methods like the second order spectral projection purification (SP2). Recent methods to compute the density matrix scale as O(N) in the number of floating point operations but are accompanied by large memory and communication overhead, and they are based on iterative use of the sparse matrix-matrix multiplication kernel (SpGEMM), which is known to be computationally irregular. In addition to irregularity in the sparse Hamiltonian H, the nonzero structure of intermediate estimates of P depends on products of H and evolves over the course of computation. On the other hand, an expansion of the density matrix P in terms of Chebyshev polynomials is straightforward and SpMV based; however, the resulting density matrix may not satisfy the required constraints exactly. In this paper, we analyze the strengths and weaknesses of the Chebyshev-Jackson polynomials and the second order spectral projection purification (SP2) method, and propose to combine them so that the accurate density matrix can be computed using the SpMV computational kernel only, and without having to store the density matrix P. Our method accomplishes these objectives by using the Chebyshev polynomial estimate as the initial guess for SP2, which is followed by using sparse matrix-vector multiplications (SpMVs) to replicate the behavior of the SP2 algorithm for purification. We demonstrate the method on a tight-binding model system of an oxide material containing more than 3 million atoms. In addition, we also present the predicted behavior of our method when applied to near-metallic Hamiltonians with a wide energy spectrum.

Semisupervised kernel marginal Fisher analysis for face recognition.

PubMed

Wang, Ziqiang; Sun, Xia; Sun, Lijun; Huang, Yuchun

2013-01-01

Dimensionality reduction is a key problem in face recognition due to the high-dimensionality of face image. To effectively cope with this problem, a novel dimensionality reduction algorithm called semisupervised kernel marginal Fisher analysis (SKMFA) for face recognition is proposed in this paper. SKMFA can make use of both labelled and unlabeled samples to learn the projection matrix for nonlinear dimensionality reduction. Meanwhile, it can successfully avoid the singularity problem by not calculating the matrix inverse. In addition, in order to make the nonlinear structure captured by the data-dependent kernel consistent with the intrinsic manifold structure, a manifold adaptive nonparameter kernel is incorporated into the learning process of SKMFA. Experimental results on three face image databases demonstrate the effectiveness of our proposed algorithm.

METCAN-PC - METAL MATRIX COMPOSITE ANALYZER

NASA Technical Reports Server (NTRS)

Murthy, P. L.

1994-01-01

High temperature metal matrix composites offer great potential for use in advanced aerospace structural applications. The realization of this potential however, requires concurrent developments in (1) a technology base for fabricating high temperature metal matrix composite structural components, (2) experimental techniques for measuring their thermal and mechanical characteristics, and (3) computational methods to predict their behavior. METCAN (METal matrix Composite ANalyzer) is a computer program developed to predict this behavior. METCAN can be used to computationally simulate the non-linear behavior of high temperature metal matrix composites (HT-MMC), thus allowing the potential payoff for the specific application to be assessed. It provides a comprehensive analysis of composite thermal and mechanical performance. METCAN treats material nonlinearity at the constituent (fiber, matrix, and interphase) level, where the behavior of each constituent is modeled accounting for time-temperature-stress dependence. The composite properties are synthesized from the constituent instantaneous properties by making use of composite micromechanics and macromechanics. Factors which affect the behavior of the composite properties include the fabrication process variables, the fiber and matrix properties, the bonding between the fiber and matrix and/or the properties of the interphase between the fiber and matrix. The METCAN simulation is performed as point-wise analysis and produces composite properties which are readily incorporated into a finite element code to perform a global structural analysis. After the global structural analysis is performed, METCAN decomposes the composite properties back into the localized response at the various levels of the simulation. At this point the constituent properties are updated and the next iteration in the analysis is initiated. This cyclic procedure is referred to as the integrated approach to metal matrix composite analysis. METCAN-PC is written in FORTRAN 77 for IBM PC series and compatible computers running MS-DOS. An 80286 machine with an 80287 math co-processor is required for execution. The executable requires at least 640K of RAM and DOS 3.1 or higher. The package includes sample executables which were compiled under Microsoft FORTRAN v. 5.1. The standard distribution medium for this program is one 5.25 inch 360K MS-DOS format diskette. The contents of the diskette are compressed using the PKWARE archiving tools. The utility to unarchive the files, PKUNZIP.EXE, is included. METCAN-PC was developed in 1992.

Import of a major mitochondrial enzyme depends on synergy between two distinct helices of its presequence

USDA-ARS?s Scientific Manuscript database

The human mitochondrial glutamate dehydrogenase isozymes (hGDH1 and 2) are abundant matrix-localized proteins encoded by nuclear genes. The proteins are synthesized in the cytoplasm, with an atypically long N-terminal mitochondrial targeting sequence (MTS). The results of secondary structure predi...

Some Properties of Estimated Scale Invariant Covariance Structures.

ERIC Educational Resources Information Center

Dijkstra, T. K.

1990-01-01

An example of scale invariance is provided via the LISREL model that is subject only to classical normalizations and zero constraints on the parameters. Scale invariance implies that the estimated covariance matrix must satisfy certain equations, and the nature of these equations depends on the fitting function used. (TJH)

Temporal patterns in Saturnidae (silk moth) and Sphingidae (hawk moth) assemblages in protected forests of central Uganda

PubMed Central

Akite, Perpetra; Telford, Richard J; Waring, Paul; Akol, Anne M; Vandvik, Vigdis

2015-01-01

Forest-dependent biodiversity is threatened throughout the tropics by habitat loss and land-use intensification of the matrix habitats. We resampled historic data on two moth families, known to play central roles in many ecosystem processes, to evaluate temporal changes in species richness and community structure in three protected forests in central Uganda in a rapidly changing matrix. Our results show some significant declines in the moth species richness and the relative abundance and richness of forest-dependent species over the last 20–40 years. The observed changes in species richness and composition among different forests, ecological types, and moth groups highlight the need to repeatedly monitor biodiversity even within protected and relatively intact forests. PMID:25937916

Global Failure Modes in High Temperature Composite Structures

NASA Technical Reports Server (NTRS)

Knauss, W. G.

1998-01-01

Composite materials have been considered for many years as the major advance in the construction of energy efficient aerospace structures. Notable advances have been made in understanding the special design considerations that set composites apart from the usual "isotropic" engineering materials such as the metals. As a result, a number of significant engineering designs have been accomplished. However, one shortcoming of the currently favored composites is their relatively unforgiving behavior with respect to failure (brittleness) under seemingly mild impact conditions and large efforts are underway to rectify that situation, much along the lines of introducing thermoplastic matrix materials. Because of their relatively more pronounced (thermo) viscoelastic behavior these materials respond with "toughness" in fracture situations. From the point of view of applications requiring material strength, this property is highly desirable. This feature impacts several important and distinct engineering problems which have been' considered under this grant and cover the 1) effect of impact damage on structural (buckling) stability of composite panels, the 2) effect of time dependence on the progression of buckling instabilities, and the 3) evolution of damage and fracture at generic thickness discontinuities in structures. The latter topic has serious implications for structural stability problems (buckling failure in reinforced shell structures) as well as failure progression in stringer-reinforced shell structures. This grant has dealt with these issues. Polymer "toughness" is usually associated with uncrosslinked or thermo-plastic polymers. But, by comparison with their thermoset counterparts they tend to exhibit more pronounced time dependent material behavior; also, that time dependence can occur at lower temperatures which places restriction in the high temperature use of these "newer and tougher" materials that are not quite so serious with the thermoset matrix materials. From a structural point of view the implications of this material behavior are potentially severe in that structural failure characteristics are no longer readily observed in short term qualification tests so characteristic for aerospace structures built from typical engineering metals.

Analytical development of disturbed matrix eigenvalue problem applied to mixed convection stability analysis in Darcy media

NASA Astrophysics Data System (ADS)

Hamed, Haikel Ben; Bennacer, Rachid

2008-08-01

This work consists in evaluating algebraically and numerically the influence of a disturbance on the spectral values of a diagonalizable matrix. Thus, two approaches will be possible; to use the theorem of disturbances of a matrix depending on a parameter, due to Lidskii and primarily based on the structure of Jordan of the no disturbed matrix. The second approach consists in factorizing the matrix system, and then carrying out a numerical calculation of the roots of the disturbances matrix characteristic polynomial. This problem can be a standard model in the equations of the continuous media mechanics. During this work, we chose to use the second approach and in order to illustrate the application, we choose the Rayleigh-Bénard problem in Darcy media, disturbed by a filtering through flow. The matrix form of the problem is calculated starting from a linear stability analysis by a finite elements method. We show that it is possible to break up the general phenomenon into other elementary ones described respectively by a disturbed matrix and a disturbance. A good agreement between the two methods was seen. To cite this article: H.B. Hamed, R. Bennacer, C. R. Mecanique 336 (2008).

Effect of aperiodicity on the broadband reflection of silicon nanorod structures for photovoltaics.

PubMed

Lin, Chenxi; Huang, Ningfeng; Povinelli, Michelle L

2012-01-02

We carry out a systematic numerical study of the effects of aperiodicity on silicon nanorod anti-reflection structures. We use the scattering matrix method to calculate the average reflection loss over the solar spectrum for periodic and aperiodic arrangements of nanorods. We find that aperiodicity can either improve or deteriorate the anti-reflection performance, depending on the nanorod diameter. We use a guided random-walk algorithm to design optimal aperiodic structures that exhibit lower reflection loss than both optimal periodic and random aperiodic structures.

The dentin organic matrix - limitations of restorative dentistry hidden on the nanometer scale

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

Bertassoni, Luiz E; Orgel, Joseph P.R.; Antipova, Olga

The prevention and treatment of dental caries are major challenges occurring in dentistry. The foundations for modern management of this dental disease, estimated to affect 90% of adults in Western countries, rest upon the dependence of ultrafine interactions between synthetic polymeric biomaterials and nanostructured supramolecular assemblies that compose the tooth organic substrate. Research has shown, however, that this interaction imposes less than desirable long-term prospects for current resin-based dental restorations. Here we review progress in the identification of the nanostructural organization of the organic matrix of dentin, the largest component of the tooth structure, and highlight aspects relevant to understatingmore » the interaction of restorative biomaterials with the dentin substrate. We offer novel insights into the influence of the hierarchically assembled supramolecular structure of dentin collagen fibrils and their structural dependence on water molecules. Secondly, we review recent evidence for the participation of proteoglycans in composing the dentin organic network. Finally, we discuss the relation of these complexly assembled nanostructures with the protease degradative processes driving the low durability of current resin-based dental restorations. We argue in favour of the structural limitations that these complexly organized and inherently hydrated organic structures may impose on the clinical prospects of current hydrophobic and hydrolyzable dental polymers that establish ultrafine contact with the tooth substrate.« less

Classical r matrix of the su(2 vertical bar 2) super Yang-Mills spin chain

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

Torrielli, Alessandro

2007-05-15

In this note we straightforwardly derive and make use of the quantum R matrix for the su(2 vertical bar 2) super Yang-Mills spin chain in the manifest su(1 vertical bar 2)-invariant formulation, which solves the standard quantum Yang-Baxter equation, in order to obtain the correspondent (undressed) classical r matrix from the first order expansion in the 'deformation' parameter 2{pi}/{radical}({lambda}) and check that this last solves the standard classical Yang-Baxter equation. We analyze its bialgebra structure, its dependence on the spectral parameters, and its pole structure. We notice that it still preserves an su(1 vertical bar 2) subalgebra, thereby admitting anmore » expression in terms of a combination of projectors, which spans only a subspace of su(1 vertical bar 2)xsu(1 vertical bar 2). We study the residue at its simple pole at the origin and comment on the applicability of the classical Belavin-Drinfeld type of analysis.« less

The interface in tungsten fiber reinforced niobium metal-matrix composites. Final Report Ph.D. Thesis - Case Western Reserve Univ., Cleveland, OH

NASA Technical Reports Server (NTRS)

Grobstein, Toni L.

1989-01-01

The creep resistance of tungsten fiber reinforced niobium metal-matrix composites was evaluated. The interface region between the fiber and matrix was characterized by microhardness and electron probe microanalysis measurements which indicated that its properties were between those of fiber and matrix. However, the measured properties of the composite exceeded those calculated by the rule of mixtures even when the interface zone was assumed to retain all the strength of the fiber. The composite structure appeared to enhance the strengths of both the fibers and the matrix above what they exhibited in stand-alone tests. The effect of fiber orientation and matrix alloy composition on the fiber/matrix interface were also evaluated. Small alloying additions of zirconium and tungsten to the niobium matrix affected the creep resistance of the composites only slightly. A decrease in the creep resistance of the composite with increasing zirconium content in the matrix was ascribed to an increase in the diffusion rate of the fiber/matrix interdiffusion reaction, and a slight increase in the creep resistance of the composite was observed with an addition of 9 w percent tungsten to the matrix. In addition, Kirkendall void formation was observed at the fiber/matrix interface; the void distribution differed depending on the fiber orientation relative to the stress axis.

Integrating Temperature-Dependent Life Table Data into a Matrix Projection Model for Drosophila suzukii Population Estimation

PubMed Central

Wiman, Nik G.; Walton, Vaughn M.; Dalton, Daniel T.; Anfora, Gianfranco; Burrack, Hannah J.; Chiu, Joanna C.; Daane, Kent M.; Grassi, Alberto; Miller, Betsey; Tochen, Samantha; Wang, Xingeng; Ioriatti, Claudio

2014-01-01

Temperature-dependent fecundity and survival data was integrated into a matrix population model to describe relative Drosophila suzukii Matsumura (Diptera: Drosophilidae) population increase and age structure based on environmental conditions. This novel modification of the classic Leslie matrix population model is presented as a way to examine how insect populations interact with the environment, and has application as a predictor of population density. For D. suzukii, we examined model implications for pest pressure on crops. As case studies, we examined model predictions in three small fruit production regions in the United States (US) and one in Italy. These production regions have distinctly different climates. In general, patterns of adult D. suzukii trap activity broadly mimicked seasonal population levels predicted by the model using only temperature data. Age structure of estimated populations suggest that trap and fruit infestation data are of limited value and are insufficient for model validation. Thus, we suggest alternative experiments for validation. The model is advantageous in that it provides stage-specific population estimation, which can potentially guide management strategies and provide unique opportunities to simulate stage-specific management effects such as insecticide applications or the effect of biological control on a specific life-stage. The two factors that drive initiation of the model are suitable temperatures (biofix) and availability of a suitable host medium (fruit). Although there are many factors affecting population dynamics of D. suzukii in the field, temperature-dependent survival and reproduction are believed to be the main drivers for D. suzukii populations. PMID:25192013

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.

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.

Mimicking the extracellular matrix with functionalized, metal-assembled collagen peptide scaffolds.

PubMed

Hernandez-Gordillo, Victor; Chmielewski, Jean

2014-08-01

Natural and synthetic three-dimensional (3-D) scaffolds that mimic the microenvironment of the extracellular matrix (ECM), with growth factor storage/release and the display of cell adhesion signals, offer numerous advantages for regenerative medicine and in vitro morphogenesis and oncogenesis modeling. Here we report the design of collagen mimetic peptides (CMPs) that assemble into a highly crosslinked 3-D matrix in response to metal ion stimuli, that may be functionalized with His-tagged cargoes, such as green fluorescent protein (GFP-His8) and human epidermal growth factor (hEGF-His6). The bound hEGF-His6 was found to gradually release from the matrix in vitro and induce cell proliferation in the EGF-dependent cell line MCF10A. The additional incorporation of a cell adhesion sequence (RGDS) at the N-terminus of the CMP creates an environment that facilitated the organization of matrix-encapsulated MCF10A cells into spheroid structures, thus mimicking the ECM environment. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

1988-11-01

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

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

NASA Astrophysics Data System (ADS)

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

1988-11-01

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

Systematic sparse matrix error control for linear scaling electronic structure calculations.

PubMed

Rubensson, Emanuel H; Sałek, Paweł

2005-11-30

Efficient truncation criteria used in multiatom blocked sparse matrix operations for ab initio calculations are proposed. As system size increases, so does the need to stay on top of errors and still achieve high performance. A variant of a blocked sparse matrix algebra to achieve strict error control with good performance is proposed. The presented idea is that the condition to drop a certain submatrix should depend not only on the magnitude of that particular submatrix, but also on which other submatrices that are dropped. The decision to remove a certain submatrix is based on the contribution the removal would cause to the error in the chosen norm. We study the effect of an accumulated truncation error in iterative algorithms like trace correcting density matrix purification. One way to reduce the initial exponential growth of this error is presented. The presented error control for a sparse blocked matrix toolbox allows for achieving optimal performance by performing only necessary operations needed to maintain the requested level of accuracy. Copyright 2005 Wiley Periodicals, Inc.

Rapid Engineering of Three-Dimensional, Multicellular Tissues With Polymeric Scaffolds

NASA Technical Reports Server (NTRS)

Gonda, Steve R.; Jordan, Jacqueline; Fraga, Denise N.

2007-01-01

A process has been developed for the rapid tissue engineering of multicellular-tissue-equivalent assemblies by the controlled enzymatic degradation of polymeric beads in a low-fluid-shear bioreactor. In this process, the porous polymeric beads serve as temporary scaffolds to support the assemblies of cells in a tissuelike 3D configuration during the critical initial growth phases of attachment of anchorage-dependent cells, aggregation of the cells, and formation of a 3D extracellular matrix. Once the cells are assembled into a 3D array and enmeshed in a structural supportive 3D extracellular matrix (ECM), the polymeric scaffolds can be degraded in the low-fluid-shear environment of the NASA-designed bioreactor. The natural 3D tissuelike assembly, devoid of any artificial support structure, is maintained in the low-shear bioreactor environment by the newly formed natural cellular/ECM. The elimination of the artificial scaffold allows normal tissue structure and function.

Collagenolytic Matrix Metalloproteinase Structure-Function Relationships: Insights From Molecular Dynamics Studies.

PubMed

Karabencheva-Christova, Tatyana G; Christov, Christo Z; Fields, Gregg B

2017-01-01

Several members of the zinc-dependent matrix metalloproteinase (MMP) family catalyze collagen degradation. Experimental data reveal a collaboration between different MMP domains in order to achieve efficient collagenolysis. Molecular dynamics (MD) simulations have been utilized to provide atomistic details of the collagenolytic process. The triple-helical structure of collagen exhibits local regions of flexibility, with modulation of interchain salt bridges and water bridges contributing to accessibility of individual chains by the enzyme. In turn, the hemopexin-like (HPX) domain of the MMP initially binds the triple helix and facilitates the presentation of individual strands to active site in the catalytic (CAT) domain. Extensive positive and negative correlated motions are observed between the CAT and HPX domains when collagen is bound. Ultimately, the MD simulation studies have complemented structural (NMR spectroscopy, X-ray crystallography) and kinetic analyses to provide a more detailed mechanistic view of MMP-catalyzed collagenolysis. © 2017 Elsevier Inc. All rights reserved.

Quantitative regulation of bone-mimetic, oriented collagen/apatite matrix structure depends on the degree of osteoblast alignment on oriented collagen substrates.

PubMed

Matsugaki, Aira; Isobe, Yoshihiro; Saku, Taro; Nakano, Takayoshi

2015-02-01

Bone tissue has a specific anisotropic morphology derived from collagen fiber alignment and the related apatite crystal orientation as a bone quality index. However, the precise mechanism of cellular regulation of the crystallographic orientation of apatite has not been clarified. In this study, anisotropic construction of cell-produced mineralized matrix in vitro was established by initiating organized cellular alignment and subsequent oriented bone-like matrix (collagen/apatite) production. The oriented collagen substrates with three anisotropic levels were prepared by a hydrodynamic method. Primary osteoblasts were cultured on the fabricated substrates until mineralized matrix formation is confirmed. Osteoblast alignment was successfully regulated by the level of substrate collagen orientation, with preferential alignment along the direction of the collagen fibers. Notably, both fibrous orientation of newly synthesized collagen matrix and c-axis of produced apatite crystals showed preferential orientation along the cell direction. Because the degree of anisotropy of the deposited apatite crystals showed dependency on the directional distribution of osteoblasts cultured on the oriented collagen substrates, the cell orientation determines the crystallographic anisotropy of produced apatite crystals. To the best of our knowledge, this is the first report demonstrating that bone tissue anisotropy, even the alignment of apatite crystals, is controllable by varying the degree of osteoblast alignment via regulating the level of substrate orientation. © 2014 Wiley Periodicals, Inc.

Vibrational excitation and dissociative attachment of a triatomic molecule: CO/sub 2/ in the collinear approximation

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

Wong, C.F.; Light, J.C.

1986-02-01

The effective R-matrix model and the R-matrix propagative method applied earlier to elec- tron--diatomic-molecule scattering are extended to treat dissociative attachment of collinear triatomic molecules. To describe the vibrational excitation and dissociative attachment of CO/sub 2/ in the 4-eV region, the nuclear dynamics is solved on a Wall-Porter potential-energy surface. A hybrid approach is developed in which the L/sup 2/ and R-matrix propagation methods are combined to evaluate the global R matrix. Our calculations show that it is easier to excite the symmetric mode vibrations than the asymmetric mode vibrations. Our results also show that the observed structures in themore » energy dependence of the dissociative attachment cross sections are due to the vibrational states of the negative ion (CO/sub 2/ /sup -/) and not to the vibrational states of the CO fragment.« less

Effect of Mechanical and Thermal Loading Histories on Residual Properties of SiCf/SiC Ceramic Matrix Composites

NASA Technical Reports Server (NTRS)

Almansour, Amjad; Kiser, Doug; Smith, Craig; Bhatt, Ram; Gorican, Dan; Phillips, Ron; McCue, Terry R.

2017-01-01

Silicon Carbide based Ceramic Matrix Composites (CMCs) are attractive materials for use in high-temperature structural applications in the aerospace and nuclear industries. Under high stresses and temperatures, creep degradation is the dominant damage mechanism in CMCs. Consequently, chemical vapor infiltration (CVI) SiCf/SiC ceramic matrix composites (CMC) incorporating SylramicTM-iBN SiC fibers coated with boron nitride (BN) interphase and CVI-SiC matrix were tested to examine creep behavior in air at a range of elevated temperatures of (2200 - 2700 F). Samples that survived creep tests were evaluated via RT fast fracture tensile tests to determine residual properties, with the use of acoustic emission (AE) to assess stress dependent damage initiation and progression. Microscopy of regions within the gage section of the tested specimens was performed. Observed material degradation mechanisms are discussed.

Thermal and damping behaviour of magnetic shape memory alloy composites

NASA Astrophysics Data System (ADS)

Glock, Susanne; Michaud, Véronique

2015-06-01

Single crystals of ferromagnetic shape memory alloys (MSMA) exhibit magnetic field and stress induced strains via energy dissipating twinning. Embedding single crystalline MSMA particles into a polymer matrix could thus produce composites with enhanced energy dissipation, suitable for damping applications. Composites of ferromagnetic, martensitic or austenitic Ni-Mn-Ga powders embedded in a standard epoxy matrix were produced by casting. The martensitic powder composites showed a crystal structure dependent damping behaviour that was more dissipative than that of austenitic powder or Cu-Ni reference powder composites and than that of the pure matrix. The loss ratio also increased with increasing strain amplitude and decreasing frequency, respectively. Furthermore, Ni-Mn-Ga powder composites exhibited an increased damping behaviour at the martensite/austenite transformation temperature of the Ni-Mn-Ga particles in addition to that at the glass transition temperature of the epoxy matrix, creating possible synergetic effects.

Ion irradiation to simulate neutron irradiation in model graphites: Consequences for nuclear graphite

NASA Astrophysics Data System (ADS)

Galy, N.; Toulhoat, N.; Moncoffre, N.; Pipon, Y.; Bérerd, N.; Ammar, M. R.; Simon, P.; Deldicque, D.; Sainsot, P.

2017-10-01

Due to its excellent moderator and reflector qualities, graphite was used in CO2-cooled nuclear reactors such as UNGG (Uranium Naturel-Graphite-Gaz). Neutron irradiation of graphite resulted in the production of 14C which is a key issue radionuclide for the management of the irradiated graphite waste. In order to elucidate the impact of neutron irradiation on 14C behavior, we carried out a systematic investigation of irradiation and its synergistic effects with temperature in Highly Oriented Pyrolitic Graphite (HOPG) model graphite used to simulate the coke grains of nuclear graphite. We used 13C implantation in order to simulate 14C displaced from its original structural site through recoil. The collision of the impinging neutrons with the graphite matrix carbon atoms induces mainly ballistic damage. However, a part of the recoil carbon atom energy is also transferred to the graphite lattice through electronic excitation. The effects of the different irradiation regimes in synergy with temperature were simulated using ion irradiation by varying Sn(nuclear)/Se(electronic) stopping power. Thus, the samples were irradiated with different ions of different energies. The structure modifications were followed by High Resolution Transmission Electron Microscopy (HRTEM) and Raman microspectrometry. The results show that temperature generally counteracts the disordering effects of irradiation but the achieved reordering level strongly depends on the initial structural state of the graphite matrix. Thus, extrapolating to reactor conditions, for an initially highly disordered structure, irradiation at reactor temperatures (200 - 500 °C) should induce almost no change of the initial structure. On the contrary, when the structure is initially less disordered, there should be a "zoning" of the reordering: In "cold" high flux irradiated zones where the ballistic damage is important, the structure should be poorly reordered; In "hot" low flux irradiated zones where the ballistic impact is lower and can therefore be counteracted by temperature, a better reordering of the structure should be achieved. Concerning 14C, except when located close to open pores where it can be removed through radiolytic corrosion, it tends to stabilize in the graphite matrix into sp2 or sp3 structures with variable proportions depending on the irradiation conditions.

The use of a combination of different MR methods to study swelling of hydrophilic xanthan matrix tablets at different pHs.

PubMed

Mikac, U; Sepe, A; Kristl, J; Baumgartner, I

2012-01-01

Modified-release matrix tablets have been extensively used by the pharmaceutical industry as one of the most successful oral drug-delivery systems. The key element in drug release from hydrophilic matrix tablets is the gel layer that regulates the penetration of water and controls drug dissolution and diffusion. Magnetic resonance imaging (MRI) is a powerful, non-invasive technique that can help improve our understanding of the gel layer formed on swellable, polymer-matrix tablets, as well as the layer's properties and its influence on the drug release. The aim was to investigate the effects of pH and ionic strength on swelling and to study the influence of structural changes in xanthan gel on drug release. For this purpose a combination of different MRI methods for accurate determination of penetration, swelling and erosion fronts was used. The position of the penetration and swelling fronts were the same, independently of the different xanthan gel structures formed under different conditions of pH and ionic strength. The position of the erosion front, on the other hand, is strongly dependent on pH and ionic strength, as reflected in different thicknesses of the gel layers.

Matrix Transformation in Boron Containing High-Temperature Co-Re-Cr Alloys

NASA Astrophysics Data System (ADS)

Strunz, Pavel; Mukherji, Debashis; Beran, Přemysl; Gilles, Ralph; Karge, Lukas; Hofmann, Michael; Hoelzel, Markus; Rösler, Joachim; Farkas, Gergely

2018-03-01

An addition of boron largely increases the ductility in polycrystalline high-temperature Co-Re alloys. Therefore, the effect of boron on the alloy structural characteristics is of high importance for the stability of the matrix at operational temperatures. Volume fractions of ɛ (hexagonal close-packed—hcp), γ (face-centered cubic—fcc) and σ (Cr2Re3 type) phases were measured at ambient and high temperatures (up to 1500 °C) for a boron-containing Co-17Re-23Cr alloy using neutron diffraction. The matrix phase undergoes an allotropic transformation from ɛ to γ structure at high temperatures, similar to pure cobalt and to the previously investigated, more complex Co-17Re-23Cr-1.2Ta-2.6C alloy. It was determined in this study that the transformation temperature depends on the boron content (0-1000 wt. ppm). Nevertheless, the transformation temperature did not change monotonically with the increase in the boron content but reached a minimum at approximately 200 ppm of boron. A probable reason is the interplay between the amount of boron in the matrix and the amount of σ phase, which binds hcp-stabilizing elements (Cr and Re). Moreover, borides were identified in alloys with high boron content.

Investigation of Super Tube Structure and Performance (Postprint)

DTIC Science & Technology

2010-04-01

thermosyphon is claimed as thermally superconductive and offers solid state mode of heat transport. A host of speculations about this claim was emerging...sealed structure and design of a conventional heat pipe or thermosyphon is claimed as thermally superconductive and offers solid state mode of heat...matrix. The tilt angle was varied to check for gravity dependence. Tests were run as step functions allowing the tube to reach steady state at a new

Regenerator filled with a matrix of polycrystalline iron whiskers

NASA Astrophysics Data System (ADS)

Eder, F. X.; Appel, H.

1982-08-01

In thermal regenerators, parameters were optimized: convection coefficient, surface of heat accumulating matrix, matrix density and heat capacity, and frequency of cycle inversions. The variation of heat capacity with working temperature was also computed. Polycrystalline iron whiskers prove a good compromise as matrix for heat regenerators at working temperatures ranging from 300 to 80 K. They were compared with wire mesh screens and microspheres of bronze and stainless steel. For theses structures and materials, thermal conductivity, pressure drop, heat transfer and yield were calculated and related to the experimental values. As transport heat gas, helium, argon, and dry nitrogen were applied at pressures up to 20 bar. Experimental and theoretical studies result in a set of formulas for calculating pressure drop, heat capacity, and heat transfer rate for a given thermal regenerator in function of mass flow. It is proved that a whisker matrix has an efficiency that depends strongly on gas pressure and composition. Iron whiskers make a good matrix with heat capacities of kW/cu cm per K, but their relative high pressure drop may, at low pressures, be a limitation. A regenerator expansion machine is described.

Matrix Management Structures in Higher Education. Coombe Lodge Working Paper. Information Bank Number 1394.

ERIC Educational Resources Information Center

Cuthbert, Rob

The matrix structure as an alternative to the departmental structure for colleges and universities is discussed, and the matrix system at Middlesex Polytechnic in England is used as illustration. The major impact of the introduction of a matrix structure is its effect on teaching activities within the institution. The matrix structure formally…

On structure-exploiting trust-region regularized nonlinear least squares algorithms for neural-network learning.

PubMed

Mizutani, Eiji; Demmel, James W

2003-01-01

This paper briefly introduces our numerical linear algebra approaches for solving structured nonlinear least squares problems arising from 'multiple-output' neural-network (NN) models. Our algorithms feature trust-region regularization, and exploit sparsity of either the 'block-angular' residual Jacobian matrix or the 'block-arrow' Gauss-Newton Hessian (or Fisher information matrix in statistical sense) depending on problem scale so as to render a large class of NN-learning algorithms 'efficient' in both memory and operation costs. Using a relatively large real-world nonlinear regression application, we shall explain algorithmic strengths and weaknesses, analyzing simulation results obtained by both direct and iterative trust-region algorithms with two distinct NN models: 'multilayer perceptrons' (MLP) and 'complementary mixtures of MLP-experts' (or neuro-fuzzy modular networks).

Non-Finite Complements in Russian, Serbian/Croatian, and Macedonian

ERIC Educational Resources Information Center

Kim, Bo Ra

2010-01-01

This study investigates the coherence properties of non-finite complements in Russian, Serbian/Croatian, and Macedonian. I demonstrate that Slavic non-finite complements do not project a uniform syntactic structure. The maximal projection of non-finite complements is not fixed but depends on the selectional properties of the matrix verb. I present…

Time Delay Embedding Increases Estimation Precision of Models of Intraindividual Variability

ERIC Educational Resources Information Center

von Oertzen, Timo; Boker, Steven M.

2010-01-01

This paper investigates the precision of parameters estimated from local samples of time dependent functions. We find that "time delay embedding," i.e., structuring data prior to analysis by constructing a data matrix of overlapping samples, increases the precision of parameter estimates and in turn statistical power compared to standard…

Nanoscale Viscoelasticity of Extracellular Matrix Proteins in Soft Tissues: a Multiscale Approach

PubMed Central

Miri, Amir K.; Heris, Hossein K.; Mongeau, Luc; Javid, Farhad

2013-01-01

We propose that the bulk viscoelasticity of soft tissues results from two length-scale-dependent mechanisms: the time-dependent response of extracellular matrix proteins (ECM) at the nanometer scale and the biophysical interactions between the ECM solid structure and interstitial fluid at the micrometer scale. The latter was modeled using the poroelasticity theory with an assumption of free motion of the interstitial fluid within the porous ECM structure. Following a recent study (Heris, H.K., Miri, A.K., Tripathy, U., Barthelat, F., Mongeau, L., 2013. Journal of the Mechanical Behavior of Biomedical Materials), atomic force microscopy was used to perform creep loading and 50-nm sinusoidal oscillations on porcine vocal folds. The proposed model was calibrated by a finite element model to accurately predict the nanoscale viscoelastic moduli of ECM. A linear correlation was observed between the in-depth distribution of the viscoelastic moduli and that of hyaluronic acids in the vocal fold tissue. We conclude that hyaluronic acids may regulate the vocal fold viscoelasticity at nanoscale. The proposed methodology offers a characterization tool for biomaterials used in vocal fold augmentations. PMID:24317493

[Spatial scale effect of land use landscape pattern in Yongdeng County, Gansu Province, China.

PubMed

Liu, Yuan Yuan; Liu, Xue Lu

2016-04-22

Based on "patch-corridor-matrix" pattern, spatial scale effect of landscape pattern was studied in Yongdeng County of Lanzhou City, Gansu Province, China. The results showed that the grassland was the matrix of landscape structure in the studied area, road and river played the corridor role, and the other landscape elements (cultivated land, forest land, garden land, residential land, industrial and mineral land, public management and service land, and the other land) acted as patches. The patch level index and the landscape level index all showed obvious dependence on spatial extent. The scale effect of patch index of different landscape elements existed differently in different extent intervals, so did the scale effect of the landscape level index. Within the extent of 1-20 km, the scale effect showed the most obvious difference between the element types and the index types, while it became smaller in 21-90 km, and disappeared beyond 90 km. 90 km×90 km might be the effective extent to study the dependence of spatial extent of landscape structure.

The Dimer Interface of the Membrane Type 1 Matrix Metalloproteinase Hemopexin Domain

PubMed Central

Tochowicz, Anna; Goettig, Peter; Evans, Richard; Visse, Robert; Shitomi, Yasuyuki; Palmisano, Ralf; Ito, Noriko; Richter, Klaus; Maskos, Klaus; Franke, Daniel; Svergun, Dmitri; Nagase, Hideaki; Bode, Wolfram; Itoh, Yoshifumi

2011-01-01

Homodimerization is an essential step for membrane type 1 matrix metalloproteinase (MT1-MMP) to activate proMMP-2 and to degrade collagen on the cell surface. To uncover the molecular basis of the hemopexin (Hpx) domain-driven dimerization of MT1-MMP, a crystal structure of the Hpx domain was solved at 1.7 Å resolution. Two interactions were identified as potential biological dimer interfaces in the crystal structure, and mutagenesis studies revealed that the biological dimer possesses a symmetrical interaction where blades II and III of molecule A interact with blades III and II of molecule B. The mutations of amino acids involved in the interaction weakened the dimer interaction of Hpx domains in solution, and incorporation of these mutations into the full-length enzyme significantly inhibited dimer-dependent functions on the cell surface, including proMMP-2 activation, collagen degradation, and invasion into the three-dimensional collagen matrix, whereas dimer-independent functions, including gelatin film degradation and two-dimensional cell migration, were not affected. These results shed light on the structural basis of MT1-MMP dimerization that is crucial to promote cellular invasion. PMID:21193411

Flat band in disorder-driven non-Hermitian Weyl semimetals

NASA Astrophysics Data System (ADS)

Zyuzin, A. A.; Zyuzin, A. Yu.

2018-01-01

We study the interplay of disorder and band-structure topology in a Weyl semimetal with a tilted conical spectrum around the Weyl points. The spectrum of particles is given by the eigenvalues of a non-Hermitian matrix, which contains contributions from a Weyl Hamiltonian and complex self-energy due to electron elastic scattering on disorder. We find that the tilt-induced matrix structure of the self-energy gives rise to either a flat band or a nodal line segment at the interface of the electron and hole pockets in the bulk band structure of type-II Weyl semimetals depending on the Weyl cone inclination. For the tilt in a single direction in momentum space, each Weyl point expands into a flat band lying on the plane, which is transverse to the direction of the tilt. The spectrum of the flat band is fully imaginary and is separated from the in-plane dispersive part of the spectrum by the "exceptional nodal ring" where the matrix of the Green's function in momentum-frequency space is defective. The tilt in two directions might shrink a flat band into a nodal line segment with "exceptional edge points." We discuss the connection to the non-Hermitian topological theory.

Predicting drug-target interactions by dual-network integrated logistic matrix factorization

NASA Astrophysics Data System (ADS)

Hao, Ming; Bryant, Stephen H.; Wang, Yanli

2017-01-01

In this work, we propose a dual-network integrated logistic matrix factorization (DNILMF) algorithm to predict potential drug-target interactions (DTI). The prediction procedure consists of four steps: (1) inferring new drug/target profiles and constructing profile kernel matrix; (2) diffusing drug profile kernel matrix with drug structure kernel matrix; (3) diffusing target profile kernel matrix with target sequence kernel matrix; and (4) building DNILMF model and smoothing new drug/target predictions based on their neighbors. We compare our algorithm with the state-of-the-art method based on the benchmark dataset. Results indicate that the DNILMF algorithm outperforms the previously reported approaches in terms of AUPR (area under precision-recall curve) and AUC (area under curve of receiver operating characteristic) based on the 5 trials of 10-fold cross-validation. We conclude that the performance improvement depends on not only the proposed objective function, but also the used nonlinear diffusion technique which is important but under studied in the DTI prediction field. In addition, we also compile a new DTI dataset for increasing the diversity of currently available benchmark datasets. The top prediction results for the new dataset are confirmed by experimental studies or supported by other computational research.

Efficient Algorithms for Estimating the Absorption Spectrum within Linear Response TDDFT

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

Brabec, Jiri; Lin, Lin; Shao, Meiyue

We present two iterative algorithms for approximating the absorption spectrum of molecules within linear response of time-dependent density functional theory (TDDFT) framework. These methods do not attempt to compute eigenvalues or eigenvectors of the linear response matrix. They are designed to approximate the absorption spectrum as a function directly. They take advantage of the special structure of the linear response matrix. Neither method requires the linear response matrix to be constructed explicitly. They only require a procedure that performs the multiplication of the linear response matrix with a vector. These methods can also be easily modified to efficiently estimate themore » density of states (DOS) of the linear response matrix without computing the eigenvalues of this matrix. We show by computational experiments that the methods proposed in this paper can be much more efficient than methods that are based on the exact diagonalization of the linear response matrix. We show that they can also be more efficient than real-time TDDFT simulations. We compare the pros and cons of these methods in terms of their accuracy as well as their computational and storage cost.« less

Role for Tyrosine Phosphorylation of A-kinase Anchoring Protein 8 (AKAP8) in Its Dissociation from Chromatin and the Nuclear Matrix.

PubMed

Kubota, Sho; Morii, Mariko; Yuki, Ryuzaburo; Yamaguchi, Noritaka; Yamaguchi, Hiromi; Aoyama, Kazumasa; Kuga, Takahisa; Tomonaga, Takeshi; Yamaguchi, Naoto

2015-04-24

Protein-tyrosine phosphorylation regulates a wide variety of cellular processes at the plasma membrane. Recently, we showed that nuclear tyrosine kinases induce global nuclear structure changes, which we called chromatin structural changes. However, the mechanisms are not fully understood. In this study we identify protein kinase A anchoring protein 8 (AKAP8/AKAP95), which associates with chromatin and the nuclear matrix, as a nuclear tyrosine-phosphorylated protein. Tyrosine phosphorylation of AKAP8 is induced by several tyrosine kinases, such as Src, Fyn, and c-Abl but not Syk. Nucleus-targeted Lyn and c-Src strongly dissociate AKAP8 from chromatin and the nuclear matrix in a kinase activity-dependent manner. The levels of tyrosine phosphorylation of AKAP8 are decreased by substitution of multiple tyrosine residues on AKAP8 into phenylalanine. Importantly, the phenylalanine mutations of AKAP8 inhibit its dissociation from nuclear structures, suggesting that the association/dissociation of AKAP8 with/from nuclear structures is regulated by its tyrosine phosphorylation. Furthermore, the phenylalanine mutations of AKAP8 suppress the levels of nuclear tyrosine kinase-induced chromatin structural changes. In contrast, AKAP8 knockdown increases the levels of chromatin structural changes. Intriguingly, stimulation with hydrogen peroxide induces chromatin structural changes accompanied by the dissociation of AKAP8 from nuclear structures. These results suggest that AKAP8 is involved in the regulation of chromatin structural changes through nuclear tyrosine phosphorylation. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

An Uncertainty Structure Matrix for Models and Simulations

NASA Technical Reports Server (NTRS)

Green, Lawrence L.; Blattnig, Steve R.; Hemsch, Michael J.; Luckring, James M.; Tripathi, Ram K.

2008-01-01

Software that is used for aerospace flight control and to display information to pilots and crew is expected to be correct and credible at all times. This type of software is typically developed under strict management processes, which are intended to reduce defects in the software product. However, modeling and simulation (M&S) software may exhibit varying degrees of correctness and credibility, depending on a large and complex set of factors. These factors include its intended use, the known physics and numerical approximations within the M&S, and the referent data set against which the M&S correctness is compared. The correctness and credibility of an M&S effort is closely correlated to the uncertainty management (UM) practices that are applied to the M&S effort. This paper describes an uncertainty structure matrix for M&S, which provides a set of objective descriptions for the possible states of UM practices within a given M&S effort. The columns in the uncertainty structure matrix contain UM elements or practices that are common across most M&S efforts, and the rows describe the potential levels of achievement in each of the elements. A practitioner can quickly look at the matrix to determine where an M&S effort falls based on a common set of UM practices that are described in absolute terms that can be applied to virtually any M&S effort. The matrix can also be used to plan those steps and resources that would be needed to improve the UM practices for a given M&S effort.

A cellular Potts model for the MMP-dependent and -independent cancer cell migration in matrix microtracks of different dimensions

NASA Astrophysics Data System (ADS)

Scianna, Marco; Preziosi, Luigi

2014-03-01

Cell migration is fundamental in a wide variety of physiological and pathological phenomena, among other in cancer invasion and development. In particular, the migratory/invasive capability of single metastatic cells is fundamental in determining the malignancy of a solid tumor. Specific cell migration phenotypes result for instance from the reciprocal interplay between the biophysical and biochemical properties of both the malignant cells themselves and of the surrounding environment. In particular, the extracellular matrices (ECMs) forming connective tissues can provide both loosely organized zones and densely packed barriers, which may impact cell invasion mode and efficiency. The critical processes involved in cell movement within confined spaces are (i) the proteolytic activity of matrix metalloproteinases (MMPs) and (ii) the deformation of the entire cell body, and in particular of the nucleus. We here present an extended cellular Potts model (CPM) to simulate a bio-engineered matrix system, which tests the active motile behavior of a single cancer cell into narrow channels of different widths. As distinct features of our approach, the cell is modeled as a compartmentalized discrete element, differentiated in the nucleus and in the cytosolic region, while a directional shape-dependent movement is explicitly driven by the evolution of its polarity vector. As outcomes, we find that, in a large track, the tumor cell is not able to maintain a directional movement. On the contrary, a structure of subcellular width behaves as a contact guidance sustaining cell persistent locomotion. In particular, a MMP-deprived cell is able to repolarize and follow the micropattern geometry, while a full MMP activity leads to a secondary track expansion by degrading the matrix structure. Finally, we confirm that cell movement within a subnuclear structure can be achieved either by pericellular proteolysis or by a significant deformation of cell nucleus.

Double matrix effect in Low Energy Ion Scattering from La surfaces

NASA Astrophysics Data System (ADS)

Zameshin, Andrey A.; Yakshin, Andrey E.; Sturm, Jacobus M.; Brongerma, Hidde H.; Bijkerk, Fred

2018-05-01

Low Energy Ion Scattering (LEIS) has been performed on several lanthanum-based surfaces. Strong subsurface matrix effects - dependence of surface scattered He+ ion yield on the composition of subsurface layer - have been observed. The ion yield of He+ scattered by La differed by a factor of up to 2.5 for different surfaces, while only the La peak was visible in the spectra. To study these effects and enable surface quantification, He+ ion yields have been measured in a range of incident He+ energies from 1000 to 7500 eV for LaB6, La2O3, oxidized La and pure La surfaces. The investigation showed that as many as two simultaneous matrix effects are present, each one driven by a separate charge exchange mechanism. The first one is a resonant neutralization from the conduction band of La to an excited state of the He+ ion. It depends on the work function of the surface, which is lowered significantly when La interacts with O or B. The second mechanism is quasiresonant charge transfer between bound La levels and He 1s, which creates characteristic oscillations in the energy dependence of ion yields. The exact structure of the oscillations depends on small changes in binding energies of interacting La levels. This is the first time quasiresonant charge transfer is proven to be present in La. It is likely that La 5p orbitals participate in this resonance, which can be the first clear observation of a resonance between p and s orbitals in LEIS. This type of resonance was previously believed to be absent because of strong damping. We also demonstrated that despite the complex matrix effect precise measurements over a wide energy range allow quantification of the atomic composition of La-based surfaces.

The amino-terminal matrix assembly domain of fibronectin stabilizes cell shape and prevents cell cycle progression.

PubMed

Christopher, R A; Judge, S R; Vincent, P A; Higgins, P J; McKeown-Longo, P J

1999-10-01

Adhesion to the extracellular matrix modulates the cellular response to growth factors and is critical for cell cycle progression. The present study was designed to address the relationship between fibronectin matrix assembly and cell shape or shape dependent cellular processes. The binding of fibronectin's amino-terminal matrix assembly domain to adherent cells represents the initial step in the assembly of exogenous fibronectin into the extracellular matrix. When added to monolayers of pulmonary artery endothelial cells, the 70 kDa fragment of fibronectin (which contains the matrix assembly domain) stabilized both the extracellular fibronectin matrix as well as the actin cytoskeleton against cytochalasin D-mediated structural reorganization. This activity appeared to require specific fibronectin sequences as fibronectin fragments containing the cell adhesion domain as well as purified vitronectin were ineffective inhibitors of cytochalasin D-induced cytoarchitectural restructuring. Such pronounced morphologic consequences associated with exposure to the 70 kDa fragment suggested that this region of the fibronectin molecule may affect specific growth traits known to be influenced by cell shape. To assess this possibility, the 70 kDa fragment was added to scrape-wounded monolayers of bovine microvessel endothelium and the effects on two shape-dependent processes (i.e. migration and proliferation) were measured as a function of time after injury and location from the wound. The addition of amino-terminal fragments of fibronectin to the monolayer significantly inhibited (by >50%) wound closure. Staining of wounded monolayers with BrdU, moreover, indicated that either the 70 kDa or 25 kDa amino-terminal fragments of fibronectin, but not the 40 kDa collagen binding fragment, also inhibited cell cycle progression. These results suggest that the binding of fibronectin's amino-terminal region to endothelial cell layers inhibits cell cycle progression by stabilizing cell shape.

Cell shape, cytoskeletal mechanics, and cell cycle control in angiogenesis

NASA Technical Reports Server (NTRS)

Ingber, D. E.; Prusty, D.; Sun, Z.; Betensky, H.; Wang, N.

1995-01-01

Capillary endothelial cells can be switched between growth and differentiation by altering cell-extracellular matrix interactions and thereby, modulating cell shape. Studies were carried out to determine when cell shape exerts its growth-regulatory influence during cell cycle progression and to explore the role of cytoskeletal structure and mechanics in this control mechanism. When G0-synchronized cells were cultured in basic fibroblast growth factor (FGF)-containing defined medium on dishes coated with increasing densities of fibronectin or a synthetic integrin ligand (RGD-containing peptide), cell spreading, nuclear extension, and DNA synthesis all increased in parallel. To determine the minimum time cells must be adherent and spread on extracellular matrix (ECM) to gain entry into S phase, cells were removed with trypsin or induced to retract using cytochalasin D at different times after plating. Both approaches revealed that cells must remain extended for approximately 12-15 h and hence, most of G1, in order to enter S phase. After this restriction point was passed, normally 'anchorage-dependent' endothelial cells turned on DNA synthesis even when round and in suspension. The importance of actin-containing microfilaments in shape-dependent growth control was confirmed by culturing cells in the presence of cytochalasin D (25-1000 ng ml-1): dose-dependent inhibition of cell spreading, nuclear extension, and DNA synthesis resulted. In contrast, induction of microtubule disassembly using nocodazole had little effect on cell or nuclear spreading and only partially inhibited DNA synthesis. Interestingly, combination of nocodazole with a suboptimal dose of cytochalasin D (100 ng ml-1) resulted in potent inhibition of both spreading and growth, suggesting that microtubules are redundant structural elements which can provide critical load-bearing functions when microfilaments are partially compromised. Similar synergism between nocodazole and cytochalasin D was observed when cytoskeletal stiffness was measured directly in living cells using magnetic twisting cytometry. These results emphasize the importance of matrix-dependent changes in cell and nuclear shape as well as higher order structural interactions between different cytoskeletal filament systems for control of capillary cell growth during angiogenesis.

Continued-fraction representation of the Kraus map for non-Markovian reservoir damping

NASA Astrophysics Data System (ADS)

van Wonderen, A. J.; Suttorp, L. G.

2018-04-01

Quantum dissipation is studied for a discrete system that linearly interacts with a reservoir of harmonic oscillators at thermal equilibrium. Initial correlations between system and reservoir are assumed to be absent. The dissipative dynamics as determined by the unitary evolution of system and reservoir is described by a Kraus map consisting of an infinite number of matrices. For all Laplace-transformed Kraus matrices exact solutions are constructed in terms of continued fractions that depend on the pair correlation functions of the reservoir. By performing factorizations in the Kraus map a perturbation theory is set up that conserves in arbitrary perturbative order both positivity and probability of the density matrix. The latter is determined by an integral equation for a bitemporal matrix and a finite hierarchy for Kraus matrices. In the lowest perturbative order this hierarchy reduces to one equation for one Kraus matrix. Its solution is given by a continued fraction of a much simpler structure as compared to the non-perturbative case. In the lowest perturbative order our non-Markovian evolution equations are applied to the damped Jaynes–Cummings model. From the solution for the atomic density matrix it is found that the atom may remain in the state of maximum entropy for a significant time span that depends on the initial energy of the radiation field.

Establishment of substratum polarity in the blastocoel roof of the Xenopus embryo.

PubMed

Nagel, M; Winklbauer, R

1999-05-01

The fibronectin fibril matrix on the blastocoel roof of the Xenopus gastrula contains guidance cues that determine the direction of mesoderm cell migration. The underlying guidance-related polarity of the blastocoel roof is established in the late blastula under the influence of an instructive signal from the vegetal half of the embryo, in particular from the mesoderm. Formation of an oriented substratum depends on functional activin and FGF signaling pathways in the blastocoel roof. Besides being involved in tissue polarization, activin and FGF also affect fibronectin matrix assembly. Activin treatment of the blastocoel roof inhibits fibril formation, whereas FGF modulates the structure of the fibril network. The presence of intact fibronectin fibrils is permissive for directional mesoderm migration on the blastocoel roof extracellular matrix.

Variational second order density matrix study of F3-: importance of subspace constraints for size-consistency.

PubMed

van Aggelen, Helen; Verstichel, Brecht; Bultinck, Patrick; Van Neck, Dimitri; Ayers, Paul W; Cooper, David L

2011-02-07

Variational second order density matrix theory under "two-positivity" constraints tends to dissociate molecules into unphysical fractionally charged products with too low energies. We aim to construct a qualitatively correct potential energy surface for F(3)(-) by applying subspace energy constraints on mono- and diatomic subspaces of the molecular basis space. Monoatomic subspace constraints do not guarantee correct dissociation: the constraints are thus geometry dependent. Furthermore, the number of subspace constraints needed for correct dissociation does not grow linearly with the number of atoms. The subspace constraints do impose correct chemical properties in the dissociation limit and size-consistency, but the structure of the resulting second order density matrix method does not exactly correspond to a system of noninteracting units.

A Damage-Dependent Finite Element Analysis for Fiber-Reinforced Composite Laminates

NASA Technical Reports Server (NTRS)

Coats, Timothy W.; Harris, Charles E.

1998-01-01

A progressive damage methodology has been developed to predict damage growth and residual strength of fiber-reinforced composite structure with through penetrations such as a slit. The methodology consists of a damage-dependent constitutive relationship based on continuum damage mechanics. Damage is modeled using volume averaged strain-like quantities known as internal state variables and is represented in the equilibrium equations as damage induced force vectors instead of the usual degradation and modification of the global stiffness matrix.

[Bone quantitative ultrasound].

PubMed

Matsukawa, Mami

2016-01-01

The conventional ultrasonic bone densitometry system can give us information of bone as ultrasonic wave velocity and attenuation. However, the data reflect both structural and material properties of bone. In order to focus only on the bone matrix properties without the effect of bone structure, studies of microscopic Brillouin scattering technique are introduced. The wave velocity in a trabecula was anisotropic and depended on the position and structure of the cancellous bone. The glycation also affected on the wave velocities in bone. As a new bone quality, the piezoelectricity of bone is also discussed.

Eigentime identities for on weighted polymer networks

NASA Astrophysics Data System (ADS)

Dai, Meifeng; Tang, Hualong; Zou, Jiahui; He, Di; Sun, Yu; Su, Weiyi

2018-01-01

In this paper, we first analytically calculate the eigenvalues of the transition matrix of a structure with very complex architecture and their multiplicities. We call this structure polymer network. Based on the eigenvalues obtained in the iterative manner, we then calculate the eigentime identity. We highlight two scaling behaviors (logarithmic and linear) for this quantity, strongly depending on the value of the weight factor. Finally, by making use of the obtained eigenvalues, we determine the weighted counting of spanning trees.

Silicon quantum dots embedded in a SiO2 matrix: From structural study to carrier transport properties

NASA Astrophysics Data System (ADS)

Garcia-Castello, Nuria; Illera, Sergio; Guerra, Roberto; Prades, Joan Daniel; Ossicini, Stefano; Cirera, Albert

2013-08-01

We study the details of electronic transport related to the atomistic structure of silicon quantum dots embedded in a silicon dioxide matrix using ab initio calculations of the density of states. Several structural and composition features of quantum dots (QDs), such as diameter and amorphization level, are studied and correlated with transport under transfer Hamiltonian formalism. The current is strongly dependent on the QD density of states and on the conduction gap, both dependent on the dot diameter. In particular, as size increases, the available states inside the QD increase, while the QD band gap decreases due to relaxation of quantum confinement. Both effects contribute to increasing the current with the dot size. Besides, valence band offset between the band edges of the QD and the silica, and conduction band offset in a minor grade, increases with the QD diameter up to the theoretical value corresponding to planar heterostructures, thus decreasing the tunneling transmission probability and hence the total current. We discuss the influence of these parameters on electron and hole transport, evidencing a correlation between the electron (hole) barrier value and the electron (hole) current, and obtaining a general enhancement of the electron (hole) transport for larger (smaller) QD. Finally, we show that crystalline and amorphous structures exhibit enhanced probability of hole and electron current, respectively.

Metal Ion Dependence of the Matrix Metalloproteinase-1 Mechanism.

PubMed

Yang, Hao; Makaroff, Katherine; Paz, Nicholas; Aitha, Mahesh; Crowder, Michael W; Tierney, David L

2015-06-16

Matrix metalloproteinase-1 (MMP-1) plays crucial roles in disease-related physiologies and pathological processes in the human body. We report here solution studies of MMP-1, including characterization of a series of mutants designed to bind metal in either the catalytic site or the structural site (but not both). Circular dichroism and fluorescence spectroscopy of the mutants demonstrate the importance of the structural Zn(II) in maintaining both secondary and tertiary structure, while UV-visible, nuclear magnetic resonance, electron paramagnetic resonance, and extended X-ray absorption fine structure show its presence influences the catalytic metal ion's coordination number. The mutants allow us to demonstrate convincingly the preparation of a mixed-metal analogue, Co(C)Zn(S)-MMP-1, with Zn(II) in the structural site and Co(II) in the catalytic site. Stopped-flow fluorescence of the native form, Zn(C)Zn(S)-MMP-1, and the mixed-metal Co(C)Zn(S)-MMP-1 analogue shows that the internal fluorescence of a nearby Trp residue is modulated with catalysis and can be used to monitor reactivity under a number of conditions, opening the door to substrate profiling.

Multivariate analysis of scale-dependent associations between bats and landscape structure

USGS Publications Warehouse

Gorresen, P.M.; Willig, M.R.; Strauss, R.E.

2005-01-01

The assessment of biotic responses to habitat disturbance and fragmentation generally has been limited to analyses at a single spatial scale. Furthermore, methods to compare responses between scales have lacked the ability to discriminate among patterns related to the identity, strength, or direction of associations of biotic variables with landscape attributes. We present an examination of the relationship of population- and community-level characteristics of phyllostomid bats with habitat features that were measured at multiple spatial scales in Atlantic rain forest of eastern Paraguay. We used a matrix of partial correlations between each biotic response variable (i.e., species abundance, species richness, and evenness) and a suite of landscape characteristics to represent the multifaceted associations of bats with spatial structure. Correlation matrices can correspond based on either the strength (i.e., magnitude) or direction (i.e., sign) of association. Therefore, a simulation model independently evaluated correspondence in the magnitude and sign of correlations among scales, and results were combined via a meta-analysis to provide an overall test of significance. Our approach detected both species-specific differences in response to landscape structure and scale dependence in those responses. This matrix-simulation approach has broad applicability to ecological situations in which multiple intercorrelated factors contribute to patterns in space or time. ?? 2005 by the Ecological Society of America.

Distance matrix-based approach to protein structure prediction.

PubMed

Kloczkowski, Andrzej; Jernigan, Robert L; Wu, Zhijun; Song, Guang; Yang, Lei; Kolinski, Andrzej; Pokarowski, Piotr

2009-03-01

Much structural information is encoded in the internal distances; a distance matrix-based approach can be used to predict protein structure and dynamics, and for structural refinement. Our approach is based on the square distance matrix D = [r(ij)(2)] containing all square distances between residues in proteins. This distance matrix contains more information than the contact matrix C, that has elements of either 0 or 1 depending on whether the distance r (ij) is greater or less than a cutoff value r (cutoff). We have performed spectral decomposition of the distance matrices D = sigma lambda(k)V(k)V(kT), in terms of eigenvalues lambda kappa and the corresponding eigenvectors v kappa and found that it contains at most five nonzero terms. A dominant eigenvector is proportional to r (2)--the square distance of points from the center of mass, with the next three being the principal components of the system of points. By predicting r (2) from the sequence we can approximate a distance matrix of a protein with an expected RMSD value of about 7.3 A, and by combining it with the prediction of the first principal component we can improve this approximation to 4.0 A. We can also explain the role of hydrophobic interactions for the protein structure, because r is highly correlated with the hydrophobic profile of the sequence. Moreover, r is highly correlated with several sequence profiles which are useful in protein structure prediction, such as contact number, the residue-wise contact order (RWCO) or mean square fluctuations (i.e. crystallographic temperature factors). We have also shown that the next three components are related to spatial directionality of the secondary structure elements, and they may be also predicted from the sequence, improving overall structure prediction. We have also shown that the large number of available HIV-1 protease structures provides a remarkable sampling of conformations, which can be viewed as direct structural information about the dynamics. After structure matching, we apply principal component analysis (PCA) to obtain the important apparent motions for both bound and unbound structures. There are significant similarities between the first few key motions and the first few low-frequency normal modes calculated from a static representative structure with an elastic network model (ENM) that is based on the contact matrix C (related to D), strongly suggesting that the variations among the observed structures and the corresponding conformational changes are facilitated by the low-frequency, global motions intrinsic to the structure. Similarities are also found when the approach is applied to an NMR ensemble, as well as to atomic molecular dynamics (MD) trajectories. Thus, a sufficiently large number of experimental structures can directly provide important information about protein dynamics, but ENM can also provide a similar sampling of conformations. Finally, we use distance constraints from databases of known protein structures for structure refinement. We use the distributions of distances of various types in known protein structures to obtain the most probable ranges or the mean-force potentials for the distances. We then impose these constraints on structures to be refined or include the mean-force potentials directly in the energy minimization so that more plausible structural models can be built. This approach has been successfully used by us in 2006 in the CASPR structure refinement (http://predictioncenter.org/caspR).

Numerical modelling of the evolution of conglomerate deformation up to high simple-shear strain

NASA Astrophysics Data System (ADS)

Ran, Hao; Bons, Paul D.; Wang, Genhou; Steinbach, Florian; Finch, Melanie; Ran, Shuming; Liang, Xiao; Zhou, Jie

2017-04-01

Deformed conglomerates have been widely used to investigate deformation history and structural analysis, using strain analyses techniques, such as the Rf-Φ and Fry methods on deformed pebbles. Although geologists have focused on the study of deformed conglomerates for several decades, some problems of the process and mechanism of deformation, such as the development of structures in pebbles and matrix, are still not understand well. Numerical modelling provides a method to investigate the process of deformation, as a function of different controlling parameters, up to high strains at conditions that cannot be achieved in the laboratory. We use the 2D numerical modelling platform Elle coupled to the full field crystal visco-plasticity code (VPFFT) to simulate the deformation of conglomerates under simple shear conditions, achieving high finite strains of ≥10. Probably for the first time, we included the effect of an anisotropy, i.e. mica-rich matrix. Our simulations show the deformation of pebbles not only depends on the viscosity contrast between pebbles and matrix but emphasises the importance of interaction between neighbouring pebbles. Under the same finite strain shearing the pebbles of conglomerates with high pebble densities show higher Rf and lower Φ than those of conglomerates with a low density pebbles. Strain localisation can be observed at both the margin of strong pebbles and in the bridging area between the pebbles. At low to medium finite strain, local areas show the opposite (antithetic) shear sense because of the different relative rotation and movement of pebbles or clusters of pebbles. Very hard pebbles retain their original shape and may rotate, depending on the anisotropy of the matrix. σ-clasts are formed by pebbles with moderate viscosity contrast between pebble and a softer matrix. By contrast, δ-clasts are not observed in our simulations with both isotropic and anisotropic matrices, which is consistent with their relative scarcity in natural mylonites. The formation of SC-fabrics is enhanced by anisotropy of the matrix, which facilitates strain partitioning in low-strain S-domains and high strain C-domains.

Light scattering by a nematic liquid crystal droplet: Wentzel–Kramers–Brillouin approximation

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

Loiko, V. A., E-mail: loiko@dragon.bas-net.by; Konkolovich, A. V.; Miskevich, A. A.

2016-01-15

Light scattering by an optically anisotropic liquid crystal (LC) droplet of a nematic in an isotropic polymer matrix is considered in the Wentzel–Kramers–Brillouin (WKB) approximation. General relations are obtained for elements of the amplitude matrix of light scattering by a droplet of arbitrary shape and for the structure of the director field. Analytic expressions for the amplitude matrices are derived for spherical LC droplets with a uniformly oriented structure of local optical axes for strictly forward and strictly backward scattering. The efficiency factors of extinction and backward scattering for a spherical nonabsorbing LC droplet depending on the LC optical anisotropy,more » refractive index of the polymer, illumination conditions, and orientation of the optical axis of the droplet are analyzed. Verification of the obtained solutions has been performed.« less

Non-convex Statistical Optimization for Sparse Tensor Graphical Model

PubMed Central

Sun, Wei; Wang, Zhaoran; Liu, Han; Cheng, Guang

2016-01-01

We consider the estimation of sparse graphical models that characterize the dependency structure of high-dimensional tensor-valued data. To facilitate the estimation of the precision matrix corresponding to each way of the tensor, we assume the data follow a tensor normal distribution whose covariance has a Kronecker product structure. The penalized maximum likelihood estimation of this model involves minimizing a non-convex objective function. In spite of the non-convexity of this estimation problem, we prove that an alternating minimization algorithm, which iteratively estimates each sparse precision matrix while fixing the others, attains an estimator with the optimal statistical rate of convergence as well as consistent graph recovery. Notably, such an estimator achieves estimation consistency with only one tensor sample, which is unobserved in previous work. Our theoretical results are backed by thorough numerical studies. PMID:28316459

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.

The Role of Structural Extracellular Matrix Proteins in Urothelial Bladder Cancer (Review)

PubMed Central

Brunner, Andrea; Tzankov, Alexandar

2007-01-01

The extracellular matrix (ECM) plays a key role in the modulation of cancer cell invasion. In urothelial carcinoma of the bladder (UC) the role of ECM proteins has been widely studied. The mechanisms, which are involved in the development of invasion, progression and generalization, are complex, depending on the interaction of ECM proteins with each other as well as with cancer cells. The following review will focus on the pathogenetic role and prognostic value of structural proteins, such as laminins, collagens, fibronectin (FN), tenascin (Tn-C) and thrombospondin 1 (TSP1) in UC. In addition, the role of integrins mediating the interaction of ECM molecules and cancer cells will be addressed, since integrin-mediated FN, Tn-C and TSP1 interactions seem to play an important role during tumor cell invasion and angiogenesis. PMID:19662222

Exciton emission of quasi-2D InGaN in GaN matrix grown by molecular beam epitaxy

PubMed Central

Ma, Dingyu; Rong, Xin; Zheng, Xiantong; Wang, Weiying; Wang, Ping; Schulz, Tobias; Albrecht, Martin; Metzner, Sebastian; Müller, Mathias; August, Olga; Bertram, Frank; Christen, Jürgen; Jin, Peng; Li, Mo; Zhang, Jian; Yang, Xuelin; Xu, Fujun; Qin, Zhixin; Ge, Weikun; Shen, Bo; Wang, Xinqiang

2017-01-01

We investigate the emission from confined excitons in the structure of a single-monolayer-thick quasi-two-dimensional (quasi-2D) InxGa1−xN layer inserted in GaN matrix. This quasi-2D InGaN layer was successfully achieved by molecular beam epitaxy (MBE), and an excellent in-plane uniformity in this layer was confirmed by cathodoluminescence mapping study. The carrier dynamics have also been investigated by time-resolved and excitation-power-dependent photoluminescence, proving that the recombination occurs via confined excitons within the ultrathin quasi-2D InGaN layer even at high temperature up to ~220 K due to the enhanced exciton binding energy. This work indicates that such structure affords an interesting opportunity for developing high-performance photonic devices. PMID:28417975

φq-field theory for portfolio optimization: “fat tails” and nonlinear correlations

NASA Astrophysics Data System (ADS)

Sornette, D.; Simonetti, P.; Andersen, J. V.

2000-08-01

Physics and finance are both fundamentally based on the theory of random walks (and their generalizations to higher dimensions) and on the collective behavior of large numbers of correlated variables. The archetype examplifying this situation in finance is the portfolio optimization problem in which one desires to diversify on a set of possibly dependent assets to optimize the return and minimize the risks. The standard mean-variance solution introduced by Markovitz and its subsequent developments is basically a mean-field Gaussian solution. It has severe limitations for practical applications due to the strongly non-Gaussian structure of distributions and the nonlinear dependence between assets. Here, we present in details a general analytical characterization of the distribution of returns for a portfolio constituted of assets whose returns are described by an arbitrary joint multivariate distribution. In this goal, we introduce a non-linear transformation that maps the returns onto Gaussian variables whose covariance matrix provides a new measure of dependence between the non-normal returns, generalizing the covariance matrix into a nonlinear covariance matrix. This nonlinear covariance matrix is chiseled to the specific fat tail structure of the underlying marginal distributions, thus ensuring stability and good conditioning. The portfolio distribution is then obtained as the solution of a mapping to a so-called φq field theory in particle physics, of which we offer an extensive treatment using Feynman diagrammatic techniques and large deviation theory, that we illustrate in details for multivariate Weibull distributions. The interaction (non-mean field) structure in this field theory is a direct consequence of the non-Gaussian nature of the distribution of asset price returns. We find that minimizing the portfolio variance (i.e. the relatively “small” risks) may often increase the large risks, as measured by higher normalized cumulants. Extensive empirical tests are presented on the foreign exchange market that validate satisfactorily the theory. For “fat tail” distributions, we show that an adequate prediction of the risks of a portfolio relies much more on the correct description of the tail structure rather than on their correlations. For the case of asymmetric return distributions, our theory allows us to generalize the return-risk efficient frontier concept to incorporate the dimensions of large risks embedded in the tail of the asset distributions. We demonstrate that it is often possible to increase the portfolio return while decreasing the large risks as quantified by the fourth and higher-order cumulants. Exact theoretical formulas are validated by empirical tests.

Expression, purification and crystallization of a lyssavirus matrix (M) protein

PubMed Central

Assenberg, René; Delmas, Olivier; Graham, Stephen C.; Verma, Anil; Berrow, Nick; Stuart, David I.; Owens, Raymond J.; Bourhy, Hervé; Grimes, Jonathan M.

2008-01-01

The matrix (M) proteins of lyssaviruses (family Rhabdoviridae) are crucial to viral morphogenesis as well as in modulating replication and transcription of the viral genome. To date, no high-resolution structural information has been obtained for full-length rhabdovirus M. Here, the cloning, expression and purification of the matrix proteins from three lyssaviruses, Lagos bat virus (LAG), Mokola virus and Thailand dog virus, are described. Crystals have been obtained for the full-length M protein from Lagos bat virus (LAG M). Successful crystallization depended on a number of factors, in particular the addition of an N-terminal SUMO fusion tag to increase protein solubility. Diffraction data have been recorded from crystals of native and selenomethionine-labelled LAG M to 2.75 and 3.0 Å resolution, respectively. Preliminary analysis indicates that these crystals belong to space group P6122 or P6522, with unit-cell parameters a = b = 56.9–57.2, c = 187.9–188.6 Å, consistent with the presence of one molecule per asymmetric unit, and structure determination is currently in progress. PMID:18391421

Tuning of optical properties of CdS nanoparticles synthesized in a glass matrix

NASA Astrophysics Data System (ADS)

Popov, Ivan D.; Kuznetsova, Yulia V.; Rempel, Svetlana V.; Rempel, Andrey A.

2018-03-01

Attempts were made to provide the data concerning directed synthesis of semiconductor nanoparticles in a dielectric silica-based glass matrix. These attempts involve finding out the connections between the structure, size of CdS nanoparticles, and optical properties of the nanocomposites produced. High-resolution focused ion beam scanning electron microscopy images of CdS nanoparticles incorporated in glass and SAXS results confirm the formation of uniformly distributed spherical CdS nanoparticles with an average diameter of about 6.2 nm. UV-Vis measurements show that CdS composites possess a direct bandgap wider than 2.45 eV depending on the heat treatment conditions; thus, heat treatment can be used to control nanoparticle size in each selected composite. The emission spectra showed a maximum at about 603 nm and a red shift of about 100 nm with increasing annealing temperature that is associated with the presence of defect states in the nanoparticles. In addition, semiconductor phase concentration in the glass matrix was found by using optical absorption data for the first time, which allows understanding the effect of nanocomposite structure on luminescence properties.

Tribological Properties of AlSi12-Al₂O₃ Interpenetrating Composite Layers in Comparison with Unreinforced Matrix Alloy.

PubMed

Dolata, Anna Janina

2017-09-06

Alumina-Aluminum composites with interpenetrating network structures are a new class of advanced materials with potentially better properties than composites reinforced by particles or fibers. Local casting reinforcement was proposed to take into account problems with the machinability of this type of materials and the shaping of the finished products. The centrifugal infiltration process fabricated composite castings in the form of locally reinforced shafts. The main objective of the research presented in this work was to compare the tribological properties (friction coefficient, wear resistance) of AlSi12/Al₂O₃ interpenetrating composite layers with unreinforced AlSi12 matrix areas. Profilometric tests enabled both quantitative and qualitative analyses of the wear trace that formed on investigated surfaces. It has been shown that interpenetrating composite layers are characterized by lower and more stable coefficients of friction (μ), as well as higher wear resistance than unreinforced matrix areas. At the present stage, the study confirmed that the tribological properties of the composite layers depend on the spatial structure of the ceramic reinforcement, and primarily the volume and size of alumina foam cells.

Multi-Scale CNT-Based Reinforcing Polymer Matrix Composites for Lightweight Structures

NASA Technical Reports Server (NTRS)

Eberly, Daniel; Ou, Runqing; Karcz, Adam; Skandan, Ganesh; Mather, Patrick; Rodriguez, Erika

2013-01-01

Reinforcing critical areas in carbon polymer matrix composites (PMCs), also known as fiber reinforced composites (FRCs), is advantageous for structural durability. Since carbon nanotubes (CNTs) have extremely high tensile strength, they can be used as a functional additive to enhance the mechanical properties of FRCs. However, CNTs are not readily dispersible in the polymer matrix, which leads to lower than theoretically predicted improvement in mechanical, thermal, and electrical properties of CNT composites. The inability to align CNTs in a polymer matrix is also a known issue. The feasibility of incorporating aligned CNTs into an FRC was demonstrated using a novel, yet commercially viable nanofiber approach, termed NRMs (nanofiber-reinforcing mats). The NRM concept of reinforcement allows for a convenient and safe means of incorporating CNTs into FRC structural components specifically where they are needed during the fabrication process. NRMs, fabricated through a novel and scalable process, were incorporated into FRC test panels using layup and vacuum bagging techniques, where alternating layers of the NRM and carbon prepreg were used to form the reinforced FRC structure. Control FRC test panel coupons were also fabricated in the same manner, but comprised of only carbon prepreg. The FRC coupons were machined to size and tested for flexural, tensile, and compression properties. This effort demonstrated that FRC structures can be fabricated using the NRM concept, with an increased average load at break during flexural testing versus that of the control. The NASA applications for the developed technologies are for lightweight structures for in-space and launch vehicles. In addition, the developed technologies would find use in NASA aerospace applications such as rockets, aircraft, aircraft/spacecraft propulsion systems, and supporting facilities. The reinforcing aspect of the technology will allow for more efficient joining of fiber composite parts, thus offering additional weight savings. More robust structures capable of withstanding micrometeoroid and space debris impacts will be possible with the enhanced mechanical properties imparted by the aligned CNTs incorporated into the fiber composite structure, as well as the potential for improved electrical and thermal properties. The materials fabrication approach developed in the present effort is a platform for customer applications where additional reinforcement is required or would be beneficial, especially in FRC structures and component parts. Depending upon the specific customer application, the NRM could be tailored to the specific matrix resin and desired property enhancement.

Autofluorescence lifetime metrology for label-free detection of cartilage matrix degradation

NASA Astrophysics Data System (ADS)

Nickdel, Mohammad B.; Lagarto, João. L.; Kelly, Douglas J.; Manning, Hugh B.; Yamamoto, Kazuhiro; Talbot, Clifford B.; Dunsby, Christopher; French, Paul; Itoh, Yoshifumi

2014-03-01

Degradation of articular cartilage extracellular matrix (ECM) by proteolytic enzyme is the hallmark of arthritis that leads to joint destruction. Detection of early biochemical changes in cartilage before irreversible structural damages become apparent is highly desirable. Here we report that the autofluorescence decay profile of cartilage is significantly affected by proteolytic degradation of cartilage ECM and can be characterised by measurements of the autofluorescence lifetime (AFL). A multidimensional fluorometer utilizing ultraviolet excitation at 355 nm or 375 nm coupled to a fibreoptic probe was developed for single point time-resolved AFL measurements of porcine articular cartilage explants treated with different proteinases. Degradation of cartilage matrix components by treating with bacterial collagenase, matrix metalloproteinase 1, or trypsin resulted in significant reduction of AFL of the cartilage in both a dose and time dependent manner. Differences in cartilage AFL were also confirmed by fluorescence lifetime imaging microscopy (FLIM). Our data suggest that AFL of cartilage tissue is a potential non-invasive readout to monitor cartilage matrix integrity that may be utilized for diagnosis of arthritis as well as monitoring the efficacy of anti-arthritic therapeutic agents.

Structure of the two-neutrino double-β decay matrix elements within perturbation theory

NASA Astrophysics Data System (ADS)

Štefánik, Dušan; Šimkovic, Fedor; Faessler, Amand

2015-06-01

The two-neutrino double-β Gamow-Teller and Fermi transitions are studied within an exactly solvable model, which allows a violation of both spin-isospin SU(4) and isospin SU(2) symmetries, and is expressed with generators of the SO(8) group. It is found that this model reproduces the main features of realistic calculation within the quasiparticle random-phase approximation with isospin symmetry restoration concerning the dependence of the two-neutrino double-β decay matrix elements on isovector and isoscalar particle-particle interactions. By using perturbation theory an explicit dependence of the two-neutrino double-β decay matrix elements on the like-nucleon pairing, particle-particle T =0 and T =1 , and particle-hole proton-neutron interactions is obtained. It is found that double-β decay matrix elements do not depend on the mean field part of Hamiltonian and that they are governed by a weak violation of both SU(2) and SU(4) symmetries by the particle-particle interaction of Hamiltonian. It is pointed out that there is a dominance of two-neutrino double-β decay transition through a single state of intermediate nucleus. The energy position of this state relative to energies of initial and final ground states is given by a combination of strengths of residual interactions. Further, energy-weighted Fermi and Gamow-Teller sum rules connecting Δ Z =2 nuclei are discussed. It is proposed that these sum rules can be used to study the residual interactions of the nuclear Hamiltonian, which are relevant for charge-changing nuclear transitions.

Deposition of tropoelastin into the extracellular matrix requires a competent elastic fiber scaffold but not live cells.

PubMed

Kozel, Beth A; Ciliberto, Christopher H; Mecham, Robert P

2004-04-01

The initial steps of elastic fiber assembly were investigated using an in vitro assembly model in which purified recombinant tropoelastin (rbTE) was added to cultures of live or dead cells. The ability of tropoelastin to associate with preexisting elastic fibers or microfibrils in the extracellular matrix was then assessed by immunofluorescence microscopy using species-specific tropoelastin antibodies. Results show that rbTE can associate with elastic fiber components in the absence of live cells through a process that does not depend on crosslink formation. Time course studies show a transformation of the deposited protein from an initial globular appearance early in culture to a more fibrous structure as the matrix matures. Deposition required the C-terminal region of tropoelastin and correlated with the presence of preexisting elastic fibers or microfibrils. Association of exogenously added tropoelastin to the cellular extracellular matrix was inhibited by the addition of heparan sulfate but not chondroitin sulfate sugars. Together, these results suggest that the matrix elaborated by the cell is sufficient for the initial deposition of tropoelastin in the extracellular space and that elastin assembly may be influenced by the composition of sulfated proteoglycans in the matrix.

Distance learning in discriminative vector quantization.

PubMed

Schneider, Petra; Biehl, Michael; Hammer, Barbara

2009-10-01

Discriminative vector quantization schemes such as learning vector quantization (LVQ) and extensions thereof offer efficient and intuitive classifiers based on the representation of classes by prototypes. The original methods, however, rely on the Euclidean distance corresponding to the assumption that the data can be represented by isotropic clusters. For this reason, extensions of the methods to more general metric structures have been proposed, such as relevance adaptation in generalized LVQ (GLVQ) and matrix learning in GLVQ. In these approaches, metric parameters are learned based on the given classification task such that a data-driven distance measure is found. In this letter, we consider full matrix adaptation in advanced LVQ schemes. In particular, we introduce matrix learning to a recent statistical formalization of LVQ, robust soft LVQ, and we compare the results on several artificial and real-life data sets to matrix learning in GLVQ, a derivation of LVQ-like learning based on a (heuristic) cost function. In all cases, matrix adaptation allows a significant improvement of the classification accuracy. Interestingly, however, the principled behavior of the models with respect to prototype locations and extracted matrix dimensions shows several characteristic differences depending on the data sets.

Factors Controlling Stress Rupture of Fiber-Reinforced Ceramic Composites

NASA Technical Reports Server (NTRS)

DiCarlo, J. A.; Yun, H. M.

1999-01-01

The successful application of fiber-reinforced ceramic matrix composites (CMC) depends strongly on maximizing material rupture life over a wide range of temperatures and applied stresses. The objective of this paper is to examine the various intrinsic and extrinsic factors that control the high-temperature stress rupture of CMC for stresses below and above those required for cracking of the 0 C plies (Regions I and II, respectively). Using creep-rupture results for a variety of ceramic fibers and rupture data for CMC reinforced by these fibers, it is shown that in those cases where the matrix carries little structural load, CMC rupture conditions can be predicted very well from the fiber behavior measured under the appropriate test environment. As such, one can then examine the intrinsic characteristics of the fibers in order to develop design guidelines for selecting fibers and fiber microstructures in order to maximize CMC rupture life. For those cases where the fiber interfacial coatings are unstable in the test environment, CMC lives are generally worse than those predicted by fiber behavior alone. For those cases where the matrix can support structural load, CMC life can even be greater provided matrix creep behavior is properly controlled. Thus the achievement of long CMC rupture life requires understanding and optimizing the behavior of all constituents in the proper manner.

A new decentralised controller design method for a class of strongly interconnected systems

NASA Astrophysics Data System (ADS)

Duan, Zhisheng; Jiang, Zhong-Ping; Huang, Lin

2017-02-01

In this paper, two interconnected structures are first discussed, under which some closed-loop subsystems must be unstable to make the whole interconnected system stable, which can be viewed as a kind of strongly interconnected systems. Then, comparisons with small gain theorem are discussed and large gain interconnected characteristics are shown. A new approach for the design of decentralised controllers is presented by determining the Lyapunov function structure previously, which allows the existence of unstable subsystems. By fully utilising the orthogonal space information of input matrix, some new understandings are presented for the construction of Lyapunov matrix. This new method can deal with decentralised state feedback, static output feedback and dynamic output feedback controllers in a unified framework. Furthermore, in order to reduce the design conservativeness and deal with robustness, a new robust decentralised controller design method is given by combining with the parameter-dependent Lyapunov function method. Some basic rules are provided for the choice of initial variables in Lyapunov matrix or new introduced slack matrices. As byproducts, some linear matrix inequality based sufficient conditions are established for centralised static output feedback stabilisation. Effects of unstable subsystems in nonlinear Lur'e systems are further discussed. The corresponding decentralised controller design method is presented for absolute stability. The examples illustrate that the new method is significantly effective.

Aging-associated modifications of collagen affect its degradation by matrix metalloproteinases.

PubMed

Panwar, Preety; Butler, Georgina S; Jamroz, Andrew; Azizi, Pouya; Overall, Christopher M; Brömme, Dieter

2018-01-01

The natural aging process and various pathologies correlate with alterations in the composition and the structural and mechanical integrity of the connective tissue. Collagens represent the most abundant matrix proteins and provide for the overall stiffness and resilience of tissues. The structural changes of collagens and their susceptibility to degradation are associated with skin wrinkling, bone and cartilage deterioration, as well as cardiovascular and respiratory malfunctions. Here, matrix metalloproteinases (MMPs) are major contributors to tissue remodeling and collagen degradation. During aging, collagens are modified by mineralization, accumulation of advanced glycation end-products (AGEs), and the depletion of glycosaminoglycans (GAGs), which affect fiber stability and their susceptibility to MMP-mediated degradation. We found a reduced collagenolysis in mineralized and AGE-modified collagen fibers when compared to native fibrillar collagen. GAGs had no effect on MMP-mediated degradation of collagen. In general, MMP digestion led to a reduction in the mechanical strength of native and modified collagen fibers. Successive fiber degradation with MMPs and the cysteine-dependent collagenase, cathepsin K (CatK), resulted in their complete degradation. In contrast, MMP-generated fragments were not or only poorly cleaved by non-collagenolytic cathepsins such as cathepsin V (CatV). In conclusion, our data indicate that aging and disease-associated collagen modifications reduce tissue remodeling by MMPs and decrease the structural and mechanic integrity of collagen fibers, which both may exacerbate extracellular matrix pathology. Copyright © 2017 Elsevier B.V. All rights reserved.

Stretching the boundaries of extracellular matrix research.

PubMed

Hynes, Richard O

2014-12-01

Extracellular matrix (ECM) proteins constitute >1% of the proteome and interact with many modifiers and growth factors to affect most aspects of cellular behaviour during development and normal physiology, as well as in diseases such as fibroses, cancer and many genetic disorders. In addition to biochemical signals provided to cells by ECM proteins, important cell–ECM interactions involve bidirectional mechanotransduction influences, which are dependent on the physical structure and organization of the ECM. These are beginning to be understood using twenty-first-century approaches, including biophysics, nanotechnology, biological engineering and modern microscopy. Articles in this issue of Nature Reviews Molecular Cell Biology review progress in our understanding of the ECM.

Statistical properties of the stock and credit market: RMT and network topology

NASA Astrophysics Data System (ADS)

Lim, Kyuseong; Kim, Min Jae; Kim, Sehyun; Kim, Soo Yong

We analyzed the dependence structure of the credit and stock market using random matrix theory and network topology. The dynamics of both markets have been spotlighted throughout the subprime crisis. In this study, we compared these two markets in view of the market-wide effect from random matrix theory and eigenvalue analysis. We found that the largest eigenvalue of the credit market as a whole preceded that of the stock market in the beginning of the financial crisis and that of two markets tended to be synchronized after the crisis. The correlation between the companies of both markets became considerably stronger after the crisis as well.

Markov model of the loan portfolio dynamics considering influence of management and external economic factors

NASA Astrophysics Data System (ADS)

Bozhalkina, Yana; Timofeeva, Galina

2016-12-01

Mathematical model of loan portfolio in the form of a controlled Markov chain with discrete time is considered. It is assumed that coefficients of migration matrix depend on corrective actions and external factors. Corrective actions include process of receiving applications, interaction with existing solvent and insolvent clients. External factors are macroeconomic indicators, such as inflation and unemployment rates, exchange rates, consumer price indices, etc. Changes in corrective actions adjust the intensity of transitions in the migration matrix. The mathematical model for forecasting the credit portfolio structure taking into account a cumulative impact of internal and external changes is obtained.

Cucheb: A GPU implementation of the filtered Lanczos procedure

NASA Astrophysics Data System (ADS)

Aurentz, Jared L.; Kalantzis, Vassilis; Saad, Yousef

2017-11-01

This paper describes the software package Cucheb, a GPU implementation of the filtered Lanczos procedure for the solution of large sparse symmetric eigenvalue problems. The filtered Lanczos procedure uses a carefully chosen polynomial spectral transformation to accelerate convergence of the Lanczos method when computing eigenvalues within a desired interval. This method has proven particularly effective for eigenvalue problems that arise in electronic structure calculations and density functional theory. We compare our implementation against an equivalent CPU implementation and show that using the GPU can reduce the computation time by more than a factor of 10. Program Summary Program title: Cucheb Program Files doi:http://dx.doi.org/10.17632/rjr9tzchmh.1 Licensing provisions: MIT Programming language: CUDA C/C++ Nature of problem: Electronic structure calculations require the computation of all eigenvalue-eigenvector pairs of a symmetric matrix that lie inside a user-defined real interval. Solution method: To compute all the eigenvalues within a given interval a polynomial spectral transformation is constructed that maps the desired eigenvalues of the original matrix to the exterior of the spectrum of the transformed matrix. The Lanczos method is then used to compute the desired eigenvectors of the transformed matrix, which are then used to recover the desired eigenvalues of the original matrix. The bulk of the operations are executed in parallel using a graphics processing unit (GPU). Runtime: Variable, depending on the number of eigenvalues sought and the size and sparsity of the matrix. Additional comments: Cucheb is compatible with CUDA Toolkit v7.0 or greater.

Transport properties of electrons in fractal magnetic-barrier structures

NASA Astrophysics Data System (ADS)

Sun, Lifeng; Fang, Chao; Guo, Yong

2010-09-01

Quantum transport properties in fractal magnetically modulated structures are studied by the transfer-matrix method. It is found that the transmission spectra depend sensitively not only on the incident energy and the direction of the wave vector but also on the stage of the fractal structures. Resonance splitting, enhancement, and position shift of the resonance peaks under different magnetic modulation are observed at four different fractal stages, and the relationship between the conductance in the fractal structure and magnetic modulation is also revealed. The results indicate the spectra of the transmission can be considered as fingerprints for the fractal structures, which show the subtle correspondence between magnetic structures and transport behaviors.

The Exopolysaccharide Matrix

PubMed Central

Koo, H.; Falsetta, M.L.; Klein, M.I.

2013-01-01

Many infectious diseases in humans are caused or exacerbated by biofilms. Dental caries is a prime example of a biofilm-dependent disease, resulting from interactions of microorganisms, host factors, and diet (sugars), which modulate the dynamic formation of biofilms on tooth surfaces. All biofilms have a microbial-derived extracellular matrix as an essential constituent. The exopolysaccharides formed through interactions between sucrose- (and starch-) and Streptococcus mutans-derived exoenzymes present in the pellicle and on microbial surfaces (including non-mutans) provide binding sites for cariogenic and other organisms. The polymers formed in situ enmesh the microorganisms while forming a matrix facilitating the assembly of three-dimensional (3D) multicellular structures that encompass a series of microenvironments and are firmly attached to teeth. The metabolic activity of microbes embedded in this exopolysaccharide-rich and diffusion-limiting matrix leads to acidification of the milieu and, eventually, acid-dissolution of enamel. Here, we discuss recent advances concerning spatio-temporal development of the exopolysaccharide matrix and its essential role in the pathogenesis of dental caries. We focus on how the matrix serves as a 3D scaffold for biofilm assembly while creating spatial heterogeneities and low-pH microenvironments/niches. Further understanding on how the matrix modulates microbial activity and virulence expression could lead to new approaches to control cariogenic biofilms. PMID:24045647

The exopolysaccharide matrix: a virulence determinant of cariogenic biofilm.

PubMed

Koo, H; Falsetta, M L; Klein, M I

2013-12-01

Many infectious diseases in humans are caused or exacerbated by biofilms. Dental caries is a prime example of a biofilm-dependent disease, resulting from interactions of microorganisms, host factors, and diet (sugars), which modulate the dynamic formation of biofilms on tooth surfaces. All biofilms have a microbial-derived extracellular matrix as an essential constituent. The exopolysaccharides formed through interactions between sucrose- (and starch-) and Streptococcus mutans-derived exoenzymes present in the pellicle and on microbial surfaces (including non-mutans) provide binding sites for cariogenic and other organisms. The polymers formed in situ enmesh the microorganisms while forming a matrix facilitating the assembly of three-dimensional (3D) multicellular structures that encompass a series of microenvironments and are firmly attached to teeth. The metabolic activity of microbes embedded in this exopolysaccharide-rich and diffusion-limiting matrix leads to acidification of the milieu and, eventually, acid-dissolution of enamel. Here, we discuss recent advances concerning spatio-temporal development of the exopolysaccharide matrix and its essential role in the pathogenesis of dental caries. We focus on how the matrix serves as a 3D scaffold for biofilm assembly while creating spatial heterogeneities and low-pH microenvironments/niches. Further understanding on how the matrix modulates microbial activity and virulence expression could lead to new approaches to control cariogenic biofilms.

Power law tails in phylogenetic systems.

PubMed

Qin, Chongli; Colwell, Lucy J

2018-01-23

Covariance analysis of protein sequence alignments uses coevolving pairs of sequence positions to predict features of protein structure and function. However, current methods ignore the phylogenetic relationships between sequences, potentially corrupting the identification of covarying positions. Here, we use random matrix theory to demonstrate the existence of a power law tail that distinguishes the spectrum of covariance caused by phylogeny from that caused by structural interactions. The power law is essentially independent of the phylogenetic tree topology, depending on just two parameters-the sequence length and the average branch length. We demonstrate that these power law tails are ubiquitous in the large protein sequence alignments used to predict contacts in 3D structure, as predicted by our theory. This suggests that to decouple phylogenetic effects from the interactions between sequence distal sites that control biological function, it is necessary to remove or down-weight the eigenvectors of the covariance matrix with largest eigenvalues. We confirm that truncating these eigenvectors improves contact prediction.

Analyte-Size-Dependent Ionization and Quantification of Monosaccharides in Human Plasma Using Cation-Exchanged Smectite Layers.

PubMed

Ding, Yuqi; Kawakita, Kento; Xu, Jiawei; Akiyama, Kazuhiko; Fujino, Tatsuya

2015-08-04

Smectite, a synthetic inorganic polymer with a saponite structure, was subjected to matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Typical organic matrix molecules 2,4,6-trihydroxyacetophenone (THAP) and 2,5-dihydroxybenzoic acid (DHBA) were intercalated into the layer spacing of cation-exchanged smectite, and the complex was used as a new matrix for laser desorption/ionization mass spectrometry. Because of layer spacing limitations, only a small analyte that could enter the layer and bind to THAP or DHBA could be ionized. This was confirmed by examining different analyte/matrix preparation methods and by measuring saccharides with different molecular sizes. Because of the homogeneous distribution of THAP molecules in the smectite layer spacing, high reproducibility of the analyte peak intensity was achieved. By using isotope-labeled (13)C6-d-glucose as the internal standard, quantitative analysis of monosaccharides in pretreated human plasma sample was performed, and the value of 8.6 ± 0.3 μg/mg was estimated.

Quantum confinement of nanocrystals within amorphous matrices

NASA Astrophysics Data System (ADS)

Lusk, Mark T.; Collins, Reuben T.; Nourbakhsh, Zahra; Akbarzadeh, Hadi

2014-02-01

Nanocrystals encapsulated within an amorphous matrix are computationally analyzed to quantify the degree to which the matrix modifies the nature of their quantum-confinement power—i.e., the relationship between nanocrystal size and the gap between valence- and conduction-band edges. A special geometry allows exactly the same amorphous matrix to be applied to nanocrystals of increasing size to precisely quantify changes in confinement without the noise typically associated with encapsulating structures that are different for each nanocrystal. The results both explain and quantify the degree to which amorphous matrices redshift the character of quantum confinement. The character of this confinement depends on both the type of encapsulating material and the separation distance between the nanocrystals within it. Surprisingly, the analysis also identifies a critical nanocrystal threshold below which quantum confinement is not possible—a feature unique to amorphous encapsulation. Although applied to silicon nanocrystals within an amorphous silicon matrix, the methodology can be used to accurately analyze the confinement softening of other amorphous systems as well.

Notes on quantitative structure-properties relationships (QSPR) (1): A discussion on a QSPR dimensionality paradox (QSPR DP) and its quantum resolution.

PubMed

Carbó-Dorca, Ramon; Gallegos, Ana; Sánchez, Angel J

2009-05-01

Classical quantitative structure-properties relationship (QSPR) statistical techniques unavoidably present an inherent paradoxical computational context. They rely on the definition of a Gram matrix in descriptor spaces, which is used afterwards to reduce the original dimension via several possible kinds of algebraic manipulations. From there, effective models for the computation of unknown properties of known molecular structures are obtained. However, the reduced descriptor dimension causes linear dependence within the set of discrete vector molecular representations, leading to positive semi-definite Gram matrices in molecular spaces. To resolve this QSPR dimensionality paradox (QSPR DP) here is proposed to adopt as starting point the quantum QSPR (QQSPR) computational framework perspective, where density functions act as infinite dimensional descriptors. The fundamental QQSPR equation, deduced from employing quantum expectation value numerical evaluation, can be approximately solved in order to obtain models exempt of the QSPR DP. The substitution of the quantum similarity matrix by an empirical Gram matrix in molecular spaces, build up with the original non manipulated discrete molecular descriptor vectors, permits to obtain classical QSPR models with the same characteristics as in QQSPR, that is: possessing a certain degree of causality and explicitly independent of the descriptor dimension. 2008 Wiley Periodicals, Inc.

Graphite nanoplatelets-modified PLA/PCL: Effect of blend ratio and nanofiller localization on structure and properties.

PubMed

Kelnar, Ivan; Kratochvíl, Jaroslav; Kaprálková, Ludmila; Zhigunov, Alexander; Nevoralová, Martina

2017-07-01

Structure and properties of poly(lactic acid) (PLA)/poly (ɛ-caprolactone) (PCL) influenced by graphite nanoplatelets (GNP) were studied in dependence on blend composition. Electron microscopy indicates predominant localization of GNP in PCL. GNP-induced changes in viscosity hinder refinement of PCL inclusions, support PCL continuity in the co-continuous system, and lead to reduction of PLA inclusions size without GNP being present at the interface in the PCL-matrix blend. Negligible differences in crystallinity of both phases indicate that mechanical behaviour is mainly influenced by reinforcement and GNP-induced changes in morphology. Addition of 5 parts of GNP leads to ~40% and ~25% increase of stiffness in the PCL- and PLA-matrix systems, respectively, whereas the reinforcing effect is practically eliminated in the co-continuous systems due to GNP-induced lower continuity of PLA which enhances toughness. Impact resistance of the 80/20 blend shows increase with 5 parts content due to synergistic effect of PCL/GNP stacks, whereas minor increase in the blend of the ductile PCL matrix with brittle PLA inclusions is caused by GNP-modification of the component parameters. Results indicate high potential of GNP in preparing biocompatible systems with wide range of structure and properties. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Effective Potential Energy Surfaces of the Nonadiabatic Collision

DTIC Science & Technology

2009-03-01

effective PESs data was extracted for the equilibrium H2 bond length and used to calculate inelastic scattering matrix elements using the time ...very grateful not only for the time he devoted each week to discussing the status of the work, but also his infectious love of learning that is...33 Structure of the Asymptotic Representation ................................................................. 43 The Time -Dependent

Positional information in axolotl and mouse limb extracellular matrix is mediated via heparan sulfate and fibroblast growth factor during limb regeneration in the axolotl (Ambystoma mexicanum).

PubMed

Phan, Anne Q; Lee, Jangwoo; Oei, Michelle; Flath, Craig; Hwe, Caitlyn; Mariano, Rachele; Vu, Tiffany; Shu, Cynthia; Dinh, Andrew; Simkin, Jennifer; Muneoka, Ken; Bryant, Susan V; Gardiner, David M

2015-08-01

Urodele amphibians are unique among adult vertebrates in their ability to regenerate complex body structures after traumatic injury. In salamander regeneration, the cells maintain a memory of their original position and use this positional information to recreate the missing pattern. We used an in vivo gain-of-function assay to determine whether components of the extracellular matrix (ECM) have positional information required to induce formation of new limb pattern during regeneration. We discovered that salamander limb ECM has a position-specific ability to either inhibit regeneration or induce de novo limb structure, and that this difference is dependent on heparan sulfates that are associated with differential expression of heparan sulfate sulfotransferases. We also discovered that an artificial ECM containing only heparan sulfate was sufficient to induce de novo limb pattern in salamander limb regeneration. Finally, ECM from mouse limbs is capable of inducing limb pattern in axolotl blastemas in a position-specific, developmental-stage-specific, and heparan sulfate-dependent manner. This study demonstrates a mechanism for positional information in regeneration and establishes a crucial functional link between salamander regeneration and mammals.

Positional information in axolotl and mouse limb extracellular matrix is mediated via heparan sulfate and fibroblast growth factor during limb regeneration in the axolotl (Ambystoma mexicanum)

PubMed Central

Phan, Anne Q.; Lee, Jangwoo; Oei, Michelle; Flath, Craig; Hwe, Caitlyn; Mariano, Rachele; Vu, Tiffany; Shu, Cynthia; Dinh, Andrew; Simkin, Jennifer; Muneoka, Ken; Bryant, Susan V.

2015-01-01

Abstract Urodele amphibians are unique among adult vertebrates in their ability to regenerate complex body structures after traumatic injury. In salamander regeneration, the cells maintain a memory of their original position and use this positional information to recreate the missing pattern. We used an in vivo gain‐of‐function assay to determine whether components of the extracellular matrix (ECM) have positional information required to induce formation of new limb pattern during regeneration. We discovered that salamander limb ECM has a position‐specific ability to either inhibit regeneration or induce de novo limb structure, and that this difference is dependent on heparan sulfates that are associated with differential expression of heparan sulfate sulfotransferases. We also discovered that an artificial ECM containing only heparan sulfate was sufficient to induce de novo limb pattern in salamander limb regeneration. Finally, ECM from mouse limbs is capable of inducing limb pattern in axolotl blastemas in a position‐specific, developmental‐stage‐specific, and heparan sulfate‐dependent manner. This study demonstrates a mechanism for positional information in regeneration and establishes a crucial functional link between salamander regeneration and mammals. PMID:27499874

Nanoscale viscoelasticity of extracellular matrix proteins in soft tissues: A multiscale approach.

PubMed

Miri, Amir K; Heris, Hossein K; Mongeau, Luc; Javid, Farhad

2014-02-01

It is hypothesized that the bulk viscoelasticity of soft tissues is determined by two length-scale-dependent mechanisms: the time-dependent response of the extracellular matrix (ECM) proteins at the nanometer scale and the biophysical interactions between the ECM solid structure and interstitial fluid at the micrometer scale. The latter is governed by poroelasticity theory assuming free motion of the interstitial fluid within the porous ECM structure. In a recent study (Heris, H.K., Miri, A.K., Tripathy, U., Barthelat, F., Mongeau, L., 2013. J. Mech. Behav. Biomed. Mater.), atomic force microscopy was used to measure the response of porcine vocal folds to a creep loading and a 50-nm sinusoidal oscillation. A constitutive model was calibrated and verified using a finite element model to accurately predict the nanoscale viscoelastic moduli of ECM. A generally good correlation was obtained between the predicted variation of the viscoelastic moduli with depth and that of hyaluronic acids in vocal fold tissue. We conclude that hyaluronic acids may regulate vocal fold viscoelasticity. The proposed methodology offers a characterization tool for biomaterials used in vocal fold augmentations. © 2013 Elsevier Ltd. All rights reserved.

Study on dissolution mechanism of cortisol and cortisone from hair matrix with liquid chromatography-tandem mass spectrometry.

PubMed

Xing, Xue; Chen, Zheng; Li, Jifeng; Zhang, Jing; Deng, Huihua; Lu, Zuhong

2013-06-05

Hair cortisol has been used as a biomarker of chronic stress. The detected contents of hair cortisol might depend on the incubation duration in solvents for no-milled hair samples with 3-layer structure. However, there was no research on the dissolution mechanism of hair analytes. After uniform mixture, no-milled hair samples were incubated in methanol and water for the 12 different durations and milled hair was done as comparison. Hair cortisol and cortisone were determined with high performance liquid chromatography-tandem mass spectrometry (LC-MS/MS). The measured concentrations of hair cortisol and cortisone showed ≥2 maxima during the entire incubation in methanol and water from 5 min to 72 h for no-milled hair. Hair cortisol concentration measured by LC-MS/MS was increased with the incubation duration. Conversely, it was not held when hair was powdered prior to the incubation in methanol. Hair cortisol and cortisone were dissolved from hair matrix through the 2-stage or multistage mechanism, which might depend on the hair 3-layer structure and its degree of damage. Copyright © 2013 Elsevier B.V. All rights reserved.

Quasi-stationary states of an electron with linearly dependent effective mass in an open nanostructure within transmission coefficient and S-matrix methods

NASA Astrophysics Data System (ADS)

Seti, Julia; Tkach, Mykola; Voitsekhivska, Oxana

2018-03-01

The exact solutions of the Schrödinger equation for a double-barrier open semiconductor plane nanostructure are obtained by using two different approaches, within the model of the rectangular potential profile and the continuous position-dependent effective mass of the electron. The transmission coefficient and scattering matrix are calculated for the double-barrier nanostructure. The resonance energies and resonance widths of the electron quasi-stationary states are analyzed as a function of the size of the near-interface region between wells and barriers, where the effective mass linearly depends on the coordinate. It is established that, in both methods, the increasing size affects in a qualitatively similar way the spectral characteristics of the states, shifting the resonance energies into the low- or high-energy region and increasing the resonance widths. It is shown that the relative difference of resonance energies and widths of a certain state, obtained in the model of position-dependent effective mass and in the widespread abrupt model in physically correct range of near-interface sizes, does not exceed 0.5% and 5%, respectively, independently of the other geometrical characteristics of the structure.

Time dependent Schrödinger equation for black hole evaporation: No information loss

NASA Astrophysics Data System (ADS)

Corda, Christian

2015-02-01

In 1976 S. Hawking claimed that "Because part of the information about the state of the system is lost down the hole, the final situation is represented by a density matrix rather than a pure quantum state".1 In a series of papers, together with collaborators, we naturally interpreted BH quasi-normal modes (QNMs) in terms of quantum levels discussing a model of excited BH somewhat similar to the historical semi-classical Bohr model of the structure of a hydrogen atom. Here we explicitly write down, for the same model, a time dependent Schrödinger equation for the system composed by Hawking radiation and BH QNMs. The physical state and the correspondent wave function are written in terms of a unitary evolution matrix instead of a density matrix. Thus, the final state results to be a pure quantum state instead of a mixed one. Hence, Hawking's claim is falsified because BHs result to be well defined quantum mechanical systems, having ordered, discrete quantum spectra, which respect 't Hooft's assumption that Schrödinger equations can be used universally for all dynamics in the universe. As a consequence, information comes out in BH evaporation in terms of pure states in a unitary time dependent evolution. In Section 4 of this paper we show that the present approach permits also to solve the entanglement problem connected with the information paradox.

Mesenchymal Stem Cells Sense Three Dimensional Type I Collagen through Discoidin Domain Receptor 1.

PubMed

Lund, A W; Stegemann, J P; Plopper, G E

2009-01-01

The extracellular matrix provides structural and organizational cues for tissue development and defines and maintains cellular phenotype during cell fate determination. Multipotent mesenchymal stem cells use this matrix to tightly regulate the balance between their differentiation potential and self-renewal in the native niche. When understood, the mechanisms that govern cell-matrix crosstalk during differentiation will allow for efficient engineering of natural and synthetic matrices to specifically direct and maintain stem cell phenotype. This work identifies the discoidin domain receptor 1 (DDR1), a collagen activated receptor tyrosine kinase, as a potential link through which stem cells sense and respond to the 3D organization of their extracellular matrix microenvironment. DDR1 is dependent upon both the structure and proteolytic state of its collagen ligand and is specifically expressed and localized in three dimensional type I collagen culture. Inhibition of DDR1 expression results in decreased osteogenic potential, increased cell spreading, stress fiber formation and ERK1/2 phosphorylation. Additionally, loss of DDR1 activity alters the cell-mediated organization of the naïve type I collagen matrix. Taken together, these results demonstrate a role for DDR1 in the stem cell response to and interaction with three dimensional type I collagen. Dynamic changes in cell shape in 3D culture and the tuning of the local ECM microstructure, directs crosstalk between DDR1 and two dimensional mechanisms of osteogenesis that can alter their traditional roles.

Structural and optical properties of vanadium ion-implanted GaN

NASA Astrophysics Data System (ADS)

Macková, A.; Malinský, P.; Jagerová, A.; Sofer, Z.; Klímová, K.; Sedmidubský, D.; Mikulics, M.; Lorinčík, J.; Veselá, D.; Böttger, R.; Akhmadaliev, S.

2017-09-01

The field of advanced electronic and optical devices searches for a new generation of transistors and lasers. The practical development of these novel devices depends on the availability of materials with the appropriate magnetic and optical properties, which is strongly connected to the internal morphology and the structural properties of the prepared doped structures. In this contribution, we present the characterisation of V ion-doped GaN epitaxial layers. GaN layers, oriented along the (0 0 0 1) crystallographic direction, grown by low-pressure metal-organic vapour-phase epitaxy (MOVPE) on c-plane sapphire substrates were implanted with 400 keV V+ ions at fluences of 5 × 1015 and 5 × 1016 cm-2. Elemental depth profiling was accomplished by Rutherford Backscattering Spectrometry (RBS) and Secondary Ion Mass Spectrometry (SIMS) to obtain precise information about the dopant distribution. Structural investigations are needed to understand the influence of defect distribution on the crystal-matrix recovery and the desired structural and optical properties. The structural properties of the ion-implanted layers were characterised by RBS-channelling and Raman spectroscopy to get a comprehensive insight into the structural modification of implanted GaN and to study the influence of subsequent annealing on the crystalline matrix reconstruction. Photoluminescence measurement was carried out to check the optical properties of the prepared structures.

Structural and optical properties of Sb65Se35-xGex thin films

NASA Astrophysics Data System (ADS)

Saleh, S. A.; Al-Hajry, A.; Ali, H. M.

2011-07-01

Sb65Se35-xGex (x=0-20 at.%) thin films, prepared by the electron beam evaporation technique on ultrasonically cleaned glass substrates at 300 K, were investigated. The amorphous structure of the thin films was confirmed by x-ray diffraction analysis. The structure was deduced from the Raman spectra measured for all germanium contents in the Sb-Se-Ge matrix. The absorption coefficient (α) of the films was determined by optical transmission measurements. The compositional dependence of the optical band gap is discussed in light of topological and chemical ordered network models.

Structure of CdTe nanoparticles in glass

NASA Astrophysics Data System (ADS)

Hayes, T. M.; Nagpal, Swati; Persans, P. D.

2000-03-01

Optical long-pass wavelength filters are generally made by growing small crystallites of appropriate semiconductors in a transparent glass matrix. Depending on the semiconductor, these systems are candidates for interesting and important nonlinear optical switching applications. The structure of these nanocrystals has been shown to be a valuable indicator of the chemical and thermodynamic processes during crystallite growth and dissolution. We have used x-ray absorption spectroscopy to study the structure of the crystallites produced during heat treatment of filter glasses containing Cd and Te and producing optical absorption edges at the band gap of bulk CdTe. The results will be discussed.

Landscape ecology of interactions between seagrass and mobile epifauna: The matrix matters

NASA Astrophysics Data System (ADS)

Tanner, Jason E.

2006-07-01

There is increasing interest among ecologists about how the type of matrix surrounding a habitat patch influences the organisms living in that patch. This question is virtually unstudied in marine systems. In this paper I show that the mobile faunal assemblage in seagrass patches does depend on the surrounding matrix. Faunal assemblages in patches of Posidonia surrounded by sand are different than in those surrounded by Heterozostera, another seagrass, having more than double the abundance of both amphipods and polychaetes. However, the differences are not simply due to spillover from the matrix habitat, but rather are an emergent property of the patch context that cannot be predicted. Posidonia surrounded by sand actually has an assemblage that is intermediate between Heterozostera and Posidonia surrounded by Heterozostera. Differences in habitat structure do not account for this pattern, as seagrass biomass did not vary, and the same result was found in artificial seagrass. The faunal assemblage did not vary depending on the location within the patch (edge or centre) for Heterozostera, Posidonia or artificial seagrass. Patch size, however, did have an effect for Heterozostera, with smaller patches having 2-3 times as many isopods per sample as large, but less than half the number of some amphipod families. These results suggest that the landscape context is as important in marine systems as it is known to be in terrestrial systems.

Dependence structure of the commodity and stock markets, and relevant multi-spread strategy

NASA Astrophysics Data System (ADS)

Kim, Min Jae; Kim, Sehyun; Jo, Yong Hwan; Kim, Soo Yong

2011-10-01

Understanding the dependence structure between the commodity and stock markets is a crucial issue in constructing a portfolio. It can also help us to discover new opportunities to implement spread trading using multiple assets classified in the two different markets. This study analyzed the dependence structure of the commodity and stock markets using the random matrix theory technique and network analysis. Our results show that the stock and commodity markets must be handled as completely separated asset classes except for the oil and gold markets, so the performance enhancement of the mean-variance portfolio is significant as expected. In light of the fact that WTI 1 month futures and four oil-related stocks are strongly correlated, they were selected as basic ingredients to complement the multi-spread convergence trading strategy using a machine learning technique called the AdaBoost algorithm. The performance of this strategy for non-myopic investors, who can endure short-term loss, can be enhanced significantly on a risk measurement basis.

Commensurate vortex configurations in thin superconducting films nanostructured by square lattice of magnetic dots

NASA Astrophysics Data System (ADS)

Milošević, M. V.; Peeters, F. M.

2004-05-01

Within the phenomenological Ginzburg-Landau (GL) theory, we investigate the vortex structure of a thin superconducting film (SC) with a regular matrix of ferromagnetic dots (FD) deposited on top of it. The vortex pinning properties of such a magnetic lattice are studied, and the field polarity dependent votex pinning is observed. The exact vortex configuration depends on the size of the magnetic dots, their polarity, periodicity of the FD-rooster and the properties of the SC expressed through the effective Ginzburg-Landau parameter κ*.

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

Conn, Charlotte E.; Darmanin, Connie; Sagnella, Sharon M.

The dopamine D2 long (D2L) receptor and bacteriorhodopsin (bR), which are integral membraneproteins, have been incorporated within bicontinuous cubic mesophases formed by the lipids anandamide and H-farnesoyl monoethanolamide, which have been specifically investigated by us for use as in mesocrystallization media. We show that the incorporated membraneprotein affects the structure of the cubic phases with the particular effect observed dependent on the geometry of the underlying cubic phase. The results are complementary to those obtained in Part 1 of this series, where we demonstrated that the structural effects observed depend on the structure of the membraneprotein. Importantly protein concentrations commonlymore » used for crystallization can destroy the cubic phase matrix, particularly where there is a large discrepancy between the hydrophilic and the hydrophobic spans of the membraneprotein, and the hydrophilic and hydrophobic domain sizes of the cubic phase.« less

Time-dependent deformation of titanium metal matrix composites

NASA Technical Reports Server (NTRS)

Bigelow, C. A.; Bahei-El-din, Y. A.; Mirdamadi, M.

1995-01-01

A three-dimensional finite element program called VISCOPAC was developed and used to conduct a micromechanics analysis of titanium metal matrix composites. The VISCOPAC program uses a modified Eisenberg-Yen thermo-viscoplastic constitutive model to predict matrix behavior under thermomechanical fatigue loading. The analysis incorporated temperature-dependent elastic properties in the fiber and temperature-dependent viscoplastic properties in the matrix. The material model was described and the necessary material constants were determined experimentally. Fiber-matrix interfacial behavior was analyzed using a discrete fiber-matrix model. The thermal residual stresses due to the fabrication cycle were predicted with a failed interface, The failed interface resulted in lower thermal residual stresses in the matrix and fiber. Stresses due to a uniform transverse load were calculated at two temperatures, room temperature and an elevated temperature of 650 C. At both temperatures, a large stress concentration was calculated when the interface had failed. The results indicate the importance of accuracy accounting for fiber-matrix interface failure and the need for a micromechanics-based analytical technique to understand and predict the behavior of titanium metal matrix composites.

Crazing of nanocomposites with polymer-tethered nanoparticles

DOE PAGES

Meng, Dong; Kumar, Sanat K.; Ge, Ting; ...

2016-09-07

The crazing behavior of polymer nanocomposites formed by blending polymer grafted nanoparticles with an entangled polymer melt is studied by molecular dynamics simulations. We focus on the three key differences in the crazing behavior of a composite relative to the pure homopolymer matrix, namely, a lower yield stress, a smaller extension ratio, and a grafted chain length dependent failure stress. The yield behavior is found to be mostly controlled by the local nanoparticle-grafted polymer interfacial energy, with the grafted polymer-polymer matrix interfacial structure being of little to no relevance. Increasing the attraction between nanoparticle core and the grafted polymer inhibitsmore » void nucleation and leads to a higher yield stress. In the craze growth regime, the presence of “grafted chain” sections of ≈100 monomers alters the mechanical response of composite samples, giving rise to smaller extension ratios and higher drawing stresses than for the homopolymer matrix. As a result, the dominant failure mechanism of composite samples depends strongly on the length of the grafted chains, with disentanglement being the dominant mechanism for short chains, while bond breaking is the failure mode for chain lengths >10N e, where N e is the entanglement length.« less

The Role of Species Traits in Mediating Functional Recovery during Matrix Restoration

PubMed Central

Barnes, Andrew D.; Emberson, Rowan M.; Krell, Frank-Thorsten; Didham, Raphael K.

2014-01-01

Reversing anthropogenic impacts on habitat structure is frequently successful through restoration, but the mechanisms linking habitat change, community reassembly and recovery of ecosystem functioning remain unknown. We test for the influence of edge effects and matrix habitat restoration on the reassembly of dung beetle communities and consequent recovery of dung removal rates across tropical forest edges. Using path modelling, we disentangle the relative importance of community-weighted trait means and functional trait dispersion from total biomass effects on rates of dung removal. Community trait composition and biomass of dung beetle communities responded divergently to edge effects and matrix habitat restoration, yielding opposing effects on dung removal. However, functional dispersion—used in this study as a measure of niche complementarity—did not explain a significant amount of variation in dung removal rates across habitat edges. Instead, we demonstrate that the path to functional recovery of these altered ecosystems depends on the trait-mean composition of reassembling communities, over and above purely biomass-dependent processes that would be expected under neutral theory. These results suggest that any ability to manage functional recovery of ecosystems during habitat restoration will demand knowledge of species' roles in ecosystem processes. PMID:25502448

The role of species traits in mediating functional recovery during matrix restoration.

PubMed

Barnes, Andrew D; Emberson, Rowan M; Krell, Frank-Thorsten; Didham, Raphael K

2014-01-01

Reversing anthropogenic impacts on habitat structure is frequently successful through restoration, but the mechanisms linking habitat change, community reassembly and recovery of ecosystem functioning remain unknown. We test for the influence of edge effects and matrix habitat restoration on the reassembly of dung beetle communities and consequent recovery of dung removal rates across tropical forest edges. Using path modelling, we disentangle the relative importance of community-weighted trait means and functional trait dispersion from total biomass effects on rates of dung removal. Community trait composition and biomass of dung beetle communities responded divergently to edge effects and matrix habitat restoration, yielding opposing effects on dung removal. However, functional dispersion--used in this study as a measure of niche complementarity--did not explain a significant amount of variation in dung removal rates across habitat edges. Instead, we demonstrate that the path to functional recovery of these altered ecosystems depends on the trait-mean composition of reassembling communities, over and above purely biomass-dependent processes that would be expected under neutral theory. These results suggest that any ability to manage functional recovery of ecosystems during habitat restoration will demand knowledge of species' roles in ecosystem processes.

Covariance, correlation matrix, and the multiscale community structure of networks.

PubMed

Shen, Hua-Wei; Cheng, Xue-Qi; Fang, Bin-Xing

2010-07-01

Empirical studies show that real world networks often exhibit multiple scales of topological descriptions. However, it is still an open problem how to identify the intrinsic multiple scales of networks. In this paper, we consider detecting the multiscale community structure of network from the perspective of dimension reduction. According to this perspective, a covariance matrix of network is defined to uncover the multiscale community structure through the translation and rotation transformations. It is proved that the covariance matrix is the unbiased version of the well-known modularity matrix. We then point out that the translation and rotation transformations fail to deal with the heterogeneous network, which is very common in nature and society. To address this problem, a correlation matrix is proposed through introducing the rescaling transformation into the covariance matrix. Extensive tests on real world and artificial networks demonstrate that the correlation matrix significantly outperforms the covariance matrix, identically the modularity matrix, as regards identifying the multiscale community structure of network. This work provides a novel perspective to the identification of community structure and thus various dimension reduction methods might be used for the identification of community structure. Through introducing the correlation matrix, we further conclude that the rescaling transformation is crucial to identify the multiscale community structure of network, as well as the translation and rotation transformations.

Chirality dependence of dipole matrix element of carbon nanotubes in axial magnetic field: A third neighbor tight binding approach

NASA Astrophysics Data System (ADS)

Chegel, Raad; Behzad, Somayeh

2014-02-01

We have studied the electronic structure and dipole matrix element, D, of carbon nanotubes (CNTs) under magnetic field, using the third nearest neighbor tight binding model. It is shown that the 1NN and 3NN-TB band structures show differences such as the spacing and mixing of neighbor subbands. Applying the magnetic field leads to breaking the degeneracy behavior in the D transitions and creates new allowed transitions corresponding to the band modifications. It is found that |D| is proportional to the inverse tube radius and chiral angle. Our numerical results show that amount of filed induced splitting for the first optical peak is proportional to the magnetic field by the splitting rate ν11. It is shown that ν11 changes linearly and parabolicly with the chiral angle and radius, respectively.

Internal strain drives spontaneous periodic buckling in collagen and regulates remodeling.

PubMed

Dittmore, Andrew; Silver, Jonathan; Sarkar, Susanta K; Marmer, Barry; Goldberg, Gregory I; Neuman, Keir C

2016-07-26

Fibrillar collagen, an essential structural component of the extracellular matrix, is remarkably resistant to proteolysis, requiring specialized matrix metalloproteinases (MMPs) to initiate its remodeling. In the context of native fibrils, remodeling is poorly understood; MMPs have limited access to cleavage sites and are inhibited by tension on the fibril. Here, single-molecule recordings of fluorescently labeled MMPs reveal cleavage-vulnerable binding regions arrayed periodically at ∼1-µm intervals along collagen fibrils. Binding regions remain periodic even as they migrate on the fibril, indicating a collective process of thermally activated and self-healing defect formation. An internal strain relief model involving reversible structural rearrangements quantitatively reproduces the observed spatial patterning and fluctuations of defects and provides a mechanism for tension-dependent stabilization of fibrillar collagen. This work identifies internal-strain-driven defects that may have general and widespread regulatory functions in self-assembled biological filaments.

Dirac R -matrix calculations for the electron-impact excitation of neutral tungsten providing noninvasive diagnostics for magnetic confinement fusion

NASA Astrophysics Data System (ADS)

Smyth, R. T.; Ballance, C. P.; Ramsbottom, C. A.; Johnson, C. A.; Ennis, D. A.; Loch, S. D.

2018-05-01

Neutral tungsten is the primary candidate as a wall material in the divertor region of the International Thermonuclear Experimental Reactor (ITER). The efficient operation of ITER depends heavily on precise atomic physics calculations for the determination of reliable erosion diagnostics, helping to characterize the influx of tungsten impurities into the core plasma. The following paper presents detailed calculations of the atomic structure of neutral tungsten using the multiconfigurational Dirac-Fock method, drawing comparisons with experimental measurements where available, and includes a critical assessment of existing atomic structure data. We investigate the electron-impact excitation of neutral tungsten using the Dirac R -matrix method, and by employing collisional-radiative models, we benchmark our results with recent Compact Toroidal Hybrid measurements. The resulting comparisons highlight alternative diagnostic lines to the widely used 400.88-nm line.

Conductivity and properties of polysiloxane-polyether cluster-LiTFSI networks as hybrid polymer electrolytes

NASA Astrophysics Data System (ADS)

Boaretto, Nicola; Joost, Christine; Seyfried, Mona; Vezzù, Keti; Di Noto, Vito

2016-09-01

This report describes the synthesis and the properties of a series of polymer electrolytes, composed of a hybrid inorganic-organic matrix doped with LiTFSI. The matrix is based on ring-like oligo-siloxane clusters, bearing pendant, partially cross-linked, polyether chains. The dependency of the thermo-mechanic and of the transport properties on several structural parameters, such as polyether chains' length, cross-linkers' concentration, and salt concentration is studied. Altogether, the materials show good thermo-mechanical and electrochemical stabilities, with conductivities reaching, at best, 8·10-5 S cm-1 at 30 °C. In conclusion, the cell performances of one representative sample are shown. The scope of this report is to analyze the correlations between structure and properties in networked and hybrid polymer electrolytes. This could help the design of optimized polymer electrolytes for application in lithium metal batteries.

Internal strain drives spontaneous periodic buckling in collagen and regulates remodeling

PubMed Central

Dittmore, Andrew; Silver, Jonathan; Sarkar, Susanta K.; Marmer, Barry; Goldberg, Gregory I.; Neuman, Keir C.

2016-01-01

Fibrillar collagen, an essential structural component of the extracellular matrix, is remarkably resistant to proteolysis, requiring specialized matrix metalloproteinases (MMPs) to initiate its remodeling. In the context of native fibrils, remodeling is poorly understood; MMPs have limited access to cleavage sites and are inhibited by tension on the fibril. Here, single-molecule recordings of fluorescently labeled MMPs reveal cleavage-vulnerable binding regions arrayed periodically at ∼1-µm intervals along collagen fibrils. Binding regions remain periodic even as they migrate on the fibril, indicating a collective process of thermally activated and self-healing defect formation. An internal strain relief model involving reversible structural rearrangements quantitatively reproduces the observed spatial patterning and fluctuations of defects and provides a mechanism for tension-dependent stabilization of fibrillar collagen. This work identifies internal–strain-driven defects that may have general and widespread regulatory functions in self-assembled biological filaments. PMID:27402741

Structural symmetry in evolutionary games.

PubMed

McAvoy, Alex; Hauert, Christoph

2015-10-06

In evolutionary game theory, an important measure of a mutant trait (strategy) is its ability to invade and take over an otherwise-monomorphic population. Typically, one quantifies the success of a mutant strategy via the probability that a randomly occurring mutant will fixate in the population. However, in a structured population, this fixation probability may depend on where the mutant arises. Moreover, the fixation probability is just one quantity by which one can measure the success of a mutant; fixation time, for instance, is another. We define a notion of homogeneity for evolutionary games that captures what it means for two single-mutant states, i.e. two configurations of a single mutant in an otherwise-monomorphic population, to be 'evolutionarily equivalent' in the sense that all measures of evolutionary success are the same for both configurations. Using asymmetric games, we argue that the term 'homogeneous' should apply to the evolutionary process as a whole rather than to just the population structure. For evolutionary matrix games in graph-structured populations, we give precise conditions under which the resulting process is homogeneous. Finally, we show that asymmetric matrix games can be reduced to symmetric games if the population structure possesses a sufficient degree of symmetry. © 2015 The Author(s).

Structural symmetry in evolutionary games

PubMed Central

McAvoy, Alex; Hauert, Christoph

2015-01-01

In evolutionary game theory, an important measure of a mutant trait (strategy) is its ability to invade and take over an otherwise-monomorphic population. Typically, one quantifies the success of a mutant strategy via the probability that a randomly occurring mutant will fixate in the population. However, in a structured population, this fixation probability may depend on where the mutant arises. Moreover, the fixation probability is just one quantity by which one can measure the success of a mutant; fixation time, for instance, is another. We define a notion of homogeneity for evolutionary games that captures what it means for two single-mutant states, i.e. two configurations of a single mutant in an otherwise-monomorphic population, to be ‘evolutionarily equivalent’ in the sense that all measures of evolutionary success are the same for both configurations. Using asymmetric games, we argue that the term ‘homogeneous’ should apply to the evolutionary process as a whole rather than to just the population structure. For evolutionary matrix games in graph-structured populations, we give precise conditions under which the resulting process is homogeneous. Finally, we show that asymmetric matrix games can be reduced to symmetric games if the population structure possesses a sufficient degree of symmetry. PMID:26423436

Efficient reanalysis of structures by a direct modification method. [local stiffness modifications of large structures

NASA Technical Reports Server (NTRS)

Raibstein, A. I.; Kalev, I.; Pipano, A.

1976-01-01

A procedure for the local stiffness modifications of large structures is described. It enables structural modifications without an a priori definition of the changes in the original structure and without loss of efficiency due to multiple loading conditions. The solution procedure, implemented in NASTRAN, involved the decomposed stiffness matrix and the displacement vectors of the original structure. It solves the modified structure exactly, irrespective of the magnitude of the stiffness changes. In order to investigate the efficiency of the present procedure and to test its applicability within a design environment, several real and large structures were solved. The results of the efficiency studies indicate that the break-even point of the procedure varies between 8% and 60% stiffness modifications, depending upon the structure's characteristics and the options employed.

Microstructure and phase composition characterization in a Co{sub 38}Ni{sub 33}Al{sub 29} ferromagnetic shape memory alloy

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

Lu, J.B.

2016-08-15

Transmission electron microscopy was performed to investigate the microstructures of a secondary phase and its surrounding matrix in a Co{sub 38}Ni{sub 33}Al{sub 29} ferromagnetic shape memory alloy. The secondary phase shows a γ′ L1{sub 2} structure exhibiting a dendritic morphology with enclosed B2 austenite regions while the matrix shows the L1{sub 0} martensitic structure. A secondary phase-austenite-martensite sandwich structure with residual austenite ranging from several hundred nanometers to several micrometers wide is observed at the secondary phase-martensite interface due to the depletion of Co and enrichment of Al in the chemical gradient zone and the effect of the strong martensiticmore » start temperature dependency of the element concentrations. The crystallographic orientation relationship of the secondary phase and the B2 austenite fits the Kurdjumov-Sachs relationship. - Highlights: •The secondary phase has a γ′ L1{sub 2} structure exhibiting a dendritic morphology. •A secondary phase-austenite-martensite sandwich structure is observed. •The structural sandwich structure is due to elemental composition variation. •The secondary phase and the B2 austenite fit the Kurdjumov-Sachs relationship.« less

The extracellular matrix: Structure, composition, age-related differences, tools for analysis and applications for tissue engineering.

PubMed

Kular, Jaspreet K; Basu, Shouvik; Sharma, Ram I

2014-01-01

The extracellular matrix is a structural support network made up of diverse proteins, sugars and other components. It influences a wide number of cellular processes including migration, wound healing and differentiation, all of which is of particular interest to researchers in the field of tissue engineering. Understanding the composition and structure of the extracellular matrix will aid in exploring the ways the extracellular matrix can be utilised in tissue engineering applications especially as a scaffold. This review summarises the current knowledge of the composition, structure and functions of the extracellular matrix and introduces the effect of ageing on extracellular matrix remodelling and its contribution to cellular functions. Additionally, the current analytical technologies to study the extracellular matrix and extracellular matrix-related cellular processes are also reviewed.

Past matrix stiffness primes epithelial cells and regulates their future collective migration through a mechanical memory.

PubMed

Nasrollahi, Samila; Walter, Christopher; Loza, Andrew J; Schimizzi, Gregory V; Longmore, Gregory D; Pathak, Amit

2017-11-01

During morphogenesis and cancer metastasis, grouped cells migrate through tissues of dissimilar stiffness. Although the influence of matrix stiffness on cellular mechanosensitivity and motility are well-recognized, it remains unknown whether these matrix-dependent cellular features persist after cells move to a new microenvironment. Here, we interrogate whether priming of epithelial cells by a given matrix stiffness influences their future collective migration on a different matrix - a property we refer to as the 'mechanical memory' of migratory cells. To prime cells on a defined matrix and track their collective migration onto an adjoining secondary matrix of dissimilar stiffness, we develop a modular polyacrylamide substrate through step-by-step polymerization of different PA compositions. We report that epithelial cells primed on a stiff matrix migrate faster, display higher actomyosin expression, form larger focal adhesions, and retain nuclear YAP even after arriving onto a soft secondary matrix, as compared to their control behavior on a homogeneously soft matrix. Priming on a soft ECM causes a reverse effect. The depletion of YAP dramatically reduces this memory-dependent migration. Our results present a previously unidentified regulation of mechanosensitive collective cell migration by past matrix stiffness, in which mechanical memory depends on YAP activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Advancing Renewable Materials by Light and X-ray Scattering

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

Akpalu, Yvonne A

With the ultimate goal to design PHA polymer nanocomposites with tailored properties, we have completed systematic study of the influence of cooling rate [Xie et al, J. Appl. Poly. Sci., 2008] and nanofiller [Xie et al, Polymer 2009] characteristics on model bionanocomposites. Structure-property relationships for a model bionanocomposites system were investigated. These results yielded new fundamental knowledge that supports the discovery of cost-effective manufacturing technologies for a family of promising polyhydroxyalkanoates (PHAs) polyesters, with the potential to replace polyethylene and polypropylene (see Noda letter). Our results show that simple two-phase composite models do not account for the data. Although improvementmore » of the mechanical properties (stiffness/modulus and toughness) must be due to alteration of the matrix by the nanoparticle filler, the observed improvement was not caused by the change of crystallinity or spherulitic morphology. Instead, improvement depends on the molecular weight of the polymer matrix and unknown filler-matrix interactions.« less

A study of the parallel algorithm for large-scale DC simulation of nonlinear systems

NASA Astrophysics Data System (ADS)

Cortés Udave, Diego Ernesto; Ogrodzki, Jan; Gutiérrez de Anda, Miguel Angel

Newton-Raphson DC analysis of large-scale nonlinear circuits may be an extremely time consuming process even if sparse matrix techniques and bypassing of nonlinear models calculation are used. A slight decrease in the time required for this task may be enabled on multi-core, multithread computers if the calculation of the mathematical models for the nonlinear elements as well as the stamp management of the sparse matrix entries are managed through concurrent processes. This numerical complexity can be further reduced via the circuit decomposition and parallel solution of blocks taking as a departure point the BBD matrix structure. This block-parallel approach may give a considerable profit though it is strongly dependent on the system topology and, of course, on the processor type. This contribution presents the easy-parallelizable decomposition-based algorithm for DC simulation and provides a detailed study of its effectiveness.

Approximate equiangular tight frames for compressed sensing and CDMA applications

NASA Astrophysics Data System (ADS)

Tsiligianni, Evaggelia; Kondi, Lisimachos P.; Katsaggelos, Aggelos K.

2017-12-01

Performance guarantees for recovery algorithms employed in sparse representations, and compressed sensing highlights the importance of incoherence. Optimal bounds of incoherence are attained by equiangular unit norm tight frames (ETFs). Although ETFs are important in many applications, they do not exist for all dimensions, while their construction has been proven extremely difficult. In this paper, we construct frames that are close to ETFs. According to results from frame and graph theory, the existence of an ETF depends on the existence of its signature matrix, that is, a symmetric matrix with certain structure and spectrum consisting of two distinct eigenvalues. We view the construction of a signature matrix as an inverse eigenvalue problem and propose a method that produces frames of any dimensions that are close to ETFs. Due to the achieved equiangularity property, the so obtained frames can be employed as spreading sequences in synchronous code-division multiple access (s-CDMA) systems, besides compressed sensing.

Matrix metalloproteinases: their functional role in lung cancer.

PubMed

Merchant, Neha; Nagaraju, Ganji Purnachandra; Rajitha, Balney; Lammata, Saipriya; Jella, Kishore Kumar; Buchwald, Zachary S; Lakka, Sajani S; Ali, Arif N

2017-08-01

Lung malignancy is the foremost cause of cancer-related deaths globally and is frequently related to long-term tobacco smoking. Recent studies reveal that the expression of matrix metalloproteinases (MMPs) is extremely high in lung tumors compared with non-malignant lung tissue. MMPs are zinc-dependent proteases and are involved in the degradation of extracellular matrix (ECM). Several investigations have shown that MMPs manipulate the activity of non-ECM molecules, including cytokines, growth factors and receptors that control the tumor microenvironment. In this review, we have summarized and critically reviewed the published works on the role of MMPs in non-small-cell lung cancer. We have also explored the structure of MMPs, their various types and roles in lung cancer metastasis including invasion, migration and angiogenesis. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Mechanistic understanding of nanoparticles' interactions with extracellular matrix: the cell and immune system.

PubMed

Engin, Ayse Basak; Nikitovic, Dragana; Neagu, Monica; Henrich-Noack, Petra; Docea, Anca Oana; Shtilman, Mikhail I; Golokhvast, Kirill; Tsatsakis, Aristidis M

2017-06-24

Extracellular matrix (ECM) is an extraordinarily complex and unique meshwork composed of structural proteins and glycosaminoglycans. The ECM provides essential physical scaffolding for the cellular constituents, as well as contributes to crucial biochemical signaling. Importantly, ECM is an indispensable part of all biological barriers and substantially modulates the interchange of the nanotechnology products through these barriers. The interactions of the ECM with nanoparticles (NPs) depend on the morphological characteristics of intercellular matrix and on the physical characteristics of the NPs and may be either deleterious or beneficial. Importantly, an altered expression of ECM molecules ultimately affects all biological processes including inflammation. This review critically discusses the specific behavior of NPs that are within the ECM domain, and passing through the biological barriers. Furthermore, regenerative and toxicological aspects of nanomaterials are debated in terms of the immune cells-NPs interactions.

Matrix models for size-structured populations: unrealistic fast growth or simply diffusion?

PubMed

Picard, Nicolas; Liang, Jingjing

2014-01-01

Matrix population models are widely used to study population dynamics but have been criticized because their outputs are sensitive to the dimension of the matrix (or, equivalently, to the class width). This sensitivity is concerning for the population growth rate (λ) because this is an intrinsic characteristic of the population that should not depend on the model specification. It has been suggested that the sensitivity of λ to matrix dimension was linked to the existence of fast pathways (i.e. the fraction of individuals that systematically move up a class), whose proportion increases when class width increases. We showed that for matrix population models with growth transition only from class i to class i + 1, λ was independent of the class width when the mortality and the recruitment rates were constant, irrespective of the growth rate. We also showed that if there were indeed fast pathways, there were also in about the same proportion slow pathways (i.e. the fraction of individuals that systematically remained in the same class), and that they jointly act as a diffusion process (where diffusion here is the movement in size of an individual whose size increments are random according to a normal distribution with mean zero). For 53 tree species from a tropical rain forest in the Central African Republic, the diffusion resulting from common matrix dimensions was much stronger than would be realistic. Yet, the sensitivity of λ to matrix dimension for a class width in the range 1-10 cm was small, much smaller than the sampling uncertainty on the value of λ. Moreover, λ could either increase or decrease when class width increased depending on the species. Overall, even if the class width should be kept small enough to limit diffusion, it had little impact on the estimate of λ for tree species.

Atomic spectral-product representations of molecular electronic structure: metric matrices and atomic-product composition of molecular eigenfunctions.

PubMed

Ben-Nun, M; Mills, J D; Hinde, R J; Winstead, C L; Boatz, J A; Gallup, G A; Langhoff, P W

2009-07-02

Recent progress is reported in development of ab initio computational methods for the electronic structures of molecules employing the many-electron eigenstates of constituent atoms in spectral-product forms. The approach provides a universal atomic-product description of the electronic structure of matter as an alternative to more commonly employed valence-bond- or molecular-orbital-based representations. The Hamiltonian matrix in this representation is seen to comprise a sum over atomic energies and a pairwise sum over Coulombic interaction terms that depend only on the separations of the individual atomic pairs. Overall electron antisymmetry can be enforced by unitary transformation when appropriate, rather than as a possibly encumbering or unnecessary global constraint. The matrix representative of the antisymmetrizer in the spectral-product basis, which is equivalent to the metric matrix of the corresponding explicitly antisymmetric basis, provides the required transformation to antisymmetric or linearly independent states after Hamiltonian evaluation. Particular attention is focused in the present report on properties of the metric matrix and on the atomic-product compositions of molecular eigenstates as described in the spectral-product representations. Illustrative calculations are reported for simple but prototypically important diatomic (H(2), CH) and triatomic (H(3), CH(2)) molecules employing algorithms and computer codes devised recently for this purpose. This particular implementation of the approach combines Slater-orbital-based one- and two-electron integral evaluations, valence-bond constructions of standard tableau functions and matrices, and transformations to atomic eigenstate-product representations. The calculated metric matrices and corresponding potential energy surfaces obtained in this way elucidate a number of aspects of the spectral-product development, including the nature of closure in the representation, the general redundancy or linear dependence of its explicitly antisymmetrized form, the convergence of the apparently disparate atomic-product and explicitly antisymmetrized atomic-product forms to a common invariant subspace, and the nature of a chemical bonding descriptor provided by the atomic-product compositions of molecular eigenstates. Concluding remarks indicate additional studies in progress and the prognosis for performing atomic spectral-product calculations more generally and efficiently.

Exchange bias in multiferroic Ca3Mn2O7 effected by Dzyaloshinskii-Moriya interaction

NASA Astrophysics Data System (ADS)

Sahlot, Pooja; Jana, Anupam; Awasthi, A. M.

2018-04-01

Ruddlesden-Popper manganite Ca3Mn2O7 has been synthesized in single phase orthorhombic structure with Cmcm space group. Temperature dependent magnetization M(T) shows that Ca3Mn2O7 undergoes long range antiferromagnetic (AFM) transition below 123 K, with weak ferromagnetism (WFM) at lower temperatures. Field dependent magnetization M(H) confirms WFM character below ˜110 K in the AFM-base magnetic structure. Detailed analysis of the zero field cooled magnetic hysteresis loops reveals a measurable exchange bias (EB) effect in the sample. EB is attributed to the high anisotropy in the sample and the presence of Dzyaloshinskii-Moriya (D-M) interaction, responsible for the canted interfacial-spins that couple "FM-clusters" with the "AFM-matrix". Temperature dependence of horizontal shifts of the M(H) loops in terms of the coercive fields (Hc±) and vertical shifts in terms of the remnant magnetizations (Mr±) is presented.

Mn concentration and quantum size effects on spin-polarized transport through CdMnTe based magnetic resonant tunneling diode.

PubMed

Mnasri, S; Abdi-Ben Nasrallahl, S; Sfina, N; Lazzari, J L; Saïd, M

2012-11-01

Theoretical studies on spin-dependent transport in magnetic tunneling diodes with giant Zeeman splitting of the valence band are carried out. The studied structure consists of two nonmagnetic layers CdMgTe separated by a diluted magnetic semiconductor barrier CdMnTe, the hole is surrounded by two p-doped CdTe layers. Based on the parabolic valence band effective mass approximation and the transfer matrix method, the magnetization and the current densities for holes with spin-up and spin-down are studied in terms of the Mn concentration, the well and barrier thicknesses as well as the voltage. It is found that, the current densities depend strongly on these parameters and by choosing suitable values; this structure can be a good spin filter. Such behaviors are originated from the enhancement and suppression in the spin-dependent resonant states.

Thermal conductivity of pillared graphene-epoxy nanocomposites using molecular dynamics

NASA Astrophysics Data System (ADS)

Lakshmanan, A.; Srivastava, S.; Ramazani, A.; Sundararaghavan, V.

2018-04-01

Thermal conductivity in a pillared graphene-epoxy nanocomposite (PGEN) is studied using equilibrium molecular dynamics simulations. PGEN is a proposed material for advanced thermal management applications because it combines high in-plane conductivity of graphene with high axial conductivity of a nanotube to significantly enhance the overall conductivity of the epoxy matrix material. Anisotropic conductivity of PGEN has been compared with that of pristine and functionalized carbon nanotube-epoxy nanocomposites, showcasing the advantages of the unique hierarchical structure of PGEN. Compared to pure carbon allotropes, embedding the epoxy matrix also promotes a weaker dependence of conductivity on thermal variations. These features make this an attractive material for thermal management applications.

Wavelength dependent SHG imaging and scattering probes of extracellular matrix (ECM) alterations in ovarian cancer (Conference Presentation)

NASA Astrophysics Data System (ADS)

Campagnola, Paul J.; Tilbury, Karissa B.; Campbell, Kirby R.; Eliceiri, Kevin W.; Patankar, Manish

2017-02-01

Ovarian cancer remains the most deadly gynecological cancer with a poor aggregate survival rate. To improve upon this situation, we utilized collagen-specific Second Harmonic Generation (SHG) imaging microscopy and optical scattering measurements to probe structural differences in the extracellular matrix of normal stroma, benign tumors, endometrioid tumors, and low and high-grade serous (LGS and HGS) tumors. The SHG signatures of the emission directionality and conversion efficiency as well as the optical scattering are related to the organization of collagen on the sub-micron size. The wavelength dependence of these readouts adds additional characterization of the size and distribution of collagen fibrils/fibers relative to the interrogating wavelengths. We found strong wavelength dependent dependencies of these metrics that were different between the different tumors that are related to respective structural attributes in the collagen organization. These sub-resolution determinations are consistent with the dualistic classification of type I and II serous tumors. However, type I endometrioid tumors have strongly differing ECM architecture than the serous malignancies. Moreover, our analyses are further consistent with LGS and benign tumors having similar etiology. We identified optimal wavelengths for the SHG metrics as well as optical scattering measurements. The SHG metrics and optical scattering measurements were then used to form a linear discriminant model to classify the tissues, and we obtained high accuracy ( 90%) between the tissue types. This delineation is superior to current clinical performance and has potential applicability in supplementing histological analysis, understanding the etiology, as well as development of an in vivo screening tool.

The Impact of Goal Setting and Empowerment on Governmental Matrix Organizations

DTIC Science & Technology

1993-09-01

shared. In a study of matrix management, Eduardo Vasconcellos further describes various matrix structures in the Galbraith model. In a functional...Technology/LAR, Wright-Patterson AFB OH, 1992. Vasconcellos , Eduardo . "A Model For a Better Understanding of the Matrix Structure," IEEE Transactions on...project matrix, the project manager maintains more influence and the structure lies to the right-of center ( Vasconcellos , 1979:58). Different Types of

Temperature-sensitive elastin-mimetic dendrimers: Effect of peptide length and dendrimer generation to temperature sensitivity.

PubMed

Kojima, Chie; Irie, Kotaro; Tada, Tomoko; Tanaka, Naoki

2014-06-01

Dendrimers are synthetic macromolecules with unique structure, which are a potential scaffold for peptides. Elastin is one of the main components of extracellular matrix and a temperature-sensitive biomacromolecule. Previously, Val-Pro-Gly-Val-Gly peptides have been conjugated to a dendrimer for designing an elastin-mimetic dendrimer. In this study, various elastin-mimetic dendrimers using different length peptides and different dendrimer generations were synthesized to control the temperature dependency. The elastin-mimetic dendrimers formed β-turn structure by heating, which was similar to the elastin-like peptides. The elastin-mimetic dendrimers exhibited an inverse phase transition, largely depending on the peptide length and slightly depending on the dendrimer generation. The elastin-mimetic dendrimers formed aggregates after the phase transition. The endothermal peak was observed in elastin-mimetic dendrimers with long peptides, but not with short ones. The peptide length and the dendrimer generation are important factors to tune the temperature dependency on the elastin-mimetic dendrimer. Copyright © 2013 Wiley Periodicals, Inc.

Optimal matrix rigidity for stress fiber polarization in stem cells

PubMed Central

Rehfeldt, F.; Brown, A. E. X.; Discher, D. E.; Safran, S. A.

2010-01-01

The shape and differentiation of human mesenchymal stem cells is especially sensitive to the rigidity of their environment; the physical mechanisms involved are unknown. A theoretical model and experiments demonstrate here that the polarization/alignment of stress-fibers within stem cells is a non-monotonic function of matrix rigidity. We treat the cell as an active elastic inclusion in a surrounding matrix whose polarizability, unlike dead matter, depends on the feedback of cellular forces that develop in response to matrix stresses. The theory correctly predicts the monotonic increase of the cellular forces with the matrix rigidity and the alignment of stress-fibers parallel to the long axis of cells. We show that the anisotropy of this alignment depends non-monotonically on matrix rigidity and demonstrate it experimentally by quantifying the orientational distribution of stress-fibers in stem cells. These findings offer a first physical insight for the dependence of stem cell differentiation on tissue elasticity. PMID:20563235

High-resolution high-sensitivity and truly distributed optical frequency domain reflectometry for structural crack detection

NASA Astrophysics Data System (ADS)

Li, Wenhai; Bao, Xiaoyi; Chen, Liang

2014-05-01

Optical Frequency Domain Reflectometry (OFDR) with the use of polarization maintaining fiber (PMF) is capable of distinguishing strain and temperature, which is critical for successful field applications such as structural health monitoring (SHM) and smart material. Location-dependent measurement sensitivities along PMF are compensated by cross- and auto-correlations measurements of the spectra form a distributed parameter matrix. Simultaneous temperature and strain measurement accuracy of 1μstrain and 0.1°C is achieved with 2.5mm spatial resolution in over 180m range.

Constrained Sintering in Fabrication of Solid Oxide Fuel Cells

PubMed Central

Lee, Hae-Weon; Park, Mansoo; Hong, Jongsup; Kim, Hyoungchul; Yoon, Kyung Joong; Son, Ji-Won; Lee, Jong-Ho; Kim, Byung-Kook

2016-01-01

Solid oxide fuel cells (SOFCs) are inevitably affected by the tensile stress field imposed by the rigid substrate during constrained sintering, which strongly affects microstructural evolution and flaw generation in the fabrication process and subsequent operation. In the case of sintering a composite cathode, one component acts as a continuous matrix phase while the other acts as a dispersed phase depending upon the initial composition and packing structure. The clustering of dispersed particles in the matrix has significant effects on the final microstructure, and strong rigidity of the clusters covering the entire cathode volume is desirable to obtain stable pore structure. The local constraints developed around the dispersed particles and their clusters effectively suppress generation of major process flaws, and microstructural features such as triple phase boundary and porosity could be readily controlled by adjusting the content and size of the dispersed particles. However, in the fabrication of the dense electrolyte layer via the chemical solution deposition route using slow-sintering nanoparticles dispersed in a sol matrix, the rigidity of the cluster should be minimized for the fine matrix to continuously densify, and special care should be taken in selecting the size of the dispersed particles to optimize the thermodynamic stability criteria of the grain size and film thickness. The principles of constrained sintering presented in this paper could be used as basic guidelines for realizing the ideal microstructure of SOFCs. PMID:28773795

The multifacet graphically contracted function method. I. Formulation and implementation

NASA Astrophysics Data System (ADS)

Shepard, Ron; Gidofalvi, Gergely; Brozell, Scott R.

2014-08-01

The basic formulation for the multifacet generalization of the graphically contracted function (MFGCF) electronic structure method is presented. The analysis includes the discussion of linear dependency and redundancy of the arc factor parameters, the computation of reduced density matrices, Hamiltonian matrix construction, spin-density matrix construction, the computation of optimization gradients for single-state and state-averaged calculations, graphical wave function analysis, and the efficient computation of configuration state function and Slater determinant expansion coefficients. Timings are given for Hamiltonian matrix element and analytic optimization gradient computations for a range of model problems for full-CI Shavitt graphs, and it is observed that both the energy and the gradient computation scale as O(N2n4) for N electrons and n orbitals. The important arithmetic operations are within dense matrix-matrix product computational kernels, resulting in a computationally efficient procedure. An initial implementation of the method is used to present applications to several challenging chemical systems, including N2 dissociation, cubic H8 dissociation, the symmetric dissociation of H2O, and the insertion of Be into H2. The results are compared to the exact full-CI values and also to those of the previous single-facet GCF expansion form.

The multifacet graphically contracted function method. I. Formulation and implementation.

PubMed

Shepard, Ron; Gidofalvi, Gergely; Brozell, Scott R

2014-08-14

The basic formulation for the multifacet generalization of the graphically contracted function (MFGCF) electronic structure method is presented. The analysis includes the discussion of linear dependency and redundancy of the arc factor parameters, the computation of reduced density matrices, Hamiltonian matrix construction, spin-density matrix construction, the computation of optimization gradients for single-state and state-averaged calculations, graphical wave function analysis, and the efficient computation of configuration state function and Slater determinant expansion coefficients. Timings are given for Hamiltonian matrix element and analytic optimization gradient computations for a range of model problems for full-CI Shavitt graphs, and it is observed that both the energy and the gradient computation scale as O(N(2)n(4)) for N electrons and n orbitals. The important arithmetic operations are within dense matrix-matrix product computational kernels, resulting in a computationally efficient procedure. An initial implementation of the method is used to present applications to several challenging chemical systems, including N2 dissociation, cubic H8 dissociation, the symmetric dissociation of H2O, and the insertion of Be into H2. The results are compared to the exact full-CI values and also to those of the previous single-facet GCF expansion form.

Osteoblasts extracellular matrix induces vessel like structures through glycosylated collagen I

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

Palmieri, D.; Valli, M.; Viglio, S.

2010-03-10

Extracellular matrix (ECM) plays a fundamental role in angiogenesis affecting endothelial cells proliferation, migration and differentiation. Vessels-like network formation in vitro is a reliable test to study the inductive effects of ECM on angiogenesis. Here we utilized matrix deposed by osteoblasts as substrate where the molecular and structural complexity of the endogenous ECM is preserved, to test if it induces vessel-like network formation by endothelial cells in vitro. ECM is more similar to the physiological substrate in vivo than other substrates previously utilized for these studies in vitro. Osteogenic ECM, prepared in vitro from mature osteoblasts at the phase ofmore » maximal deposition and glycosylation of collagen I, induces EAhy926, HUVEC, and HDMEC endothelial cells to form vessels-like structures and promotes the activation of metalloproteinase-2 (MMP-2); the functionality of the p-38/MAPK signaling pathway is required. Osteogenic ECM also induces a transient increase of CXCL12 and a decrease of the receptor CXCR4. The induction of vessel-like networks is dependent from proper glycosylation of collagens and does not occur on osteogenic ECMs if deglycosylated by -galactosidase or on less glycosylated ECMs derived from preosteoblasts and normal fibroblasts, while is sustained on ECM from osteogenesis imperfecta fibroblasts only when their mutation is associated with over-glycosylation of collagen type I. These data support that post-translational glycosylation has a role in the induction in endothelial cells in vitro of molecules conductive to self-organization in vessels-like structures.« less

Regulation of Extracellular Matrix Synthesis by Shell Extracts from the Marine Bivalve Pecten maximus in Human Articular Chondrocytes- Application for Cartilage Engineering.

PubMed

Bouyoucef, Mouloud; Rakic, Rodolphe; Gómez-Leduc, Tangni; Latire, Thomas; Marin, Frédéric; Leclercq, Sylvain; Carreiras, Franck; Serpentini, Antoine; Lebel, Jean-Marc; Galéra, Philippe; Legendre, Florence

2018-04-07

The shells of the bivalve mollusks are organo-mineral structures predominantly composed of calcium carbonate, but also of a minor organic matrix, a mixture of proteins, glycoproteins, and polysaccharides. These proteins are involved in mineral deposition and, more generally, in the spatial organization of the shell crystallites in well-defined microstructures. In this work, we extracted different organic shell extracts (acid-soluble matrix, acid-insoluble matrix, water-soluble matrix, guanidine HCl/EDTA-extracted matrix, referred as ASM, AIM, WSM, and EDTAM, respectively) from the shell of the scallop Pecten maximus and studied their biological activities on human articular chondrocytes (HACs). We found that these extracts differentially modulate the biological activities of HACs, depending on the type of extraction and the concentration used. Furthermore, we showed that, unlike ASM and AIM, WSM promotes maintenance of the chondrocyte phenotype in monolayer culture. WSM increased the expression of chondrocyte-specific markers (aggrecan and type II collagen), without enhancing that of the main chondrocyte dedifferentiation marker (type I collagen). We also demonstrated that WSM could favor redifferentiation of chondrocyte in collagen sponge scaffold in hypoxia. Thus, this study suggests that the organic matrix of Pecten maximus, particularly WSM, may contain interesting molecules with chondrogenic effects. Our research emphasizes the potential use of WSM of Pecten maximus for cell therapy of cartilage.

Frequency-dependent population dynamics: effect of sex ratio and mating system on the elasticity of population growth rate.

PubMed

Haridas, C V; Eager, Eric Alan; Rebarber, Richard; Tenhumberg, Brigitte

2014-11-01

When vital rates depend on population structure (e.g., relative frequencies of males or females), an important question is how the long-term population growth rate λ responds to changes in rates. For instance, availability of mates may depend on the sex ratio of the population and hence reproductive rates could be frequency-dependent. In such cases change in any vital rate alters the structure, which in turn, affect frequency-dependent rates. We show that the elasticity of λ to a rate is the sum of (i) the effect of the linear change in the rate and (ii) the effect of nonlinear changes in frequency-dependent rates. The first component is always positive and is the classical elasticity in density-independent models obtained directly from the population projection matrix. The second component can be positive or negative and is absent in density-independent models. We explicitly express each component of the elasticity as a function of vital rates, eigenvalues and eigenvectors of the population projection matrix. We apply this result to a two-sex model, where male and female fertilities depend on adult sex ratio α (ratio of females to males) and the mating system (e.g., polygyny) through a harmonic mating function. We show that the nonlinear component of elasticity to a survival rate is negligible only when the average number of mates (per male) is close to α. In a strictly monogamous species, elasticity to female survival is larger than elasticity to male survival when α<1 (less females). In a polygynous species, elasticity to female survival can be larger than that of male survival even when sex ratio is female biased. Our results show how demography and mating system together determine the response to selection on sex-specific vital rates. Copyright © 2014 Elsevier Inc. All rights reserved.

Development of FRP composite structural biomaterials: ultimate strength of the fiber/matrix interfacial bond in in vivo simulated environments.

PubMed

Latour, R A; Black, J

1992-05-01

Fiber reinforced polymer (FRP) composites are being developed as alternatives to metals for structural orthopedic implant applications. FRP composite fracture behavior and environmental interactions are distinctly different from those which occur in metals. These differences must be accounted for in the design and evaluation of implant performance. Fiber/matrix interfacial bond strength in a FRP composite is known to strongly influence fracture behavior. The interfacial bond strength of four candidate fiber/matrix combinations (carbon fiber/polycarbonate, carbon fiber/polysulfone, polyaramid fiber/polycarbonate, polyaramid fiber/polysulfone) were investigated at 37 degrees C in dry and in vivo simulated (saline, exudate) environments. Ultimate bond strength was measured by a single fiber-microdroplet pull-out test. Dry bond strengths were significantly decreased following exposure to either saline or exudate with bond strength loss being approximately equal in both the saline and exudate. Bond strength loss is attributed to the diffusion of water and/or salt ions into the sample and their interaction with interfacial bonding. Because bond degradation is dependent upon diffusion, diffusional equilibrium must be obtained in composite test samples before the full effect of the test environment upon composite mechanical behavior can be determined.

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

Assenberg, René; Delmas, Olivier; Graham, Stephen C.

The expression, purification and crystallization of the full-length matrix protein from three lyssaviruses is described. The matrix (M) proteins of lyssaviruses (family Rhabdoviridae) are crucial to viral morphogenesis as well as in modulating replication and transcription of the viral genome. To date, no high-resolution structural information has been obtained for full-length rhabdovirus M. Here, the cloning, expression and purification of the matrix proteins from three lyssaviruses, Lagos bat virus (LAG), Mokola virus and Thailand dog virus, are described. Crystals have been obtained for the full-length M protein from Lagos bat virus (LAG M). Successful crystallization depended on a number ofmore » factors, in particular the addition of an N-terminal SUMO fusion tag to increase protein solubility. Diffraction data have been recorded from crystals of native and selenomethionine-labelled LAG M to 2.75 and 3.0 Å resolution, respectively. Preliminary analysis indicates that these crystals belong to space group P6{sub 1}22 or P6{sub 5}22, with unit-cell parameters a = b = 56.9–57.2, c = 187.9–188.6 Å, consistent with the presence of one molecule per asymmetric unit, and structure determination is currently in progress.« less

Tribological Properties of AlSi12-Al2O3 Interpenetrating Composite Layers in Comparison with Unreinforced Matrix Alloy

PubMed Central

Dolata, Anna Janina

2017-01-01

Alumina–Aluminum composites with interpenetrating network structures are a new class of advanced materials with potentially better properties than composites reinforced by particles or fibers. Local casting reinforcement was proposed to take into account problems with the machinability of this type of materials and the shaping of the finished products. The centrifugal infiltration process fabricated composite castings in the form of locally reinforced shafts. The main objective of the research presented in this work was to compare the tribological properties (friction coefficient, wear resistance) of AlSi12/Al2O3 interpenetrating composite layers with unreinforced AlSi12 matrix areas. Profilometric tests enabled both quantitative and qualitative analyses of the wear trace that formed on investigated surfaces. It has been shown that interpenetrating composite layers are characterized by lower and more stable coefficients of friction (μ), as well as higher wear resistance than unreinforced matrix areas. At the present stage, the study confirmed that the tribological properties of the composite layers depend on the spatial structure of the ceramic reinforcement, and primarily the volume and size of alumina foam cells. PMID:28878162

miR-132 Regulates Dendritic Spine Structure by Direct Targeting of Matrix Metalloproteinase 9 mRNA.

PubMed

Jasińska, Magdalena; Miłek, Jacek; Cymerman, Iwona A; Łęski, Szymon; Kaczmarek, Leszek; Dziembowska, Magdalena

2016-09-01

Mir-132 is a neuronal activity-regulated microRNA that controls the morphology of dendritic spines and neuronal transmission. Similar activities have recently been attributed to matrix metalloproteinase-9 (MMP-9), an extrasynaptic protease. In the present study, we provide evidence that miR-132 directly regulates MMP-9 mRNA in neurons to modulate synaptic plasticity. With the use of luciferase reporter system, we show that miR-132 binds to the 3'UTR of MMP-9 mRNA to regulate its expression in neurons. The overexpression of miR-132 in neurons reduces the level of endogenous MMP-9 protein secretion. In synaptoneurosomes, metabotropic glutamate receptor (mGluR)-induced signaling stimulates the dissociation of miR-132 from polyribosomal fractions and shifts it towards the messenger ribonucleoprotein (mRNP)-containing fraction. Furthermore, we demonstrate that the overexpression of miR-132 in the cultured hippocampal neurons from Fmr1 KO mice that have increased synaptic MMP-9 level provokes enlargement of the dendritic spine heads, a process previously implicated in enhanced synaptic plasticity. We propose that activity-dependent miR-132 regulates structural plasticity of dendritic spines through matrix metalloproteinase 9.

Drove roads: Keystone structures that promote ant diversity in Mediterranean forest landscapes

NASA Astrophysics Data System (ADS)

Azcárate, Francisco M.; Seoane, Javier; Castro, Sara; Peco, Begoña

2013-05-01

Drove roads are the traditional corridors used by pastoralists for seasonal movements of livestock (transhumance). They cover a considerable land area in Mediterranean countries and, although they are an obvious source of landscape diversity, their influence on the diversity and composition of animal assemblages has not been documented. Ant communities were studied on four active drove roads, two in forests (submediterranean and conifer) and two in open environments (croplands and rangelands). They were compared with the respective matrix communities and their contribution to local species richness was evaluated. The effects were heavily dependent on the open or closed nature of the matrix. In forest environments, drove roads increased ant species richness at the local scale, acting as clear keystone structures. Their species richness and functional diversity were highest on the fine scale, species composition was different, and a slight edge effect in the matrix was detected. In contrast, drove roads had little or even a negative effect in open environment locations. We conclude that drove roads have a high conservation value for ants in Mediterranean forest environments, in addition to their importance as reservoirs of plant biodiversity and generators of ecological goods and services.

Modeling extracellular matrix (ECM) alterations in ovarian cancer by multiphoton excited fabrication of stromal models (Conference Presentation)

NASA Astrophysics Data System (ADS)

Campagnola, Paul J.; Ajeti, Visar; Lara, Jorge; Eliceiri, Kevin W.; Patankar, Mansh

2016-04-01

A profound remodeling of the extracellular matrix (ECM) occurs in human ovarian cancer but it unknown how this affects tumor growth, where this understanding could lead to better diagnostics and therapeutic approaches. We investigate the role of these ECM alterations by using multiphoton excited (MPE) polymerization to fabricate biomimetic models to investigate operative cell-matrix interactions in invasion/metastasis. First, we create nano/microstructured gradients mimicking the basal lamina to study adhesion/migration dynamics of ovarian cancer cells of differing metastatic potential. We find a strong haptotactic response that depends on both contact guidance and ECM binding cues. While we found enhanced migration for more invasive cells, the specifics of alignment and directed migration also depend on cell polarity. We further use MPE fabrication to create collagen scaffolds with complex, 3D submicron morphology. The stromal scaffold designs are derived directly from "blueprints" based on SHG images of normal, high risk, and malignant ovarian tissues. The models are seeded with different cancer cell lines and this allows decoupling of the roles of cell characteristics (metastatic potential) and ECM structure and composition (normal vs cancer) on adhesion/migration dynamics. We found the malignant stroma structure promotes enhanced migration and proliferation and also cytoskeletal alignment. Creating synthetic models based on fibers patterns further allows decoupling the topographic roles of the fibers themselves vs their alignment within the tissue. These models cannot be synthesized by other conventional fabrication methods and we suggest the MPE image-based fabrication method will enable a variety of studies in cancer biology.

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

Bai, Zhaojun; Yang, Chao

What is common among electronic structure calculation, design of MEMS devices, vibrational analysis of high speed railways, and simulation of the electromagnetic field of a particle accelerator? The answer: they all require solving large scale nonlinear eigenvalue problems. In fact, these are just a handful of examples in which solving nonlinear eigenvalue problems accurately and efficiently is becoming increasingly important. Recognizing the importance of this class of problems, an invited minisymposium dedicated to nonlinear eigenvalue problems was held at the 2005 SIAM Annual Meeting. The purpose of the minisymposium was to bring together numerical analysts and application scientists to showcasemore » some of the cutting edge results from both communities and to discuss the challenges they are still facing. The minisymposium consisted of eight talks divided into two sessions. The first three talks focused on a type of nonlinear eigenvalue problem arising from electronic structure calculations. In this type of problem, the matrix Hamiltonian H depends, in a non-trivial way, on the set of eigenvectors X to be computed. The invariant subspace spanned by these eigenvectors also minimizes a total energy function that is highly nonlinear with respect to X on a manifold defined by a set of orthonormality constraints. In other applications, the nonlinearity of the matrix eigenvalue problem is restricted to the dependency of the matrix on the eigenvalues to be computed. These problems are often called polynomial or rational eigenvalue problems In the second session, Christian Mehl from Technical University of Berlin described numerical techniques for solving a special type of polynomial eigenvalue problem arising from vibration analysis of rail tracks excited by high-speed trains.« less

Finite element solution of transient fluid-structure interaction problems

NASA Technical Reports Server (NTRS)

Everstine, Gordon C.; Cheng, Raymond S.; Hambric, Stephen A.

1991-01-01

A finite element approach using NASTRAN is developed for solving time-dependent fluid-structure interaction problems, with emphasis on the transient scattering of acoustic waves from submerged elastic structures. Finite elements are used for modeling both structure and fluid domains to facilitate the graphical display of the wave motion through both media. For the liquid, the use of velocity potential as the fundamental unknown results in a symmetric matrix equation. The approach is illustrated for the problem of transient scattering from a submerged elastic spherical shell subjected to an incident tone burst. The use of an analogy between the equations of elasticity and the wave equation of acoustics, a necessary ingredient to the procedure, is summarized.

Implementation of Fiber Substructuring Into Strain Rate Dependent Micromechanics Analysis of Polymer Matrix Composites

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.

2001-01-01

A research program is in progress to develop strain rate dependent deformation and failure models for the analysis of polymer matrix composites subject to impact loads. Previously, strain rate dependent inelastic constitutive equations developed to model the polymer matrix were incorporated into a mechanics of materials based micromechanics method. In the current work, the micromechanics method is revised such that the composite unit cell is divided into a number of slices. Micromechanics equations are then developed for each slice, with laminate theory applied to determine the elastic properties, effective stresses and effective inelastic strains for the unit cell. Verification studies are conducted using two representative polymer matrix composites with a nonlinear, strain rate dependent deformation response. The computed results compare well to experimentally obtained values.

An Efficient Scheme for Updating Sparse Cholesky Factors

NASA Technical Reports Server (NTRS)

Raghavan, Padma

2002-01-01

Raghavan had earlier developed the software package DCSPACK which can be used for solving sparse linear systems where the coefficient matrix is symmetric and positive definite (this project was not funded by NASA but by agencies such as NSF). DSCPACK-S is the serial code and DSCPACK-P is a parallel implementation suitable for multiprocessors or networks-of-workstations with message passing using MCI. The main algorithm used is the Cholesky factorization of a sparse symmetric positive positive definite matrix A = LL(T). The code can also compute the factorization A = LDL(T). The complexity of the software arises from several factors relating to the sparsity of the matrix A. A sparse N x N matrix A has typically less that cN nonzeroes where c is a small constant. If the matrix were dense, it would have O(N2) nonzeroes. The most complicated part of such sparse Cholesky factorization relates to fill-in, i.e., zeroes in the original matrix that become nonzeroes in the factor L. An efficient implementation depends to a large extent on complex data structures and on techniques from graph theory to reduce, identify, and manage fill. DSCPACK is based on an efficient multifrontal implementation with fill-managing algorithms and implementation arising from earlier research by Raghavan and others. Sparse Cholesky factorization is typically a four step process: (1) ordering to compute a fill-reducing numbering, (2) symbolic factorization to determine the nonzero structure of L, (3) numeric factorization to compute L, and, (4) triangular solution to solve L(T)x = y and Ly = b. The first two steps are symbolic and are performed using the graph of the matrix. The numeric factorization step is of dominant cost and there are several schemes for improving performance by exploiting the nested and dense structure of groups of columns in the factor. The latter are aimed at better utilization of the cache-memory hierarchy on modem processors to prevent cache-misses and provide execution rates (operations/second) that are close to the peak rates for dense matrix computations. Currently, EPISCOPACY is being used in an application at NASA directed by J. Newman and M. James. We propose the implementation of efficient schemes for updating the LL(T) or LDL(T) factors computed in DSCPACK-S to meet the computational requirements of their project. A brief description is provided in the next section.

Analytical modeling of polarization transformation of laser radiation of various spectral ranges by birefringent structures

NASA Astrophysics Data System (ADS)

Motrich, A. V.; Ushenko, O. G.

2018-01-01

The results of statistical dependence and correlation structures of two-dimensional Mueller matrix elements in various spectral regions of laser radiation by changes in the distribution of orientations of optical axes and birefringence of protein crystals. Namely, a two-wave ("red-blue") approach - layer of biological tissues irradiated by He-Ne laser (λ1 = 0,63μm ) and He-Cd laser (λ1 = 0,41μm )was used Conducted analysis of polarimetric sensitivity was made, a state of polarization points that contain volumetric structures of biological objects to spectral region of laser radiation was detected.

Effects of landscape matrix on population connectivity of an arboreal mammal, Petaurus breviceps.

PubMed

Malekian, Mansoureh; Cooper, Steven J B; Saint, Kathleen M; Lancaster, Melanie L; Taylor, Andrea C; Carthew, Susan M

2015-09-01

Ongoing habitat loss and fragmentation is considered a threat to biodiversity as it can create small, isolated populations that are at increased risk of extinction. Tree-dependent species are predicted to be highly sensitive to forest and woodland loss and fragmentation, but few studies have tested the influence of different types of landscape matrix on gene flow and population structure of arboreal species. Here, we examine the effects of landscape matrix on population structure of the sugar glider (Petaurus breviceps) in a fragmented landscape in southeastern South Australia. We collected 250 individuals across 12 native Eucalyptus forest remnants surrounded by cleared agricultural land or exotic Pinus radiata plantations and a large continuous eucalypt forest. Fifteen microsatellite loci were genotyped and analyzed to infer levels of population differentiation and dispersal. Genetic differentiation among most forest patches was evident. We found evidence for female philopatry and restricted dispersal distances for females relative to males, suggesting there is male-biased dispersal. Among the environmental variables, spatial variables including geographic location, minimum distance to neighboring patch, and degree of isolation were the most important in explaining genetic variation. The permeability of a cleared agricultural matrix to dispersing gliders was significantly higher than that of a pine matrix, with the gliders dispersing shorter distances across the latter. Our results added to previous findings for other species of restricted dispersal and connectivity due to habitat fragmentation in the same region, providing valuable information for the development of strategies to improve the connectivity of populations in the future.

The modelling of the flow-induced vibrations of periodic flat and axial-symmetric structures with a wave-based method

NASA Astrophysics Data System (ADS)

Errico, F.; Ichchou, M.; De Rosa, S.; Bareille, O.; Franco, F.

2018-06-01

The stochastic response of periodic flat and axial-symmetric structures, subjected to random and spatially-correlated loads, is here analysed through an approach based on the combination of a wave finite element and a transfer matrix method. Although giving a lower computational cost, the present approach keeps the same accuracy of classic finite element methods. When dealing with homogeneous structures, the accuracy is also extended to higher frequencies, without increasing the time of calculation. Depending on the complexity of the structure and the frequency range, the computational cost can be reduced more than two orders of magnitude. The presented methodology is validated both for simple and complex structural shapes, under deterministic and random loads.

Extracellular DNA and lipoteichoic acids interact with exopolysaccharides in the extracellular matrix of Streptococcus mutans biofilms.

PubMed

Castillo Pedraza, Midian C; Novais, Tatiana F; Faustoferri, Roberta C; Quivey, Robert G; Terekhov, Anton; Hamaker, Bruce R; Klein, Marlise I

2017-10-01

Streptococcus mutans-derived exopolysaccharides are virulence determinants in the matrix of biofilms that cause caries. Extracellular DNA (eDNA) and lipoteichoic acid (LTA) are found in cariogenic biofilms, but their functions are unclear. Therefore, strains of S. mutans carrying single deletions that would modulate matrix components were used: eDNA - ∆lytS and ∆lytT; LTA - ∆dltA and ∆dltD; and insoluble exopolysaccharide - ΔgtfB. Single-species (parental strain S. mutans UA159 or individual mutant strains) and mixed-species (UA159 or mutant strain, Actinomyces naeslundii and Streptococcus gordonii) biofilms were evaluated. Distinct amounts of matrix components were detected, depending on the inactivated gene. eDNA was found to be cooperative with exopolysaccharide in early phases, while LTA played a larger role in the later phases of biofilm development. The architecture of mutant strains biofilms was distinct (vs UA159), demonstrating that eDNA and LTA influence exopolysaccharide distribution and microcolony organization. Thus, eDNA and LTA may shape exopolysaccharide structure, affecting strategies for controlling pathogenic biofilms.

Mixed Matrix Carbon Molecular Sieve and Alumina (CMS-Al2O3) Membranes

NASA Astrophysics Data System (ADS)

Song, Yingjun; Wang, David K.; Birkett, Greg; Martens, Wayde; Duke, Mikel C.; Smart, Simon; Diniz da Costa, João C.

2016-07-01

This work shows mixed matrix inorganic membranes prepared by the vacuum-assisted impregnation method, where phenolic resin precursors filled the pore of α-alumina substrates. Upon carbonisation, the phenolic resin decomposed into several fragments derived from the backbone of the resin matrix. The final stages of decomposition (>650 °C) led to a formation of carbon molecular sieve (CMS) structures, reaching the lowest average pore sizes of ~5 Å at carbonisation temperatures of 700 °C. The combination of vacuum-assisted impregnation and carbonisation led to the formation of mixed matrix of CMS and α-alumina particles (CMS-Al2O3) in a single membrane. These membranes were tested for pervaporative desalination and gave very high water fluxes of up to 25 kg m-2 h-1 for seawater (NaCl 3.5 wt%) at 75 °C. Salt rejection was also very high varying between 93-99% depending on temperature and feed salt concentration. Interestingly, the water fluxes remained almost constant and were not affected as feed salt concentration increased from 0.3, 1 and 3.5 wt%.

Extracellular DNA and lipoteichoic acids interact with exopolysaccharides in the extracellular matrix of Streptococcus mutans biofilms

PubMed Central

Castillo Pedraza, Midian C.; Novais, Tatiana F.; Faustoferri, Roberta C.; Quivey, Robert G.; Terekhov, Anton; Hamaker, Bruce R.; Klein, Marlise I.

2018-01-01

Streptococcus mutans -derived exopolysaccharides are virulence determinants in the matrix of biofilms that cause caries. Extracellular DNA (eDNA) and lipoteichoic acid (LTA) are found in cariogenic biofilms, but their functions are unclear. Therefore, strains of S. mutans carrying single deletions that would modulate matrix components were used: eDNA – ΔlytS and ΔlytT; LTA – ΔdltA and ΔdltD; and insoluble exopolysaccharide – ΔgtfB. Single-species (parental strain S. mutans UA159 or individual mutant strains) and mixed-species (UA159 or mutant strain, Actinomyces naeslundii and Streptococcus gordonii) biofilms were evaluated. Distinct amounts of matrix components were detected, depending on the inactivated gene. eDNA was found to be cooperative with exopolysaccharide in early phases, while LTA played a larger role in the later phases of biofilm development. The architecture of mutant strains biofilms was distinct (vs UA159), demonstrating that eDNA and LTA influence exopolysaccharide distribution and microcolony organization. Thus, eDNA and LTA may shape exopolysaccharide structure, affecting strategies for controlling pathogenic biofilms. PMID:28946780

Mixed Matrix Carbon Molecular Sieve and Alumina (CMS-Al2O3) Membranes.

PubMed

Song, Yingjun; Wang, David K; Birkett, Greg; Martens, Wayde; Duke, Mikel C; Smart, Simon; Diniz da Costa, João C

2016-07-29

This work shows mixed matrix inorganic membranes prepared by the vacuum-assisted impregnation method, where phenolic resin precursors filled the pore of α-alumina substrates. Upon carbonisation, the phenolic resin decomposed into several fragments derived from the backbone of the resin matrix. The final stages of decomposition (>650 °C) led to a formation of carbon molecular sieve (CMS) structures, reaching the lowest average pore sizes of ~5 Å at carbonisation temperatures of 700 °C. The combination of vacuum-assisted impregnation and carbonisation led to the formation of mixed matrix of CMS and α-alumina particles (CMS-Al2O3) in a single membrane. These membranes were tested for pervaporative desalination and gave very high water fluxes of up to 25 kg m(-2) h(-1) for seawater (NaCl 3.5 wt%) at 75 °C. Salt rejection was also very high varying between 93-99% depending on temperature and feed salt concentration. Interestingly, the water fluxes remained almost constant and were not affected as feed salt concentration increased from 0.3, 1 and 3.5 wt%.

A Glimpse of Matrix Metalloproteinases in Diabetic Nephropathy

PubMed Central

Xu, X.; Xiao, L.; Xiao, P.; Yang, S.; Chen, G.; Liu, F.; Kanwar, Y.Y.; Sun, L.

2014-01-01

Matrix metalloproteinases (MMPs) are proteolytic enzymes belonging to the family of zinc-dependent endopeptidases that are capable of degrading almost all the proteinaceous components of the extracellular matrix (ECM). It is known that MMPs play a role in a number of renal diseases, such as, various forms of glomerulonephritis and tubular diseases, including some of the inherited kidney diseases. In this regard, ECM accumulation is considered to be a hallmark morphologic finding of diabetic nephropathy, which not only is related to the excessive synthesis of matrix proteins, but also to their decreased degradation by the MMPs. In recent years, increasing evidence suggest that there is a good correlation between the activity or expression of MMPs and progression of renal disease in patients with diabetic nephropathy in humans and in various experimental animal models. In such a diabetic milieu, the expression of MMPs is modulated by high glucose, advanced glycation end products (AGEs), TGF-β, reactive oxygen species (ROS), transcription factors and some of the microRNAs. In this review, we focused on the structure and functions of MMPs, and their role in the pathogenesis of diabetic nephropathy. PMID:25039784

Modeling of biologically motivated self-learning equivalent-convolutional recurrent-multilayer neural structures (BLM_SL_EC_RMNS) for image fragments clustering and recognition

NASA Astrophysics Data System (ADS)

Krasilenko, Vladimir G.; Lazarev, Alexander A.; Nikitovich, Diana V.

2018-03-01

The biologically-motivated self-learning equivalence-convolutional recurrent-multilayer neural structures (BLM_SL_EC_RMNS) for fragments images clustering and recognition will be discussed. We shall consider these neural structures and their spatial-invariant equivalental models (SIEMs) based on proposed equivalent two-dimensional functions of image similarity and the corresponding matrix-matrix (or tensor) procedures using as basic operations of continuous logic and nonlinear processing. These SIEMs can simply describe the signals processing during the all training and recognition stages and they are suitable for unipolar-coding multilevel signals. The clustering efficiency in such models and their implementation depends on the discriminant properties of neural elements of hidden layers. Therefore, the main models and architecture parameters and characteristics depends on the applied types of non-linear processing and function used for image comparison or for adaptive-equivalent weighing of input patterns. We show that these SL_EC_RMNSs have several advantages, such as the self-study and self-identification of features and signs of the similarity of fragments, ability to clustering and recognize of image fragments with best efficiency and strong mutual correlation. The proposed combined with learning-recognition clustering method of fragments with regard to their structural features is suitable not only for binary, but also color images and combines self-learning and the formation of weight clustered matrix-patterns. Its model is constructed and designed on the basis of recursively continuous logic and nonlinear processing algorithms and to k-average method or method the winner takes all (WTA). The experimental results confirmed that fragments with a large numbers of elements may be clustered. For the first time the possibility of generalization of these models for space invariant case is shown. The experiment for an images of different dimensions (a reference array) and fragments with diferent dimensions for clustering is carried out. The experiments, using the software environment Mathcad showed that the proposed method is universal, has a significant convergence, the small number of iterations is easily, displayed on the matrix structure, and confirmed its prospects. Thus, to understand the mechanisms of self-learning equivalence-convolutional clustering, accompanying her to the competitive processes in neurons, and the neural auto-encoding-decoding and recognition principles with the use of self-learning cluster patterns is very important which used the algorithm and the principles of non-linear processing of two-dimensional spatial functions of images comparison. The experimental results show that such models can be successfully used for auto- and hetero-associative recognition. Also they can be used to explain some mechanisms, known as "the reinforcementinhibition concept". Also we demonstrate a real model experiments, which confirm that the nonlinear processing by equivalent function allow to determine the neuron-winners and customize the weight matrix. At the end of the report, we will show how to use the obtained results and to propose new more efficient hardware architecture of SL_EC_RMNS based on matrix-tensor multipliers. Also we estimate the parameters and performance of such architectures.

Testability analysis on a hydraulic system in a certain equipment based on simulation model

NASA Astrophysics Data System (ADS)

Zhang, Rui; Cong, Hua; Liu, Yuanhong; Feng, Fuzhou

2018-03-01

Aiming at the problem that the complicated structure and the shortage of fault statistics information in hydraulic systems, a multi value testability analysis method based on simulation model is proposed. Based on the simulation model of AMESim, this method injects the simulated faults and records variation of test parameters ,such as pressure, flow rate, at each test point compared with those under normal conditions .Thus a multi-value fault-test dependency matrix is established. Then the fault detection rate (FDR) and fault isolation rate (FIR) are calculated based on the dependency matrix. Finally the system of testability and fault diagnosis capability are analyzed and evaluated, which can only reach a lower 54%(FDR) and 23%(FIR). In order to improve testability performance of the system,. number and position of the test points are optimized on the system. Results show the proposed test placement scheme can be used to solve the problems that difficulty, inefficiency and high cost in the system maintenance.

Wideband Direction of Arrival Estimation in the Presence of Unknown Mutual Coupling

PubMed Central

Li, Weixing; Zhang, Yue; Lin, Jianzhi; Guo, Rui; Chen, Zengping

2017-01-01

This paper investigates a subarray based algorithm for direction of arrival (DOA) estimation of wideband uniform linear array (ULA), under the presence of frequency-dependent mutual coupling effects. Based on the Toeplitz structure of mutual coupling matrices, the whole array is divided into the middle subarray and the auxiliary subarray. Then two-sided correlation transformation is applied to the correlation matrix of the middle subarray instead of the whole array. In this way, the mutual coupling effects can be eliminated. Finally, the multiple signal classification (MUSIC) method is utilized to derive the DOAs. For the condition when the blind angles exist, we refine DOA estimation by using a simple approach based on the frequency-dependent mutual coupling matrixes (MCMs). The proposed method can achieve high estimation accuracy without any calibration sources. It has a low computational complexity because iterative processing is not required. Simulation results validate the effectiveness and feasibility of the proposed algorithm. PMID:28178177

Sensitivity analysis of reactive ecological dynamics.

PubMed

Verdy, Ariane; Caswell, Hal

2008-08-01

Ecological systems with asymptotically stable equilibria may exhibit significant transient dynamics following perturbations. In some cases, these transient dynamics include the possibility of excursions away from the equilibrium before the eventual return; systems that exhibit such amplification of perturbations are called reactive. Reactivity is a common property of ecological systems, and the amplification can be large and long-lasting. The transient response of a reactive ecosystem depends on the parameters of the underlying model. To investigate this dependence, we develop sensitivity analyses for indices of transient dynamics (reactivity, the amplification envelope, and the optimal perturbation) in both continuous- and discrete-time models written in matrix form. The sensitivity calculations require expressions, some of them new, for the derivatives of equilibria, eigenvalues, singular values, and singular vectors, obtained using matrix calculus. Sensitivity analysis provides a quantitative framework for investigating the mechanisms leading to transient growth. We apply the methodology to a predator-prey model and a size-structured food web model. The results suggest predator-driven and prey-driven mechanisms for transient amplification resulting from multispecies interactions.

Reflection by absorbing periodically stratified media

NASA Astrophysics Data System (ADS)

Lekner, John

2014-03-01

Existing theory gives the optical properties of a periodically stratified medium in terms of a two by two matrix. This theory is valid also for absorbing media, because the matrix remains unimodular. The main effect of absorption is that the reflection (of either polarization) becomes independent of the number of periods N, and of the substrate properties, provided N exceeds a certain value which depends on the absorption. The s and p reflections are then given by simple formulae. The stop-band structure, which gives total reflection in bands of frequency and angle of incidence in the non-absorbing case, remains influential in weakly absorbing media, causing strong variations in reflectivity. The theory is applied to the frequency dependence of the normal-incidence reflectivity of a quarter-wave stack in which the high-index and low-index layers both absorb weakly. Analytical expressions are obtained for the frequency at which the reflectivity is maximum, the maximum reflectivity, and also for the reflectivity at the band edges of the stop band of the non-absorbing stack.

A constitutive material model for nonlinear finite element structural analysis using an iterative matrix approach

NASA Technical Reports Server (NTRS)

Koenig, Herbert A.; Chan, Kwai S.; Cassenti, Brice N.; Weber, Richard

1988-01-01

A unified numerical method for the integration of stiff time dependent constitutive equations is presented. The solution process is directly applied to a constitutive model proposed by Bodner. The theory confronts time dependent inelastic behavior coupled with both isotropic hardening and directional hardening behaviors. Predicted stress-strain responses from this model are compared to experimental data from cyclic tests on uniaxial specimens. An algorithm is developed for the efficient integration of the Bodner flow equation. A comparison is made with the Euler integration method. An analysis of computational time is presented for the three algorithms.

Implementation of a Matrix Organizational Structure: A Case Study.

ERIC Educational Resources Information Center

Whorton, David M.

The implementation of a matrix structure as an alternative to the traditional collegial/bureaucratic form at a college of education in a medium-size state university is described. Matrix organizational structures are differentiated from hierarchical bureaucratic structures by dividing the organization's tasks into functional units across which an…

Recent development in deciphering the structure of luminescent silver nanodots

NASA Astrophysics Data System (ADS)

Choi, Sungmoon; Yu, Junhua

2017-05-01

Matrix-stabilized silver clusters and stable luminescent few-atom silver clusters, referred to as silver nanodots, show notable difference in their photophysical properties. We present recent research on deciphering the nature of silver clusters and nanodots and understanding the factors that lead to variations in luminescent mechanisms. Due to their relatively simple structure, the matrix-stabilized clusters have been well studied. However, the single-stranded DNA (ssDNA)-stabilized silver nanodots that show the most diverse emission wavelengths and the best photophysical properties remain mysterious species. It is clear that their photophysical properties highly depend on their protection scaffolds. Analyses from combinations of high-performance liquid chromatography, inductively coupled plasma-atomic emission spectroscopy, electrophoresis, and mass spectrometry indicate that about 10 to 20 silver atoms form emissive complexes with ssDNA. However, it is possible that not all of the silver atoms in the complex form effective emission centers. Investigation of the nanodot structure will help us understand why luminescent silver nanodots are stable in aqueous solution and how to further improve their chemical and photophysical properties.

Nanoscale assembly of high-temperature oxidation-resistant nanocomposites.

PubMed

Peng, Xiao

2010-02-01

Structural considerations for designing a high-temperature oxidation-resistant metallic material are proposed, based on the dependence of the material structure on a promotion of the development of a protective scale of chromia or alumina. The material should have numerous sites on its surface for nucleating the protective oxides at the onset of oxidation and abundant grain boundaries in deeper areas for simultaneously supplying sufficient flux of the protective-oxide-forming elements toward the surface for a rapid linkage of the oxide nuclei through their lateral growth. Based on these considerations, we fabricated, using an electrochemical deposition method, novel nanocomposites which have a nanocrystalline metal matrix containing Cr and/or Al nanoparticles dispersed at the nano length scale. The validity of the design considerations is verified by comparing the high-temperature oxidation of a typical Ni-Cr nanocomposite system with two types of conventional Ni-Cr materials having similar or higher Cr content but different structure: one is a composite having a nanocrystalline Ni matrix containing Cr microparticles dispersed at the microscale and the other are micron-grained Ni-Cr alloys with the Cr distribution at the atomic length scale.

Nanoscale assembly of high-temperature oxidation-resistant nanocomposites

NASA Astrophysics Data System (ADS)

Peng, Xiao

2010-02-01

Structural considerations for designing a high-temperature oxidation-resistant metallic material are proposed, based on the dependence of the material structure on a promotion of the development of a protective scale of chromia or alumina. The material should have numerous sites on its surface for nucleating the protective oxides at the onset of oxidation and abundant grain boundaries in deeper areas for simultaneously supplying sufficient flux of the protective-oxide-forming elements toward the surface for a rapid linkage of the oxide nuclei through their lateral growth. Based on these considerations, we fabricated, using an electrochemical deposition method, novel nanocomposites which have a nanocrystalline metal matrix containing Cr and/or Al nanoparticles dispersed at the nano length scale. The validity of the design considerations is verified by comparing the high-temperature oxidation of a typical Ni-Cr nanocomposite system with two types of conventional Ni-Cr materials having similar or higher Cr content but different structure: one is a composite having a nanocrystalline Ni matrix containing Cr microparticles dispersed at the microscale and the other are micron-grained Ni-Cr alloys with the Cr distribution at the atomic length scale.

High temperature composite analyzer (HITCAN) user's manual, version 1.0

NASA Technical Reports Server (NTRS)

Lackney, J. J.; Singhal, S. N.; Murthy, P. L. N.; Gotsis, P.

1993-01-01

This manual describes 'how-to-use' the computer code, HITCAN (HIgh Temperature Composite ANalyzer). HITCAN is a general purpose computer program for predicting nonlinear global structural and local stress-strain response of arbitrarily oriented, multilayered high temperature metal matrix composite structures. This code combines composite mechanics and laminate theory with an internal data base for material properties of the constituents (matrix, fiber and interphase). The thermo-mechanical properties of the constituents are considered to be nonlinearly dependent on several parameters including temperature, stress and stress rate. The computation procedure for the analysis of the composite structures uses the finite element method. HITCAN is written in FORTRAN 77 computer language and at present has been configured and executed on the NASA Lewis Research Center CRAY XMP and YMP computers. This manual describes HlTCAN's capabilities and limitations followed by input/execution/output descriptions and example problems. The input is described in detail including (1) geometry modeling, (2) types of finite elements, (3) types of analysis, (4) material data, (5) types of loading, (6) boundary conditions, (7) output control, (8) program options, and (9) data bank.

Advanced Constituents and Processes for Ceramic Composite Engine Components

NASA Technical Reports Server (NTRS)

Yun, H. M.; DiCarlo, J. A.; Bhatt, R. T.

2004-01-01

The successful replacement of metal alloys by ceramic matrix composites (CMC) in hot-section engine components will depend strongly on optimizing the processes and properties of the CMC microstructural constituents so that they can synergistically provide the total CMC system with improved temperature capability and with the key properties required by the components for long-term structural service. This presentation provides the results of recent activities at NASA aimed at developing advanced silicon carbide (Sic) fiber-reinforced hybrid Sic matrix composite systems that can operate under mechanical loading and oxidizing conditions for hundreds of hours at 2400 and 2600 F, temperatures well above current metal capability. These SiC/SiC composite systems are lightweight (-30% metal density) and, in comparison to monolithic ceramics and carbon fiber-reinforced ceramic composites, are able to reliably retain their structural properties for long times under aggressive engine environments. It is shown that the improved temperature capability of the SiC/SiC systems is related first to the NASA development of the Sylramic-iBN Sic fiber, which displays high thermal stability, creep resistance, rupture resistance, and thermal conductivity, and possesses an in-situ grown BN surface layer for added environmental durability. This fiber is simply derived from Sylramic Sic fiber type that is currently produced at ATK COI Ceramics. Further capability is then derived by using chemical vapor infiltration (CVI) to form the initial portion of the hybrid Sic matrix. Because of its high creep resistance and thermal conductivity, the CVI Sic matrix is a required base constituent for all the high temperature SiC/SiC systems. By subsequently thermo- mechanical-treating the CMC preform, which consists of the S ylramic-iBN fibers and CVI Sic matrix, process-related defects in the matrix are removed, further improving matrix and CMC creep resistance and conductivity.

ELSI: A unified software interface for Kohn–Sham electronic structure solvers

DOE PAGES

Yu, Victor Wen-zhe; Corsetti, Fabiano; Garcia, Alberto; ...

2017-09-15

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aimsmore » to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. As a result, comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.« less

ELSI: A unified software interface for Kohn-Sham electronic structure solvers

NASA Astrophysics Data System (ADS)

Yu, Victor Wen-zhe; Corsetti, Fabiano; García, Alberto; Huhn, William P.; Jacquelin, Mathias; Jia, Weile; Lange, Björn; Lin, Lin; Lu, Jianfeng; Mi, Wenhui; Seifitokaldani, Ali; Vázquez-Mayagoitia, Álvaro; Yang, Chao; Yang, Haizhao; Blum, Volker

2018-01-01

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aims to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. Comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.

Origin of the biomechanical properties of wood related to the fine structure of the multi-layered cell wall.

PubMed

Yamamoto, H; Kojima, Y; Okuyama, T; Abasolo, W P; Gril, J

2002-08-01

In this study, a basic model is introduced to describe the biomechanical properties of the wood from the viewpoint of the composite structure of its cell wall. First, the mechanical interaction between the cellulose microfibril (CMF) as a bundle framework and the lignin-hemicellulose as a matrix (MT) skeleton in the secondary wall is formulated based on "the two phase approximation." Thereafter, the origins of (1) tree growth stress, (2) shrinkage or swelling anisotropy of the wood, and (3) moisture dependency of the Young's modulus of wood along the grain were simulated using the newly introduced model. Through the model formulation; (1) the behavior of the cellulose microfibril (CMF) and the matrix substance (MT) during cell wall maturation was estimated; (2) the moisture reactivity of each cell wall constituent was investigated; and (3) a realistic model of the fine composite structure of the matured cell wall was proposed. Thus, it is expected that the fine structure and internal property of each cell wall constituent can be estimated through the analyses of the macroscopic behaviors of wood based on the two phase approximation.

ELSI: A unified software interface for Kohn–Sham electronic structure solvers

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

Yu, Victor Wen-zhe; Corsetti, Fabiano; Garcia, Alberto

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aimsmore » to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. As a result, comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.« less

Thermoelectric Properties of a Ferromagnetic Semiconductor Based on a Dirac Semimetal (Cd3As2) under High Pressure

NASA Astrophysics Data System (ADS)

Melnikova, N. V.; Tebenkov, A. V.; Sukhanova, G. V.; Babushkin, A. N.; Saipulaeva, L. A.; Zakhvalinskii, V. S.; Gabibov, S. F.; Alibekov, A. G.; Mollaev, A. Yu.

2018-03-01

The pressure dependences of thermal emf (a parameter that ranks among the most sensitive to phase transformations) are studied for the purpose of identifying baric phase transitions in the 10-50 GPa interval in the Cd3As2 + MnAs (44.7% MnAs) structure formed by ferromagnetic MnAs granules in a semiconductor Cd3As2 matrix.

High Strain Rate Deformation Modeling of a Polymer Matrix Composite. Part 1; Matrix Constitutive Equations

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.; Stouffer, Donald C.

1998-01-01

Recently applications have exposed polymer matrix composite materials to very high strain rate loading conditions, requiring an ability to understand and predict the material behavior under these extreme conditions. In this first paper of a two part report, background information is presented, along with the constitutive equations which will be used to model the rate dependent nonlinear deformation response of the polymer matrix. Strain rate dependent inelastic constitutive models which were originally developed to model the viscoplastic deformation of metals have been adapted to model the nonlinear viscoelastic deformation of polymers. The modified equations were correlated by analyzing the tensile/ compressive response of both 977-2 toughened epoxy matrix and PEEK thermoplastic matrix over a variety of strain rates. For the cases examined, the modified constitutive equations appear to do an adequate job of modeling the polymer deformation response. A second follow-up paper will describe the implementation of the polymer deformation model into a composite micromechanical model, to allow for the modeling of the nonlinear, rate dependent deformation response of polymer matrix composites.

Effects of Complex Structured Anodic Oxide Dielectric Layer Grown in Pore Matrix for Aluminum Capacitor.

PubMed

Shin, Jin-Ha; Yun, Sook Young; Lee, Chang Hyoung; Park, Hwa-Sun; Suh, Su-Jeong

2015-11-01

Anodization of aluminum is generally divided up into two types of anodic aluminum oxide structures depending on electrolyte type. In this study, an anodization process was carried out in two steps to obtain high dielectric strength and break down voltage. In the first step, evaporated high purity Al on Si wafer was anodized in oxalic acidic aqueous solution at various times at a constant temperature of 5 degrees C. In the second step, citric acidic aqueous solution was used to obtain a thickly grown sub-barrier layer. During the second anodization process, the anodizing potential of various ranges was applied at room temperature. An increased thickness of the sub-barrier layer in the porous matrix was obtained according to the increment of the applied anodizing potential. The microstructures and the growth of the sub-barrier layer were then observed with an increasing anodizing potential of 40 to 300 V by using a scanning electron microscope (SEM). An impedance analyzer was used to observe the change of electrical properties, including the capacitance, dissipation factor, impedance, and equivalent series resistance (ESR) depending on the thickness increase of the sub-barrier layer. In addition, the breakdown voltage was measured. The results revealed that dielectric strength was improved with the increase of sub-barrier layer thickness.

Time-evolving collagen-like structural fibers in soft tissues: biaxial loading and spherical inflation

NASA Astrophysics Data System (ADS)

Topol, Heiko; Demirkoparan, Hasan; Pence, Thomas J.; Wineman, Alan

2017-02-01

This work considers a previously developed constitutive theory for the time dependent mechanical response of fibrous soft tissue resulting from the time dependent remodeling of a collagen fiber network that is embedded in a ground substance matrix. The matrix is taken to be an incompressible nonlinear elastic solid. The remodeling process consists of the continual dissolution of existing fibers and the creation of new fibers. Motivated by experimental reports on the enzyme degradation of collagen fibers, the remodeling is governed by first order chemical kinetics such that the dissolution rate is dependent upon the fiber stretch. The resulting time dependent mechanical response is sensitive to the natural configuration of the fibers when they are created, and different assumptions on the nature of the fiber's stress free state are considered here. The response under biaxial loading, a type of loading that has particular significance for the characterization of biological materials, is studied. The inflation of a spherical membrane is then analyzed in terms of the equal biaxial stretch that occurs in the membrane approximation. Different assumptions on the natural configuration of the fibers, combined with their time dependent dissolution and reforming, are shown to emulate alternative forms of creep and relaxation response. This formal similarity to viscoelastic phenomena occurs even though the underlying mechanisms are fundamentally different from the mechanism of macromolecular reconfiguration that one typically associates with viscoelastic response.

The nuclear matrix prepared by amine modification

PubMed Central

Wan, Katherine M.; Nickerson, Jeffrey A.; Krockmalnic, Gabriela; Penman, Sheldon

1999-01-01

The nucleus is spatially ordered by attachments to a nonchromatin nuclear structure, the nuclear matrix. The nuclear matrix and chromatin are intimately connected and integrated structures, and so a major technical challenge in nuclear matrix research has been to remove chromatin while retaining a native nuclear matrix. Most methods for removing chromatin require first a nuclease digestion and then a salt extraction to remove cut chromatin. We have hypothesized that cut chromatin is held in place by charge interactions involving nucleosomal amino groups. We have tested this hypothesis by chemically modifying amino groups after nuclease digestion. By using this protocol, chromatin could be effectively removed at physiological ionic strength. We compared the ultrastructure and composition of this nuclear matrix preparation with the traditional high-salt nuclear matrix and with the third nuclear matrix preparation that we have developed from which chromatin is removed after extensive crosslinking. All three matrix preparations reveal internal nuclear matrix structures that are built on a network of branched filaments of about 10 nm diameter. That such different chromatin-removal protocols reveal similar principles of nuclear matrix construction increases our confidence that we are observing important architectural elements of the native structure in the living cell. PMID:9927671

Comparison of two matrix data structures for advanced CSM testbed applications

NASA Technical Reports Server (NTRS)

Regelbrugge, M. E.; Brogan, F. A.; Nour-Omid, B.; Rankin, C. C.; Wright, M. A.

1989-01-01

The first section describes data storage schemes presently used by the Computational Structural Mechanics (CSM) testbed sparse matrix facilities and similar skyline (profile) matrix facilities. The second section contains a discussion of certain features required for the implementation of particular advanced CSM algorithms, and how these features might be incorporated into the data storage schemes described previously. The third section presents recommendations, based on the discussions of the prior sections, for directing future CSM testbed development to provide necessary matrix facilities for advanced algorithm implementation and use. The objective is to lend insight into the matrix structures discussed and to help explain the process of evaluating alternative matrix data structures and utilities for subsequent use in the CSM testbed.

The cabABC Operon Essential for Biofilm and Rugose Colony Development in Vibrio vulnificus

PubMed Central

Park, Jin Hwan; Jo, Youmi; Jang, Song Yee; Kwon, Haenaem; Irie, Yasuhiko; Parsek, Matthew R.; Kim, Myung Hee; Choi, Sang Ho

2015-01-01

A transcriptome analysis identified Vibrio vulnificus cabABC genes which were preferentially expressed in biofilms. The cabABC genes were transcribed as a single operon. The cabA gene was induced by elevated 3′,5′-cyclic diguanylic acid (c-di-GMP) and encoded a calcium-binding protein CabA. Comparison of the biofilms produced by the cabA mutant and its parent strain JN111 in microtiter plates using crystal-violet staining demonstrated that CabA contributed to biofilm formation in a calcium-dependent manner under elevated c-di-GMP conditions. Genetic and biochemical analyses revealed that CabA was secreted to the cell exterior through functional CabB and CabC, distributed throughout the biofilm matrix, and produced as the biofilm matured. These results, together with the observation that CabA also contributes to the development of rugose colony morphology, indicated that CabA is a matrix-associated protein required for maturation, rather than adhesion involved in the initial attachment, of biofilms. Microscopic comparison of the structure of biofilms produced by JN111 and the cabA mutant demonstrated that CabA is an extracellular matrix component essential for the development of the mature biofilm structures in flow cells and on oyster shells. Exogenously providing purified CabA restored the biofilm- and rugose colony-forming abilities of the cabA mutant when calcium was available. Circular dichroism and size exclusion analyses revealed that calcium binding induces CabA conformational changes which may lead to multimerization. Extracellular complementation experiments revealed that CabA can assemble a functional matrix only when exopolysaccharides coexist. Consequently, the combined results suggested that CabA is a structural protein of the extracellular matrix and multimerizes to a conformation functional in building robust biofilms, which may render V. vulnificus to survive in hostile environments and reach a concentrated infective dose. PMID:26406498

Evaluating Process Improvement Courses of Action Through Modeling and Simulation

DTIC Science & Technology

2017-09-16

changes to a process is time consuming and has potential to overlook stochastic effects. By modeling a process as a Numerical Design Structure Matrix...13 Methods to Evaluate Process Performance ................................................................15 The Design Structure...Matrix ......................................................................................16 Numerical Design Structure Matrix

Effects of a petunia scaffold/matrix attachment region on copy number dependency and stability of transgene expression in Nicotiana tabacum.

PubMed

Dietz-Pfeilstetter, Antje; Arndt, Nicola; Manske, Ulrike

2016-04-01

Transgenes in genetically modified plants are often not reliably expressed during development or in subsequent generations. Transcriptional gene silencing (TGS) as well as post-transcriptional gene silencing (PTGS) have been shown to occur in transgenic plants depending on integration pattern, copy number and integration site. In an effort to reduce position effects, to prevent read-through transcription and to provide a more accessible chromatin structure, a P35S-ß-glucuronidase (P35S-gus) transgene flanked by a scaffold/matrix attachment region from petunia (Petun-SAR), was introduced in Nicotiana tabacum plants by Agrobacterium tumefaciens mediated transformation. It was found that Petun-SAR mediates enhanced expression and copy number dependency up to 2 gene copies, but did not prevent gene silencing in transformants with multiple and rearranged gene copies. However, in contrast to the non-SAR transformants where silencing was irreversible and proceeded during long-term vegetative propagation and in progeny plants, gus expression in Petun-SAR plants was re-established in the course of development. Gene silencing was not necessarily accompanied by DNA methylation, while the gus transgene could still be expressed despite considerable CG methylation within the coding region.

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.

X-ray absorption studies of gamma irradiated Nd doped phosphate glass

NASA Astrophysics Data System (ADS)

Rai, V. N.; Rajput, Parasmani; Jha, S. N.; Bhattacharyya, D.

2015-06-01

This paper presents the X-ray absorption near edge structure (XANES) studies of Nd doped phosphate glasses before and after gamma irradiation. The intensity and location of LIII edge white line peak of Nd changes depending on its concentration as well as on the ratio of O/Nd in the glass matrix. The decrease in the peak intensity of white line after gamma irradiation indicates towards reduction of Nd3+ to Nd2+ in the glass matrix, which increases with an increase in the doses of gamma irradiation. Similarity in the XANES spectra of Nd doped phosphate glasses and Nd2O3 suggests that coordination geometry around Nd3+ in glass samples may be identical to that of Nd2O3.

Method of joining metallic and composite components

NASA Technical Reports Server (NTRS)

Semmes, Edmund B. (Inventor)

2010-01-01

A method is provided for joining a metallic member to a structure made of a composite matrix material. One or more surfaces of a portion of the metallic member that is to be joined to the composite matrix structure is provided with a plurality of outwardly projecting studs. The surface including the studs is brought into engagement with a portion of an uncured composite matrix material so that fibers of the composite matrix material intertwine with the studs, and the metallic member and composite structure form an assembly. The assembly is then companion cured so as to join the metallic member to the composite matrix material structure.

Arterial elastic fiber structure. Function and potential roles in acute aortic dissection.

PubMed

Pratt, B; Curci, J

2010-10-01

The lethality of acute aortic dissection is well recognized. Successful treatment and prevention of aortic dissection is going to be dependent upon an improved understanding of the molecular and physiologic events which predispose to dissection development and propagation. In this review, we will focus on the elastic fiber, one of the critical elements of the aortic wall matrix. Mechanical or functional failure of the elastin in the wall of the aorta likely predisposes to dissection as well as the post-dissection aortic degeneration with aneurysm formation. Insight into the role of the elastin and the elastic fiber in aortic dissection has recently been accelerated by research into the molecular mechanisms associated with hereditary propensity for aortic dissection, such as Marfan syndrome. These studies have implicated both structural and metabolic contributions of alterations in the scaffolding proteins in matrix elastic fibers. In particular, increased transforming growth factor-β (TGF-β) activity may play a prominent role in predisposing the aortic wall to dissection. The events which predispose to post-dissection aortic degeneration are somewhat less well defined. However, the loss of the structural integrity of the remaining elastic fibers leaves the wall weaker and prone to dilatation and rupture. It appears likely that the upregulation of several potent proteases, particularly those of the matrix metalloproteinase (MMP) family such as MMP-9, are participating in the subsequent matrix damage. Novel medical treatments based on this pathologic data have been proposed and in some cases have made it to clinical trials. The ongoing study evaluating whether therapeutic inhibition of TGF-β may be useful in reducing the risk of aortic dissection in patients at high risk represents one promising new strategy in the treatment of this deadly disease.

Matrix Metalloproteinases as Regulators of Vein Structure and Function: Implications in Chronic Venous Disease.

PubMed

MacColl, Elisabeth; Khalil, Raouf A

2015-12-01

Lower-extremity veins have efficient wall structure and function and competent valves that permit upward movement of deoxygenated blood toward the heart against hydrostatic venous pressure. Matrix metalloproteinases (MMPs) play an important role in maintaining vein wall structure and function. MMPs are zinc-binding endopeptidases secreted as inactive pro-MMPs by fibroblasts, vascular smooth muscle (VSM), and leukocytes. Pro-MMPs are activated by various activators including other MMPs and proteinases. MMPs cause degradation of extracellular matrix (ECM) proteins such as collagen and elastin, and could have additional effects on the endothelium, as well as VSM cell migration, proliferation, Ca(2+) signaling, and contraction. Increased lower-extremity hydrostatic venous pressure is thought to induce hypoxia-inducible factors and other MMP inducers/activators such as extracellular matrix metalloproteinase inducer, prostanoids, chymase, and hormones, leading to increased MMP expression/activity, ECM degradation, VSM relaxation, and venous dilation. Leukocyte infiltration and inflammation of the vein wall cause further increases in MMPs, vein wall dilation, valve degradation, and different clinical stages of chronic venous disease (CVD), including varicose veins (VVs). VVs are characterized by ECM imbalance, incompetent valves, venous reflux, wall dilation, and tortuosity. VVs often show increased MMP levels, but may show no change or decreased levels, depending on the VV region (atrophic regions with little ECM versus hypertrophic regions with abundant ECM) and MMP form (inactive pro-MMP versus active MMP). Management of VVs includes compression stockings, venotonics, and surgical obliteration or removal. Because these approaches do not treat the causes of VVs, alternative methods are being developed. In addition to endogenous tissue inhibitors of MMPs, synthetic MMP inhibitors have been developed, and their effects in the treatment of VVs need to be examined. Copyright © 2015 by The American Society for Pharmacology and Experimental Therapeutics.

Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix

PubMed Central

Borlee, Bradley R; Goldman, Aaron D; Murakami, Keiji; Samudrala, Ram; Wozniak, Daniel J; Parsek, Matthew R

2010-01-01

Pseudomonas aeruginosa, the principal pathogen of cystic fibrosis patients, forms antibiotic-resistant biofilms promoting chronic colonization of the airways. The extracellular (EPS) matrix is a crucial component of biofilms that provides the community multiple benefits. Recent work suggests that the secondary messenger, cyclic-di-GMP, promotes biofilm formation. An analysis of factors specifically expressed in P. aeruginosa under conditions of elevated c-di-GMP, revealed functions involved in the production and maintenance of the biofilm extracellular matrix. We have characterized one of these components, encoded by the PA4625 gene, as a putative adhesin and designated it cdrA. CdrA shares structural similarities to extracellular adhesins that belong to two-partner secretion systems. The cdrA gene is in a two gene operon that also encodes a putative outer membrane transporter, CdrB. The cdrA gene encodes a 220 KDa protein that is predicted to be rod-shaped protein harbouring a β-helix structural motif. Western analysis indicates that the CdrA is produced as a 220 kDa proprotein and processed to 150 kDa before secretion into the extracellular medium. We demonstrated that cdrAB expression is minimal in liquid culture, but is elevated in biofilm cultures. CdrAB expression was found to promote biofilm formation and auto-aggregation in liquid culture. Aggregation mediated by CdrA is dependent on the Psl polysaccharide and can be disrupted by adding mannose, a key structural component of Psl. Immunoprecipitation of Psl present in culture supernatants resulted in co-immunoprecipitation of CdrA, providing additional evidence that CdrA directly binds to Psl. A mutation in cdrA caused a decrease in biofilm biomass and resulted in the formation of biofilms exhibiting decreased structural integrity. Psl-specific lectin staining suggests that CdrA either cross-links Psl polysaccharide polymers and/or tethers Psl to the cells, resulting in increased biofilm structural stability. Thus, this study identifies a key protein structural component of the P. aeruginosa EPS matrix. PMID:20088866

Bayesian hierarchical model for large-scale covariance matrix estimation.

PubMed

Zhu, Dongxiao; Hero, Alfred O

2007-12-01

Many bioinformatics problems implicitly depend on estimating large-scale covariance matrix. The traditional approaches tend to give rise to high variance and low accuracy due to "overfitting." We cast the large-scale covariance matrix estimation problem into the Bayesian hierarchical model framework, and introduce dependency between covariance parameters. We demonstrate the advantages of our approaches over the traditional approaches using simulations and OMICS data analysis.

Pore-Scale Simulation and Sensitivity Analysis of Apparent Gas Permeability in Shale Matrix

PubMed Central

Zhang, Pengwei; Hu, Liming; Meegoda, Jay N.

2017-01-01

Extremely low permeability due to nano-scale pores is a distinctive feature of gas transport in a shale matrix. The permeability of shale depends on pore pressure, porosity, pore throat size and gas type. The pore network model is a practical way to explain the macro flow behavior of porous media from a microscopic point of view. In this research, gas flow in a shale matrix is simulated using a previously developed three-dimensional pore network model that includes typical bimodal pore size distribution, anisotropy and low connectivity of the pore structure in shale. The apparent gas permeability of shale matrix was calculated under different reservoir pressures corresponding to different gas exploitation stages. Results indicate that gas permeability is strongly related to reservoir gas pressure, and hence the apparent permeability is not a unique value during the shale gas exploitation, and simulations suggested that a constant permeability for continuum-scale simulation is not accurate. Hence, the reservoir pressures of different shale gas exploitations should be considered. In addition, a sensitivity analysis was also performed to determine the contributions to apparent permeability of a shale matrix from petro-physical properties of shale such as pore throat size and porosity. Finally, the impact of connectivity of nano-scale pores on shale gas flux was analyzed. These results would provide an insight into understanding nano/micro scale flows of shale gas in the shale matrix. PMID:28772465

Pore-Scale Simulation and Sensitivity Analysis of Apparent Gas Permeability in Shale Matrix.

PubMed

Zhang, Pengwei; Hu, Liming; Meegoda, Jay N

2017-01-25

Extremely low permeability due to nano-scale pores is a distinctive feature of gas transport in a shale matrix. The permeability of shale depends on pore pressure, porosity, pore throat size and gas type. The pore network model is a practical way to explain the macro flow behavior of porous media from a microscopic point of view. In this research, gas flow in a shale matrix is simulated using a previously developed three-dimensional pore network model that includes typical bimodal pore size distribution, anisotropy and low connectivity of the pore structure in shale. The apparent gas permeability of shale matrix was calculated under different reservoir pressures corresponding to different gas exploitation stages. Results indicate that gas permeability is strongly related to reservoir gas pressure, and hence the apparent permeability is not a unique value during the shale gas exploitation, and simulations suggested that a constant permeability for continuum-scale simulation is not accurate. Hence, the reservoir pressures of different shale gas exploitations should be considered. In addition, a sensitivity analysis was also performed to determine the contributions to apparent permeability of a shale matrix from petro-physical properties of shale such as pore throat size and porosity. Finally, the impact of connectivity of nano-scale pores on shale gas flux was analyzed. These results would provide an insight into understanding nano/micro scale flows of shale gas in the shale matrix.

The controversial nuclear matrix: a balanced point of view.

PubMed

Martelli, A M; Falcieri, E; Zweyer, M; Bortul, R; Tabellini, G; Cappellini, A; Cocco, L; Manzoli, L

2002-10-01

The nuclear matrix is defined as the residual framework after the removal of the nuclear envelope, chromatin, and soluble components by sequential extractions. According to several investigators the nuclear matrix provides the structural basis for intranuclear order. However, the existence itself and the nature of this structure is still uncertain. Although the techniques used for the visualization of the nuclear matrix have improved over the years, it is still unclear to what extent the isolated nuclear matrix corresponds to an in vivo existing structure. Therefore, considerable skepticism continues to surround the nuclear matrix fraction as an accurate representation of the situation in living cells. Here, we summarize the experimental evidence in favor of, or against, the presence of a diffuse nucleoskeleton as a facilitating organizational nonchromatin structure of the nucleus.

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.

Analysis of Crushing Response of Composite Crashworthy Structures

NASA Astrophysics Data System (ADS)

David, Matthew; Johnson, Alastair F.; Voggenreiter, H.

2013-10-01

The paper describes quasi-static and dynamic tests to characterise the energy absorption properties of polymer composite crash energy absorbing segment elements under axial loads. Detailed computer tomography scans of failed specimens are used to identify local compression crush failure mechanisms at the crush front. The varied crushing morphology between the compression strain rates identified in this paper is observed to be due to the differences in the response modes and mechanical properties of the strain dependent epoxy matrix. The importance of understanding the role of strain rate effects in composite crash energy absorbing structures is highlighted in this paper.

Moments of the neutron g₂ structure function at intermediate Q²

DOE PAGES

Solvignon-Slifer, Patricia H.

2015-07-15

We present new experimental results of the ³He spin structure function g₂ in the resonance region at Q² values between 1.2 and 3.0 (GeV/c)². Spin dependent moments of the neutron were then extracted.Our main result, the inelastic contribution to the neutron d₂ matrix element, was found to be small (Q²) = 2.4 (GeV/c)² and in agreement with the Lattice QCD calculation. The Burkhardt-Cottingham sum rule for ³He neutron was tested with the measured data and using the Wandzura-Wilczek relation for the low x unmeasured region.

Hybrid type-I InAs/GaAs and type-II GaSb/GaAs quantum dot structure with enhanced photoluminescence

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

Ji, Hai-Ming; Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083; Liang, Baolai, E-mail: bliang@cnsi.ucla.edu

2015-03-09

We investigate the photoluminescence (PL) properties of a hybrid type-I InAs/GaAs and type-II GaSb/GaAs quantum dot (QD) structure grown in a GaAs matrix by molecular beam epitaxy. This hybrid QD structure exhibits more intense PL with a broader spectral range, compared with control samples that contain only InAs or GaSb QDs. This enhanced PL performance is attributed to additional electron and hole injection from the type-I InAs QDs into the adjacent type-II GaSb QDs. We confirm this mechanism using time-resolved and power-dependent PL. These hybrid QD structures show potential for high efficiency QD solar cell applications.

[Nuclear protein matrix from giant nuclei of Chironomus plumosus determinates polythene chromosome organization].

PubMed

Makarov, M S; Chentsov, Iu S

2010-01-01

Giant nuclei from salivary glands of Chironomus plumosus were treated in situ with detergent, 2 M NaCl and nucleases in order to reveal residual nuclear matrix proteins (NMP). It was shown, that preceding stabilization of non-histone proteins with 2 mM CuCl2 allowed to visualize the structure of polythene chromosomes at every stage of the extraction of histones and DNA. Stabilized NPM of polythene chromosomes maintains their morphology and banding patterns, which is observed by light and electron microscopy, whereas internal fibril net or residual nucleoli are not found. In stabilized NPM of polythene chromosomes, topoisomerase IIalpha and SMC1 retain their localization that is typical of untreated chromosomes. NPM of polythene chromosomes also includes sites of DNA replication, visualized with BrDU incubation, and some RNA-components. So, we can conclude that structure of NPM from giant nuclei is equal to NPM from normal interphase nuclei, and that morphological features of polythene chromosomes depend on the presence of NMP.

Experimental Verification of a Progressive Damage Model for IM7/5260 Laminates Subjected to Tension-Tension Fatigue

NASA Technical Reports Server (NTRS)

Coats, Timothy W.; Harris, Charles E.

1995-01-01

The durability and damage tolerance of laminated composites are critical design considerations for airframe composite structures. Therefore, the ability to model damage initiation and growth and predict the life of laminated composites is necessary to achieve structurally efficient and economical designs. The purpose of this research is to experimentally verify the application of a continuum damage model to predict progressive damage development in a toughened material system. Damage due to monotonic and tension-tension fatigue was documented for IM7/5260 graphite/bismaleimide laminates. Crack density and delamination surface area were used to calculate matrix cracking and delamination internal state variables to predict stiffness loss in unnotched laminates. A damage dependent finite element code predicted the stiffness loss for notched laminates with good agreement to experimental data. It was concluded that the continuum damage model can adequately predict matrix damage progression in notched and unnotched laminates as a function of loading history and laminate stacking sequence.

Lightweight bio-composites based on hemp fibres produced by conventional and unconventional processes

NASA Astrophysics Data System (ADS)

Boccarusso, L.; Durante, M.; Formisano, A.; Langella, A.; Minutolo, F. Memola Capece

2017-10-01

Considering that nowadays the interest in the use of bio-composite materials is increasing more and more, this work is focused on the manufacturing of lightweight components based on hemp fibres for future applications, for example as a core for sandwich structures. Three different no-complex processes were used: a conventional hand lay-up, an unconventional infusion process and a hand lay-up process followed by injection moulding. They were used to produce bio-composite structures using an epoxy resin and/or a polyurethane foam as matrix. Depending on the process used for the manufacturing, laminates with different values of density were obtained. A detailed study in terms of both static and dynamic properties was carried out and the different mechanical behaviour for each sample typology was highlighted. The results showed that the process in which both the epoxy resin and the polyurethane foam were used as matrix allowed to obtain laminates with lower density and higher specific mechanical properties.

Keeping the Vimentin Network under Control: Cell–Matrix Adhesion–associated Plectin 1f Affects Cell Shape and Polarity of Fibroblasts

PubMed Central

Burgstaller, Gerald; Gregor, Martin; Winter, Lilli

2010-01-01

Focal adhesions (FAs) located at the ends of actin/myosin-containing contractile stress fibers form tight connections between fibroblasts and their underlying extracellular matrix. We show here that mature FAs and their derivative fibronectin fibril-aligned fibrillar adhesions (FbAs) serve as docking sites for vimentin intermediate filaments (IFs) in a plectin isoform 1f (P1f)-dependent manner. Time-lapse video microscopy revealed that FA-associated P1f captures mobile vimentin filament precursors, which then serve as seeds for de novo IF network formation via end-to-end fusion with other mobile precursors. As a consequence of IF association, the turnover of FAs is reduced. P1f-mediated IF network formation at FbAs creates a resilient cage-like core structure that encases and positions the nucleus while being stably connected to the exterior of the cell. We show that the formation of this structure affects cell shape with consequences for cell polarization. PMID:20702585

Rapid Mueller matrix polarimetry imaging based on four photoelastic modulators with no moving parts (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gribble, Adam; Alali, Sanaz; Vitkin, Alex

2016-03-01

Polarized light has many applications in biomedical imaging. The interaction of a biological sample with polarized light reveals information about its composition, both structural and functional. For example, the polarimetry-derived metric of linear retardance (birefringence) is dependent on tissue structural organization (anisotropy) and can be used to diagnose myocardial infarct; circular birefringence (optical rotation) can measure glucose concentrations. The most comprehensive type of polarimetry analysis is to measure the Mueller matrix, a polarization transfer function that completely describes how a sample interacts with polarized light. To derive this 4x4 matrix it is necessary to observe how a tissue interacts with different polarizations. A well-suited approach for tissue polarimetry is to use photoelastic modulators (PEMs), which dynamically modulate the polarization of light. Previously, we have demonstrated a rapid time-gated Stokes imaging system that is capable of characterizing the state of polarized light (the Stokes vector) over a large field, after interacting with any turbid media. This was accomplished by synchronizing CCD camera acquisition times relative to two PEMs using a field-programmable gate array (FPGA). Here, we extend this technology to four PEMs, yielding a polarimetry system that is capable of rapidly measuring the complete sample Mueller matrix over a large field of view, with no moving parts and no beam steering. We describe the calibration procedure and evaluate the accuracy of the measurements. Results are shown for tissue-mimicking phantoms, as well as initial biological samples.

Metal matrix composite micromechanics: In-situ behavior influence on composite properties

NASA Technical Reports Server (NTRS)

Murthy, P. L. N.; Hopkins, D. A.; Chamis, C. C.

1989-01-01

Recent efforts in computational mechanics methods for simulating the nonlinear behavior of metal matrix composites have culminated in the implementation of the Metal Matrix Composite Analyzer (METCAN) computer code. In METCAN material nonlinearity is treated at the constituent (fiber, matrix, and interphase) level where the current material model describes a time-temperature-stress dependency of the constituent properties in a material behavior space. The composite properties are synthesized from the constituent instantaneous properties by virtue of composite micromechanics and macromechanics models. The behavior of metal matrix composites depends on fabrication process variables, in situ fiber and matrix properties, bonding between the fiber and matrix, and/or the properties of an interphase between the fiber and matrix. Specifically, the influence of in situ matrix strength and the interphase degradation on the unidirectional composite stress-strain behavior is examined. These types of studies provide insight into micromechanical behavior that may be helpful in resolving discrepancies between experimentally observed composite behavior and predicted response.

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

Three-dimensional matrix fiber alignment modulates cell migration and MT1-MMP utility by spatially and temporally directing protrusions

NASA Astrophysics Data System (ADS)

Fraley, Stephanie I.; Wu, Pei-Hsun; He, Lijuan; Feng, Yunfeng; Krisnamurthy, Ranjini; Longmore, Gregory D.; Wirtz, Denis

2015-10-01

Multiple attributes of the three-dimensional (3D) extracellular matrix (ECM) have been independently implicated as regulators of cell motility, including pore size, crosslink density, structural organization, and stiffness. However, these parameters cannot be independently varied within a complex 3D ECM protein network. We present an integrated, quantitative study of these parameters across a broad range of complex matrix configurations using self-assembling 3D collagen and show how each parameter relates to the others and to cell motility. Increasing collagen density resulted in a decrease and then an increase in both pore size and fiber alignment, which both correlated significantly with cell motility but not bulk matrix stiffness within the range tested. However, using the crosslinking enzyme Transglutaminase II to alter microstructure independently of density revealed that motility is most significantly predicted by fiber alignment. Cellular protrusion rate, protrusion orientation, speed of migration, and invasion distance showed coupled biphasic responses to increasing collagen density not predicted by 2D models or by stiffness, but instead by fiber alignment. The requirement of matrix metalloproteinase (MMP) activity was also observed to depend on microstructure, and a threshold of MMP utility was identified. Our results suggest that fiber topography guides protrusions and thereby MMP activity and motility.

Tensor-GMRES method for large sparse systems of nonlinear equations

NASA Technical Reports Server (NTRS)

Feng, Dan; Pulliam, Thomas H.

1994-01-01

This paper introduces a tensor-Krylov method, the tensor-GMRES method, for large sparse systems of nonlinear equations. This method is a coupling of tensor model formation and solution techniques for nonlinear equations with Krylov subspace projection techniques for unsymmetric systems of linear equations. Traditional tensor methods for nonlinear equations are based on a quadratic model of the nonlinear function, a standard linear model augmented by a simple second order term. These methods are shown to be significantly more efficient than standard methods both on nonsingular problems and on problems where the Jacobian matrix at the solution is singular. A major disadvantage of the traditional tensor methods is that the solution of the tensor model requires the factorization of the Jacobian matrix, which may not be suitable for problems where the Jacobian matrix is large and has a 'bad' sparsity structure for an efficient factorization. We overcome this difficulty by forming and solving the tensor model using an extension of a Newton-GMRES scheme. Like traditional tensor methods, we show that the new tensor method has significant computational advantages over the analogous Newton counterpart. Consistent with Krylov subspace based methods, the new tensor method does not depend on the factorization of the Jacobian matrix. As a matter of fact, the Jacobian matrix is never needed explicitly.

The multifacet graphically contracted function method. I. Formulation and implementation

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

Shepard, Ron; Brozell, Scott R.; Gidofalvi, Gergely

2014-08-14

The basic formulation for the multifacet generalization of the graphically contracted function (MFGCF) electronic structure method is presented. The analysis includes the discussion of linear dependency and redundancy of the arc factor parameters, the computation of reduced density matrices, Hamiltonian matrix construction, spin-density matrix construction, the computation of optimization gradients for single-state and state-averaged calculations, graphical wave function analysis, and the efficient computation of configuration state function and Slater determinant expansion coefficients. Timings are given for Hamiltonian matrix element and analytic optimization gradient computations for a range of model problems for full-CI Shavitt graphs, and it is observed that bothmore » the energy and the gradient computation scale as O(N{sup 2}n{sup 4}) for N electrons and n orbitals. The important arithmetic operations are within dense matrix-matrix product computational kernels, resulting in a computationally efficient procedure. An initial implementation of the method is used to present applications to several challenging chemical systems, including N{sub 2} dissociation, cubic H{sub 8} dissociation, the symmetric dissociation of H{sub 2}O, and the insertion of Be into H{sub 2}. The results are compared to the exact full-CI values and also to those of the previous single-facet GCF expansion form.« less

Contractility of the cell rear drives invasion of breast tumor cells in 3D Matrigel

PubMed Central

Poincloux, Renaud; Collin, Olivier; Lizárraga, Floria; Romao, Maryse; Debray, Marcel; Piel, Matthieu; Chavrier, Philippe

2011-01-01

Cancer cells use different modes of migration, including integrin-dependent mesenchymal migration of elongated cells along elements of the 3D matrix as opposed to low-adhesion-, contraction-based amoeboid motility of rounded cells. We report that MDA-MB-231 human breast adenocarcinoma cells invade 3D Matrigel with a characteristic rounded morphology and with F-actin and myosin-IIa accumulating at the cell rear in a uropod-like structure. MDA-MB-231 cells display neither lamellipodia nor bleb extensions at the leading edge and do not require Arp2/3 complex activity for 3D invasion in Matrigel. Accumulation of phospho-MLC and blebbing activity were restricted to the uropod as reporters of actomyosin contractility, and velocimetric analysis of fluorescent beads embedded within the 3D matrix showed that pulling forces exerted to the matrix are restricted to the side and rear of cells. Inhibition of actomyosin contractility or β1 integrin function interferes with uropod formation, matrix deformation, and invasion through Matrigel. These findings support a model whereby actomyosin-based uropod contractility generates traction forces on the β1 integrin adhesion system to drive cell propulsion within the 3D matrix, with no contribution of lamellipodia extension or blebbing to movement. PMID:21245302

Energy Absorption Capacity in Natural Fiber Reinforcement Composites Structures

PubMed Central

López-Alba, Elías; Díaz, Francisco

2018-01-01

The study of natural fiber reinforcement composite structures has focused the attention of the automobile industry due to the new regulation in relation to the recyclability and the reusability of the materials preserving and/or improving the mechanical characteristics. The influence of different parameters on the material behavior of natural fiber reinforced plastic structures has been investigated, showing the potential for transport application in energy absorbing structures. Two different woven fabrics (twill and hopsack) made of flax fibers as well as a non-woven mat made of a mixture of hemp and kenaf fibers were employed as reinforcing materials. These reinforcing textiles were impregnated with both HD-PE (high-density polyethylen) and PLA (polylactic acid) matrix, using a continuous compression molding press. The impregnated semi-finished laminates (so-called organic sheets) were thermoformed in a second step to half-tubes that were assembled through vibration-welding process to cylindric crash absorbers. The specimens were loaded by compression to determine the specific energy absorption capacity. Quasi-static test results were compared to dynamic test data obtained on a catapult arrangement. The differences on the specific energies absorption (SEA) as a function of different parameters, such as the wall thickness, the weave material type, the reinforced textiles, and the matrix used, depending on the velocity rate application were quantified. In the case of quasi-static analysis it is observed a 20% increment in the SEA value when wove Hopsack fabric reinforcement is employed. No velocity rate influence from the material was observed on the SEA evaluation at higher speeds used to perform the experiments. The influence of the weave configuration (Hopsack) seems to be more stable against buckling effects at low loading rates with 10% higher SEA values. An increase of SEA level of up to 72% for PLA matrix was observed when compared with HD-PE matrix. PMID:29534003

Energy Absorption Capacity in Natural Fiber Reinforcement Composites Structures.

PubMed

López-Alba, Elías; Schmeer, Sebastian; Díaz, Francisco

2018-03-13

The study of natural fiber reinforcement composite structures has focused the attention of the automobile industry due to the new regulation in relation to the recyclability and the reusability of the materials preserving and/or improving the mechanical characteristics. The influence of different parameters on the material behavior of natural fiber reinforced plastic structures has been investigated, showing the potential for transport application in energy absorbing structures. Two different woven fabrics (twill and hopsack) made of flax fibers as well as a non-woven mat made of a mixture of hemp and kenaf fibers were employed as reinforcing materials. These reinforcing textiles were impregnated with both HD-PE (high-density polyethylen) and PLA (polylactic acid) matrix, using a continuous compression molding press. The impregnated semi-finished laminates (so-called organic sheets) were thermoformed in a second step to half-tubes that were assembled through vibration-welding process to cylindric crash absorbers. The specimens were loaded by compression to determine the specific energy absorption capacity. Quasi-static test results were compared to dynamic test data obtained on a catapult arrangement. The differences on the specific energies absorption (SEA) as a function of different parameters, such as the wall thickness, the weave material type, the reinforced textiles, and the matrix used, depending on the velocity rate application were quantified. In the case of quasi-static analysis it is observed a 20% increment in the SEA value when wove Hopsack fabric reinforcement is employed. No velocity rate influence from the material was observed on the SEA evaluation at higher speeds used to perform the experiments. The influence of the weave configuration (Hopsack) seems to be more stable against buckling effects at low loading rates with 10% higher SEA values. An increase of SEA level of up to 72% for PLA matrix was observed when compared with HD-PE matrix.

Photoelectron Pumped Phosphors,

DTIC Science & Technology

1989-07-01

result of SEE, if the screen is made from a dielectric or a semi- conductor with a high resistivity . The CL brightness depends on the energy of the...1. The rare-earth ion activated high resistance phos- phors based on the materials with garnet, spinel and diamond structure can be considered as the...most prospective CL materials, especially in the compounds that include the rare-earth elements in their host matrix. 2. The low resistance CL oxides

Macroscopic Modeling of A3B15A3 Triblock Copolymers in B Solvent

DTIC Science & Technology

2010-11-01

matrix composed of the midblock (2). Some examples of TPEs are poly[styrene-butadiene-styrene] (SBS), poly[styrene- isoprene -styrene] (SIS), poly[styrene...92. 19. Hadziioannou, G.; Skoulios, A. Molecular Weight Dependence of Lamellar Structure in Styrene Isoprene Two- and Three-block Copolymers...Microphase Seperation in Styrene- Isoprene Block Copolymers. Macromolecules 1994, 27. 42. Mckay, K. W.; Gros, W. A.; Diehl, C. F. The Influence of

Development of a hybrid wave based-transfer matrix model for sound transmission analysis.

PubMed

Dijckmans, A; Vermeir, G

2013-04-01

In this paper, a hybrid wave based-transfer matrix model is presented that allows for the investigation of the sound transmission through finite multilayered structures placed between two reverberant rooms. The multilayered structure may consist of an arbitrary configuration of fluid, elastic, or poro-elastic layers. The field variables (structural displacements and sound pressures) are expanded in terms of structural and acoustic wave functions. The boundary and continuity conditions in the rooms determine the participation factors in the pressure expansions. The displacement of the multilayered structure is determined by the mechanical impedance matrix, which gives a relation between the pressures and transverse displacements at both sides of the structure. The elements of this matrix are calculated with the transfer matrix method. First, the hybrid model is numerically validated. Next a comparison is made with sound transmission loss measurements of a hollow brick wall and a sandwich panel. Finally, numerical simulations show the influence of structural damping, room dimensions and plate dimensions on the sound transmission loss of multilayered structures.

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

The dependence of the tunneling characteristic on the electronic energy bands and the carrier’s states of Graphene superlattice

NASA Astrophysics Data System (ADS)

Yang, C. H.; Shen, G. Z.; Ao, Z. M.; Xu, Y. W.

2016-09-01

Using the transfer matrix method, the carrier tunneling properties in graphene superlattice generated by the Thue-Morse sequence and Kolakoski sequence are investigated. The positions and strength of the transmission can be modulated by the barrier structures, the incident energy and angle, the height and width of the potential. These carriers tunneling characteristic can be understood from the energy band structures in the corresponding superlattice systems and the carrier’s states in well/barriers. The transmission peaks above the critical incident angle rely on the carrier’s resonance in the well regions. The structural diversity can modulate the electronic and transport properties, thus expanding its applications.

Effects of sample size on estimates of population growth rates calculated with matrix models.

PubMed

Fiske, Ian J; Bruna, Emilio M; Bolker, Benjamin M

2008-08-28

Matrix models are widely used to study the dynamics and demography of populations. An important but overlooked issue is how the number of individuals sampled influences estimates of the population growth rate (lambda) calculated with matrix models. Even unbiased estimates of vital rates do not ensure unbiased estimates of lambda-Jensen's Inequality implies that even when the estimates of the vital rates are accurate, small sample sizes lead to biased estimates of lambda due to increased sampling variance. We investigated if sampling variability and the distribution of sampling effort among size classes lead to biases in estimates of lambda. Using data from a long-term field study of plant demography, we simulated the effects of sampling variance by drawing vital rates and calculating lambda for increasingly larger populations drawn from a total population of 3842 plants. We then compared these estimates of lambda with those based on the entire population and calculated the resulting bias. Finally, we conducted a review of the literature to determine the sample sizes typically used when parameterizing matrix models used to study plant demography. We found significant bias at small sample sizes when survival was low (survival = 0.5), and that sampling with a more-realistic inverse J-shaped population structure exacerbated this bias. However our simulations also demonstrate that these biases rapidly become negligible with increasing sample sizes or as survival increases. For many of the sample sizes used in demographic studies, matrix models are probably robust to the biases resulting from sampling variance of vital rates. However, this conclusion may depend on the structure of populations or the distribution of sampling effort in ways that are unexplored. We suggest more intensive sampling of populations when individual survival is low and greater sampling of stages with high elasticities.

Integration of Posttranscriptional Gene Networks into Metabolic Adaptation and Biofilm Maturation in Candida albicans

PubMed Central

Harrison, Paul F.; Lo, Tricia L.; Quenault, Tara; Dagley, Michael J.; Bellousoff, Matthew; Powell, David R.; Beilharz, Traude H.; Traven, Ana

2015-01-01

The yeast Candida albicans is a human commensal and opportunistic pathogen. Although both commensalism and pathogenesis depend on metabolic adaptation, the regulatory pathways that mediate metabolic processes in C. albicans are incompletely defined. For example, metabolic change is a major feature that distinguishes community growth of C. albicans in biofilms compared to suspension cultures, but how metabolic adaptation is functionally interfaced with the structural and gene regulatory changes that drive biofilm maturation remains to be fully understood. We show here that the RNA binding protein Puf3 regulates a posttranscriptional mRNA network in C. albicans that impacts on mitochondrial biogenesis, and provide the first functional data suggesting evolutionary rewiring of posttranscriptional gene regulation between the model yeast Saccharomyces cerevisiae and C. albicans. A proportion of the Puf3 mRNA network is differentially expressed in biofilms, and by using a mutant in the mRNA deadenylase CCR4 (the enzyme recruited to mRNAs by Puf3 to control transcript stability) we show that posttranscriptional regulation is important for mitochondrial regulation in biofilms. Inactivation of CCR4 or dis-regulation of mitochondrial activity led to altered biofilm structure and over-production of extracellular matrix material. The extracellular matrix is critical for antifungal resistance and immune evasion, and yet of all biofilm maturation pathways extracellular matrix biogenesis is the least understood. We propose a model in which the hypoxic biofilm environment is sensed by regulators such as Ccr4 to orchestrate metabolic adaptation, as well as the regulation of extracellular matrix production by impacting on the expression of matrix-related cell wall genes. Therefore metabolic changes in biofilms might be intimately linked to a key biofilm maturation mechanism that ultimately results in untreatable fungal disease. PMID:26474309

Operator bases, S-matrices, and their partition functions

NASA Astrophysics Data System (ADS)

Henning, Brian; Lu, Xiaochuan; Melia, Tom; Murayama, Hitoshi

2017-10-01

Relativistic quantum systems that admit scattering experiments are quantitatively described by effective field theories, where S-matrix kinematics and symmetry considerations are encoded in the operator spectrum of the EFT. In this paper we use the S-matrix to derive the structure of the EFT operator basis, providing complementary descriptions in (i) position space utilizing the conformal algebra and cohomology and (ii) momentum space via an algebraic formulation in terms of a ring of momenta with kinematics implemented as an ideal. These frameworks systematically handle redundancies associated with equations of motion (on-shell) and integration by parts (momentum conservation). We introduce a partition function, termed the Hilbert series, to enumerate the operator basis — correspondingly, the S-matrix — and derive a matrix integral expression to compute the Hilbert series. The expression is general, easily applied in any spacetime dimension, with arbitrary field content and (linearly realized) symmetries. In addition to counting, we discuss construction of the basis. Simple algorithms follow from the algebraic formulation in momentum space. We explicitly compute the basis for operators involving up to n = 5 scalar fields. This construction universally applies to fields with spin, since the operator basis for scalars encodes the momentum dependence of n-point amplitudes. We discuss in detail the operator basis for non-linearly realized symmetries. In the presence of massless particles, there is freedom to impose additional structure on the S- matrix in the form of soft limits. The most na¨ıve implementation for massless scalars leads to the operator basis for pions, which we confirm using the standard CCWZ formulation for non-linear realizations. Although primarily discussed in the language of EFT, some of our results — conceptual and quantitative — may be of broader use in studying conformal field theories as well as the AdS/CFT correspondence.

Micromechanics effects in creep of metal-matrix composites

NASA Astrophysics Data System (ADS)

Davis, L. C.; Allison, J. E.

1995-12-01

The creep of metal-matrix composites is analyzed by finite element techniques. An axisymmetric unit-cell model with spherical reinforcing particles is used. Parameters appropriate to TiC particles in a precipitation-hardened (2219) Al matrix are chosen. The effects of matrix plasticity and residual stresses on the creep of the composite are calculated. We confirm (1) that the steady-state rate is independent of the particle elastic moduli and the matrix elastic and plastic properties, (2) that the ratio of composite to matrix steady-state rates depends only on the volume fraction and geometry of the reinforcing phase, and (3) that this ratio can be determined from a calculation of the stress-strain relation for the geometrically identical composite (same phase volume and geometry) with rigid particles in the appropriate power-law hardening matrix. The values of steady-state creep are compared to experimental ones (Krajewski et al.). Continuum mechanics predictions give a larger reduction of the composite creep relative to the unreinforced material than measured, suggesting that the effective creep rate of the matrix is larger than in unreinforced precipitation-hardened Al due to changes in microstructure, dislocation density, or creep mechanism. Changes in matrix creep properties are also suggested by the comparison of calculated and measured creep strain rates in the primary creep regime, where significantly different time dependencies are found. It is found that creep calculations performed for a timeindependent matrix creep law can be transformed to obtain the creep for a time-dependent creep law.

Multi-cut solutions in Chern-Simons matrix models

NASA Astrophysics Data System (ADS)

Morita, Takeshi; Sugiyama, Kento

2018-04-01

We elaborate the Chern-Simons (CS) matrix models at large N. The saddle point equations of these matrix models have a curious structure which cannot be seen in the ordinary one matrix models. Thanks to this structure, an infinite number of multi-cut solutions exist in the CS matrix models. Particularly we exactly derive the two-cut solutions at finite 't Hooft coupling in the pure CS matrix model. In the ABJM matrix model, we argue that some of multi-cut solutions might be interpreted as a condensation of the D2-brane instantons.

Bond-strength inversion in (In,Ga)As semiconductor alloys

NASA Astrophysics Data System (ADS)

Eckner, Stefanie; Ritter, Konrad; Schöppe, Philipp; Haubold, Erik; Eckner, Erich; Rensberg, Jura; Röder, Robert; Ridgway, Mark C.; Schnohr, Claudia S.

2018-05-01

The atomic-scale structure and vibrational properties of semiconductor alloys are determined by the energy required for stretching and bending the individual bonds. Using temperature-dependent extended x-ray absorption fine-structure spectroscopy, we have determined the element-specific In-As and Ga-As effective bond-stretching force constants in (In,Ga)As as a function of the alloy composition. The results reveal a striking inversion of the bond strength where the originally stiffer bond in the parent materials becomes the softer bond in the alloy and vice versa. Our findings clearly demonstrate that changes of both the individual bond length and the surrounding matrix affect the bond-stretching force constants. We thus show that the previously used common assumptions about the element-specific force constants in semiconductor alloys do not reproduce the composition dependence determined experimentally for (In,Ga)As.

Detailed Analysis of the Structural Changes of Bone Matrix During the Demineralization Process Using Raman Spectroscopy

NASA Astrophysics Data System (ADS)

Timchenko, E. V.; Zherdeva, L. A.; Timchenko, P. E.; Volova, L. T.; Ponomareva, U. V.

The results of experimental research of human cortical bone tissue depending on demineralization time were represented using Raman spectroscopy. Depending on demineralization time the ratio of the mineral (РO43- and CO32-) and organic components (amide I) of bone tissue, as well as changes in the spectral regions responsible for the structural integrity of the collagen fibers in bone tissue (1200-1460 cm-1 and 2880-3000 cm-1) were investigated. The observed changes show a decrease in mineral components: thus, the value of Raman band intensity at 956 and 1069 cm-1 for 5 minutes demineralization is 68.5 and 77.3%, for 20 minutes - 55.1 and 61.1%, for 120 minutes - 32.8 and 37% from Raman intensity values of not demineralized tissue objects respectively.

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

Time evolution of photon-pulse propagation in scattering and absorbing media: The dynamic radiative transfer system

NASA Astrophysics Data System (ADS)

Georgakopoulos, A.; Politopoulos, K.; Georgiou, E.

2018-03-01

A new dynamic-system approach to the problem of radiative transfer inside scattering and absorbing media is presented, directly based on first-hand physical principles. This method, the Dynamic Radiative Transfer System (DRTS), employs a dynamical system formality using a global sparse matrix, which characterizes the physical, optical and geometrical properties of the material-volume of interest. The new system state is generated by the above time-independent matrix, using simple matrix-vector multiplication for each subsequent time step. DRTS is capable of calculating accurately the time evolution of photon propagation in media of complex structure and shape. The flexibility of DRTS allows the integration of time-dependent sources, boundary conditions, different media and several optical phenomena like reflection and refraction in a unified and consistent way. Various examples of DRTS simulation results are presented for ultra-fast light pulse 3-D propagation, demonstrating greatly reduced computational cost and resource requirements compared to other methods.

Storm water runoff concentration matrix for urban areas.

PubMed

Göbel, P; Dierkes, C; Coldewey, W G

2007-04-01

The infrastructure (roads, sidewalk, commercial and residential structures) added during the land development and urbanisation process is designed to collect precipitation and convey it out of the watershed, typically in existing surface water channels, such as streams and rivers. The quality of surface water, seepage water and ground water is influenced by pollutants that collect on impervious surfaces and that are carried by urban storm water runoff. Heavy metals, e.g. lead (Pb), zinc (Zn), copper (Cu), cadmium (Cd), polycyclic aromatic hydrocarbons (PAH), mineral oil hydrocarbons (MOH) and readily soluble salts in runoff, contribute to the degradation of water. An intensive literature search on the distribution and concentration of the surface-dependent runoff water has been compiled. Concentration variations of several pollutants derived from different surfaces have been averaged. More than 300 references providing about 1300 data for different pollutants culminate in a representative concentration matrix consisting of medians and extreme values. This matrix can be applied to long-term valuations and numerical modelling of storm water treatment facilities.

Matrix metalloproteinase inhibition negatively affects muscle stem cell behavior

PubMed Central

Bellayr, Ian; Holden, Kyle; Mu, Xiaodong; Pan, Haiying; Li, Yong

2013-01-01

Skeletal muscle is a large and complex system that is crucial for structural support, movement and function. When injured, the repair of skeletal muscle undergoes three phases: inflammation and degeneration, regeneration and fibrosis formation in severe injuries. During fibrosis formation, muscle healing is impaired because of the accumulation of excess collagen. A group of zinc-dependent endopeptidases that have been found to aid in the repair of skeletal muscle are matrix metalloproteinases (MMPs). MMPs are able to assist in tissue remodeling through the regulation of extracellular matrix (ECM) components, as well as contributing to cell migration, proliferation, differentiation and angiogenesis. In the present study, the effect of GM6001, a broad-spectrum MMP inhibitor, on muscle-derived stem cells (MDSCs) is investigated. We find that MMP inhibition negatively impacts skeletal muscle healing by impairing MDSCs in migratory and multiple differentiation abilities. These results indicate that MMP signaling plays an essential role in the wound healing of muscle tissue because their inhibition is detrimental to stem cells residing in skeletal muscle. PMID:23329998

Identification of hair shaft progenitors that create a niche for hair pigmentation

PubMed Central

Liao, Chung-Ping; Booker, Reid C.; Morrison, Sean J.; Le, Lu Q.

2017-01-01

Hair differentiates from follicle stem cells through progenitor cells in the matrix. In contrast to stem cells in the bulge, the identities of the progenitors and the mechanisms by which they regulate hair shaft components are poorly understood. Hair is also pigmented by melanocytes in the follicle. However, the niche that regulates follicular melanocytes is not well characterized. Here, we report the identification of hair shaft progenitors in the matrix that are differentiated from follicular epithelial cells expressing transcription factor KROX20. Depletion of Krox20 lineage cells results in arrest of hair growth, confirming the critical role of KROX20+ cells as antecedents of structural cells found in hair. Expression of stem cell factor (SCF) by these cells is necessary for the maintenance of differentiated melanocytes and for hair pigmentation. Our findings reveal the identities of hair matrix progenitors that regulate hair growth and pigmentation, partly by creating an SCF-dependent niche for follicular melanocytes. PMID:28465357

Identification of hair shaft progenitors that create a niche for hair pigmentation.

PubMed

Liao, Chung-Ping; Booker, Reid C; Morrison, Sean J; Le, Lu Q

2017-04-15

Hair differentiates from follicle stem cells through progenitor cells in the matrix. In contrast to stem cells in the bulge, the identities of the progenitors and the mechanisms by which they regulate hair shaft components are poorly understood. Hair is also pigmented by melanocytes in the follicle. However, the niche that regulates follicular melanocytes is not well characterized. Here, we report the identification of hair shaft progenitors in the matrix that are differentiated from follicular epithelial cells expressing transcription factor KROX20. Depletion of Krox20 lineage cells results in arrest of hair growth, confirming the critical role of KROX20 + cells as antecedents of structural cells found in hair. Expression of stem cell factor (SCF) by these cells is necessary for the maintenance of differentiated melanocytes and for hair pigmentation. Our findings reveal the identities of hair matrix progenitors that regulate hair growth and pigmentation, partly by creating an SCF-dependent niche for follicular melanocytes. © 2017 Liao et al.; Published by Cold Spring Harbor Laboratory Press.

Explicit formula for the Holevo bound for two-parameter qubit-state estimation problem

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

Suzuki, Jun, E-mail: junsuzuki@uec.ac.jp

The main contribution of this paper is to derive an explicit expression for the fundamental precision bound, the Holevo bound, for estimating any two-parameter family of qubit mixed-states in terms of quantum versions of Fisher information. The obtained formula depends solely on the symmetric logarithmic derivative (SLD), the right logarithmic derivative (RLD) Fisher information, and a given weight matrix. This result immediately provides necessary and sufficient conditions for the following two important classes of quantum statistical models; the Holevo bound coincides with the SLD Cramér-Rao bound and it does with the RLD Cramér-Rao bound. One of the important results ofmore » this paper is that a general model other than these two special cases exhibits an unexpected property: the structure of the Holevo bound changes smoothly when the weight matrix varies. In particular, it always coincides with the RLD Cramér-Rao bound for a certain choice of the weight matrix. Several examples illustrate these findings.« less

Ideal regularization for learning kernels from labels.

PubMed

Pan, Binbin; Lai, Jianhuang; Shen, Lixin

2014-08-01

In this paper, we propose a new form of regularization that is able to utilize the label information of a data set for learning kernels. The proposed regularization, referred to as ideal regularization, is a linear function of the kernel matrix to be learned. The ideal regularization allows us to develop efficient algorithms to exploit labels. Three applications of the ideal regularization are considered. Firstly, we use the ideal regularization to incorporate the labels into a standard kernel, making the resulting kernel more appropriate for learning tasks. Next, we employ the ideal regularization to learn a data-dependent kernel matrix from an initial kernel matrix (which contains prior similarity information, geometric structures, and labels of the data). Finally, we incorporate the ideal regularization to some state-of-the-art kernel learning problems. With this regularization, these learning problems can be formulated as simpler ones which permit more efficient solvers. Empirical results show that the ideal regularization exploits the labels effectively and efficiently. Copyright © 2014 Elsevier Ltd. All rights reserved.

The influence of matrix microstructure and particle reinforcement on the creep behavior of 2219 aluminum

NASA Astrophysics Data System (ADS)

Krajewski, P. E.; Allison, J. E.; Jones, J. W.

1993-12-01

The influence of matrix microstructure and reinforcement with 15 vol pct of TiC particles on the creep behavior of 2219 aluminum has been examined in the temperature range of 150 ‡C to 250 ‡C. At 150 ‡C, reinforcement led to an improvement in creep resistance, while at 250 ‡C, both materials exhibited essentially identical creep behavior. Precipitate spacing in the matrix exerted the predominant influence on minimum creep rate in both the unreinforced and the reinforced materials over the temperature range studied. This behavior and the high-stress dependence of minimum creep rate are explained using existing constant structure models where, in the present study, precipitate spacing is identified as the pertinent substructure dimension. A modest microstructure-independent strengthening from particle reinforcement was observed at 150 ‡C and was accurately modeled by existing continuum mechanical models. The absence of reinforcement creep strengthening at 250 ‡C can be attributed to diffusional relaxation processes at the higher temperature.

Fracture Mechanisms For SiC Fibers And SiC/SiC Composites Under Stress-Rupture Conditions at High Temperatures

NASA Technical Reports Server (NTRS)

DiCarlo, James A.; Yun, Hee Mann; Hurst, Janet B.; Viterna, L. (Technical Monitor)

2002-01-01

The successful application of SiC/SiC ceramic matrix composites as high-temperature structural materials depends strongly on maximizing the fracture or rupture life of the load-bearing fiber and matrix constituents. Using high-temperature data measured under stress-rupture test conditions, this study examines in a mechanistic manner the effects of various intrinsic and extrinsic factors on the creep and fracture behavior of a variety of SiC fiber types. It is shown that although some fiber types fracture during a large primary creep stage, the fiber creep rate just prior to fracture plays a key role in determining fiber rupture time (Monkman-Grant theory). If it is assumed that SiC matrices rupture in a similar manner as fibers with the same microstructures, one can develop simple mechanistic models to analyze and optimize the stress-rupture behavior of SiC/SiC composites for applied stresses that are initially below matrix cracking.

Structural Studies of dielectric HDPE+ZrO2 polymer nanocomposites: filler concentration dependences

NASA Astrophysics Data System (ADS)

Nabiyev, A. A.; Islamov, A. Kh; Maharramov, A. M.; Nuriyev, M. A.; Ismayilova, R. S.; Doroshkevic, A. S.; Pawlukojc, A.; Turchenko, V. A.; Olejniczak, A.; Rulev, M. İ.; Almasan, V.; Kuklin, A. I.

2018-03-01

Structural properties of HDPE+ZrO2 polymer nanocomposites thin films of 80-100μm thicknesses were investigated using SANS, XRD, Laser Raman and FTIR spectroscopy. The mass fraction of the filler was 1, 3, 10, and 20%. Results of XRD analysis showed that ZrO2 powder was crystallized both in monoclinic and in cubic phase under normal conditions. The percentages of monoclinic and cubic phase were found to be 99.8% and 0.2%, respectively. It was found that ZrO2 nanoparticles did not affect the main crystal and chemical structure of HDPE, but the degree of crystallinity of the polymer decreases with increasing concentration of zirconium oxide. SANS experiments showed that at ambient conditions ZrO2 nanoparticles mainly distributed like mono-particles in the polymer matrix at all concentrations of filler.The structure of HDPE+ZrO2 does not changes up to 132°C at 1-3% of filler, excepting changing of the polymer structure at temperatures upper 82°C. At high concentrations of filler 10-20% the aggregation of ZrO2 nanoparticles occurs, forming domains of 2.5μm. The results of Raman and FTIR spectroscopy did not show additional specific chemical bonds between the filler and the polymer matrix. New peaks formation was not observed. These results suggest that core-shell structure does not exist in the polymer nanocomposite system.

Enhanced osteoprogenitor elongated collagen fiber matrix formation by bioactive glass ionic silicon dependent on Sp7 (osterix) transcription.

PubMed

Varanasi, Venu G; Odatsu, Tetsurou; Bishop, Timothy; Chang, Joyce; Owyoung, Jeremy; Loomer, Peter M

2016-10-01

Bioactive glasses release ions, those enhance osteoblast collagen matrix synthesis and osteogenic marker expression during bone healing. Collagen matrix density and osteogenic marker expression depend on osteogenic transcription factors, (e.g., Osterix (OSX)). We hypothesize that enhanced expression and formation of collagen by Si(4+) depends on enhanced expression of OSX transcription. Experimental bioactive glass (6P53-b) and commercial Bioglass(TM) (45S5) were dissolved in basal medium to make glass conditioned medium (GCM). ICP-MS analysis was used to measure bioactive glass ion release rates. MC3T3-E1 cells were cultured for 20 days, and gene expression and extracellular matrix collagen formation was analyzed. In a separate study, siRNA was used to determine the effect of OSX knockdown on impacting the effect of Si(4+) on osteogenic markers and matrix collagen formation. Each bioactive glass exhibited similar ion release rates for all ions, except Mg(2+) released by 6P53-b. Gene expression results showed that GCM markedly enhanced many osteogenic markers, and 45S5 GCM showed higher levels of expression and collagen matrix fiber bundle density than 6P53-b GCM. Upon knockdown of OSX transcription, collagen type 5, alkaline phosphatase, and matrix density were not enhanced as compared to wild type cells. This study illustrates that the enhancement of elongated collagen fiber matrix formation by Si(±) depends on OSX transcription. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 2604-2615, 2016. © 2016 Wiley Periodicals, Inc.

A model for the progressive failure of laminated composite structural components

NASA Technical Reports Server (NTRS)

Allen, D. H.; Lo, D. C.

1991-01-01

Laminated continuous fiber polymeric composites are capable of sustaining substantial load induced microstructural damage prior to component failure. Because this damage eventually leads to catastrophic failure, it is essential to capture the mechanics of progressive damage in any cogent life prediction model. For the past several years the authors have been developing one solution approach to this problem. In this approach the mechanics of matrix cracking and delamination are accounted for via locally averaged internal variables which account for the kinematics of microcracking. Damage progression is predicted by using phenomenologically based damage evolution laws which depend on the load history. The result is a nonlinear and path dependent constitutive model which has previously been implemented to a finite element computer code for analysis of structural components. Using an appropriate failure model, this algorithm can be used to predict component life. In this paper the model will be utilized to demonstrate the ability to predict the load path dependence of the damage and stresses in plates subjected to fatigue loading.

Pairing matrix elements and pairing gaps with bare, effective, and induced interactions

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

Barranco, F.; Bortignon, P.F.; Colo, G.

2005-11-01

The dependence on the single-particle states of the pairing matrix elements of the Gogny force and of the bare low-momentum nucleon-nucleon potential v{sub low-k}--designed so as to reproduce the low-energy observables avoiding the use of a repulsive core--is studied for a typical finite, superfluid nucleus ({sup 120}Sn). It is found that the matrix elements of v{sub low-k} follow closely those of v{sub Gogny} on a wide range of energy values around the Fermi energy e{sub F}, those associated with v{sub low-k} being less attractive. This result explains the fact that around e{sub F} the pairing gap {delta}{sub Gogny} associated withmore » the Gogny interaction (and with a density of single-particle levels corresponding to an effective k mass m{sub k}{approx_equal}0.7 m) is a factor of about 2 larger than {delta}{sub low-k}, being in agreement with {delta}{sub exp}=1.4 MeV. The exchange of low-lying collective surface vibrations among pairs of nucleons moving in time-reversal states gives rise to an induced pairing interaction v{sub ind} peaked at e{sub F}. The interaction (v{sub low-k}+v{sub ind}) Z{sub {omega}} arising from the renormalization of the bare nucleon-nucleon potential and of the single-particle motion ({omega}-mass and quasiparticle strength Z{sub {omega}}) associated with the particle-vibration coupling mechanism, leads to a value of the pairing gap at the Fermi energy {delta}{sub ren} that accounts for the experimental value. An important question that remains to be studied quantitatively is to what extent {delta}{sub Gogny}, which depends on average parameters, and {delta}{sub ren}, which explicitly depends on the parameters describing the (low-energy) nuclear structure, display or not a similar isotopic dependence and whether this dependence is borne out by the data.« less

How cells (might) sense microgravity

NASA Technical Reports Server (NTRS)

Ingber, D.

1999-01-01

This article is a summary of a lecture presented at an ESA/NASA Workshop on Cell and Molecular Biology Research in Space that convened in Leuven, Belgium, in June 1998. Recent studies are reviewed which suggest that cells may sense mechanical stresses, including those due to gravity, through changes in the balance of forces that are transmitted across transmembrane adhesion receptors that link the cytoskeleton to the extracellular matrix and to other cells (e.g., integrins, cadherins, selectins). The mechanism by which these mechanical signals are transduced and converted into a biochemical response appears to be based, in part, on the finding that living cells use a tension-dependent form of architecture, known as tensegrity, to organize and stabilize their cytoskeleton. Because of tensegrity, the cellular response to stress differs depending on the level of pre-stress (pre-existing tension) in the cytoskeleton and it involves all three cytoskeletal filament systems as well as nuclear scaffolds. Recent studies confirm that alterations in the cellular force balance can influence intracellular biochemistry within focal adhesion complexes that form at the site of integrin binding as well as gene expression in the nucleus. These results suggest that gravity sensation may not result from direct activation of any single gravioreceptor molecule. Instead, gravitational forces may be experienced by individual cells in the living organism as a result of stress-dependent changes in cell, tissue, or organ structure that, in turn, alter extracellular matrix mechanics, cell shape, cytoskeletal organization, or internal pre-stress in the cell-tissue matrix.--Ingber, D. How cells (might) sense microgravity.

Time dependent Schrödinger equation for black hole evaporation: No information loss

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

Corda, Christian, E-mail: cordac.galilei@gmail.com

2015-02-15

In 1976 S. Hawking claimed that “Because part of the information about the state of the system is lost down the hole, the final situation is represented by a density matrix rather than a pure quantum state”. This was the starting point of the popular “black hole (BH) information paradox”. In a series of papers, together with collaborators, we naturally interpreted BH quasi-normal modes (QNMs) in terms of quantum levels discussing a model of excited BH somewhat similar to the historical semi-classical Bohr model of the structure of a hydrogen atom. Here we explicitly write down, for the same model,more » a time dependent Schrödinger equation for the system composed by Hawking radiation and BH QNMs. The physical state and the correspondent wave function are written in terms of a unitary evolution matrix instead of a density matrix. Thus, the final state results to be a pure quantum state instead of a mixed one. Hence, Hawking’s claim is falsified because BHs result to be well defined quantum mechanical systems, having ordered, discrete quantum spectra, which respect ’t Hooft’s assumption that Schrödinger equations can be used universally for all dynamics in the universe. As a consequence, information comes out in BH evaporation in terms of pure states in a unitary time dependent evolution. In Section 4 of this paper we show that the present approach permits also to solve the entanglement problem connected with the information paradox.« less

Matrix Pseudospectral Method for (Visco)Elastic Tides Modeling of Planetary Bodies

NASA Astrophysics Data System (ADS)

Zabranova, Eliska; Hanyk, Ladidslav; Matyska, Ctirad

2010-05-01

We deal with the equations and boundary conditions describing deformation and gravitational potential of prestressed spherically symmetric elastic bodies by decomposing governing equations into a series of boundary value problems (BVP) for ordinary differential equations (ODE) of the second order. In contrast to traditional Runge-Kutta integration techniques, highly accurate pseudospectral schemes are employed to directly discretize the BVP on Chebyshev grids and a set of linear algebraic equations with an almost block diagonal matrix is derived. As a consequence of keeping the governing ODEs of the second order instead of the usual first-order equations, the resulting algebraic system is half-sized but derivatives of the model parameters are required. Moreover, they can be easily evaluated for models, where structural parametres are piecewise polynomially dependent. Both accuracy and efficiency of the method are tested by evaluating the tidal Love numbers for the Earth's model PREM. Finally, we also derive complex Love numbers for models with the Maxwell viscoelastic rheology, where viscosity is a depth-dependent function. The method is applied to evaluation of the tidal Love numbers for models of Mars and Venus. The Love numbers of the two Martian models - the former optimized to cosmochemical data and the latter to the moment of inertia (Sohl and Spohn, 1997) - are h2=0.172 (0.212) and k2=0.093 (0.113). For Venus, the value of k2=0.295 (Konopliv and Yoder, 1996), obtained from the gravity-field analysis, is consistent with the results for our model with the liquid-core radius of 3110 km (Zábranová et al., 2009). Together with rapid evaluation of free oscillation periods by an analogous method, this combined matrix approach could by employed as an efficient numerical tool in structural studies of planetary bodies. REFERENCES Konopliv, A. S. and Yoder, C. F., 1996. Venusian k2 tidal Love number from Magellan and PVO tracking data, Geophys. Res. Lett., 23, 1857-1860. Sohl, F., and Spohn, T., 1997. The interior structure of Mars: Implications from SNC meteorites, J. Geophys. Res., 102, 1613-1635. Zabranova, E., Hanyk L. and Matyska, C.: Matrix Pseudospectral Method for Elastic Tides Modeling. In: Holota P. (Ed.): Mission and Passion: Science. A volume dedicated to Milan Bursa on the occasion of his 80th birthday. Published by the Czech National Committee of Geodesy and Geophysics. Prague, 2009, pp. 243-260.

Exploration of polyamide structure-property relationships by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Barrère, Caroline; Rejaibi, Majed; Curat, Aurélien; Hubert-Roux, Marie; Lavanant, Hélène; Afonso, Carlos; Kebir, Nasreddine; Desilles, Nicolas; Lecamp, Laurence; Burel, Fabrice; Loutelier-Bourhis, Corinne

2014-08-15

Polyamides (PA) are among the most used classes of polymers because of their attractive properties. Depending on the nature and proportion of the co-monomers used for their synthesis, they can exhibit a very large range of melting temperatures (Tm ). This study aims at the correlation of data from mass spectrometry (MS) with differential scanning calorimetry (DSC) and X-ray diffraction analyses to relate molecular structure to physical properties such as melting temperature, enthalpy change and crystallinity rate. Six different PA copolymers with molecular weights around 3500 g mol(-1) were synthesized with varying proportions of different co-monomers (amino-acid AB/di-amine AA/di-acid BB). Their melting temperature, enthalpy change and crystallinity rate were measured by DSC and X-ray diffraction. Their structural characterization was carried out by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Because of the poor solubility of PA, a solvent-free sample preparation strategy was used with 2,5-dihydroxybenzoic acid (2,5-DHB) as the matrix and sodium iodide as the cationizing agent. The different proportions of the repeating unit types led to the formation of PA with melting temperatures ranging from 115°C to 185°C. The structural characterization of these samples by MALDI-TOF-MS revealed a collection of different ion distributions with different sequences of repeating units (AA, BB; AB/AA, BB and AB) in different proportions according to the mixture of monomers used in the synthesis. The relative intensities of these ion distributions were related to sample complexity and structure. They were correlated to DSC and X-ray results, to explain the observed physical properties. The structural information obtained by MALDI-TOF-MS provided a better understanding of the variation of the PA melting temperature and established a structure-properties relationship. This work will allow future PA designs to be monitored. Copyright © 2014 John Wiley & Sons, Ltd.

Mueller matrix imaging study to detect the dental demineralization

NASA Astrophysics Data System (ADS)

Chen, Qingguang; Shen, Huanbo; Wang, Binqiang

2018-01-01

Mueller matrix is an optical parameter invasively to reveal the structure information of anisotropic material. Dental tissue has the ordered structure including dental enamel prism and dentinal tubule. The ordered structure of teeth surface will be destroyed by demineralization. The structure information has the possibility to reflect the dental demineralization. In the paper, the experiment setup was built to obtain the Mueller matrix images based on the dual- wave plate rotation method. Two linear polarizer and two quarter-wave plate were rotated by electric control revolving stage respectively to capture 16 images at different group of polarization states. Therefore, Mueller matrix image can be calculated from the 16 images. On this basis, depolarization index, the diattenuation index and retardance index of the Mueller matrix were analyzed by Lu-Chipman polarization decomposition method. Mueller matrix images of artificial demineralized enamels at different stages were analyzed and the results show the possibility to detect the dental demineralization using Mueller matrix imaging method.

Advances in biomimetic regeneration of elastic matrix structures

PubMed Central

Sivaraman, Balakrishnan; Bashur, Chris A.

2012-01-01

Elastin is a vital component of the extracellular matrix, providing soft connective tissues with the property of elastic recoil following deformation and regulating the cellular response via biomechanical transduction to maintain tissue homeostasis. The limited ability of most adult cells to synthesize elastin precursors and assemble them into mature crosslinked structures has hindered the development of functional tissue-engineered constructs that exhibit the structure and biomechanics of normal native elastic tissues in the body. In diseased tissues, the chronic overexpression of proteolytic enzymes can cause significant matrix degradation, to further limit the accumulation and quality (e.g., fiber formation) of newly deposited elastic matrix. This review provides an overview of the role and importance of elastin and elastic matrix in soft tissues, the challenges to elastic matrix generation in vitro and to regenerative elastic matrix repair in vivo, current biomolecular strategies to enhance elastin deposition and matrix assembly, and the need to concurrently inhibit proteolytic matrix disruption for improving the quantity and quality of elastogenesis. The review further presents biomaterial-based options using scaffolds and nanocarriers for spatio-temporal control over the presentation and release of these biomolecules, to enable biomimetic assembly of clinically relevant native elastic matrix-like superstructures. Finally, this review provides an overview of recent advances and prospects for the application of these strategies to regenerating tissue-type specific elastic matrix structures and superstructures. PMID:23355960

Macro- to microscale strain transfer in fibrous tissues is heterogeneous and tissue-specific.

PubMed

Han, Woojin M; Heo, Su-Jin; Driscoll, Tristan P; Smith, Lachlan J; Mauck, Robert L; Elliott, Dawn M

2013-08-06

Mechanical deformation applied at the joint or tissue level is transmitted through the macroscale extracellular matrix to the microscale local matrix, where it is transduced to cells within these tissues and modulates tissue growth, maintenance, and repair. The objective of this study was to investigate how applied tissue strain is transferred through the local matrix to the cell and nucleus in meniscus, tendon, and the annulus fibrosus, as well as in stem cell-seeded scaffolds engineered to reproduce the organized microstructure of these native tissues. To carry out this study, we developed a custom confocal microscope-mounted tensile testing device and simultaneously monitored strain across multiple length scales. Results showed that mean strain was heterogeneous and significantly attenuated, but coordinated, at the local matrix level in native tissues (35-70% strain attenuation). Conversely, freshly seeded scaffolds exhibited very direct and uniform strain transfer from the tissue to the local matrix level (15-25% strain attenuation). In addition, strain transfer from local matrix to cells and nuclei was dependent on fiber orientation and tissue type. Histological analysis suggested that different domains exist within these fibrous tissues, with most of the tissue being fibrous, characterized by an aligned collagen structure and elongated cells, and other regions being proteoglycan (PG)-rich, characterized by a dense accumulation of PGs and rounder cells. In meniscus, the observed heterogeneity in strain transfer correlated strongly with cellular morphology, where rounder cells located in PG-rich microdomains were shielded from deformation, while elongated cells in fibrous microdomains deformed readily. Collectively, these findings suggest that different tissues utilize distinct strain-attenuating mechanisms according to their unique structure and cellular phenotype, and these differences likely alter the local biologic response of such tissues and constructs in response to mechanical perturbation. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A Rhizobium leguminosarum CHDL- (Cadherin-Like-) Lectin Participates in Assembly and Remodeling of the Biofilm Matrix

PubMed Central

Vozza, Nicolás F.; Abdian, Patricia L.; Russo, Daniela M.; Mongiardini, Elías J.; Lodeiro, Aníbal R.; Molin, Søren; Zorreguieta, Angeles

2016-01-01

In natural environments most bacteria live in multicellular structures called biofilms. These cell aggregates are enclosed in a self-produced polymeric extracellular matrix, which protects the cells, provides mechanical stability and mediates cellular cohesion and adhesion to surfaces. Although important advances were made in the identification of the genetic and extracellular factors required for biofilm formation, the mechanisms leading to biofilm matrix assembly, and the roles of extracellular proteins in these processes are still poorly understood. The symbiont Rhizobium leguminosarum requires the synthesis of the acidic exopolysaccharide and the PrsDE secretion system to develop a mature biofilm. PrsDE is responsible for the secretion of the Rap family of proteins that share one or two Ra/CHDL (cadherin-like-) domains. RapA2 is a calcium-dependent lectin with a cadherin-like β sheet structure that specifically recognizes the exopolysaccharide, either as a capsular polysaccharide (CPS) or in its released form [extracellular polysaccharide (EPS)]. In this study, using gain and loss of function approaches combined with phenotypic and microscopic studies we demonstrated that RapA lectins are involved in biofilm matrix development and cellular cohesion. While the absence of any RapA protein increased the compactness of bacterial aggregates, high levels of RapA1 expanded distances between cells and favored the production of a dense matrix network. Whereas endogenous RapA(s) are predominantly located at one bacterial pole, we found that under overproduction conditions, RapA1 surrounded the cell in a way that was reminiscent of the capsule. Accordingly, polysaccharide analyses showed that the RapA lectins promote CPS formation at the expense of lower EPS production. Besides, polysaccharide analysis suggests that RapA modulates the EPS size profile. Collectively, these results show that the interaction of RapA lectins with the polysaccharide is involved in rhizobial biofilm matrix assembly and remodeling. PMID:27790205

Decellularized Matrix from Tumorigenic Human Mesenchymal Stem Cells Promotes Neovascularization with Galectin-1 Dependent Endothelial Interaction

PubMed Central

Burns, Jorge S.; Kristiansen, Malthe; Kristensen, Lars P.; Larsen, Kenneth H.; Nielsen, Maria O.; Christiansen, Helle; Nehlin, Jan; Andersen, Jens S.; Kassem, Moustapha

2011-01-01

Background Acquisition of a blood supply is fundamental for extensive tumor growth. We recently described vascular heterogeneity in tumours derived from cell clones of a human mesenchymal stem cell (hMSC) strain (hMSC-TERT20) immortalized by retroviral vector mediated human telomerase (hTERT) gene expression. Histological analysis showed that cells of the most vascularized tumorigenic clone, -BD11 had a pericyte-like alpha smooth muscle actin (ASMA+) and CD146+ positive phenotype. Upon serum withdrawal in culture, -BD11 cells formed cord-like structures mimicking capillary morphogenesis. In contrast, cells of the poorly tumorigenic clone, -BC8 did not stain for ASMA, tumours were less vascularized and serum withdrawal in culture led to cell death. By exploring the heterogeneity in hMSC-TERT20 clones we aimed to understand molecular mechanisms by which mesenchymal stem cells may promote neovascularization. Methodology/Principal Findings Quantitative qRT-PCR analysis revealed similar mRNA levels for genes encoding the angiogenic cytokines VEGF and Angiopoietin-1 in both clones. However, clone-BD11 produced a denser extracellular matrix that supported stable ex vivo capillary morphogenesis of human endothelial cells and promoted in vivo neovascularization. Proteomic characterization of the -BD11 decellularized matrix identified 50 extracellular angiogenic proteins, including galectin-1. siRNA knock down of galectin-1 expression abrogated the ex vivo interaction between decellularized -BD11 matrix and endothelial cells. More stable shRNA knock down of galectin-1 expression did not prevent -BD11 tumorigenesis, but greatly reduced endothelial migration into -BD11 cell xenografts. Conclusions Decellularized hMSC matrix had significant angiogenic potential with at least 50 angiogenic cell surface and extracellular proteins, implicated in attracting endothelial cells, their adhesion and activation to form tubular structures. hMSC -BD11 surface galectin-1 expression was required to bring about matrix-endothelial interactions and for xenografted hMSC -BD11 cells to optimally recruit host vasculature. PMID:21779348

Micromechanical analysis on anisotropy of structured magneto-rheological elastomer

NASA Astrophysics Data System (ADS)

Li, R.; Zhang, Z.; Chen, S. W.; Wang, X. J.

2015-07-01

This paper investigates the equivalent elastic modulus of structured magneto-rheological elastomer (MRE) in the absence of magnetic field. We assume that both matrix and ferromagnetic particles are linear elastic materials, and ferromagnetic particles are embedded in matrix with layer-like structure. The structured composite could be divided into matrix layer and reinforced layer, in which the reinforced layer is composed of matrix and the homogenously distributed ferromagnetic particles in matrix. The equivalent elastic modulus of reinforced layer is analysed by the Mori-Tanaka method. Finite Element Method (FEM) is also carried out to illustrate the relationship between the elastic modulus and the volume fraction of ferromagnetic particles. The results show that the anisotropy of elastic modulus becomes noticeable, as the volume fraction of particles increases.

Discretized torsional dynamics and the folding of an RNA chain.

PubMed

Fernández, A; Salthú, R; Cendra, H

1999-08-01

The aim of this work is to implement a discrete coarse codification of local torsional states of the RNA chain backbone in order to explore the long-time limit dynamics and ultimately obtain a coarse solution to the RNA folding problem. A discrete representation of the soft-mode dynamics is turned into an algorithm for a rough structure prediction. The algorithm itself is inherently parallel, as it evaluates concurrent folding possibilities by pattern recognition, but it may be implemented in a personal computer as a chain of perturbation-translation-renormalization cycles performed on a binary matrix of local topological constraints. This requires suitable representational tools and a periodic quenching of the dynamics for system renormalization. A binary coding of local topological constraints associated with each structural motif is introduced, with each local topological constraint corresponding to a local torsional state. This treatment enables us to adopt a computation time step far larger than hydrodynamic drag time scales. Accordingly, the solvent is no longer treated as a hydrodynamic drag medium. Instead we incorporate its capacity for forming local conformation-dependent dielectric domains. Each translation of the matrix of local topological constraints (LTM's) depends on the conformation-dependent local dielectric created by a confined solvent. Folding pathways are resolved as transitions between patterns of locally encoded structural signals which change within the 1 ns-100 ms time scale range. These coarse folding pathways are generated by a search at regular intervals for structural patterns in the LTM. Each pattern is recorded as a base-pairing pattern (BPP) matrix, a consensus-evaluation operation subject to a renormalization feedback loop. Since several mutually conflicting consensus evaluations might occur at a given time, the need arises for a probabilistic approach appropriate for an ensemble of RNA molecules. Thus, a statistical dynamics of consensus formation is determined by the time evolution of the base pairing probability matrix. These dynamics are generated for a functional RNA molecule, a representative of the so-called group I ribozymes, in order to test the model. The resulting ensemble of conformations is sharply peaked and the most probable structure features the predominance of all phylogenetically conserved intrachain helices tantamount to ribozyme function. Furthermore, the magnesium-aided cooperativity that leads to the shaping of the catalytic core is elucidated. Once the predictive folding algorithm has been implemented, the validity of the so-called "adiabatic approximation" is tested. This approximation requires that conformational microstates be lumped up into BPP's which are treated as quasiequilibrium states, while folding pathways are coarsely represented as sequences of BPP transitions. To test the validity of this adiabatic ansatz, a computation of the coarse Shannon information entropy sigma associated to the specific partition of conformation space into BPP's is performed taking into account the LTM evolution and contrasted with the adiabatic computation. The results reveal a subordination of torsional microstate dynamics to BPP transitions within time scales relevant to folding. This adiabatic entrainment in the long-time limit is thus identified as responsible for the expediency of the folding process.

Process and Microstructure to Achieve Ultra-high Dielectric Constant in Ceramic-Polymer Composites.

PubMed

Zhang, Lin; Shan, Xiaobing; Bass, Patrick; Tong, Yang; Rolin, Terry D; Hill, Curtis W; Brewer, Jeffrey C; Tucker, Dennis S; Cheng, Z-Y

2016-10-21

Influences of process conditions on microstructure and dielectric properties of ceramic-polymer composites are systematically studied using CaCu 3 Ti 4 O 12 (CCTO) as filler and P(VDF-TrFE) 55/45 mol.% copolymer as the matrix by combining solution-cast and hot-pressing processes. It is found that the dielectric constant of the composites can be significantly enhanced-up to about 10 times - by using proper processing conditions. The dielectric constant of the composites can reach more than 1,000 over a wide temperature range with a low loss (tan δ ~ 10 -1 ). It is concluded that besides the dense structure of composites, the uniform distribution of the CCTO particles in the matrix plays a key role on the dielectric enhancement. Due to the influence of the CCTO on the microstructure of the polymer matrix, the composites exhibit a weaker temperature dependence of the dielectric constant than the polymer matrix. Based on the results, it is also found that the loss of the composites at low temperatures, including room temperature, is determined by the real dielectric relaxation processes including the relaxation process induced by the mixing.

Process and Microstructure to Achieve Ultra-high Dielectric Constant in Ceramic-Polymer Composites

NASA Astrophysics Data System (ADS)

Zhang, Lin; Shan, Xiaobing; Bass, Patrick; Tong, Yang; Rolin, Terry D.; Hill, Curtis W.; Brewer, Jeffrey C.; Tucker, Dennis S.; Cheng, Z.-Y.

2016-10-01

Influences of process conditions on microstructure and dielectric properties of ceramic-polymer composites are systematically studied using CaCu3Ti4O12 (CCTO) as filler and P(VDF-TrFE) 55/45 mol.% copolymer as the matrix by combining solution-cast and hot-pressing processes. It is found that the dielectric constant of the composites can be significantly enhanced-up to about 10 times - by using proper processing conditions. The dielectric constant of the composites can reach more than 1,000 over a wide temperature range with a low loss (tan δ ~ 10-1). It is concluded that besides the dense structure of composites, the uniform distribution of the CCTO particles in the matrix plays a key role on the dielectric enhancement. Due to the influence of the CCTO on the microstructure of the polymer matrix, the composites exhibit a weaker temperature dependence of the dielectric constant than the polymer matrix. Based on the results, it is also found that the loss of the composites at low temperatures, including room temperature, is determined by the real dielectric relaxation processes including the relaxation process induced by the mixing.

Properties of five toughened matrix composite materials

NASA Technical Reports Server (NTRS)

Cano, Roberto J.; Dow, Marvin B.

1992-01-01

The use of toughened matrix composite materials offers an attractive solution to the problem of poor damage tolerance associated with advanced composite materials. In this study, the unidirectional laminate strengths and moduli, notched (open-hole) and unnotched tension and compression properties of quasi-isotropic laminates, and compression-after-impact strengths of five carbon fiber/toughened matrix composites, IM7/E7T1-2, IM7/X1845, G40-800X/5255-3, IM7/5255-3, and IM7/5260 have been evaluated. The compression-after-impact (CAI) strengths were determined primarily by impacting quasi-isotropic laminates with the NASA Langley air gun. A few CAI tests were also made with a drop-weight impactor. For a given impact energy, compression after impact strengths were determined to be dependent on impactor velocity. Properties and strengths for the five materials tested are compared with NASA data on other toughened matrix materials (IM7/8551-7, IM6/1808I, IM7/F655, and T800/F3900). This investigation found that all five materials were stronger and more impact damage tolerant than more brittle carbon/epoxy composite materials currently used in aircraft structures.

A hybrid mathematical model of solid tumour invasion: the importance of cell adhesion.

PubMed

Anderson, Alexander R A

2005-06-01

In this paper we present a hybrid mathematical model of the invasion of healthy tissue by a solid tumour. In particular we consider early vascular growth, just after angiogenesis has occurred. We examine how the geometry of the growing tumour is affected by tumour cell heterogeneity caused by genetic mutations. As the tumour grows, mutations occur leading to a heterogeneous tumour cell population with some cells having a greater ability to migrate, proliferate or degrade the surrounding tissue. All of these cell properties are closely controlled by cell-cell and cell-matrix interactions and as such the physical geometry of the whole tumour will be dependent on these individual cell interactions. The hybrid model we develop focuses on four key variables implicated in the invasion process: tumour cells, host tissue (extracellular matrix), matrix-degradative enzymes and oxygen. The model is considered to be hybrid since the latter three variables are continuous (i.e. concentrations) and the tumour cells are discrete (i.e. individuals). With this hybrid model we examine how individual-based cell interactions (with one another and the matrix) can affect the tumour shape and discuss which of these interactions is perhaps most crucial in influencing the tumour's final structure.

Process and Microstructure to Achieve Ultra-high Dielectric Constant in Ceramic-Polymer Composites

PubMed Central

Zhang, Lin; Shan, Xiaobing; Bass, Patrick; Tong, Yang; Rolin, Terry D.; Hill, Curtis W.; Brewer, Jeffrey C.; Tucker, Dennis S.; Cheng, Z.-Y.

2016-01-01

Influences of process conditions on microstructure and dielectric properties of ceramic-polymer composites are systematically studied using CaCu3Ti4O12 (CCTO) as filler and P(VDF-TrFE) 55/45 mol.% copolymer as the matrix by combining solution-cast and hot-pressing processes. It is found that the dielectric constant of the composites can be significantly enhanced–up to about 10 times – by using proper processing conditions. The dielectric constant of the composites can reach more than 1,000 over a wide temperature range with a low loss (tan δ ~ 10−1). It is concluded that besides the dense structure of composites, the uniform distribution of the CCTO particles in the matrix plays a key role on the dielectric enhancement. Due to the influence of the CCTO on the microstructure of the polymer matrix, the composites exhibit a weaker temperature dependence of the dielectric constant than the polymer matrix. Based on the results, it is also found that the loss of the composites at low temperatures, including room temperature, is determined by the real dielectric relaxation processes including the relaxation process induced by the mixing. PMID:27767184

Infrared spectroscopy of water clusters isolated in methane matrices: Effects of isotope substitution and annealing

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

Yamakawa, Koichiro, E-mail: koichiro.yamakawa@gakushuin.ac.jp; Ehara, Namika; Ozawa, Nozomi

2016-07-15

Using infrared-active solvents of CH{sub 4} and CD{sub 4} for matrix isolation, we measured infrared spectra of H{sub 2}O and D{sub 2}O clusters at 7 K. The solute-concentration dependence of the spectrum of H{sub 2}O clusters in a CH{sub 4} matrix was investigated and was used for the peak assignment. Annealing procedures were found to promote the size growth of water clusters in methane matrices for all the combinations of (H{sub 2}O, CH{sub 4}), (H{sub 2}O, CD{sub 4}), (D{sub 2}O, CH{sub 4}), and (D{sub 2}O, CD{sub 4}). We also monitored the ν{sub 3} absorption due to methane to find themore » annealing-induced structural change only of solid CH{sub 4}. The matrix effects on the vibrations of the clusters are discussed on the basis of “T{sub c} plots”, where their frequencies are plotted as a function of the square root of the matrix critical temperature, T{sub c}. The obtained plots assure the validity of the assignment of the cluster peaks.« less

Clustering Tree-structured Data on Manifold

PubMed Central

Lu, Na; Miao, Hongyu

2016-01-01

Tree-structured data usually contain both topological and geometrical information, and are necessarily considered on manifold instead of Euclidean space for appropriate data parameterization and analysis. In this study, we propose a novel tree-structured data parameterization, called Topology-Attribute matrix (T-A matrix), so the data clustering task can be conducted on matrix manifold. We incorporate the structure constraints embedded in data into the non-negative matrix factorization method to determine meta-trees from the T-A matrix, and the signature vector of each single tree can then be extracted by meta-tree decomposition. The meta-tree space turns out to be a cone space, in which we explore the distance metric and implement the clustering algorithm based on the concepts like Fréchet mean. Finally, the T-A matrix based clustering (TAMBAC) framework is evaluated and compared using both simulated data and real retinal images to illus trate its efficiency and accuracy. PMID:26660696

Process depending morphology and resulting physical properties of TPU

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

Frick, Achim, E-mail: achim.frick@hs-aalen.de; Spadaro, Marcel, E-mail: marcel.spadaro@hs-aalen.de

2015-12-17

Thermoplastic polyurethane (TPU) is a rubber like material with outstanding properties, e.g. for seal applications. TPU basically provides high strength, low frictional behavior and excellent wear resistance. Though, due to segmented structure of TPU, which is composed of hard segments (HSs) and soft segments (SSs), physical properties depend strongly on the morphological arrangement of the phase separated HSs at a certain ratio of HSs to SSs. It is obvious that the TPU deforms differently depending on its bulk morphology. Basically, the morphology can either consist of HSs segregated into small domains, which are well dispersed in the SS matrix ormore » of few strongly phase separated large size HS domains embedded in the SS matrix. The morphology development is hardly ruled by the melt processing conditions of the TPU. Depending on the morphology, TPU provides quite different physical properties with respect to strength, deformation behavior, thermal stability, creep resistance and tribological performance. The paper deals with the influence of important melt processing parameters, such as temperature, pressure and shear conditions, on the resulting physical properties tested by tensile and relaxation experiments. Furthermore the morphology is studied employing differential scanning calorimeter (DSC), transmission light microscopy (TLM), scanning electron beam microscopy (SEM) and transmission electron beam microscopy (TEM) investigations. Correlations between processing conditions and resulting TPU material properties are elaborated. Flow and shear simulations contribute to the understanding of thermal and flow induced morphology development.« less

Molecular weight dependence of carrier mobility and recombination rate in neat P3HT films

DOE PAGES

Dixon, Alex G.; Visvanathan, Rayshan; Clark, Noel A.; ...

2017-11-02

The microstructure dependence of carrier mobility and recombination rates of neat films of poly 3-hexylthyophene (P3HT) were determined for a range of materials of weight-average molecular weights, Mw, ranging from 14 to 331 kDa. This variation has previously been shown to modify the polymer microstructure, with low molecular weights forming a one-phase, paraffinic-like structure comprised of chain-extended crystallites, and higher molecular weights forming a semicrystalline structure with crystalline domains being embedded in an amorphous matrix. Using Charge Extraction by Linearly Increasing Voltage (CELIV), we show here that the carrier mobility in P3HT devices peaks for materials of Mw = 48more » kDa, and that the recombination rate decreases monotonically with increasing molecular weight. This trend is likely due to the development of a semicrystalline, two-phase structure with increasing Mw, which allows for the spatial separation of holes and electrons into the amorphous and crystalline regions, respectively. This separation leads to decreased recombination.« less

Molecular weight dependence of carrier mobility and recombination rate in neat P3HT films

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

Dixon, Alex G.; Visvanathan, Rayshan; Clark, Noel A.

The microstructure dependence of carrier mobility and recombination rates of neat films of poly 3-hexylthyophene (P3HT) were determined for a range of materials of weight-average molecular weights, Mw, ranging from 14 to 331 kDa. This variation has previously been shown to modify the polymer microstructure, with low molecular weights forming a one-phase, paraffinic-like structure comprised of chain-extended crystallites, and higher molecular weights forming a semicrystalline structure with crystalline domains being embedded in an amorphous matrix. Using Charge Extraction by Linearly Increasing Voltage (CELIV), we show here that the carrier mobility in P3HT devices peaks for materials of Mw = 48more » kDa, and that the recombination rate decreases monotonically with increasing molecular weight. This trend is likely due to the development of a semicrystalline, two-phase structure with increasing Mw, which allows for the spatial separation of holes and electrons into the amorphous and crystalline regions, respectively. This separation leads to decreased recombination.« less

Spectral statistics of random geometric graphs

NASA Astrophysics Data System (ADS)

Dettmann, C. P.; Georgiou, O.; Knight, G.

2017-04-01

We use random matrix theory to study the spectrum of random geometric graphs, a fundamental model of spatial networks. Considering ensembles of random geometric graphs we look at short-range correlations in the level spacings of the spectrum via the nearest-neighbour and next-nearest-neighbour spacing distribution and long-range correlations via the spectral rigidity Δ3 statistic. These correlations in the level spacings give information about localisation of eigenvectors, level of community structure and the level of randomness within the networks. We find a parameter-dependent transition between Poisson and Gaussian orthogonal ensemble statistics. That is the spectral statistics of spatial random geometric graphs fits the universality of random matrix theory found in other models such as Erdős-Rényi, Barabási-Albert and Watts-Strogatz random graphs.

Fractal Model of Fission Product Release in Nuclear Fuel

NASA Astrophysics Data System (ADS)

Stankunas, Gediminas

2012-09-01

A model of fission gas migration in nuclear fuel pellet is proposed. Diffusion process of fission gas in granular structure of nuclear fuel with presence of inter-granular bubbles in the fuel matrix is simulated by fractional diffusion model. The Grunwald-Letnikov derivative parameter characterizes the influence of porous fuel matrix on the diffusion process of fission gas. A finite-difference method for solving fractional diffusion equations is considered. Numerical solution of diffusion equation shows correlation of fission gas release and Grunwald-Letnikov derivative parameter. Calculated profile of fission gas concentration distribution is similar to that obtained in the experimental studies. Diffusion of fission gas is modeled for real RBMK-1500 fuel operation conditions. A functional dependence of Grunwald-Letnikov derivative parameter with fuel burn-up is established.

Quantum correlation properties in Matrix Product States of finite-number spin rings

NASA Astrophysics Data System (ADS)

Zhu, Jing-Min; He, Qi-Kai

2018-02-01

The organization and structure of quantum correlation (QC) of quantum spin-chains are very rich and complex. Hence the depiction and measures about the QC of finite-number spin rings deserved to be investigated intensively by using Matrix Product States(MPSs) in addition to the case with infinite-number. Here the dependencies of the geometric quantum discord(GQD) of two spin blocks on the total spin number, the spacing spin number and the environment parameter are presented in detail. We also compare the GQD with the total correlation(TC) and the classical correlation(CC) and illustrate its characteristics. Predictably, our findings may provide the potential of designing the optimal QC experimental detection proposals and pave the way for the designation of optimal quantum information processing schemes.

Ultrafine Ceramic Grains Embedded in Metallic Glass Matrix: Achieving Superior Wear Resistance via Increase in Both Hardness and Toughness.

PubMed

Yang, Lina; Wen, Mao; Dai, Xuan; Cheng, Gang; Zhang, Kan

2018-05-09

As structural materials, crystalline or metallic glass materials have attracted scientific and practical interests. However, some mechanisms involving critical size and shear bands have adverse effects on their mechanical properties. Here, we counter these two effects by introducing a special structure with ultrafine ceramic grains (with a diameter of ∼2.0 nm) embedded into a metallic glass matrix, wherein the grains are mainly composed of a Ta-W-N solid solution structure in nature, surrounded by a W-based amorphous matrix that contains Ta and N atoms. Such a structure is in situ formed during preparation, which combines the merits of both phases to achieve simultaneous increase in hardness and toughness relative to references (pure TaN and W) and thus superior wear resistance. Even more remarkable, a favorable variation of increased hardness but reduced elasticity modulus can be induced by this structure. Intrinsically, ultrafine ceramic grains (free of dislocations), embedded in the metallic glass matrix, could prevent shear band propagation within the glass matrix and further improve the hardness of the matrix material. In return, such glass matrix allows for stiffness neutralization and structural relaxation to reduce the elasticity modulus of ceramic grains. This study will offer a new guidance to fabricate ultrahigh-performance metal-based composites.

Computationally efficient modeling and simulation of large scale systems

NASA Technical Reports Server (NTRS)

Jain, Jitesh (Inventor); Cauley, Stephen F. (Inventor); Li, Hong (Inventor); Koh, Cheng-Kok (Inventor); Balakrishnan, Venkataramanan (Inventor)

2010-01-01

A method of simulating operation of a VLSI interconnect structure having capacitive and inductive coupling between nodes thereof. A matrix X and a matrix Y containing different combinations of passive circuit element values for the interconnect structure are obtained where the element values for each matrix include inductance L and inverse capacitance P. An adjacency matrix A associated with the interconnect structure is obtained. Numerical integration is used to solve first and second equations, each including as a factor the product of the inverse matrix X.sup.1 and at least one other matrix, with first equation including X.sup.1Y, X.sup.1A, and X.sup.1P, and the second equation including X.sup.1A and X.sup.1P.

Crystal Structure and Theoretical Analysis of Green Gold Au 30 (S- t Bu) 18 Nanomolecules and Their Relation to Au 30 S(S- t Bu) 18

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

Dass, Amala; Jones, Tanya; Rambukwella, Milan

We report the complete X-ray crystallographic structure as determined through single crystal X-ray diffraction and a thorough theoretical analysis of the green gold Au30(S-tBu)18. While the structure of Au30S(S-tBu)18 with 19 sulfur atoms has been reported, the crystal structure of Au30(S-tBu)18 without the μ3-sulfur has remained elusive until now, though matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) and electrospray ionization mass spectrometry (ESI-MS) data unequivocally shows its presence in abundance. The Au30(S-tBu)18 nanomolecule is not only distinct in its crystal structure but has unique temperature dependent optical properties. Structure determination allows a rigorous comparison and an excellent agreement with theoreticalmore » predictions of structure, stability, and optical response.« less

A chimeric protein composed of NuMA fused to the DNA binding domain of LANA is sufficient for the ori-P-dependent DNA replication

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

Ohsaki, Eriko; Ueda, Keiji, E-mail: kueda@virus.me

The Kaposi's sarcoma-associated herpesvirus (KSHV) genome is stably maintained in KSHV-infected PEL cell lines during cell division. We previously showed that accumulation of LANA in the nuclear matrix fraction could be important for the latent DNA replication, and that the functional significance of LANA should be its recruitment of ori-P to the nuclear matrix. Here, we investigated whether the forced localization of the LANA-DNA binding domain (DBD) to the nuclear matrix facilitated ori-P-containing plasmid replication. We demonstrated that chimeric proteins constructed by fusion of LANA DBD with the nuclear mitotic apparatus protein (NuMA), which is one of the components ofmore » the nuclear matrix, could bind with ori-P and enhance replication of an ori-P-containing plasmid, compared with that in the presence of DBD alone. These results further suggested that the ori-P recruitment to the nuclear matrix through the binding with DBD is important for latent viral DNA replication. - Highlights: •KSHV replication in latency depends on LANA localization to the nuclear matrix. •LANA DBD was fused with NuMA, a nuclear matrix protein, at the N- and C-terminus. •NuMA-DBD was in the nuclear matrix and supported the ori-P dependent replication. •LANA in the nuclear matrix should be important for the KSHV replication in latency.« less

An overview of cartilage tissue engineering.

PubMed

Kim, H W; Han, C D

2000-12-01

Articular cartilage regeneration refers to the formation of new tissue that is indistinguishable from the native articular cartilage with respect to zonal organization, biochemical composition, and mechanical properties. Due to a limited capacity to repair cartilage, scar tissue frequently has a poorly organized structure and lacks the functional characteristics of normal cartilage. The degree of success to date achieved using a purely cell- or biological-based approach has been modest. Potentially the development of a hybrid strategy, whereby, chondrocytes or chondrogenic stem cells are combined with a matrix, making cartilage in vitro, which is then subsequently transplanted, offers a route towards a new successful treatment modality. The success of this approach depends upon the material being biocompatible, processable into a suitable three-dimensional structure and eventually biodegradable without harmful effects. In addition, the material should have a sufficient porosity to facilitate high cell loading and tissue ingrowth, and it should be able to support cell proliferation, differentiation, and function. The cell-polymer-bioreactor system provides a basis for studying the structural and functional properties of the cartilaginous matrix during its development, because tissue concentrations of glycosaminoglycan and collagen can be modulated by altering the conditions of tissue cultivation.

Near-Edge X-ray Absorption Fine Structure Studies of Electrospun Poly(dimethylsiloxane)/Poly (methyl methacrylate)/Multiwall Carbon Nanotube Composites

PubMed Central

Winter, A. Douglas; Larios, Eduardo; Alamgir, Faisal M.; Jaye, Cherno; Fischer, Daniel; Campo, Eva M.

2014-01-01

This work describes the near conduction band edge structure of electrospun mats of MWCNT-PDMS-PMMA by near edge X-Ray absorption fine structure (NEXAFS) spectroscopy. Effects of adding nanofillers of different sizes were addressed. Despite observed morphological variations and inhomogeneous carbon nanotube distribution, spun mats appeared homogeneous under NEXAFS analysis. Spectra revealed differences in emissions from glancing and normal spectra; which may evidence phase separation within the bulk of the micron-size fibers. Further, dichroic ratios show polymer chains did not align, even in the presence of nanofillers. Addition of nanofillers affected emissions in the C-H, C=O and C-C regimes, suggesting their involvement in interfacial matrix-carbon nanotube bonding. Spectral differences at glancing angles between pristine and composite mats suggest that geometric conformational configurations are taking place between polymeric chains and carbon nanotubes. These differences appear to be carbon nanotube-dimension dependent, and are promoted upon room temperature mixing and shear flow during electrospinning. CH-π bonding between polymer chains and graphitic walls, as well as H-bonds between impurities in the as-grown CNTs and polymer pendant groups are proposed bonding mechanisms promoting matrix conformation. PMID:24308286

Raman Spectrum of Er-Y-codoped ZrO2 and Fluorescence Properties of Er3+

NASA Astrophysics Data System (ADS)

He, Jun; Luo, Meng-fei; Jin, Ling-yun; He, Mai; Fang, Ping; Xie, Yun-long

2007-02-01

Er-Y-codoped ZrO2 mixed oxides with monoclinic, tetragonal and cubic structures were prepared by a sol-gel method. The crystal structure of ZrO2 matrix and the effect of the ZrO2 phases on the fluorescence properties of Er3+ were studied using Raman spectroscopy. The results indicated that the fluorescence properties of Er3+ depend on its local ZrO2 crystal structures. As ZrO2 matrix transferred from monoclinic to tetragonal and cubic phase, the Raman and fluorescence bands of Er3+ decreased in intensities and tended to form a single peak. With 632.8 nm excitation, the bands between 640 and 680 nm were attributed to the fluorescence of Er3+ in the ZrO2 environment. However, only the fluorescence was observed and no Raman spectra were seen under 514.5 nm excitation, while only Raman spectra were observed under 325 nm excitation. UV Raman spectroscopy was found to be more sensitive in the surface region while the information provided by XRD mainly came from the bulk. The phase with lower symmetry forms more easily on the surface than in the bulk.

The nesprin-cytoskeleton interface probed directly on single nuclei is a mechanically rich system.

PubMed

Balikov, Daniel A; Brady, Sonia K; Ko, Ung Hyun; Shin, Jennifer H; de Pereda, Jose M; Sonnenberg, Arnoud; Sung, Hak-Joon; Lang, Matthew J

2017-09-03

The cytoskeleton provides structure and plays an important role in cellular function such as migration, resisting compression forces, and transport. The cytoskeleton also reacts to physical cues such as fluid shear stress or extracellular matrix remodeling by reorganizing filament associations, most commonly focal adhesions and cell-cell cadherin junctions. These mechanical stimuli can result in genome-level changes, and the physical connection of the cytoskeleton to the nucleus provides an optimal conduit for signal transduction by interfacing with nuclear envelope proteins, called nesprins, within the LINC (linker of the nucleus to the cytoskeleton) complex. Using single-molecule on single nuclei assays, we report that the interactions between the nucleus and the cytoskeleton, thought to be nesprin-cytoskeleton interactions, are highly sensitive to force magnitude and direction depending on whether cells are historically interfaced with the matrix or with cell aggregates. Application of ∼10-30 pN forces to these nesprin linkages yielded structural transitions, with a base transition size of 5-6 nm, which are speculated to be associated with partial unfoldings of the spectrin domains of the nesprins and/or structural changes of histones within the nucleus.

Nanoscale movements of cellulose microfibrils in primary cell walls.

PubMed

Zhang, Tian; Vavylonis, Dimitrios; Durachko, Daniel M; Cosgrove, Daniel J

2017-04-28

The growing plant cell wall is commonly considered to be a fibre-reinforced structure whose strength, extensibility and anisotropy depend on the orientation of crystalline cellulose microfibrils, their bonding to the polysaccharide matrix and matrix viscoelasticity 1-4 . Structural reinforcement of the wall by stiff cellulose microfibrils is central to contemporary models of plant growth, mechanics and meristem dynamics 4-12 . Although passive microfibril reorientation during wall extension has been inferred from theory and from bulk measurements 13-15 , nanometre-scale movements of individual microfibrils have not been directly observed. Here we combined nanometre-scale imaging of wet cell walls by atomic force microscopy (AFM) with a stretching device and endoglucanase treatment that induces wall stress relaxation and creep, mimicking wall behaviours during cell growth. Microfibril movements during forced mechanical extensions differ from those during creep of the enzymatically loosened wall. In addition to passive angular reorientation, we observed a diverse repertoire of microfibril movements that reveal the spatial scale of molecular connections between microfibrils. Our results show that wall loosening alters microfibril connectivity, enabling microfibril dynamics not seen during mechanical stretch. These insights into microfibril movements and connectivities need to be incorporated into refined models of plant cell wall structure, growth and morphogenesis.

Hyaluronic acid-based scaffolds for tissue engineering.

PubMed

Chircov, Cristina; Grumezescu, Alexandru Mihai; Bejenaru, Ludovic Everard

2018-01-01

Hyaluronic acid (HA) is a natural glycosaminoglycan found in the extracellular matrix of most connective tissues. Due to its chemical structure, HA is a hydrophilic polymer and it is characterized by a fast degradation rate. HA-based scaffolds for tissue engineering are intensively studied due to their increased biocompatibility, biodegradability and chemical modification. Depending on the processing technique, scaffolds can be prepared in the form of hydrogels, sponges, cryogels, and injectable hydrogels, all discussed in this review.

A new method for determining the optimal lagged ensemble

PubMed Central

DelSole, T.; Tippett, M. K.; Pegion, K.

2017-01-01

Abstract We propose a general methodology for determining the lagged ensemble that minimizes the mean square forecast error. The MSE of a lagged ensemble is shown to depend only on a quantity called the cross‐lead error covariance matrix, which can be estimated from a short hindcast data set and parameterized in terms of analytic functions of time. The resulting parameterization allows the skill of forecasts to be evaluated for an arbitrary ensemble size and initialization frequency. Remarkably, the parameterization also can estimate the MSE of a burst ensemble simply by taking the limit of an infinitely small interval between initialization times. This methodology is applied to forecasts of the Madden Julian Oscillation (MJO) from version 2 of the Climate Forecast System version 2 (CFSv2). For leads greater than a week, little improvement is found in the MJO forecast skill when ensembles larger than 5 days are used or initializations greater than 4 times per day. We find that if the initialization frequency is too infrequent, important structures of the lagged error covariance matrix are lost. Lastly, we demonstrate that the forecast error at leads ≥10 days can be reduced by optimally weighting the lagged ensemble members. The weights are shown to depend only on the cross‐lead error covariance matrix. While the methodology developed here is applied to CFSv2, the technique can be easily adapted to other forecast systems. PMID:28580050

Genetic Background is a Key Determinant of Glomerular Extracellular Matrix Composition and Organization

PubMed Central

Randles, Michael J.; Woolf, Adrian S.; Huang, Jennifer L.; Byron, Adam; Humphries, Jonathan D.; Price, Karen L.; Kolatsi-Joannou, Maria; Collinson, Sophie; Denny, Thomas; Knight, David; Mironov, Aleksandr; Starborg, Toby; Korstanje, Ron; Humphries, Martin J.; Long, David A.

2015-01-01

Glomerular disease often features altered histologic patterns of extracellular matrix (ECM). Despite this, the potential complexities of the glomerular ECM in both health and disease are poorly understood. To explore whether genetic background and sex determine glomerular ECM composition, we investigated two mouse strains, FVB and B6, using RNA microarrays of isolated glomeruli combined with proteomic glomerular ECM analyses. These studies, undertaken in healthy young adult animals, revealed unique strain- and sex-dependent glomerular ECM signatures, which correlated with variations in levels of albuminuria and known predisposition to progressive nephropathy. Among the variation, we observed changes in netrin 4, fibroblast growth factor 2, tenascin C, collagen 1, meprin 1-α, and meprin 1-β. Differences in protein abundance were validated by quantitative immunohistochemistry and Western blot analysis, and the collective differences were not explained by mutations in known ECM or glomerular disease genes. Within the distinct signatures, we discovered a core set of structural ECM proteins that form multiple protein–protein interactions and are conserved from mouse to man. Furthermore, we found striking ultrastructural changes in glomerular basement membranes in FVB mice. Pathway analysis of merged transcriptomic and proteomic datasets identified potential ECM regulatory pathways involving inhibition of matrix metalloproteases, liver X receptor/retinoid X receptor, nuclear factor erythroid 2-related factor 2, notch, and cyclin-dependent kinase 5. These pathways may therefore alter ECM and confer susceptibility to disease. PMID:25896609

Further Developments in Modeling Creep Effects Within Structural SiC/SiC Components

NASA Technical Reports Server (NTRS)

Lang, Jerry; DiCarlo, James A.

2008-01-01

Anticipating the implementation of advanced SiC/SiC composites into turbine section components of future aero-propulsion engines, the primary objective of this on-going study is to develop physics-based analytical and finite-element modeling tools to predict the effects of constituent creep on SiC/SiC component service life. A second objective is to understand how to possibly manipulate constituent materials and processes in order to minimize these effects. Focusing on SiC/SiC components experiencing through-thickness stress gradients (e.g., airfoil leading edge), prior NASA creep modeling studies showed that detrimental residual stress effects can develop globally within the component walls which can increase the risk of matrix cracking. These studies assumed that the SiC/SiC composites behaved as isotropic viscoelastic continuum materials with creep behavior that was linear and symmetric with stress and that the creep parameters could be obtained from creep data as experimentally measured in-plane in the fiber direction of advanced thin-walled 2D SiC/SiC panels. The present study expands on those prior efforts by including constituent behavior with non-linear stress dependencies in order to predict such key creep-related SiC/SiC properties as time-dependent matrix stress, constituent creep and content effects on composite creep rates and rupture times, and stresses on fiber and matrix during and after creep.

Effect of storage and processing on plasmid, yeast and plant genomic DNA stability in juice from genetically modified oranges.

PubMed

Weiss, Julia; Ros-Chumillas, Maria; Peña, Leandro; Egea-Cortines, Marcos

2007-01-30

Recombinant DNA technology is an important tool in the development of plant varieties with new favourable features. There is strong opposition towards this technology due to the potential risk of horizontal gene transfer between genetically modified plant material and food-associated bacteria, especially if genes for antibiotic resistance are involved. Since horizontal transfer efficiency depends on size and length of homologous sequences, we investigated the effect of conditions required for orange juice processing on the stability of DNA from three different origins: plasmid DNA, yeast genomic DNA and endogenous genomic DNA from transgenic sweet orange (C. sinensis L. Osb.). Acidic orange juice matrix had a strong degrading effect on plasmid DNA which becomes apparent in a conformation change from supercoiled structure to nicked, linear structure within 5h of storage at 4 degrees C. Genomic yeast DNA was degraded during exposure to acidic orange juice matrix within 4 days, and also the genomic DNA of C. sinensis suffered degradation within 2 days of storage as indicated by amplification results from transgene markers. Standard pasteurization procedures affected DNA integrity depending on the method and time used. Our data show that the current standard industrial procedures to pasteurize orange juice as well as its acidic nature causes a strong degradation of both yeast and endogenous genomic DNA below sizes reported to be suitable for horizontal gene transfer.

Theoretical modeling of heating and structure alterations in cartilage under laser radiation with regard to water evaporation and diffusion dominance

NASA Astrophysics Data System (ADS)

Sobol, Emil N.; Kitai, Moishe S.; Jones, Nicholas; Sviridov, Alexander P.; Milner, Thomas E.; Wong, Brian

1998-05-01

We develop a theoretical model to calculate the temperature field and the size of modified structure area in cartilaginous tissue. The model incorporates both thermal and mass transfer in a tissue regarding bulk absorption of laser radiation, water evaporation from a surface and temperature dependence of diffusion coefficient. It is proposed that due to bound- to free-phase transition of water in cartilage heated to about 70 degrees Celsius, some parts of cartilage matrix (proteoglycan units) became more mobile. The movement of these units takes place only when temperature exceed 70 degrees Celsius and results in alteration of tissue structure (denaturation). It is shown that (1) the maximal temperature is reached not on the surface irradiated at some distance from the surface; (2) surface temperature reaches a plateau quicker that the maximal temperature; (3) the depth of denatured area strongly depends on laser fluence and wavelength, exposure time and thickness of cartilage. The model allows to predict and control temperature and depth of structure alterations in the course of laser reshaping and treatment of cartilage.

Molecular weight dependent structure and charge transport in MAPLE-deposited poly(3-hexylthiophene) thin films

DOE PAGES

Dong, Ban Xuan; Smith, Mitchell; Strzalka, Joseph; ...

2018-02-06

In this work, poly(3-hexylthiophene) (P3HT) films prepared using the matrix-assisted pulsed laser evaporation (MAPLE) technique are shown to possess morphological structures that are dependent on molecular weight (MW). Specifically, the structures of low MW samples of MAPLE-deposited film are composed of crystallites/aggregates embedded within highly disordered environments, whereas those of high MW samples are composed of aggregated domains connected by long polymer chains. Additionally, the crystallite size along the side-chain (100) direction decreases, whereas the conjugation length increases with increasing molecular weight. This is qualitatively similar to the structure of spin-cast films, though the MAPLE-deposited films are more disordered. In-planemore » carrier mobilities in the MAPLE-deposited samples increase with MW, consistent with the notion that longer chains bridge adjacent aggregated domains thereby facilitating more effective charge transport. The carrier mobilities in the MAPLE-deposited simples are consistently lower than those in the solvent-cast samples for all molecular weights, consistent with the shorter conjugation length in samples prepared by this deposition technique.« less

Molecular weight dependent structure and charge transport in MAPLE-deposited poly(3-hexylthiophene) thin films

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

Dong, Ban Xuan; Smith, Mitchell; Strzalka, Joseph

In this work, poly(3-hexylthiophene) (P3HT) films prepared using the matrix-assisted pulsed laser evaporation (MAPLE) technique are shown to possess morphological structures that are dependent on molecular weight (MW). Specifically, the structures of low MW samples of MAPLE-deposited film are composed of crystallites/aggregates embedded within highly disordered environments, whereas those of high MW samples are composed of aggregated domains connected by long polymer chains. Additionally, the crystallite size along the side-chain (100) direction decreases, whereas the conjugation length increases with increasing molecular weight. This is qualitatively similar to the structure of spin-cast films, though the MAPLE-deposited films are more disordered. In-planemore » carrier mobilities in the MAPLE-deposited samples increase with MW, consistent with the notion that longer chains bridge adjacent aggregated domains thereby facilitating more effective charge transport. The carrier mobilities in the MAPLE-deposited simples are consistently lower than those in the solvent-cast samples for all molecular weights, consistent with the shorter conjugation length in samples prepared by this deposition technique.« less

Zero-inflated count models for longitudinal measurements with heterogeneous random effects.

PubMed

Zhu, Huirong; Luo, Sheng; DeSantis, Stacia M

2017-08-01

Longitudinal zero-inflated count data arise frequently in substance use research when assessing the effects of behavioral and pharmacological interventions. Zero-inflated count models (e.g. zero-inflated Poisson or zero-inflated negative binomial) with random effects have been developed to analyze this type of data. In random effects zero-inflated count models, the random effects covariance matrix is typically assumed to be homogeneous (constant across subjects). However, in many situations this matrix may be heterogeneous (differ by measured covariates). In this paper, we extend zero-inflated count models to account for random effects heterogeneity by modeling their variance as a function of covariates. We show via simulation that ignoring intervention and covariate-specific heterogeneity can produce biased estimates of covariate and random effect estimates. Moreover, those biased estimates can be rectified by correctly modeling the random effects covariance structure. The methodological development is motivated by and applied to the Combined Pharmacotherapies and Behavioral Interventions for Alcohol Dependence (COMBINE) study, the largest clinical trial of alcohol dependence performed in United States with 1383 individuals.

A procedure for utilization of a damage-dependent constitutive model for laminated composites

NASA Technical Reports Server (NTRS)

Lo, David C.; Allen, David H.; Harris, Charles E.

1992-01-01

Described here is the procedure for utilizing a damage constitutive model to predict progressive damage growth in laminated composites. In this model, the effects of the internal damage are represented by strain-like second order tensorial damage variables and enter the analysis through damage dependent ply level and laminate level constitutive equations. The growth of matrix cracks due to fatigue loading is predicted by an experimentally based damage evolutionary relationship. This model is incorporated into a computer code called FLAMSTR. This code is capable of predicting the constitutive response and matrix crack damage accumulation in fatigue loaded laminated composites. The structure and usage of FLAMSTR are presented along with sample input and output files to assist the code user. As an example problem, an analysis of crossply laminates subjected to two stage fatigue loading was conducted and the resulting damage accumulation and stress redistribution were examined to determine the effect of variations in fatigue load amplitude applied during the first stage of the load history. It was found that the model predicts a significant loading history effect on damage evolution.

Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations.

PubMed

Linke, Max; Köfinger, Jürgen; Hummer, Gerhard

2018-05-31

We present a method to calculate the fully anisotropic rotational diffusion tensor from molecular dynamics simulations. Our approach is based on fitting the time-dependent covariance matrix of the quaternions that describe the rigid-body rotational dynamics. Explicit analytical expressions have been derived for the covariances by Favro, which are valid irrespective of the degree of anisotropy. We use these expressions to determine an optimal rotational diffusion tensor from trajectory data. The molecular structures are aligned against a reference by optimal rigid-body superposition. The quaternion covariances can then be obtained directly from the rotation matrices used in the alignment. The rotational diffusion tensor is determined by a fit to the time-dependent quaternion covariances, or directly by Laplace transformation and matrix diagonalization. To quantify uncertainties in the fit, we derive analytical expressions and compare them with the results of Brownian dynamics simulations of anisotropic rotational diffusion. We apply the method to microsecond long trajectories of the Dickerson-Drew B-DNA dodecamer and of horse heart myoglobin. The anisotropic rotational diffusion tensors calculated from simulations agree well with predictions from hydrodynamics.

Bone Formation is Affected by Matrix Advanced Glycation End Products (AGEs) In Vivo.

PubMed

Yang, Xiao; Mostafa, Ahmed Jenan; Appleford, Mark; Sun, Lian-Wen; Wang, Xiaodu

2016-10-01

Advanced glycation end products (AGEs) accumulate in bone extracellular matrix as people age. Although previous evidence shows that the accumulation of AGEs in bone matrix may impose significant effects on bone cells, the effect of matrix AGEs on bone formation in vivo is still poorly understood. To address this issue, this study used a unique rat model with autograft implant to investigate the in vivo response of bone formation to matrix AGEs. Fluorochrome biomarkers were sequentially injected into rats to label the dynamic bone formation in the presence of elevated levels of matrix AGEs. After sacrificing animals, dynamic histomorphometry was performed to determine mineral apposition rate (MAR), mineralized surface per bone surface (MS/BS), and bone formation rate (BFR). Finally, nanoindentation tests were performed to assess mechanical properties of newly formed bone tissues. The results showed that MAR, MS/BS, and BFR were significantly reduced in the vicinity of implant cores with high concentration of matrix AGEs, suggesting that bone formation activities by osteoblasts were suppressed in the presence of elevated matrix AGEs. In addition, MAR and BFR were found to be dependent on the surrounding environment of implant cores (i.e., cortical or trabecular tissues). Moreover, MS/BS and BFR were also dependent on how far the implant cores were away from the growth plate. These observations suggest that the effect of matrix AGEs on bone formation is dependent on the biological milieu around the implants. Finally, nanoindentation test results indicated that the indentation modulus and hardness of newly formed bone tissues were not affected by the presence of elevated matrix AGEs. In summary, high concentration of matrix AGEs may slow down the bone formation process in vivo, while imposing little effects on bone mineralization.

Calculating Path-Dependent Travel Time Prediction Variance and Covariance fro a Global Tomographic P-Velocity Model

NASA Astrophysics Data System (ADS)

Ballard, S.; Hipp, J. R.; Encarnacao, A.; Young, C. J.; Begnaud, M. L.; Phillips, W. S.

2012-12-01

Seismic event locations can be made more accurate and precise by computing predictions of seismic travel time through high fidelity 3D models of the wave speed in the Earth's interior. Given the variable data quality and uneven data sampling associated with this type of model, it is essential that there be a means to calculate high-quality estimates of the path-dependent variance and covariance associated with the predicted travel times of ray paths through the model. In this paper, we describe a methodology for accomplishing this by exploiting the full model covariance matrix and show examples of path-dependent travel time prediction uncertainty computed from SALSA3D, our global, seamless 3D tomographic P-velocity model. Typical global 3D models have on the order of 1/2 million nodes, so the challenge in calculating the covariance matrix is formidable: 0.9 TB storage for 1/2 of a symmetric matrix, necessitating an Out-Of-Core (OOC) blocked matrix solution technique. With our approach the tomography matrix (G which includes Tikhonov regularization terms) is multiplied by its transpose (GTG) and written in a blocked sub-matrix fashion. We employ a distributed parallel solution paradigm that solves for (GTG)-1 by assigning blocks to individual processing nodes for matrix decomposition update and scaling operations. We first find the Cholesky decomposition of GTG which is subsequently inverted. Next, we employ OOC matrix multiplication methods to calculate the model covariance matrix from (GTG)-1 and an assumed data covariance matrix. Given the model covariance matrix, we solve for the travel-time covariance associated with arbitrary ray-paths by summing the model covariance along both ray paths. Setting the paths equal and taking the square root yields the travel prediction uncertainty for the single path.

The Candida albicans Biofilm Matrix: Composition, Structure and Function.

PubMed

Pierce, Christopher G; Vila, Taissa; Romo, Jesus A; Montelongo-Jauregui, Daniel; Wall, Gina; Ramasubramanian, Anand; Lopez-Ribot, Jose L

2017-03-01

A majority of infections caused by Candida albicans -the most frequent fungal pathogen-are associated with biofilm formation. A salient feature of C. albicans biofilms is the presence of the biofilm matrix. This matrix is composed of exopolymeric materials secreted by sessile cells within the biofilm, in which all classes of macromolecules are represented, and provides protection against environmental challenges. In this review, we summarize the knowledge accumulated during the last two decades on the composition, structure, and function of the C. albicans biofilm matrix. Knowledge of the matrix components, its structure, and function will help pave the way to novel strategies to combat C. albicans biofilm infections.

The Candida albicans Biofilm Matrix: Composition, Structure and Function

PubMed Central

Pierce, Christopher G.; Vila, Taissa; Romo, Jesus A.; Montelongo-Jauregui, Daniel; Wall, Gina; Ramasubramanian, Anand; Lopez-Ribot, Jose L.

2017-01-01

A majority of infections caused by Candida albicans—the most frequent fungal pathogen—are associated with biofilm formation. A salient feature of C. albicans biofilms is the presence of the biofilm matrix. This matrix is composed of exopolymeric materials secreted by sessile cells within the biofilm, in which all classes of macromolecules are represented, and provides protection against environmental challenges. In this review, we summarize the knowledge accumulated during the last two decades on the composition, structure, and function of the C. albicans biofilm matrix. Knowledge of the matrix components, its structure, and function will help pave the way to novel strategies to combat C. albicans biofilm infections. PMID:28516088

The dynamical conductance of graphene tunnelling structures.

PubMed

Zhang, Huan; Chan, K S; Lin, Zijing

2011-12-16

The dynamical conductances of graphene tunnelling structures were numerically calculated using the scattering matrix method with the interaction effect included in a phenomenological approach. The overall single-barrier dynamical conductance is capacitative. Transmission resonances in the single-barrier structure lead to dips in the capacitative imaginary part of the response. This is different from the ac responses of typical semiconductor nanostructures, where transmission resonances usually lead to inductive peaks. The features of the dips depend on the Fermi energy. When the Fermi energy is below half of the barrier height, the dips are sharper. When the Fermi energy is higher than half of the barrier height, the dips are broader. Inductive behaviours can be observed in a double-barrier structure due to the resonances formed by reflection between the two barriers.

Clonorchis sinensis excretory-secretory products regulate migration and invasion in cholangiocarcinoma cells via extracellular signal-regulated kinase 1/2/nuclear factor-κB-dependent matrix metalloproteinase-9 expression.

PubMed

Pak, Jhang Ho; Shin, Jimin; Song, In-Sung; Shim, Sungbo; Jang, Sung-Wuk

2017-01-01

Matrix metalloproteinase-9 plays an important role in the invasion and metastasis of various types of cancer cells. We have previously reported that excretory-secretory products from Clonorchis sinensis increases matrix metalloproteinase-9 expression. However, the regulatory mechanisms through which matrix metalloproteinase-9 expression affects cholangiocarcinoma development remain unclear. In the current study, we examined the potential role of excretory-secretory products in regulating the migration and invasion of various cholangiocarcinoma cell lines. We demonstrated that excretory-secretory products significantly induced matrix metalloproteinase-9 expression and activity in a concentration-dependent manner. Reporter gene and chromatin immunoprecipitation assays showed that excretory-secretory products induced matrix metalloproteinase-9 expression by enhancing the activity of nuclear factor-kappa B. Moreover, excretory-secretory products induced the degradation and phosphorylation of IκBα and stimulated nuclear factor-kappa B p65 nuclear translocation, which was regulated by extracellular signal-regulated kinase 1/2. Taken together, our findings indicated that the excretory-secretory product-dependent enhancement of matrix metalloproteinase-9 activity and subsequent induction of IκBα and nuclear factor-kappa B activities may contribute to the progression of cholangiocarcinoma. Copyright © 2016 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

Influence of the Coulomb interaction on the exchange coupling in granular magnets.

PubMed

Udalov, O G; Beloborodov, I S

2017-04-20

We develop a theory of the exchange interaction between ferromagnetic (FM) metallic grains embedded into insulating matrix by taking into account the Coulomb blockade effects. For bulk ferromagnets separated by the insulating layer the exchange interaction strongly depends on the height and thickness of the tunneling barrier created by the insulator. We show that for FM grains embedded into insulating matrix the exchange coupling additionally depends on the dielectric properties of this matrix due to the Coulomb blockade effects. In particular, the FM coupling decreases with decreasing the dielectric permittivity of insulating matrix. We find that the change in the exchange interaction due to the Coulomb blockade effects can be a few tens of percent. Also, we study dependence of the intergrain exchange interaction on the grain size and other parameters of the system.

Matrix differentiation formulas

NASA Technical Reports Server (NTRS)

Usikov, D. A.; Tkhabisimov, D. K.

1983-01-01

A compact differentiation technique (without using indexes) is developed for scalar functions that depend on complex matrix arguments which are combined by operations of complex conjugation, transposition, addition, multiplication, matrix inversion and taking the direct product. The differentiation apparatus is developed in order to simplify the solution of extremum problems of scalar functions of matrix arguments.

Computing the Density Matrix in Electronic Structure Theory on Graphics Processing Units.

PubMed

Cawkwell, M J; Sanville, E J; Mniszewski, S M; Niklasson, Anders M N

2012-11-13

The self-consistent solution of a Schrödinger-like equation for the density matrix is a critical and computationally demanding step in quantum-based models of interatomic bonding. This step was tackled historically via the diagonalization of the Hamiltonian. We have investigated the performance and accuracy of the second-order spectral projection (SP2) algorithm for the computation of the density matrix via a recursive expansion of the Fermi operator in a series of generalized matrix-matrix multiplications. We demonstrate that owing to its simplicity, the SP2 algorithm [Niklasson, A. M. N. Phys. Rev. B2002, 66, 155115] is exceptionally well suited to implementation on graphics processing units (GPUs). The performance in double and single precision arithmetic of a hybrid GPU/central processing unit (CPU) and full GPU implementation of the SP2 algorithm exceed those of a CPU-only implementation of the SP2 algorithm and traditional matrix diagonalization when the dimensions of the matrices exceed about 2000 × 2000. Padding schemes for arrays allocated in the GPU memory that optimize the performance of the CUBLAS implementations of the level 3 BLAS DGEMM and SGEMM subroutines for generalized matrix-matrix multiplications are described in detail. The analysis of the relative performance of the hybrid CPU/GPU and full GPU implementations indicate that the transfer of arrays between the GPU and CPU constitutes only a small fraction of the total computation time. The errors measured in the self-consistent density matrices computed using the SP2 algorithm are generally smaller than those measured in matrices computed via diagonalization. Furthermore, the errors in the density matrices computed using the SP2 algorithm do not exhibit any dependence of system size, whereas the errors increase linearly with the number of orbitals when diagonalization is employed.

Identification of novel lysosomal matrix proteins by proteome analysis.

PubMed

Kollmann, Katrin; Mutenda, Kudzai E; Balleininger, Martina; Eckermann, Ellen; von Figura, Kurt; Schmidt, Bernhard; Lübke, Torben

2005-10-01

The lysosomal matrix is estimated to contain about 50 different proteins. Most of the matrix proteins are acid hydrolases that depend on mannose 6-phosphate receptors (MPR) for targeting to lysosomes. Here, we describe a comprehensive proteome analysis of MPR-binding proteins from mouse. Mouse embryonic fibroblasts defective in both MPR (MPR 46-/- and MPR 300-/-) are known to secrete the lysosomal matrix proteins. Secretions of these cells were affinity purified using an affinity matrix derivatized with MPR46 and MPR300. In the protein fraction bound to the affinity matrix and eluted with mannose 6-phosphate, 34 known lysosomal matrix proteins, 4 candidate proteins of the lysosomal matrix and 4 non-lysosomal contaminants were identified by mass spectrometry after separation by two-dimensional gel electrophoresis or by multidimensional protein identification technology. For 3 of the candidate proteins, mammalian ependymin-related protein-2 (MERP-2), retinoid-inducible serine carboxypeptidase (RISC) and the hypothetical 66.3-kDa protein we could verify that C-terminally tagged forms bound in an M6P-dependent manner to an MPR-affinity matrix and were internalized via MPR-mediated endocytosis. Hence these 3 proteins are likely to represent hitherto unrecognized lysosomal matrix proteins.

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 Management: An Organizational Alternative for Libraries.

ERIC Educational Resources Information Center

Johnson, Peggy

1990-01-01

Describes various organizational structures and models, presents matrix management as an alternative to traditional hierarchical structures, and suggests matrix management as an appropriate organizational alternative for academic libraries. Benefits that are discussed include increased flexibility, a higher level of professional independence, and…

Performance analysis of structured gradient algorithm. [for adaptive beamforming linear arrays

NASA Technical Reports Server (NTRS)

Godara, Lal C.

1990-01-01

The structured gradient algorithm uses a structured estimate of the array correlation matrix (ACM) to estimate the gradient required for the constrained least-mean-square (LMS) algorithm. This structure reflects the structure of the exact array correlation matrix for an equispaced linear array and is obtained by spatial averaging of the elements of the noisy correlation matrix. In its standard form the LMS algorithm does not exploit the structure of the array correlation matrix. The gradient is estimated by multiplying the array output with the receiver outputs. An analysis of the two algorithms is presented to show that the covariance of the gradient estimated by the structured method is less sensitive to the look direction signal than that estimated by the standard method. The effect of the number of elements on the signal sensitivity of the two algorithms is studied.

Modification of conductive polyaniline with carbon nanomaterials

NASA Astrophysics Data System (ADS)

Sedaghat, Sajjad; Alavijeh, Mahdi Soleimani

2014-08-01

The synthesis of polyaniline/single-wall nanotube, polyaniline/multi-wall nanotube and polyaniline/single-wall nanotube/graphen nanosheets nanocomposites by in situ polymerization are reported in this study. The substrates were treated with a mixture of concentrated sulfuric acid and concentrated nitric acid before usage to functionalize with carboxylic and hydroxyl groups. Aniline monomers are adsorbed and polymerized on the surface of these fillers. Structural analysis using scanning electron microscopy showed that nanomaterials dispersed into polymer matrix and made tubular structures with diameters several tens to hundreds nanometers depending on the polyaniline content. These nanocomposites can be used for production of excellent electrode materials applications in high-performance supercapacitors.

Extraction of three-dimensional silver nanostructures with supercritical fluid

NASA Astrophysics Data System (ADS)

Taguchi, Natsuo; Takeyasu, Nobuyuki; Kawata, Satoshi

2018-02-01

In a previous report, a self-growing approach was proposed for fabricating complex silver nanostructures, where silver dendrites were grown at silver nanoseeds in silver ion solution owing to plasmonic heating with ultraviolet light. Structures were deformed or destroyed when they were extracted with acetone and dried in air. In this Letter, we discuss the use of supercritical carbon dioxide fluid for the nondestructive extraction of nanostructures. We show the experimental results and discuss the laser power dependence of resultant structures. Another experiment was performed for nanostructure growth inside an agarose gel as a matrix. Silver nanostructures were immobilized without damage in an agarose skeleton network.

Organic Matrix-related mineralization of sea urchin spicules, spines, test and teeth

PubMed Central

Veis, Arthur

2012-01-01

The camarodont echinoderms have five distinct mineralized skeletal elements: the embryonic spicules and mature test; spines, lantern stereom and teeth. The embryonic spicules are transient structural elements of the larval skeleton whereas the spines and test plates are permanent structural elements. The teeth are continuously growing structures, matching wear at the incisal adoral end to the rate of new production at the aboral plumula. The mineral in all cases is a high magnesium calcite, but the magnesium content, crystal shape and growth pattern is different in each type of skeletal element. The crystal shape and organization into macro structures depends on the presence of an organic matrix which creates the spaces and controls the environments for crystal initiation and growth. The detailed mechanisms of crystal regulation are not known, but much work has been done on defining the proteins which appear to be involved. Phosphorylated matrix proteins may be of special importance. Biochemical isolation of proteins, construction and analysis of cDNA libraries, and most recently high-throughput proteomic analysis in conjunction with the sequencing of the complete genome have yielded a detailed list of protein components likely to be involved in the mineralization processes. However, the proteome-genome analyses have not yet provided insight into the mechanisms of crystallization, calcite composition, and orientation applicable to all skeletal elements. Although the embryonic pluteus and their spicules are the best studied system, it appears that spicule is not representative of the mature skeletal elements. Now armed with the compositions of most of the proteins involved, the next phase of research will have to focus on the specific localization of the proteins and individual biochemistries of each system with regard to mineral content and placement. PMID:21622194

MMpI: A WideRange of Available Compounds of Matrix Metalloproteinase Inhibitors

PubMed Central

Muvva, Charuvaka; Patra, Sanjukta; Venkatesan, Subramanian

2016-01-01

Matrix metalloproteinases (MMPs) are a family of zinc-dependent proteinases involved in the regulation of the extracellular signaling and structural matrix environment of cells and tissues. MMPs are considered as promising targets for the treatment of many diseases. Therefore, creation of database on the inhibitors of MMP would definitely accelerate the research activities in this area due to its implication in above-mentioned diseases and associated limitations in the first and second generation inhibitors. In this communication, we report the development of a new MMpI database which provides resourceful information for all researchers working in this field. It is a web-accessible, unique resource that contains detailed information on the inhibitors of MMP including small molecules, peptides and MMP Drug Leads. The database contains entries of ~3000 inhibitors including ~72 MMP Drug Leads and ~73 peptide based inhibitors. This database provides the detailed molecular and structural details which are necessary for the drug discovery and development. The MMpI database contains physical properties, 2D and 3D structures (mol2 and pdb format files) of inhibitors of MMP. Other data fields are hyperlinked to PubChem, ChEMBL, BindingDB, DrugBank, PDB, MEROPS and PubMed. The database has extensive searching facility with MMpI ID, IUPAC name, chemical structure and with the title of research article. The MMP inhibitors provided in MMpI database are optimized using Python-based Hierarchical Environment for Integrated Xtallography (Phenix) software. MMpI Database is unique and it is the only public database that contains and provides the complete information on the inhibitors of MMP. Database URL: http://clri.res.in/subramanian/databases/mmpi/index.php. PMID:27509041

Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking

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

Rumpf, Tobias; Gerhardt, Stefan; Einsle, Oliver, E-mail: einsle@biochemie.uni-freiburg.de

2015-11-18

In the present study, microseed matrix seeding was successfully applied to obtain a large number of crystals of the human sirtuin isotypes Sirt2 and Sirt3. These crystals appeared predictably in diverse crystallization conditions, diffracted to a higher resolution than reported in the literature and were subsequently used to study the protein–ligand interactions of two indole inhibitors. Sirtuins constitute a family of NAD{sup +}-dependent enzymes that catalyse the cleavage of various acyl groups from the ∊-amino group of lysines. They regulate a series of cellular processes and their misregulation has been implicated in various diseases, making sirtuins attractive drug targets. Tomore » date, only a few sirtuin modulators have been reported that are suitable for cellular research and their development has been hampered by a lack of structural information. In this work, microseed matrix seeding (MMS) was used to obtain crystals of human Sirt3 in its apo form and of human Sirt2 in complex with ADP ribose (ADPR). Crystal formation using MMS was predictable, less error-prone and yielded a higher number of crystals per drop than using conventional crystallization screening methods. The crystals were used to solve the crystal structures of apo Sirt3 and of Sirt2 in complex with ADPR at an improved resolution, as well as the crystal structures of Sirt2 in complex with ADPR and the indoles EX527 and CHIC35. These Sirt2–ADPR–indole complexes unexpectedly contain two indole molecules and provide novel insights into selective Sirt2 inhibition. The MMS approach for Sirt2 and Sirt3 may be used as the basis for structure-based optimization of Sirt2/3 inhibitors in the future.« less

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.

The Compact and Biologically Relevant Structure of Inter-α-inhibitor Is Maintained by the Chondroitin Sulfate Chain and Divalent Cations.

PubMed

Scavenius, Carsten; Nikolajsen, Camilla Lund; Stenvang, Marcel; Thøgersen, Ida B; Wyrożemski, Łukasz; Wisniewski, Hans-Georg; Otzen, Daniel E; Sanggaard, Kristian W; Enghild, Jan J

2016-02-26

Inter-α-inhibitor is a proteoglycan of unique structure. The protein consists of three subunits, heavy chain 1, heavy chain 2, and bikunin covalently joined by a chondroitin sulfate chain originating at Ser-10 of bikunin. Inter-α-inhibitor interacts with an inflammation-associated protein, tumor necrosis factor-inducible gene 6 protein, in the extracellular matrix. This interaction leads to transfer of the heavy chains from the chondroitin sulfate of inter-α-inhibitor to hyaluronan and consequently to matrix stabilization. Divalent cations and heavy chain 2 are essential co-factors in this transfer reaction. In the present study, we have investigated how divalent cations in concert with the chondroitin sulfate chain influence the structure and stability of inter-α-inhibitor. The results showed that Mg(2+) or Mn(2+), but not Ca(2+), induced a conformational change in inter-α-inhibitor as evidenced by a decrease in the Stokes radius and a bikunin chondroitin sulfate-dependent increase of the thermodynamic stability. This structure was shown to be essential for the ability of inter-α-inhibitor to participate in extracellular matrix stabilization. In addition, the data revealed that bikunin was positioned adjacent to both heavy chains and that the two heavy chains also were in close proximity. The chondroitin sulfate chain interacted with all protein components and inter-α-inhibitor dissociated when it was degraded. Conventional purification protocols result in the removal of the Mg(2+) found in plasma and because divalent cations influence the conformation and affect function it is important to consider this when characterizing the biological activity of inter-α-inhibitor. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Modeling and possible implementation of self-learning equivalence-convolutional neural structures for auto-encoding-decoding and clusterization of images

NASA Astrophysics Data System (ADS)

Krasilenko, Vladimir G.; Lazarev, Alexander A.; Nikitovich, Diana V.

2017-08-01

Self-learning equivalent-convolutional neural structures (SLECNS) for auto-coding-decoding and image clustering are discussed. The SLECNS architectures and their spatially invariant equivalent models (SI EMs) using the corresponding matrix-matrix procedures with basic operations of continuous logic and non-linear processing are proposed. These SI EMs have several advantages, such as the ability to recognize image fragments with better efficiency and strong cross correlation. The proposed clustering method of fragments with regard to their structural features is suitable not only for binary, but also color images and combines self-learning and the formation of weight clustered matrix-patterns. Its model is constructed and designed on the basis of recursively processing algorithms and to k-average method. The experimental results confirmed that larger images and 2D binary fragments with a large numbers of elements may be clustered. For the first time the possibility of generalization of these models for space invariant case is shown. The experiment for an image with dimension of 256x256 (a reference array) and fragments with dimensions of 7x7 and 21x21 for clustering is carried out. The experiments, using the software environment Mathcad, showed that the proposed method is universal, has a significant convergence, the small number of iterations is easily, displayed on the matrix structure, and confirmed its prospects. Thus, to understand the mechanisms of self-learning equivalence-convolutional clustering, accompanying her to the competitive processes in neurons, and the neural auto-encoding-decoding and recognition principles with the use of self-learning cluster patterns is very important which used the algorithm and the principles of non-linear processing of two-dimensional spatial functions of images comparison. These SIEMs can simply describe the signals processing during the all training and recognition stages and they are suitable for unipolar-coding multilevel signals. We show that the implementation of SLECNS based on known equivalentors or traditional correlators is possible if they are based on proposed equivalental two-dimensional functions of image similarity. The clustering efficiency in such models and their implementation depends on the discriminant properties of neural elements of hidden layers. Therefore, the main models and architecture parameters and characteristics depends on the applied types of non-linear processing and function used for image comparison or for adaptive-equivalental weighing of input patterns. Real model experiments in Mathcad are demonstrated, which confirm that non-linear processing on equivalent functions allows you to determine the neuron winners and adjust the weight matrix. Experimental results have shown that such models can be successfully used for auto- and hetero-associative recognition. They can also be used to explain some mechanisms known as "focus" and "competing gain-inhibition concept". The SLECNS architecture and hardware implementations of its basic nodes based on multi-channel convolvers and correlators with time integration are proposed. The parameters and performance of such architectures are estimated.

Bifurcation Analysis of a Predator-Prey System with Ratio-Dependent Functional Response

NASA Astrophysics Data System (ADS)

Jiang, Xin; She, Zhikun; Feng, Zhaosheng; Zheng, Xiuliang

2017-12-01

In this paper, we are concerned with the structural stability of a density dependent predator-prey system with ratio-dependent functional response. Starting with the geometrical analysis of hyperbolic curves, we obtain that the system has one or two positive equilibria under various conditions. Inspired by the S-procedure and semi-definite programming, we use the sum of squares decomposition based method to ensure the global asymptotic stability of the positive equilibrium through the associated polynomial Lyapunov functions. By exploring the monotonic property of the trace of the Jacobian matrix with respect to r under the given different conditions, we analytically verify that there is a corresponding unique r∗ such that the trace is equal to zero and prove the existence of Hopf bifurcation, respectively.

Spicule matrix protein LSM34 is essential for biomineralization of the sea urchin spicule.

PubMed

Peled-Kamar, Mira; Hamilton, Patricia; Wilt, Fred H

2002-01-01

Biomineralized skeletal structures are composite materials containing mineral and matrix protein(s). The cell biological mechanisms that underlie the formation, secretion, and organization of the biomineralized materials are not well understood. Although the matrix proteins influence physical properties of the structures, little is known of the role of these matrix proteins in the actual formation of the biomineralized structure. We present here results using an antisense oligonucleotide directed against a spicule matrix protein, LSM34, present in spicules of embryos of Lytechinus pictus. After injection of anti-LSM34 into the blastocoel of a sea urchin embryo, LSM34 protein in the primary mesenchyme cells decreases and biomineralization ceases, demonstrating that LSM34 function is essential for the formation of the calcareous endoskeletal spicule of the embryo. Since LSM34 is found primarily in a specialized extracellular matrix surrounding the spicule, it is probable that this matrix is important for the biomineralization process.

Effect of Kallikrein 4 Loss on Enamel Mineralization

PubMed Central

Smith, Charles E.; Richardson, Amelia S.; Hu, Yuanyuan; Bartlett, John D.; Hu, Jan C-C.; Simmer, James P.

2011-01-01

Enamel formation depends on a triad of tissue-specific matrix proteins (amelogenin, ameloblastin, and enamelin) to help initiate and stabilize progressively elongating, thin mineral ribbons of hydroxyapatite formed during an appositional growth phase. Subsequently, these proteins are eradicated to facilitate lateral expansion of the hydroxyapatite crystallites. The purpose of this study was to investigate changes in enamel mineralization occurring in mice unable to produce kallikrein 4 (Klk4), a proteinase associated with terminal extracellular degradation of matrix proteins during the maturation stage. Mice lacking functional matrix metalloproteinase 20 (Mmp20), a proteinase associated with early cleavage of matrix proteins during the secretory stage, were also analyzed as a frame of reference. The results indicated that mice lacking Klk4 produce enamel that is normal in thickness and overall organization in terms of layers and rod/inter-rod structure, but there is a developmental defect in enamel rods where they first form near the dentinoenamel junction. Mineralization is normal up to early maturation after which the enamel both retains and gains additional proteins and is unable to mature beyond 85% mineral by weight. The outmost enamel is hard, but inner regions are soft and contain much more protein than normal. The rate of mineral acquisition overall is lower by 25%. Mice lacking functional Mmp20 produce enamel that is thin and structurally abnormal. Relatively high amounts of protein remain throughout maturation, but the enamel is able to change from 67 to 75% mineral by weight during maturation. These findings reaffirm the importance of secreted proteinases to enamel mineral acquisition. PMID:21454549

A combined representation method for use in band structure calculations. 1: Method

NASA Technical Reports Server (NTRS)

Friedli, C.; Ashcroft, N. W.

1975-01-01

A representation was described whose basis levels combine the important physical aspects of a finite set of plane waves with those of a set of Bloch tight-binding levels. The chosen combination has a particularly simple dependence on the wave vector within the Brillouin Zone, and its use in reducing the standard one-electron band structure problem to the usual secular equation has the advantage that the lattice sums involved in the calculation of the matrix elements are actually independent of the wave vector. For systems with complicated crystal structures, for which the Korringa-Kohn-Rostoker (KKR), Augmented-Plane Wave (APW) and Orthogonalized-Plane Wave (OPW) methods are difficult to apply, the present method leads to results with satisfactory accuracy and convergence.

Dissecting the Impact of Matrix Anchorage and Elasticity in Cell Adhesion

PubMed Central

Pompe, Tilo; Glorius, Stefan; Bischoff, Thomas; Uhlmann, Ina; Kaufmann, Martin; Brenner, Sebastian; Werner, Carsten

2009-01-01

Abstract Extracellular matrices determine cellular fate decisions through the regulation of intracellular force and stress. Previous studies suggest that matrix stiffness and ligand anchorage cause distinct signaling effects. We show herein how defined noncovalent anchorage of adhesion ligands to elastic substrates allows for dissection of intracellular adhesion signaling pathways related to matrix stiffness and receptor forces. Quantitative analysis of the mechanical balance in cell adhesion using traction force microscopy revealed distinct scalings of the strain energy imparted by the cells on the substrates dependent either on matrix stiffness or on receptor force. Those scalings suggested the applicability of a linear elastic theoretical framework for the description of cell adhesion in a certain parameter range, which is cell-type-dependent. Besides the deconvolution of biophysical adhesion signaling, site-specific phosphorylation of focal adhesion kinase, dependent either on matrix stiffness or on receptor force, also demonstrated the dissection of biochemical signaling events in our approach. Moreover, the net contractile moment of the adherent cells and their strain energy exerted on the elastic substrate was found to be a robust measure of cell adhesion with a unifying power-law scaling exponent of 1.5 independent of matrix stiffness. PMID:19843448

Quantum non-Abelian hydrodynamics: Anyonic or spin-orbital entangled liquids, nonunitarity of scattering matrix and charge fractionalization

NASA Astrophysics Data System (ADS)

Pareek, Tribhuvan Prasad

2015-09-01

In this article, we develop an exact (nonadiabatic, nonperturbative) density matrix scattering theory for a two component quantum liquid which interacts or scatters off from a generic spin-dependent quantum potential. The generic spin dependent quantum potential [Eq. (1)] is a matrix potential, hence, adiabaticity criterion is ill-defined. Therefore the full matrix potential should be treated nonadiabatically. We succeed in doing so using the notion of vectorial matrices which allows us to obtain an exact analytical expression for the scattered density matrix (SDM), ϱsc [Eq. (30)]. We find that the number or charge density in scattered fluid, Tr(ϱsc), expressions in Eqs. (32) depends on nontrivial quantum interference coefficients, Qα β 0ijk, which arises due to quantum interference between spin-independent and spin-dependent scattering amplitudes and among spin-dependent scattering amplitudes. Further it is shown that Tr(ϱsc) can be expressed in a compact form [Eq. (39)] where the effect of quantum interference coefficients can be included using a vector Qαβ, which allows us to define a vector order parameterQ. Since the number density is obtained using an exact scattered density matrix, therefore, we do not need to prove that Q is non-zero. However, for sake of completeness, we make detailed mathematical analysis for the conditions under which the vector order parameterQ would be zero or nonzero. We find that in presence of spin-dependent interaction the vector order parameterQ is necessarily nonzero and is related to the commutator and anti-commutator of scattering matrix S with its dagger S† [Eq. (78)]. It is further shown that Q≠0, implies four physically equivalent conditions,i.e., spin-orbital entanglement is nonzero, non-Abelian scattering phase, i.e., matrices, scattering matrix is nonunitary and the broken time reversal symmetry for SDM. This also implies that quasi particle excitation are anyonic in nature, hence, charge fractionalization is a natural consequence. This aspect has also been discussed from the perspective of number or charge density conservation, which implies i.e., Tr(ϱ} sc) = Tr(ϱin). On the other hand Q = 0 turns out to be a mathematically forced unphysical solution in presence of spin-dependent potential or scattering which is equivalent to Abelian hydrodynamics, unitary scattering matrix, absence of spin-space entanglement and preserved time reversal symmetry. We have formulated the theory using mesoscopic language, specifically, we have considered two terminal systems connected to spin-dependent scattering region, which is equivalent to having two potential wells separated by a generic spin-dependent potential barrier. The formulation using mesoscopic language is practically useful because it leads directly to the measured quantities such as conductance and spin-polarization density in the leads, however, the presented formulation is not limited to the mesoscopic system only, its generality has been stressed at various places in this article.

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.

The Effect of Fiber Architecture on Matrix Cracking in Sic/sic Cmc's

NASA Technical Reports Server (NTRS)

Morscher, Gregory N.

2005-01-01

Applications incorporating silicon carbide fiber reinforced silicon carbide matrix composites (CMC's) will require a wide range of fiber architectures in order to fabricate complex shape. The stress-strain response of a given SiC/SiC system for different architectures and orientations will be required in order to design and effectively life-model future components. The mechanism for non-linear stress-strain behavior in CMC's is the formation and propagation of bridged-matrix cracks throughout the composite. A considerable amount of understanding has been achieved for the stress-dependent matrix cracking behavior of SiC fiber reinforced SiC matrix systems containing melt-infiltrated Si. This presentation will outline the effect of 2D and 3D architectures and orientation on stress-dependent matrix-cracking and how this information can be used to model material behavior and serve as the starting point foe mechanistic-based life-models.

Scleraxis is required for cell lineage differentiation and extracellular matrix remodeling during murine heart valve formation in vivo.

PubMed

Levay, Agata K; Peacock, Jacqueline D; Lu, Yinhui; Koch, Manuel; Hinton, Robert B; Kadler, Karl E; Lincoln, Joy

2008-10-24

Heart valve structures, derived from mesenchyme precursor cells, are composed of differentiated cell types and extracellular matrix arranged to facilitate valve function. Scleraxis (scx) is a transcription factor required for tendon cell differentiation and matrix organization. This study identified high levels of scx expression in remodeling heart valve structures at embryonic day 15.5 through postnatal stages using scx-GFP reporter mice and determined the in vivo function using mice null for scx. Scx(-/-) mice display significantly thickened heart valve structures from embryonic day 17.5, and valves from mutant mice show alterations in valve precursor cell differentiation and matrix organization. This is indicated by decreased expression of the tendon-related collagen type XIV, increased expression of cartilage-associated genes including sox9, as well as persistent expression of mesenchyme cell markers including msx1 and snai1. In addition, ultrastructure analysis reveals disarray of extracellular matrix and collagen fiber organization within the valve leaflet. Thickened valve structures and increased expression of matrix remodeling genes characteristic of human heart valve disease are observed in juvenile scx(-/-) mice. In addition, excessive collagen deposition in annular structures within the atrioventricular junction is observed. Collectively, our studies have identified an in vivo requirement for scx during valvulogenesis and demonstrate its role in cell lineage differentiation and matrix distribution in remodeling valve structures.

Modeling and life prediction methodology for Titanium Matrix Composites subjected to mission profiles

NASA Technical Reports Server (NTRS)

Mirdamadi, M.; Johnson, W. S.

1994-01-01

Titanium matrix composites (TMC) are being evaluated as structural materials for elevated temperature applications in future generation hypersonic vehicles. In such applications, TMC components are subjected to complex thermomechanical loading profiles at various elevated temperatures. Therefore, thermomechanical fatigue (TMF) testing, using a simulated mission profile, is essential for evaluation and development of life prediction methodologies. The objective of the research presented in this paper was to evaluate the TMF response of the (0/90)2s SCS-6/Timetal-21S subjected to a generic hypersonic flight profile and its portions with a temperature ranging from -130 C to 816 C. It was found that the composite modulus, prior to rapid degradation, had consistent values for all the profiles tested. A micromechanics based analysis was used to predict the stress-strain response of the laminate and of the constituents in each ply during thermomechanical loading conditions by using only constituent properties as input. The fiber was modeled as elastic with transverse orthotropic and temperature dependent properties. The matrix was modeled using a thermoviscoplastic constitutive relation. In the analysis, the composite modulus degradation was assumed to result from matrix cracking and was modeled by reducing the matrix modulus. Fatigue lives of the composite subjected to the complex generic hypersonic flight profile were well correlated using the predicted stress in 0 degree fibers.

Mathematical Modeling of Cancer Invasion: The Role of Membrane-Bound Matrix Metalloproteinases

PubMed Central

Deakin, Niall E.; Chaplain, Mark A. J.

2013-01-01

One of the hallmarks of cancer growth and metastatic spread is the process of local invasion of the surrounding tissue. Cancer cells achieve protease-dependent invasion by the secretion of enzymes involved in proteolysis. These overly expressed proteolytic enzymes then proceed to degrade the host tissue allowing the cancer cells to disseminate throughout the microenvironment by active migration and interaction with components of the extracellular matrix (ECM) such as collagen. In this paper we develop a mathematical model of cancer invasion which consider the role of matrix metalloproteinases (MMPs). Specifically our model will focus on two distinct types of MMP, i.e., soluble, diffusible MMPs (e.g., MMP-2) and membrane-bound MMPs (e.g., MT1-MMP), and the roles each of these plays in cancer invasion. The implications of MMP-2 activation by MMP-14 and the tissue inhibitor of metalloproteinases-2 are considered alongside the effect the architecture of the matrix may have when applied to a model of cancer invasion. Elements of the ECM architecture investigated include pore size of the matrix, since in some highly dense collagen structures such as breast tissue, the cancer cells are unable to physically fit through a porous region, and the crosslinking of collagen fibers. In this scenario, cancer cells rely on membrane-bound MMPs to forge a path through which degradation by other MMPs and movement of cancer cells becomes possible. PMID:23565505

Vitamin K-dependent carboxylation of matrix gla protein influences the risk of calciphylaxis

USDA-ARS?s Scientific Manuscript database

Matrix Gla protein (MGP) is a potent inhibitor of vascular calcification. The ability of MGP to inhibit calcification requires the activity of a vitamin K-dependent enzyme, which mediates MGP carboxylation. We investigated how MGP carboxylation influences the risk of calciphylaxis in adult patients ...

Air cathode structure manufacture

DOEpatents

Momyer, William R.; Littauer, Ernest L.

1985-01-01

An improved air cathode structure for use in primary batteries and the like. The cathode structure includes a matrix active layer, a current collector grid on one face of the matrix active layer, and a porous, nonelectrically conductive separator on the opposite face of the matrix active layer, the collector grid and separator being permanently bonded to the matrix active layer. The separator has a preselected porosity providing low IR losses and high resistance to air flow through the matrix active layer to maintain high bubble pressure during operation of the battery. In the illustrated embodiment, the separator was formed of porous polypropylene. A thin hydrophobic film is provided, in the preferred embodiment, on the current collecting metal grid.

Engineering a collagen matrix that replicates the biological properties of native extracellular matrix.

PubMed

Nam, Kwangwoo; Sakai, Yuuki; Funamoto, Seiichi; Kimura, Tsuyoshi; Kishida, Akio

2011-01-01

In this study, we aimed to replicate the function of native tissues that can be used in tissue engineering and regenerative medicine. The key to such replication is the preparation of an artificial collagen matrix that possesses a structure resembling that of the extracellular matrix. We, therefore, prepared a collagen matrix by fibrillogenesis in a NaCl/Na(2)HPO(4) aqueous solution using a dialysis cassette and investigated its biological behavior in vitro and in vivo. The in vitro cell adhesion and proliferation did not show any significant differences. The degradation rate in the living body could be controlled according to the preparation condition, where the collagen matrix with high water content (F-collagen matrix, >98%) showed fast degradation and collagen matrix with lower water content (T-collagen matrix, >80%) showed no degradation for 8 weeks. The degradation did not affect the inflammatory response at all and relatively faster wound healing response was observed. Comparing this result with that of collagen gel and decellularized cornea, it can be concluded that the structural factor is very important and no cell abnormal behavior would be observed for quaternary structured collagen matrix.

Chiral tunneling in gated inversion symmetric Weyl semimetal.

PubMed

Bai, Chunxu; Yang, Yanling; Chang, Kai

2016-02-18

Based on the chirality-resolved transfer-matrix method, we evaluate the chiral transport tunneling through Weyl semimetal multi-barrier structures created by periodic gates. It is shown that, in sharp contrast to the cases of three dimensional normal semimetals, the tunneling coefficient as a function of incident angle shows a strong anisotropic behavior. Importantly, the tunneling coefficients display an interesting periodic oscillation as a function of the crystallographic angle of the structures. With the increasement of the barriers, the tunneling current shows a Fabry-Perot type interferences. For superlattice structures, the fancy miniband effect has been revealed. Our results show that the angular dependence of the first bandgap can be reduced into a Lorentz formula. The disorder suppresses the oscillation of the tunneling conductance, but would not affect its average amplitude. This is in sharp contrast to that in multi-barrier conventional semiconductor structures. Moreover, numerical results for the dependence of the angularly averaged conductance on the incident energy and the structure parameters are presented and contrasted with those in two dimensional relativistic materials. Our work suggests that the gated Weyl semimetal opens a possible new route to access to new type nanoelectronic device.

Meta-ecosystem dynamics and functioning on finite spatial networks

PubMed Central

Marleau, Justin N.; Guichard, Frédéric; Loreau, Michel

2014-01-01

The addition of spatial structure to ecological concepts and theories has spurred integration between sub-disciplines within ecology, including community and ecosystem ecology. However, the complexity of spatial models limits their implementation to idealized, regular landscapes. We present a model meta-ecosystem with finite and irregular spatial structure consisting of local nutrient–autotrophs–herbivores ecosystems connected through spatial flows of materials and organisms. We study the effect of spatial flows on stability and ecosystem functions, and provide simple metrics of connectivity that can predict these effects. Our results show that high rates of nutrient and herbivore movement can destabilize local ecosystem dynamics, leading to spatially heterogeneous equilibria or oscillations across the meta-ecosystem, with generally increased meta-ecosystem primary and secondary production. However, the onset and the spatial scale of these emergent dynamics depend heavily on the spatial structure of the meta-ecosystem and on the relative movement rate of the autotrophs. We show how this strong dependence on finite spatial structure eludes commonly used metrics of connectivity, but can be predicted by the eigenvalues and eigenvectors of the connectivity matrix that describe the spatial structure and scale. Our study indicates the need to consider finite-size ecosystems in meta-ecosystem theory. PMID:24403323

Chiral tunneling in gated inversion symmetric Weyl semimetal

PubMed Central

Bai, Chunxu; Yang, Yanling; Chang, Kai

2016-01-01

Based on the chirality-resolved transfer-matrix method, we evaluate the chiral transport tunneling through Weyl semimetal multi-barrier structures created by periodic gates. It is shown that, in sharp contrast to the cases of three dimensional normal semimetals, the tunneling coefficient as a function of incident angle shows a strong anisotropic behavior. Importantly, the tunneling coefficients display an interesting periodic oscillation as a function of the crystallographic angle of the structures. With the increasement of the barriers, the tunneling current shows a Fabry-Perot type interferences. For superlattice structures, the fancy miniband effect has been revealed. Our results show that the angular dependence of the first bandgap can be reduced into a Lorentz formula. The disorder suppresses the oscillation of the tunneling conductance, but would not affect its average amplitude. This is in sharp contrast to that in multi-barrier conventional semiconductor structures. Moreover, numerical results for the dependence of the angularly averaged conductance on the incident energy and the structure parameters are presented and contrasted with those in two dimensional relativistic materials. Our work suggests that the gated Weyl semimetal opens a possible new route to access to new type nanoelectronic device. PMID:26888491

Enhanced nutrient transport improves the depth-dependent properties of tri-layered engineered cartilage constructs with zonal co-culture of chondrocytes and MSCs.

PubMed

Kim, Minwook; Farrell, Megan J; Steinberg, David R; Burdick, Jason A; Mauck, Robert L

2017-08-01

Biomimetic design in cartilage tissue engineering is a challenge given the complexity of the native tissue. While numerous studies have generated constructs with near-native bulk properties, recapitulating the depth-dependent features of native tissue remains a challenge. Furthermore, limitations in nutrient transport and matrix accumulation in engineered constructs hinders maturation within the central core of large constructs. To overcome these limitations, we fabricated tri-layered constructs that recapitulate the depth-dependent cellular organization and functional properties of native tissue using zonally derived chondrocytes co-cultured with MSCs. We also introduced porous hollow fibers (HFs) and HFs/cotton threads to enhance nutrient transport. Our results showed that tri-layered constructs with depth-dependent organization and properties could be fabricated. The addition of HFs or HFs/threads improved matrix accumulation in the central core region. With HF/threads, the local modulus in the deep region of tri-layered constructs nearly matched that of native tissue, though the properties in the central regions remained lower. These constructs reproduced the zonal organization and depth-dependent properties of native tissue, and demonstrate that a layer-by-layer fabrication scheme holds promise for the biomimetic repair of focal cartilage defects. Articular cartilage is a highly organized tissue driven by zonal heterogeneity of cells, extracellular matrix proteins and fibril orientations, resulting in depth-dependent mechanical properties. Therefore, the recapitulation of the functional properties of native cartilage in a tissue engineered construct requires such a biomimetic design of the morphological organization, and this has remained a challenge in cartilage tissue engineering. This study demonstrates that a layer-by-layer fabrication scheme, including co-cultures of zone-specific articular CHs and MSCs, can reproduce the depth-dependent characteristics and mechanical properties of native cartilage while minimizing the need for large numbers of chondrocytes. In addition, introduction of a porous hollow fiber (combined with a cotton thread) enhanced nutrient transport and depth-dependent properties of the tri-layered construct. Such a tri-layered construct may provide critical advantages for focal cartilage repair. These constructs hold promise for restoring native tissue structure and function, and may be beneficial in terms of zone-to-zone integration with adjacent host tissue and providing more appropriate strain transfer after implantation. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Cluster structure in the correlation coefficient matrix can be characterized by abnormal eigenvalues

NASA Astrophysics Data System (ADS)

Nie, Chun-Xiao

2018-02-01

In a large number of previous studies, the researchers found that some of the eigenvalues of the financial correlation matrix were greater than the predicted values of the random matrix theory (RMT). Here, we call these eigenvalues as abnormal eigenvalues. In order to reveal the hidden meaning of these abnormal eigenvalues, we study the toy model with cluster structure and find that these eigenvalues are related to the cluster structure of the correlation coefficient matrix. In this paper, model-based experiments show that in most cases, the number of abnormal eigenvalues of the correlation matrix is equal to the number of clusters. In addition, empirical studies show that the sum of the abnormal eigenvalues is related to the clarity of the cluster structure and is negatively correlated with the correlation dimension.

Correlation functions from a unified variational principle: Trial Lie groups

NASA Astrophysics Data System (ADS)

Balian, R.; Vénéroni, M.

2015-11-01

Time-dependent expectation values and correlation functions for many-body quantum systems are evaluated by means of a unified variational principle. It optimizes a generating functional depending on sources associated with the observables of interest. It is built by imposing through Lagrange multipliers constraints that account for the initial state (at equilibrium or off equilibrium) and for the backward Heisenberg evolution of the observables. The trial objects are respectively akin to a density operator and to an operator involving the observables of interest and the sources. We work out here the case where trial spaces constitute Lie groups. This choice reduces the original degrees of freedom to those of the underlying Lie algebra, consisting of simple observables; the resulting objects are labeled by the indices of a basis of this algebra. Explicit results are obtained by expanding in powers of the sources. Zeroth and first orders provide thermodynamic quantities and expectation values in the form of mean-field approximations, with dynamical equations having a classical Lie-Poisson structure. At second order, the variational expression for two-time correlation functions separates-as does its exact counterpart-the approximate dynamics of the observables from the approximate correlations in the initial state. Two building blocks are involved: (i) a commutation matrix which stems from the structure constants of the Lie algebra; and (ii) the second-derivative matrix of a free-energy function. The diagonalization of both matrices, required for practical calculations, is worked out, in a way analogous to the standard RPA. The ensuing structure of the variational formulae is the same as for a system of non-interacting bosons (or of harmonic oscillators) plus, at non-zero temperature, classical Gaussian variables. This property is explained by mapping the original Lie algebra onto a simpler Lie algebra. The results, valid for any trial Lie group, fulfill consistency properties and encompass several special cases: linear responses, static and time-dependent fluctuations, zero- and high-temperature limits, static and dynamic stability of small deviations.

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

Balian, R., E-mail: roger.balian@cea.fr; Vénéroni, M.

Time-dependent expectation values and correlation functions for many-body quantum systems are evaluated by means of a unified variational principle. It optimizes a generating functional depending on sources associated with the observables of interest. It is built by imposing through Lagrange multipliers constraints that account for the initial state (at equilibrium or off equilibrium) and for the backward Heisenberg evolution of the observables. The trial objects are respectively akin to a density operator and to an operator involving the observables of interest and the sources. We work out here the case where trial spaces constitute Lie groups. This choice reduces themore » original degrees of freedom to those of the underlying Lie algebra, consisting of simple observables; the resulting objects are labeled by the indices of a basis of this algebra. Explicit results are obtained by expanding in powers of the sources. Zeroth and first orders provide thermodynamic quantities and expectation values in the form of mean-field approximations, with dynamical equations having a classical Lie–Poisson structure. At second order, the variational expression for two-time correlation functions separates–as does its exact counterpart–the approximate dynamics of the observables from the approximate correlations in the initial state. Two building blocks are involved: (i) a commutation matrix which stems from the structure constants of the Lie algebra; and (ii) the second-derivative matrix of a free-energy function. The diagonalization of both matrices, required for practical calculations, is worked out, in a way analogous to the standard RPA. The ensuing structure of the variational formulae is the same as for a system of non-interacting bosons (or of harmonic oscillators) plus, at non-zero temperature, classical Gaussian variables. This property is explained by mapping the original Lie algebra onto a simpler Lie algebra. The results, valid for any trial Lie group, fulfill consistency properties and encompass several special cases: linear responses, static and time-dependent fluctuations, zero- and high-temperature limits, static and dynamic stability of small deviations.« less

The q-dependent detrended cross-correlation analysis of stock market

NASA Astrophysics Data System (ADS)

Zhao, Longfeng; Li, Wei; Fenu, Andrea; Podobnik, Boris; Wang, Yougui; Stanley, H. Eugene

2018-02-01

Properties of the q-dependent cross-correlation matrices of the stock market have been analyzed by using random matrix theory and complex networks. The correlation structures of the fluctuations at different magnitudes have unique properties. The cross-correlations among small fluctuations are much stronger than those among large fluctuations. The large and small fluctuations are dominated by different groups of stocks. We use complex network representation to study these q-dependent matrices and discover some new identities. By utilizing those q-dependent correlation-based networks, we are able to construct some portfolios of those more independent stocks which consistently perform better. The optimal multifractal order for portfolio optimization is around q  =  2 under the mean-variance portfolio framework, and q\\in[2, 6] under the expected shortfall criterion. These results have deepened our understanding regarding the collective behavior of the complex financial system.

Wavelet analysis of biological tissue's Mueller-matrix images

NASA Astrophysics Data System (ADS)

Tomka, Yu. Ya.

2008-05-01

The interrelations between statistics of the 1st-4th orders of the ensemble of Mueller-matrix images and geometric structure of birefringent architectonic nets of different morphological structure have been analyzed. The sensitivity of asymmetry and excess of statistic distributions of matrix elements Cik to changing of orientation structure of optically anisotropic protein fibrils of physiologically normal and pathologically changed biological tissues architectonics has been shown.

Salient Object Detection via Structured Matrix Decomposition.

PubMed

Peng, Houwen; Li, Bing; Ling, Haibin; Hu, Weiming; Xiong, Weihua; Maybank, Stephen J

2016-05-04

Low-rank recovery models have shown potential for salient object detection, where a matrix is decomposed into a low-rank matrix representing image background and a sparse matrix identifying salient objects. Two deficiencies, however, still exist. First, previous work typically assumes the elements in the sparse matrix are mutually independent, ignoring the spatial and pattern relations of image regions. Second, when the low-rank and sparse matrices are relatively coherent, e.g., when there are similarities between the salient objects and background or when the background is complicated, it is difficult for previous models to disentangle them. To address these problems, we propose a novel structured matrix decomposition model with two structural regularizations: (1) a tree-structured sparsity-inducing regularization that captures the image structure and enforces patches from the same object to have similar saliency values, and (2) a Laplacian regularization that enlarges the gaps between salient objects and the background in feature space. Furthermore, high-level priors are integrated to guide the matrix decomposition and boost the detection. We evaluate our model for salient object detection on five challenging datasets including single object, multiple objects and complex scene images, and show competitive results as compared with 24 state-of-the-art methods in terms of seven performance metrics.

Construction of the Dependence Matrix Based on the TRIZ Contradiction Matrix in OOD

NASA Astrophysics Data System (ADS)

Ma, Jianhong; Zhang, Quan; Wang, Yanling; Luo, Tao

In the Object-Oriented software design (OOD), design of the class and object, definition of the classes’ interface and inheritance levels and determination of dependent relations have a serious impact on the reusability and flexibility of the system. According to the concrete problems of design, how to select the right solution from the hundreds of the design schemas which has become the focus of attention of designers. After analyzing lots of software design schemas in practice and Object-Oriented design patterns, this paper constructs the dependence matrix of Object-Oriented software design filed, referring to contradiction matrix of TRIZ (Theory of Inventive Problem Solving) proposed by the former Soviet Union innovation master Altshuller. As the practice indicates, it provides a intuitive, common and standardized method for designers to choose the right design schema. Make research and communication more effectively, and also improve the software development efficiency and software quality.

Impact of Tunnel-Barrier Strength on Magnetoresistance in Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Morgan, Caitlin; Misiorny, Maciej; Metten, Dominik; Heedt, Sebastian; Schäpers, Thomas; Schneider, Claus M.; Meyer, Carola

2016-05-01

We investigate magnetoresistance in spin valves involving CoPd-contacted carbon nanotubes. Both the temperature and bias-voltage dependence clearly indicate tunneling magnetoresistance as the origin. We show that this effect is significantly affected by the tunnel-barrier strength, which appears to be one reason for the variation between devices previously detected in similar structures. Modeling the data by means of the scattering matrix approach, we find a nontrivial dependence of the magnetoresistance on the barrier strength. Furthermore, an analysis of the spin precession observed in a nonlocal Hanle measurement yields a spin lifetime of τs=1.1 ns , a value comparable with those found in silicon- or graphene-based spin-valve devices.

Restricting the high-temperature growth of nanocrystalline tin oxide

NASA Astrophysics Data System (ADS)

Savin, S.; Chadwick, A. V.

2003-01-01

The sensitivity of tin oxide is dependent on various factors, one of which is the grain size. Three methods have been investigated with the aim of stabilising the grain size in the nanometer range, namely; (i) encapsulation within a silica matrix, (ii) coating the crystallites with hexamethyldisilazane and (iii) pinning the grain boundaries with a second metal oxide nanocrystal. The resulting materials have been characterised by X-ray powder diffraction (XRPD), Extended X-ray absorption fine structure (EXAFS) and conductivity measurements.

TM4SF5 promotes metastatic behavior of cells in 3D extracellular matrix gels by reducing dependency on environmental cues

PubMed Central

Nam, Seo Hee; Cheong, Jin-Gyu; Jeong, Doyoung; Lee, Seo-Jin; Pan, Cheol-Ho; Jung, Jae Woo; Kim, Hye-Jin; Ryu, Jihye; Kim, Ji Eon; Kim, Somi; Cho, Chang Yun; Kang, Min-Kyung; Lee, Kyung-Min; Lee, Jung Weon

2017-01-01

Transmembrane 4 L six family member 5 (TM4SF5) is highly expressed in hepatocellular carcinoma tissues and enhances migration in two-dimensional environments. Here, we investigated how TM4SF5 is involved in diverse pro-metastatic phenotypes in in vivo-like three-dimensional (3D) extracellular matrix gels. TM4SF5-positive cells aggressively formed invasive foci in 3D Matrigel, depending on TM4SF5-mediated signaling activity, cytoskeletal organization, and matrix metallopeptidase (MMP) 2-mediated extracellular remodeling, whereas TM4SF5-null cells did not. The TM4SF5-null cells did, however, form invasive foci in 3D Matrigel following inhibition of Rho-associated protein kinase or addition of collagen I, suggesting that collagen I compensated for TM4SF5 expression. Similarly, TM4SF5-positive cells expressing vascular endothelial-cadherin formed network-like vasculogenic mimicry in 3D Matrigel and collagen I mixture gels, whereas TM4SF5-negative cells in the mixture gels displayed the network structures only upon further treatment with epidermal growth factor. The foci formation also required MMP2-mediated remodeling of the extracellular matrix. Co-cultures exhibited TM4SF5-positive or cancer-associated fibroblasts at the outward edges of TM4SF5-null cell clusters. Compared with TM4SF5-null cells, TM4SF5-positive cells in 3D collagen gels showed a more invasive outgrowth with dramatic invadopodia. These observations suggest that TM4SF5 plays roles in the promotion of diverse metastatic properties with fewer environmental requirements than TM4SF5-negative cells. PMID:29137358

Cardiac differentiation of cardiosphere-derived cells in scaffolds mimicking morphology of the cardiac extracellular matrix.

PubMed

Xu, Yanyi; Patnaik, Sourav; Guo, Xiaolei; Li, Zhenqing; Lo, Wilson; Butler, Ryan; Claude, Andrew; Liu, Zhenguo; Zhang, Ge; Liao, Jun; Anderson, Peter M; Guan, Jianjun

2014-08-01

Stem cell therapy has the potential to regenerate heart tissue after myocardial infarction (MI). The regeneration is dependent upon cardiac differentiation of the delivered stem cells. We hypothesized that timing of the stem cell delivery determines the extent of cardiac differentiation as cell differentiation is dependent on matrix properties such as biomechanics, structure and morphology, and these properties in cardiac extracellular matrix (ECM) continuously vary with time after MI. In order to elucidate the relationship between ECM properties and cardiac differentiation, we created an in vitro model based on ECM-mimicking fibers and a type of cardiac progenitor cell, cardiosphere-derived cells (CDCs). A simultaneous fiber electrospinning and cell electrospraying technique was utilized to fabricate constructs. By blending a highly soft hydrogel with a relatively stiff polyurethane and modulating fabrication parameters, tissue constructs with similar cell adhesion property but different global modulus, single fiber modulus, fiber density and fiber alignment were achieved. The CDCs remained alive within the constructs during a 1week culture period. CDC cardiac differentiation was dependent on the scaffold modulus, fiber volume fraction and fiber alignment. Two constructs with relatively low scaffold modulus, ∼50-60kPa, most significantly directed the CDC differentiation into mature cardiomyocytes as evidenced by gene expressions of cardiac troponin T (cTnT), calcium channel (CACNA1c) and cardiac myosin heavy chain (MYH6), and protein expressions of cardiac troponin I (cTnI) and connexin 43 (CX43). Of these two low-modulus constructs, the extent of differentiation was greater for lower fiber alignment and higher fiber volume fraction. These results suggest that cardiac ECM properties may have an effect on cardiac differentiation of delivered stem cells. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Sol-gel synthesis and in vitro bioactivity of copper and zinc-doped silicate bioactive glasses and glass-ceramics.

PubMed

Bejarano, Julian; Caviedes, Pablo; Palza, Humberto

2015-03-11

Metal doping of bioactive glasses based on ternary 60SiO2-36CaO-4P2O5 (58S) and quaternary 60SiO2-25CaO-11Na2O-4P2O5 (NaBG) mol% compositions synthesized using a sol-gel process was analyzed. In particular, the effect of incorporating 1, 5 and 10 mol% of CuO and ZnO (replacing equivalent quantities of CaO) on the texture, in vitro bioactivity, and cytocompatibility of these materials was evaluated. Our results showed that the addition of metal ions can modulate the textural property of the matrix and its crystal structure. Regarding the bioactivity, after soaking in simulated body fluid (SBF) undoped 58S and NaBG glasses developed an apatite surface layer that was reduced in the doped glasses depending on the type of metal and its concentration with Zn displaying the largest inhibitions. Both the ion release from samples and the ion adsorption from the medium depended on the type of matrix with 58S glasses showing the highest values. Pure NaBG glass was more cytocompatible to osteoblast-like cells (SaOS-2) than pure 58S glass as tested by 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay. The incorporation of metal ions decreased the cytocompatibility of the glasses depending on their concentration and on the glass matrix doped. Our results show that by changing the glass composition and by adding Cu or Zn, bioactive materials with different textures, bioactivity and cytocompatibility can be synthesized.

FaCSI: A block parallel preconditioner for fluid-structure interaction in hemodynamics

NASA Astrophysics Data System (ADS)

Deparis, Simone; Forti, Davide; Grandperrin, Gwenol; Quarteroni, Alfio

2016-12-01

Modeling Fluid-Structure Interaction (FSI) in the vascular system is mandatory to reliably compute mechanical indicators in vessels undergoing large deformations. In order to cope with the computational complexity of the coupled 3D FSI problem after discretizations in space and time, a parallel solution is often mandatory. In this paper we propose a new block parallel preconditioner for the coupled linearized FSI system obtained after space and time discretization. We name it FaCSI to indicate that it exploits the Factorized form of the linearized FSI matrix, the use of static Condensation to formally eliminate the interface degrees of freedom of the fluid equations, and the use of a SIMPLE preconditioner for saddle-point problems. FaCSI is built upon a block Gauss-Seidel factorization of the FSI Jacobian matrix and it uses ad-hoc preconditioners for each physical component of the coupled problem, namely the fluid, the structure and the geometry. In the fluid subproblem, after operating static condensation of the interface fluid variables, we use a SIMPLE preconditioner on the reduced fluid matrix. Moreover, to efficiently deal with a large number of processes, FaCSI exploits efficient single field preconditioners, e.g., based on domain decomposition or the multigrid method. We measure the parallel performances of FaCSI on a benchmark cylindrical geometry and on a problem of physiological interest, namely the blood flow through a patient-specific femoropopliteal bypass. We analyze the dependence of the number of linear solver iterations on the cores count (scalability of the preconditioner) and on the mesh size (optimality).

The concentration parameter thermal microstresses as the thermophysical characteristics of two-phase materials

NASA Astrophysics Data System (ADS)

Kuanishev, V. T.; Sachkov, I. N.; Sorogin, I. G.; Sorogina, T. I.

2017-11-01

Thermal strength is one of the main thermophysical characteristics of structural materials. For homogeneous systems it is determined by the strength characteristics of the material. While for inhomogeneous systems, in particular, multiphase ones, it is necessary to consider the nature of the microstructure. Heat resistant real materials such as steels are known to be multi-phase systems. One of the mechanisms of their destruction is associated with the presence of propagating heat fluxes that generate thermal stresses. The aim of this paper is to evaluate the patterns of the formation of spatial distributions of thermal stresses in matrix systems of round inclusions characterized by different mutual disposition. The spatial distributions of thermal stresses in a two-phase material characterized by a matrix structure with round inclusions are investigated. For the numerical solution of the problem of stationary thermal conductivity the finite element method with discretization of the medium by triangular elements is used. It was found that at certain points in the medium the values of thermal stresses are ten times higher than the average for the material. It is shown that the spatial distribution and the local magnitude of the temperature gradient depend on the shape of the particles of the phase components and the values of their thermal conductivities. It is considered that the elastic moduli of inclusion and matrix differ little from each other.

Scale-Dependent Fracture-Matrix Interactions And Their Impact on Radionuclide Transport - Final Report

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

Detwiler, Russell

Matrix diffusion and adsorption within a rock matrix are widely regarded as important mechanisms for retarding the transport of radionuclides and other solutes in fractured rock (e.g., Neretnieks, 1980; Tang et al., 1981; Maloszewski and Zuber, 1985; Novakowski and Lapcevic, 1994; Jardine et al., 1999; Zhou and Xie, 2003; Reimus et al., 2003a,b). When remediation options are being evaluated for old sources of contamination, where a large fraction of contaminants reside within the rock matrix, slow diffusion out of the matrix greatly increases the difficulty and timeframe of remediation. Estimating the rates of solute exchange between fractures and the adjacentmore » rock matrix is a critical factor in quantifying immobilization and/or remobilization of DOE-relevant contaminants within the subsurface. In principle, the most rigorous approach to modeling solute transport with fracture-matrix interaction would be based on local-scale coupled advection-diffusion/dispersion equations for the rock matrix and in discrete fractures that comprise the fracture network (Discrete Fracture Network and Matrix approach, hereinafter referred to as DFNM approach), fully resolving aperture variability in fractures and matrix property heterogeneity. However, such approaches are computationally demanding, and thus, many predictive models rely upon simplified models. These models typically idealize fracture rock masses as a single fracture or system of parallel fractures interacting with slabs of porous matrix or as a mobile-immobile or multi-rate mass transfer system. These idealizations provide tractable approaches for interpreting tracer tests and predicting contaminant mobility, but rely upon a fitted effective matrix diffusivity or mass-transfer coefficients. However, because these fitted parameters are based upon simplified conceptual models, their effectiveness at predicting long-term transport processes remains uncertain. Evidence of scale dependence of effective matrix diffusion coefficients obtained from tracer tests highlights this point and suggests that the underlying mechanisms and relationship between rock and fracture properties are not fully understood in large complex fracture networks. In this project, we developed a high-resolution DFN model of solute transport in fracture networks to explore and quantify the mechanisms that control transport in complex fracture networks and how these may give rise to observed scale-dependent matrix diffusion coefficients. Results demonstrate that small scale heterogeneity in the flow field caused by local aperture variability within individual fractures can lead to long-tailed breakthrough curves indicative of matrix diffusion, even in the absence of interactions with the fracture matrix. Furthermore, the temporal and spatial scale dependence of these processes highlights the inability of short-term tracer tests to estimate transport parameters that will control long-term fate and transport of contaminants in fractured aquifers.« less

Structure and function of matrix proteins and peptides in the biomineral formation in crustaceans.

PubMed

Nagasawa, Hiromichi

2011-01-01

Crustaceans have hard cuticle with layered structure, which is composed mainly of chitin, proteins, and calcium carbonate. Crustaceans grow by shedding the old cuticle and replacing it with a new one. Decalcification in the cuticle during the pre-molt stage and concomitant calcification in the stomach to form gastroliths observed in some crustacean species are triggered by the molting hormone. Various proteins and peptides have been identified from calcified cuticle and gastroliths, and their functions have been examined in terms of calcification and interaction with chitin. Acidic nature of matrix proteins is important for recruitment of calcium ions and interaction with calcium carbonate. Examination of the relationship between amino acid sequence containing acidic amino acid residues and calcification inhibitory activity revealed that the potency did not depend on the sequence but on the number of acidic amino acid residues. Calcium carbonate in the calcified tissues of crustaceans is amorphous in many cases. Crustaceans take a strategy to induce and maintain amorphous calcium carbonate by using low-molecular-weight phosphorus compounds.

Revisiting polarimetry near the isotropic point of an optically active, non-enantiomorphous, molecular crystal.

PubMed

Martin, Alexander T; Tan, Melissa; Nichols, Shane M; Timothy, Emily; Kahr, Bart

2018-07-01

Accurate polarimetric measurements of the optical activity of crystals along low symmetry directions are facilitated by isotropic points, frequencies where dispersion curves of eigenrays cross and the linear birefringence disappears. We report here the optical properties and structure of achiral, uniaxial (point group D 2d ) potassium trihydrogen di-(cis-4-cyclohexene-1,2-dicarboxylate) dihydrate, whose isotropic point was previously detected (S. A. Kim, C. Grieswatch, H. Küppers, Zeit. Krist. 1993; 208:219-222) and exploited for a singular measurement of optical activity normal to the optic axis. The crystal structure associated with the aforementioned study was never published. We report it here, confirming the space group assignment I 4¯c2, along with the frequency dependence of the fundamental optical properties and the constitutive tensors by fitting optical dispersion relations to measured Mueller matrix spectra. k-Space maps of circular birefringence and of the Mueller matrix near the isotropic wavelength are measured and simulated. The signs of optical rotation are correlated with the absolute crystallographic directions. © 2018 Wiley Periodicals, Inc.

Optical absorption of zigzag single walled boron nitride nanotubes in axial magnetic field

NASA Astrophysics Data System (ADS)

Chegel, Raad; Behzad, Somayeh

2013-11-01

We have investigated the effect of axial magnetic field on the band structure, dipole matrix elements and absorption spectrum in different energy ranges, using tight binding approximation. It is found that magnetic field breaks the degeneracy in the band structure and creates new allowed transitions in the dipole matrix which leads to creation of new peaks in the absorption spectrum. It is found that, unlike to CNTs which show metallic-semiconductor transition, the BNNTs remain semiconductor in any magnetic field strength. By calculation the diameter dependence of peak positions, we found that the positions of three first peaks in the lower energy region (E <5.3 eV) are proportional to n-2. In the middle energy region (7 < E < 7.5 eV) all (n, 0) zigzag BNNTs, with even and odd nanotube index, have two distinct peaks in the absence of magnetic field which these peaks may be used to identify zigzag BNNTs from other tube chiralities. For odd (even) tubes, in the middle energy region, applying the magnetic field leads to splitting of these two peaks into three (five) distinct peaks.

Optical and morphological study of disorder in opals

NASA Astrophysics Data System (ADS)

Palacios-Lidón, E.; Juárez, B. H.; Castillo-Martínez, E.; López, C.

2005-03-01

An optical and morphological study has been carried out to understand the role of intrinsic defects in the optical properties of opal-based photonic crystals. By doping poly(methylmethacrylate) (PMMA) thin-film opals with larger polystyrene (PS) spheres, structural disorder has being generated perturbing the PMMA matrix periodicity. It is shown that this disorder dramatically affects the optical response of the system worsening its photonic properties. It has been found that the effect of doping is highly dependent not only on the concentration but also on the relative size of the dopant with reference to the matrix. Through a detailed scanning electron microscopy inspection, the sort of structural defects involved, derived from the different particle size used, has been characterized. A direct relationship between the observed optical response with the different perturbations generated in the lattice has been found. In addition, from this study it can be concluded that it is possible to grow high quality alloyed photonic crystals, exhibiting intermediate photonic properties between pure PMMA and pure PS opals by simple sphere size matching and variation of the relative concentration of both components.

Separating temporal and topological effects in walk-based network centrality.

PubMed

Colman, Ewan R; Charlton, Nathaniel

2016-07-01

The recently introduced concept of dynamic communicability is a valuable tool for ranking the importance of nodes in a temporal network. Two metrics, broadcast score and receive score, were introduced to measure the centrality of a node with respect to a model of contagion based on time-respecting walks. This article examines the temporal and structural factors influencing these metrics by considering a versatile stochastic temporal network model. We analytically derive formulas to accurately predict the expectation of the broadcast and receive scores when one or more columns in a temporal edge-list are shuffled. These methods are then applied to two publicly available data sets and we quantify how much the centrality of each individual depends on structural or temporal influences. From our analysis, we highlight two practical contributions: a way to control for temporal variation when computing dynamic communicability and the conclusion that the broadcast and receive scores can, under a range of circumstances, be replaced by the row and column sums of the matrix exponential of a weighted adjacency matrix given by the data.

New Technologies for Surgery of the Congenital Cardiac Defect

PubMed Central

Kalfa, David; Bacha, Emile

2013-01-01

The surgical repair of complex congenital heart defects frequently requires additional tissue in various forms, such as patches, conduits, and valves. These devices often require replacement over a patient’s lifetime because of degeneration, calcification, or lack of growth. The main new technologies in congenital cardiac surgery aim at, on the one hand, avoiding such reoperations and, on the other hand, improving long-term outcomes of devices used to repair or replace diseased structural malformations. These technologies are: 1) new patches: CorMatrix® patches made of decellularized porcine small intestinal submucosa extracellular matrix; 2) new devices: the Melody® valve (for percutaneous pulmonary valve implantation) and tissue-engineered valved conduits (either decellularized scaffolds or polymeric scaffolds); and 3) new emerging fields, such as antenatal corrective cardiac surgery or robotically assisted congenital cardiac surgical procedures. These new technologies for structural malformation surgery are still in their infancy but certainly present great promise for the future. But the translation of these emerging technologies to routine health care and public health policy will also largely depend on economic considerations, value judgments, and political factors. PMID:23908869

Extended Stokes shift in fluorescent proteins: chromophore-protein interactions in a near-infrared TagRFP675 variant.

PubMed

Piatkevich, Kiryl D; Malashkevich, Vladimir N; Morozova, Kateryna S; Nemkovich, Nicolai A; Almo, Steven C; Verkhusha, Vladislav V

2013-01-01

Most GFP-like fluorescent proteins exhibit small Stokes shifts (10-45 nm) due to rigidity of the chromophore environment that excludes non-fluorescent relaxation to a ground state. An unusual near-infrared derivative of the red fluorescent protein mKate, named TagRFP675, exhibits the Stokes shift, which is 30 nm extended comparing to that of the parental protein. In physiological conditions, TagRFP675 absorbs at 598 nm and emits at 675 nm that makes it the most red-shifted protein of the GFP-like protein family. In addition, its emission maximum strongly depends on the excitation wavelength. Structures of TagRFP675 revealed the common DsRed-like chromophore, which, however, interacts with the protein matrix via an extensive network of hydrogen bonds capable of large flexibility. Based on the spectroscopic, biochemical, and structural analysis we suggest that the rearrangement of the hydrogen bond interactions between the chromophore and the protein matrix is responsible for the TagRFP675 spectral properties.

Optimization and control of dynamic percolationin nanostructured silicon oils

NASA Astrophysics Data System (ADS)

Badard, Mathieu; Combessis, Anthony; Allais, Arnaud; Flandin, Lionel

2017-06-01

The addition of carbonaceous fillers in polymers allows the conception of composites with optimized electrical properties. The conductivity of such material depends of the fillers structuration in matrix, especially the presence of percolated network. The objective of this paper is to understand the main aggregation mechanisms of carbon nanotubes in different media. The structuration of these filler network is probed by the use of electrical and dielectrical measurements. The innovative part of our work lies in the use of liquid matrices, especially silicon oils, to overcome mechanical constraints present in polymers on the one hand and to simplify processing on the other hand. Our work has revealed a filler aggregation over time, well known as dynamic percolation. Conductivity has been modeled as a function of time and filler content from Kirkpatrick equation. The further use of an electrical field led to conductivity enhancement as well as a decrease in percolation threshold. Finally, a study of intrinsic parameters of matrix has shown a strong effect of viscosity and surface tension on nanotubes aggregation. Contribution to the topical issue "Electrical Engineering Symposium (SGE 2016)", edited by Adel Razek

Separating temporal and topological effects in walk-based network centrality

NASA Astrophysics Data System (ADS)

Colman, Ewan R.; Charlton, Nathaniel

2016-07-01

The recently introduced concept of dynamic communicability is a valuable tool for ranking the importance of nodes in a temporal network. Two metrics, broadcast score and receive score, were introduced to measure the centrality of a node with respect to a model of contagion based on time-respecting walks. This article examines the temporal and structural factors influencing these metrics by considering a versatile stochastic temporal network model. We analytically derive formulas to accurately predict the expectation of the broadcast and receive scores when one or more columns in a temporal edge-list are shuffled. These methods are then applied to two publicly available data sets and we quantify how much the centrality of each individual depends on structural or temporal influences. From our analysis, we highlight two practical contributions: a way to control for temporal variation when computing dynamic communicability and the conclusion that the broadcast and receive scores can, under a range of circumstances, be replaced by the row and column sums of the matrix exponential of a weighted adjacency matrix given by the data.

Tensor completion for estimating missing values in visual data.

PubMed

Liu, Ji; Musialski, Przemyslaw; Wonka, Peter; Ye, Jieping

2013-01-01

In this paper, we propose an algorithm to estimate missing values in tensors of visual data. The values can be missing due to problems in the acquisition process or because the user manually identified unwanted outliers. Our algorithm works even with a small amount of samples and it can propagate structure to fill larger missing regions. Our methodology is built on recent studies about matrix completion using the matrix trace norm. The contribution of our paper is to extend the matrix case to the tensor case by proposing the first definition of the trace norm for tensors and then by building a working algorithm. First, we propose a definition for the tensor trace norm that generalizes the established definition of the matrix trace norm. Second, similarly to matrix completion, the tensor completion is formulated as a convex optimization problem. Unfortunately, the straightforward problem extension is significantly harder to solve than the matrix case because of the dependency among multiple constraints. To tackle this problem, we developed three algorithms: simple low rank tensor completion (SiLRTC), fast low rank tensor completion (FaLRTC), and high accuracy low rank tensor completion (HaLRTC). The SiLRTC algorithm is simple to implement and employs a relaxation technique to separate the dependent relationships and uses the block coordinate descent (BCD) method to achieve a globally optimal solution; the FaLRTC algorithm utilizes a smoothing scheme to transform the original nonsmooth problem into a smooth one and can be used to solve a general tensor trace norm minimization problem; the HaLRTC algorithm applies the alternating direction method of multipliers (ADMMs) to our problem. Our experiments show potential applications of our algorithms and the quantitative evaluation indicates that our methods are more accurate and robust than heuristic approaches. The efficiency comparison indicates that FaLTRC and HaLRTC are more efficient than SiLRTC and between FaLRTC an- HaLRTC the former is more efficient to obtain a low accuracy solution and the latter is preferred if a high-accuracy solution is desired.

Simulation of irradiation hardening of Zircaloy within plate-type dispersion nuclear fuel elements

NASA Astrophysics Data System (ADS)

Jiang, Yijie; Wang, Qiming; Cui, Yi; Huo, Yongzhong; Ding, Shurong

2011-06-01

Within plate-type dispersion nuclear fuel elements, the metal matrix and cladding attacked continuously by fast neutrons undergo irradiation hardening, which might have remarkable effects upon the mechanical behaviors within fuel elements. In this paper, with the irradiation hardening effect of metal materials mainly considered together with irradiation growth effect of the cladding, the three-dimensional large-deformation constitutive relations for the metal matrix and cladding are developed. The method of virtual temperature increase in the previous studies is further developed to model the irradiation swelling of fuel particles; the method of anisotropic thermal expansion is introduced to model irradiation growth of the cladding; and a method of multi-step-temperature loading is proposed to simulate the coupling features of irradiation-induced swelling of the fuel particles together with irradiation growth of the cladding. Above all, based on the developed relationship between irradiation growth at certain burnup and the loaded virtual temperatures, with considering that certain burnup corresponds to certain fast neutron fluence, the time-dependent constitutive relation due to irradiation hardening effect is replaced by the virtual-temperature-dependent one which is introduced into the commercial software to simulate the irradiation hardening effects of the matrix and cladding. Numerical simulations of the irradiation-induced mechanical behaviors are implemented with the finite element method in consideration of the micro-structure of the fuel meat. The obtained results indicate that when the irradiation hardening effects are introduced into the constitutive relations of the metal matrix and cladding: (1) higher maximum Mises stresses for certain burnup at the matrix exist with the equivalent plastic strains remaining almost the same at lower burnups; (2) the maximum Mises stresses for certain burnup at the cladding are enhanced while the maximum equivalent plastic strains are reduced; and (3) the maximum first principal stresses for certain burnup at the matrix or the cladding are lower than the ones without the hardening effect, and the differences are found to increase with burnup; and the variation rules of the interfacial stresses are similar.

Unifying time evolution and optimization with matrix product states

NASA Astrophysics Data System (ADS)

Haegeman, Jutho; Lubich, Christian; Oseledets, Ivan; Vandereycken, Bart; Verstraete, Frank

2016-10-01

We show that the time-dependent variational principle provides a unifying framework for time-evolution methods and optimization methods in the context of matrix product states. In particular, we introduce a new integration scheme for studying time evolution, which can cope with arbitrary Hamiltonians, including those with long-range interactions. Rather than a Suzuki-Trotter splitting of the Hamiltonian, which is the idea behind the adaptive time-dependent density matrix renormalization group method or time-evolving block decimation, our method is based on splitting the projector onto the matrix product state tangent space as it appears in the Dirac-Frenkel time-dependent variational principle. We discuss how the resulting algorithm resembles the density matrix renormalization group (DMRG) algorithm for finding ground states so closely that it can be implemented by changing just a few lines of code and it inherits the same stability and efficiency. In particular, our method is compatible with any Hamiltonian for which ground-state DMRG can be implemented efficiently. In fact, DMRG is obtained as a special case of our scheme for imaginary time evolution with infinite time step.

Searching for high-k RE2O3 nanoparticles embedded in SiO2 glass matrix

NASA Astrophysics Data System (ADS)

Mukherjee, S.; Lin, Y. H.; Kao, T. H.; Chou, C. C.; Yang, H. D.

2012-03-01

Significant experimental effort has been explored to search and characterize high-k materials with magnetodielectric effect (MDE) of series of rare earth (RE) oxide (RE2O3) nanoparticles (NPs) embedded in SiO2 glass matrix by a sol-gel route. Properly annealed sol-gel glass (in which RE = Sm, Gd, and Er) shows colossal response of dielectric constant along with diffuse phase transition and MDE around room temperature. The radial distribution functions, reconstructed from extended x-ray absorption fine structure, show the shortening of RE3 + -O depending on the RE2O3 NP size, which is consistent with oxygen vacancy induced dielectric anomaly. The magnetoresistive MDE is very much conditioned by magnetic property of RE2O3 NP grain, the degree of deformation of the lattice and constituent host.

A fast-initializing digital equalizer with on-line tracking for data communications

NASA Technical Reports Server (NTRS)

Houts, R. C.; Barksdale, W. J.

1974-01-01

A theory is developed for a digital equalizer for use in reducing intersymbol interference (ISI) on high speed data communications channels. The equalizer is initialized with a single isolated transmitter pulse, provided the signal-to-noise ratio (SNR) is not unusually low, then switches to a decision directed, on-line mode of operation that allows tracking of channel variations. Conditions for optimal tap-gain settings are obtained first for a transversal equalizer structure by using a mean squared error (MSE) criterion, a first order gradient algorithm to determine the adjustable equalizer tap-gains, and a sequence of isolated initializing pulses. Since the rate of tap-gain convergence depends on the eigenvalues of a channel output correlation matrix, convergence can be improved by making a linear transformation on to obtain a new correlation matrix.

Efficient swimming of an assembly of rigid spheres at low Reynolds number.

PubMed

Felderhof, B U

2015-08-01

The swimming of an assembly of rigid spheres immersed in a viscous fluid of infinite extent is studied in low-Reynolds-number hydrodynamics. The instantaneous swimming velocity and rate of dissipation are expressed in terms of the time-dependent displacements of sphere centers about their collective motion. For small-amplitude swimming with periodically oscillating displacements, optimization of the mean swimming speed at given mean power leads to an eigenvalue problem involving a velocity matrix and a power matrix. The corresponding optimal stroke permits generalization to large-amplitude motion in a model of spheres with harmonic interactions and corresponding actuating forces. The method allows straightforward calculation of the swimming performance of structures modeled as assemblies of interacting rigid spheres. A model of three collinear spheres with motion along the common axis is studied as an example.

Almost output regulation of LFT systems via gain-scheduling control

NASA Astrophysics Data System (ADS)

Yuan, Chengzhi; Duan, Chang; Wu, Fen

2018-05-01

Output regulation of general uncertain systems is a meaningful yet challenging problem. In spite of the rich literature in the field, the problem has not yet been addressed adequately due to the lack of an effective design mechanism. In this paper, we propose a new design framework for almost output regulation of uncertain systems described in the general form of linear fractional transformation (LFT) with time-varying parametric uncertainties and unknown external perturbations. A novel semi-LFT gain-scheduling output regulator structure is proposed, such that the associated control synthesis conditions guaranteeing both output regulation and ? disturbance attenuation performance are formulated as a set of linear matrix inequalities (LMIs) plus parameter-dependent linear matrix equations, which can be solved separately. A numerical example has been used to demonstrate the effectiveness of the proposed approach.

Role of Y-Al Oxides During Extended Recovery Process of a Ferritic ODS Alloy

NASA Astrophysics Data System (ADS)

Capdevila, C.; Pimentel, G.; Aranda, M. M.; Rementeria, R.; Dawson, K.; Urones-Garrote, E.; Tatlock, G. J.; Miller, M. K.

2015-08-01

The microstructural stability of Y-Al oxides during the recrystallization of Fe-Cr-Al oxide dispersion strengthened alloy is studied in this work. The goal is to determine the specific distribution pattern of oxides depending where they are located: in the matrix or at the grain boundaries. It was concluded that those located at the grain boundaries yielded a faster coarsening than the ones in the matrix, although no significant differences in composition and/or crystal structure were observed. However, the recrystallization heat treatment leads to the dissolution of the Y2O3 and its combination with Al to form the YAlO3 perovskite oxide particles process, mainly located at the grain boundaries. Finally, atom probe tomography analysis revealed a significant Ti build-up at the grain boundaries that might affect subsequent migration during recrystallization.

Protein structure estimation from NMR data by matrix completion.

PubMed

Li, Zhicheng; Li, Yang; Lei, Qiang; Zhao, Qing

2017-09-01

Knowledge of protein structures is very important to understand their corresponding physical and chemical properties. Nuclear Magnetic Resonance (NMR) spectroscopy is one of the main methods to measure protein structure. In this paper, we propose a two-stage approach to calculate the structure of a protein from a highly incomplete distance matrix, where most data are obtained from NMR. We first randomly "guess" a small part of unobservable distances by utilizing the triangle inequality, which is crucial for the second stage. Then we use matrix completion to calculate the protein structure from the obtained incomplete distance matrix. We apply the accelerated proximal gradient algorithm to solve the corresponding optimization problem. Furthermore, the recovery error of our method is analyzed, and its efficiency is demonstrated by several practical examples.

The structure of cell-matrix adhesions: the new frontier.

PubMed

Hanein, Dorit; Horwitz, Alan Rick

2012-02-01

Adhesions between the cell and the extracellular matrix (ECM) are mechanosensitive multi-protein assemblies that transmit force across the cell membrane and regulate biochemical signals in response to the chemical and mechanical environment. These combined functions in force transduction, signaling and mechanosensing contribute to cellular phenotypes that span development, homeostasis and disease. These adhesions form, mature and disassemble in response to actin organization and physical forces that originate from endogenous myosin activity or external forces by the extracellular matrix. Despite advances in our understanding of the protein composition, interactions and regulation, our understanding of matrix adhesion structure and organization, how forces affect this organization, and how these changes dictate specific signaling events is limited. Insights across multiple structural levels are acutely needed to elucidate adhesion structure and ultimately the molecular basis of signaling and mechanotransduction. Here we describe the challenges and recent advances and prospects for unraveling the structure of cell-matrix adhesions and their response to force. Copyright © 2011 Elsevier Ltd. All rights reserved.

Polymer Nanocomposites: Insights from Theory and Molecular Simulations

NASA Astrophysics Data System (ADS)

Pani, Rakhee

Advantages of polymer nanocomposites have attracted great industrial attention due to their multifunctionality and innovative technological properties. Addition of small amount of nanoparticle (nanospheres, nanotubes, nanorods, nanoplatelets, or sheets) to polymer matrix cause dramatic improvement in structural and functional properties, which is difficult to attain from those of individual components. The interaction between polymer and nanoparticle create bulk materials dominated by solid state physics at the nanoscale. Furthermore, morphology of nanocomposites depends on structural arrangements of nanoparticles. Thus, for achievement of optimized functionality like electrical, optical, mechanical and thermal properties control over the dispersion of the nanoparticle is essential. However, properties of polymer nanocomposites depend on morphology control and nature of interfacial interactions. In order to control the morphology it is necessary to understand how the processing conditions, shape and size of nanoparticle influence the structure of composite. Molecular simulations can help us to predict the parameters that control the structural changes and we could design polymer nanocomposite entailing their end-use. In this work, we addressed the following research questions: (1) the dependence of nanoparticle ligand corona structure on solvent quality and (2) the role of interfacial energy and interactions on the dispersion of molecules and nanoparticles. Specifically, this research assessed the effect of solvent interactions on the structure of nanoparticles on the example of redox core encapsulating dendrimer and ligand functionalized gold nanoparticles, role of chemical interaction on solubility of glucose in ionic liquids, diffusion of fullerene nanoparticles in polymer matrix and influence of solubility parameters on the compatibility of gold nanoparticles with diblock copolymers. Computational methods allow quantifying the structure and flexibility of the polymer chains, how energetics and surface tension change with chemical composition of the polymer/dendrimer blocks, influence of nanoparticle on structural properties of polymer and factors which may contribute to the phase separation of the polymer from nanoparticle. Interfacial characteristics are not only determined by the size-induced properties, but also the surface chemistry of the particles. Presence of solvent and the resultant interactions with the solvent are known to influence the morphology and prevent or induce aggregation of nanoparticles in polymers. We found that surface chemistry can induce change in the structure of dendrimers encapsulating a redox active core and change the solubility of the nanoparticles. The interactions between nanoparticles and polymers can also influence the morphology. We performed investigation on the role of orientation of fullerene derivatives and surface energy of polymer surface which may induce the aggregation of the fullerene nanoparticles. Furthermore, we used quantitative measurements like cluster analysis to understand the most probable orientation of the fullerene derivative with respect to the polymer chains and the diffusion of the fullerene nanoparticle, which is related to the efficiency of solar cells, can change on presence of regiorandom and regioregular polymer chains. Furthermore, we have also used different solvents based on their Hildebrand solubility parameters to investigate factors governing the morphology of polymer nanocomposite via solvent interactions. We showed that change in solvent interactions affect the compatibility, aggregation/dispersion of the gold nanoparticles, which will directly affect the morphology of polymer matrix and structural aspects which can impact their functionality. Overall, our research indicated that solvent interaction play a role in controlling the morphology of polymer nanocomposite and solubility parameter can help us to predict the resulting morphology.

Nonlinear signaling on biological networks: The role of stochasticity and spectral clustering

NASA Astrophysics Data System (ADS)

Hernandez-Hernandez, Gonzalo; Myers, Jesse; Alvarez-Lacalle, Enrique; Shiferaw, Yohannes

2017-03-01

Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different conformational states. Signaling is typically a cooperative process which requires the occurrence of multiple binding events so that reaction rates have a nonlinear dependence on the amount of signaling molecule. It is this nonlinearity that endows biological signaling networks with robust switchlike properties which are critical to their biological function. In this study we investigate how the properties of these signaling systems depend on the network architecture. Our main result is that these nonlinear networks exhibit bistability where the network activity can switch between states that correspond to a low and high activity level. We show that this bistable regime emerges at a critical coupling strength that is determined by the spectral structure of the network. In particular, the set of nodes that correspond to large components of the leading eigenvector of the adjacency matrix determines the onset of bistability. Above this transition the eigenvectors of the adjacency matrix determine a hierarchy of clusters, defined by its spectral properties, which are activated sequentially with increasing network activity. We argue further that the onset of bistability occurs either continuously or discontinuously depending upon whether the leading eigenvector is localized or delocalized. Finally, we show that at low network coupling stochastic transitions to the active branch are also driven by the set of nodes that contribute more strongly to the leading eigenvector. However, at high coupling, transitions are insensitive to network structure since the network can be activated by stochastic transitions of a few nodes. Thus this work identifies important features of biological signaling networks that may underlie their biological function.

Improved Joining of Metal Components to Composite Structures

NASA Technical Reports Server (NTRS)

Semmes, Edmund

2009-01-01

Systems requirements for complex spacecraft drive design requirements that lead to structures, components, and/or enclosures of a multi-material and multifunctional design. The varying physical properties of aluminum, tungsten, Invar, or other high-grade aerospace metals when utilized in conjunction with lightweight composites multiply system level solutions. These multi-material designs are largely dependent upon effective joining techAn improved method of joining metal components to matrix/fiber composite material structures has been invented. The method is particularly applicable to equipping such thin-wall polymer-matrix composite (PMC) structures as tanks with flanges, ceramic matrix composite (CMC) liners for high heat engine nozzles, and other metallic-to-composite attachments. The method is oriented toward new architectures and distributing mechanical loads as widely as possible in the vicinities of attachment locations to prevent excessive concentrations of stresses that could give rise to delaminations, debonds, leaks, and other failures. The method in its most basic form can be summarized as follows: A metal component is to be joined to a designated attachment area on a composite-material structure. In preparation for joining, the metal component is fabricated to include multiple studs projecting from the aforementioned face. Also in preparation for joining, holes just wide enough to accept the studs are molded into, drilled, or otherwise formed in the corresponding locations in the designated attachment area of the uncured ("wet') composite structure. The metal component is brought together with the uncured composite structure so that the studs become firmly seated in the holes, thereby causing the composite material to become intertwined with the metal component in the joining area. Alternately, it is proposed to utilize other mechanical attachment schemes whereby the uncured composite and metallic parts are joined with "z-direction" fasteners. The resulting "wet" assembly is then subjected to the composite-curing heat treatment, becoming a unitary structure. It should be noted that this new art will require different techniques for CMC s versus PMC's, but the final architecture and companion curing philosophy is the same. For instance, a chemical vapor infiltration (CVI) fabrication technique may require special integration of the pre-form and

Stress-Dependent Matrix Cracking in 2D Woven SiC-Fiber Reinforced Melt-Infiltrated SiC Matrix Composites

NASA Technical Reports Server (NTRS)

Morscher, Gregory N.

2003-01-01

The matrix cracking of a variety of SiC/SiC composites has been characterized for a wide range of constituent variation. These composites were fabricated by the 2-dimensional lay-up of 0/90 five-harness satin fabric consisting of Sylramic fiber tows that were then chemical vapor infiltrated (CVI) with BN, CVI with SiC, slurry infiltrated with SiC particles followed by molten infiltration of Si. The composites varied in number of plies, the number of tows per length, thickness, and the size of the tows. This resulted in composites with a fiber volume fraction in the loading direction that ranged from 0.12 to 0.20. Matrix cracking was monitored with modal acoustic emission in order to estimate the stress-dependent distribution of matrix cracks. It was found that the general matrix crack properties of this system could be fairly well characterized by assuming that no matrix cracks originated in the load-bearing fiber, interphase, chemical vapor infiltrated Sic tow-minicomposites, i.e., all matrix cracks originate in the 90 degree tow-minicomposites or the large unreinforced Sic-Si matrix regions. Also, it was determined that the larger tow size composites had a much narrower stress range for matrix cracking compared to the standard tow size composites.

Spacecraft structural system identification by modal test

NASA Technical Reports Server (NTRS)

Chen, J.-C.; Peretti, L. F.; Garba, J. A.

1984-01-01

A structural parameter estimation procedure using the measured natural frequencies and kinetic energy distribution as observers is proposed. The theoretical derivation of the estimation procedure is described and its constraints and limitations are explained. This procedure is applied to a large complex spacecraft structural system to identify the inertia matrix using modal test results. The inertia matrix is chosen after the stiffness matrix has been updated by the static test results.

Excitation energies from range-separated time-dependent density and density matrix functional theory.

PubMed

Pernal, Katarzyna

2012-05-14

Time-dependent density functional theory (TD-DFT) in the adiabatic formulation exhibits known failures when applied to predicting excitation energies. One of them is the lack of the doubly excited configurations. On the other hand, the time-dependent theory based on a one-electron reduced density matrix functional (time-dependent density matrix functional theory, TD-DMFT) has proven accurate in determining single and double excitations of H(2) molecule if the exact functional is employed in the adiabatic approximation. We propose a new approach for computing excited state energies that relies on functionals of electron density and one-electron reduced density matrix, where the latter is applied in the long-range region of electron-electron interactions. A similar approach has been recently successfully employed in predicting ground state potential energy curves of diatomic molecules even in the dissociation limit, where static correlation effects are dominating. In the paper, a time-dependent functional theory based on the range-separation of electronic interaction operator is rigorously formulated. To turn the approach into a practical scheme the adiabatic approximation is proposed for the short- and long-range components of the coupling matrix present in the linear response equations. In the end, the problem of finding excitation energies is turned into an eigenproblem for a symmetric matrix. Assignment of obtained excitations is discussed and it is shown how to identify double excitations from the analysis of approximate transition density matrix elements. The proposed method used with the short-range local density approximation (srLDA) and the long-range Buijse-Baerends density matrix functional (lrBB) is applied to H(2) molecule (at equilibrium geometry and in the dissociation limit) and to Be atom. The method accounts for double excitations in the investigated systems but, unfortunately, the accuracy of some of them is poor. The quality of the other excitations is in general much better than that offered by TD-DFT-LDA or TD-DMFT-BB approximations if the range-separation parameter is properly chosen. The latter remains an open problem.

Piezoresistivity of Resin-Impregnated Carbon Nanotube Film at High Temperatures.

PubMed

Li, Min; Zuo, Tianyi; Wang, Shaokai; Gu, Yizhuo; Gao, Limin; Li, Yanxia; Zhang, Zuoguang

2018-06-13

This paper presents the development of a continuous carbon nanotube (CNT) composite film sensor with a strain detecting range of 0-2% for structural composites. The strain-dependent resistance responses of continuous CNT film and its resin-impregnated composite films were investigated at temperatures as high as 200 °C. The results manifest that impregnation with resin leads to a much larger gauge factor than pristine film. Both the pristine and composite films show an increase in resistivity with increasing temperature. For different composite films, the ordering of gauge factors is consistent with that of the matrix moduli. This indicates that a resin matrix with higher modulus and strong interactions between CNTs/CNT bundles and the resin matrix are beneficial for enhancing the piezoresistive effect. The CNT/PAA composite film has a gauge factor of 4.3 at 150 °C, an order of magnitude higher than the metal foil sensor. Therefore, the CNT composite films have great potential for simultaneous application for reinforcement and as strain sensor to realise a multifunctional composite. © 2018 IOP Publishing Ltd.

Assembly and enlargement of the primary cell wall in plants

NASA Technical Reports Server (NTRS)

Cosgrove, D. J.

1997-01-01

Growing plant cells are shaped by an extensible wall that is a complex amalgam of cellulose microfibrils bonded noncovalently to a matrix of hemicelluloses, pectins, and structural proteins. Cellulose is synthesized by complexes in the plasma membrane and is extruded as a self-assembling microfibril, whereas the matrix polymers are secreted by the Golgi apparatus and become integrated into the wall network by poorly understood mechanisms. The growing wall is under high tensile stress from cell turgor and is able to enlarge by a combination of stress relaxation and polymer creep. A pH-dependent mechanism of wall loosening, known as acid growth, is characteristic of growing walls and is mediated by a group of unusual wall proteins called expansins. Expansins appear to disrupt the noncovalent bonding of matrix hemicelluloses to the microfibril, thereby allowing the wall to yield to the mechanical forces generated by cell turgor. Other wall enzymes, such as (1-->4) beta-glucanases and pectinases, may make the wall more responsive to expansin-mediated wall creep whereas pectin methylesterases and peroxidases may alter the wall so as to make it resistant to expansin-mediated creep.

Assembly and enlargement of the primary cell wall in plants.

PubMed

Cosgrove, D J

1997-01-01

Growing plant cells are shaped by an extensible wall that is a complex amalgam of cellulose microfibrils bonded noncovalently to a matrix of hemicelluloses, pectins, and structural proteins. Cellulose is synthesized by complexes in the plasma membrane and is extruded as a self-assembling microfibril, whereas the matrix polymers are secreted by the Golgi apparatus and become integrated into the wall network by poorly understood mechanisms. The growing wall is under high tensile stress from cell turgor and is able to enlarge by a combination of stress relaxation and polymer creep. A pH-dependent mechanism of wall loosening, known as acid growth, is characteristic of growing walls and is mediated by a group of unusual wall proteins called expansins. Expansins appear to disrupt the noncovalent bonding of matrix hemicelluloses to the microfibril, thereby allowing the wall to yield to the mechanical forces generated by cell turgor. Other wall enzymes, such as (1-->4) beta-glucanases and pectinases, may make the wall more responsive to expansin-mediated wall creep whereas pectin methylesterases and peroxidases may alter the wall so as to make it resistant to expansin-mediated creep.

[Extracellular matrix--regulation of cancer invasion and metastasis].

PubMed

Watanabe, Hideto

2010-11-01

Cancer cell invasion comprises steps in the destruction of the basement membrane and migration of cells into the connective tissue. These cells further migrate into lymph ducts and small vessels to reach metastasis. The extracellular matrix (ECM) provides a microenvironment for cells, and its destruction is associated with cancer cell invasion. Among matrix metalloproteinases (MMPs), both MMP-2 and 9 digest type IV collagen, a major component of the basement membrane, and MMP-14/MT1-MMP, a membrane-type MMP, activates MMP-2. Thus, these MMPs play a central role in cancer cell invasion. MMPs also cleave latent forms of growth factors and signaling molecules, releasing and activating them, which influence neo-vascularization and cancer apoptosis. Like proteins, carbohydrates are known to be involved in cancer invasion. Hyaluronan is known to both stimulate and inhibit cancer invasion, depending on its molecular size. Heparanase, which digests heparan sulfate, is known to facilitate cancer invasion and metastasis. In summary, ECM provides a microenvironment that regulates cell behavior and its structure altered by MMPs affects cancer cell invasion.

Mechanical intermixing of components in (CoMoNi)-based systems and the formation of (CoMoNi)/WC nanocomposite layers on Ti sheets under ball collisions

NASA Astrophysics Data System (ADS)

Romankov, S.; Park, Y. C.; Shchetinin, I. V.

2017-11-01

Cobalt (Co), molybdenum (Mo), and nickel (Ni) components were simultaneously introduced onto titanium (Ti) surfaces from a composed target using ball collisions. Tungsten carbide (WC) balls were selected for processing as the source of a cemented carbide reinforcement phase. During processing, ball collisions continuously introduced components from the target and the grinding media onto the Ti surface and induced mechanical intermixing of the elements, resulting in formation of a complex nanocomposite structure onto the Ti surface. The as-fabricated microstructure consisted of uniformly dispersed WC particles embedded within an integrated metallic matrix composed of an amorphous phase with nanocrystalline grains. The phase composition of the alloyed layers, atomic reactions, and the matrix grain sizes depended on the combination of components introduced onto the Ti surface during milling. The as-fabricated layer exhibited a very high hardness compared to industrial metallic alloys and tool steel materials. This approach could be used for the manufacture of both cemented carbides and amorphous matrix composite layers.

Reducing the orientation influence of Mueller matrix measurements for anisotropic scattering media

NASA Astrophysics Data System (ADS)

Sun, Minghao; He, Honghui; Zeng, Nan; Du, E.; He, Yonghong; Ma, Hui

2014-09-01

Mueller matrix polarimetry techniques contain rich micro-structural information of samples, such as the sizes and refractive indices of scatterers. Recently, Mueller matrix imaging methods have shown great potentials as powerful tools for biomedical diagnosis. However, the orientations of anisotropic fibrous structures in tissues have prominent influence on Mueller matrix measurements, resulting in difficulties for extracting micro-structural information effectively. In this paper, we apply the backscattering Mueller matrix imaging technique to biological samples with different microstructures, such as chicken heart muscle, bovine skeletal muscle, porcine liver and fat tissues. Experimental results show that the directions of the muscle fibers have prominent influence on the Mueller matrix elements. In order to reduce the orientation influence, we adopt the rotation-independent MMT and RLPI parameters, which were proposed in our previous studies, to the tissue samples. Preliminary results in this paper show that the orientation-independent parameters and their statistic features are helpful for analyzing the tissues to obtain their micro-structural properties. Since the micro-structure variations are often related to the pathological changes, the method can be applied to microscope imaging techniques and used to detect abnormal tissues such as cancer and other lesions for diagnosis purposes.

Coupled multi-disciplinary composites behavior simulation

NASA Technical Reports Server (NTRS)

Singhal, Surendra N.; Murthy, Pappu L. N.; Chamis, Christos C.

1993-01-01

The capabilities of the computer code CSTEM (Coupled Structural/Thermal/Electro-Magnetic Analysis) are discussed and demonstrated. CSTEM computationally simulates the coupled response of layered multi-material composite structures subjected to simultaneous thermal, structural, vibration, acoustic, and electromagnetic loads and includes the effect of aggressive environments. The composite material behavior and structural response is determined at its various inherent scales: constituents (fiber/matrix), ply, laminate, and structural component. The thermal and mechanical properties of the constituents are considered to be nonlinearly dependent on various parameters such as temperature and moisture. The acoustic and electromagnetic properties also include dependence on vibration and electromagnetic wave frequencies, respectively. The simulation is based on a three dimensional finite element analysis in conjunction with composite mechanics and with structural tailoring codes, and with acoustic and electromagnetic analysis methods. An aircraft engine composite fan blade is selected as a typical structural component to demonstrate the CSTEM capabilities. Results of various coupled multi-disciplinary heat transfer, structural, vibration, acoustic, and electromagnetic analyses for temperature distribution, stress and displacement response, deformed shape, vibration frequencies, mode shapes, acoustic noise, and electromagnetic reflection from the fan blade are discussed for their coupled effects in hot and humid environments. Collectively, these results demonstrate the effectiveness of the CSTEM code in capturing the coupled effects on the various responses of composite structures subjected to simultaneous multiple real-life loads.

Engineering Three-Dimensional Collagen-IKVAV Matrix to Mimic Neural Microenvironment

PubMed Central

2013-01-01

Engineering the cellular microenvironment has great potential to create a platform technology toward engineering of tissue and organs. This study aims to engineer a neural microenvironment through fabrication of three-dimensional (3D) engineered collagen matrixes mimicking in-vivo-like conditions. Collagen was chemically modified with a pentapeptide epitope consisting of isoleucine-lysine-valine-alanine-valine (IKVAV) to mimic laminin structure supports of the neural extracellular matrix (ECM). Three-dimensional collagen matrixes with and without IKVAV peptide modification were fabricated by freeze-drying technology and chemical cross-linking with glutaraldehyde. Structural information of 3D collagen matrixes indicated interconnected pores structure with an average pore size of 180 μm. Our results indicated that culture of dorsal root ganglion (DRG) cells in 3D collagen matrix was greatly influenced by 3D culture method and significantly enhanced with engineered collagen matrix conjugated with IKVAV peptide. It may be concluded that an appropriate 3D culture of neurons enables DRG to positively improve the cellular fate toward further acceleration in tissue regeneration. PMID:23705903

Hidden Markov model-derived structural alphabet for proteins: the learning of protein local shapes captures sequence specificity.

PubMed

Camproux, A C; Tufféry, P

2005-08-05

Understanding and predicting protein structures depend on the complexity and the accuracy of the models used to represent them. We have recently set up a Hidden Markov Model to optimally compress protein three-dimensional conformations into a one-dimensional series of letters of a structural alphabet. Such a model learns simultaneously the shape of representative structural letters describing the local conformation and the logic of their connections, i.e. the transition matrix between the letters. Here, we move one step further and report some evidence that such a model of protein local architecture also captures some accurate amino acid features. All the letters have specific and distinct amino acid distributions. Moreover, we show that words of amino acids can have significant propensities for some letters. Perspectives point towards the prediction of the series of letters describing the structure of a protein from its amino acid sequence.

Collagen in the spicule organic matrix of the gorgonian Leptogorgia virgulata

NASA Technical Reports Server (NTRS)

Kingsley, R. J.; Tsuzaki, M.; Watabe, N.; Mechanic, G. L.

1990-01-01

Decalcification of the calcareous spicules from the gorgonian Leptogorgia virgulata reveals an organic matrix that may be divided into water insoluble and soluble fractions. The insoluble fraction displays characteristics typical of collagen, which is an unusual component of an invertebrate calcium carbonate structure. This matrix fraction exhibits a collagenous amino acid profile and behavior upon SDS-PAGE. Furthermore, the reducible crosslink, dihydroxylysinonorleucine (DHLNL), is detected in this fraction. The composition of the matrix varies seasonally; i.e., the collagenous composition is most prevalent in the summer. These results indicate that the insoluble matrix is a dynamic structure. Potential roles of this matrix in spicule calcification are discussed.

Highly defective oxides as sinter resistant thermal barrier coating

DOEpatents

Subramanian, Ramesh

2005-08-16

A thermal barrier coating material formed of a highly defective cubic matrix structure having a concentration of a stabilizer sufficiently high that the oxygen vacancies created by the stabilizer interact within the matrix to form multi-vacancies, thereby improving the sintering resistance of the material. The concentration of stabilizer within the cubic matrix structure is greater than that concentration of stabilizer necessary to give the matrix a peak ionic conductivity value. The concentration of stabilizer may be at least 30 wt. %. Embodiments include a cubic matrix of zirconia stabilized by at least 30-50 wt. % yttria, and a cubic matrix of hafnia stabilized by at least 30-50 wt. % gadolinia.

A novel color image encryption scheme using alternate chaotic mapping structure

NASA Astrophysics Data System (ADS)

Wang, Xingyuan; Zhao, Yuanyuan; Zhang, Huili; Guo, Kang

2016-07-01

This paper proposes an color image encryption algorithm using alternate chaotic mapping structure. Initially, we use the R, G and B components to form a matrix. Then one-dimension logistic and two-dimension logistic mapping is used to generate a chaotic matrix, then iterate two chaotic mappings alternately to permute the matrix. For every iteration, XOR operation is adopted to encrypt plain-image matrix, then make further transformation to diffuse the matrix. At last, the encrypted color image is obtained from the confused matrix. Theoretical analysis and experimental results has proved the cryptosystem is secure and practical, and it is suitable for encrypting color images.

Experimental and theoretical investigation of the temperature dependent electronic quenching of O(1D) atoms in collisions with Kr

NASA Astrophysics Data System (ADS)

Nuñez-Reyes, Dianailys; Kłos, Jacek; Alexander, Millard H.; Dagdigian, Paul J.; Hickson, Kevin M.

2018-03-01

The kinetics and dynamics of the collisional electronic quenching of O(1D) atoms by Kr have been investigated in a joint experimental and theoretical study. The kinetics of quenching were measured over the temperature range 50-296 K using the Laval nozzle method. O(1D) atoms were prepared by 266 nm photolysis of ozone, and the decay of the O(1D) concentration was monitored through vacuum ultraviolet fluorescence at 115.215 nm, from which the rate constant was determined. To interpret the experiments, a quantum close-coupling treatment of the quenching transition from the 1D state to the 3Pj fine-structure levels in collisions with Kr, and also Ar and Xe, was carried out. The relevant potential energy curves and spin-orbit coupling matrix elements were obtained in electronic structure calculations. We find reasonable agreement between computed temperature-dependent O(1D)-Rg (Rg = Ar, Kr, Xe) quenching rate constants and the present measurements for Kr and earlier measurements. In particular, the temperature dependence is well described.

A Nanostructured Matrices Assessment to Study Drug Distribution in Solid Tumor Tissues by Mass Spectrometry Imaging

PubMed Central

Giordano, Silvia; Pifferi, Valentina; Morosi, Lavinia; Morelli, Melinda; Falciola, Luigi; Cappelletti, Giuseppe; Visentin, Sonja; Licandro, Simonetta A.; Frapolli, Roberta; Zucchetti, Massimo; Pastorelli, Roberta; Brunelli, Laura; D’Incalci, Maurizio; Davoli, Enrico

2017-01-01

The imaging of drugs inside tissues is pivotal in oncology to assess whether a drug reaches all cells in an adequate enough concentration to eradicate the tumor. Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI) is one of the most promising imaging techniques that enables the simultaneous visualization of multiple compounds inside tissues. The choice of a suitable matrix constitutes a critical aspect during the development of a MALDI-MSI protocol since the matrix ionization efficiency changes depending on the analyte structure and its physico-chemical properties. The objective of this study is the improvement of the MALDI-MSI technique in the field of pharmacology; developing specifically designed nanostructured surfaces that allow the imaging of different drugs with high sensitivity and reproducibility. Among several nanomaterials, we tested the behavior of gold and titanium nanoparticles, and halloysites and carbon nanotubes as possible matrices. All nanomaterials were firstly screened by co-spotting them with drugs on a MALDI plate, evaluating the drug signal intensity and the signal-to-noise ratio. The best performing matrices were tested on control tumor slices, and were spotted with drugs to check the ion suppression effect of the biological matrix. Finally; the best nanomaterials were employed in a preliminary drug distribution study inside tumors from treated mice. PMID:28336905

Free-Standing Optically Switchable Chiral Plasmonic Photonic Crystal Based on Self-Assembled Cellulose Nanorods and Gold Nanoparticles.

PubMed

Chu, Guang; Wang, Xuesi; Yin, Hang; Shi, Ying; Jiang, Haijing; Chen, Tianrui; Gao, Jianxiong; Qu, Dan; Xu, Yan; Ding, Dajun

2015-10-07

Photonic crystals incorporating with plasmonic nanoparticles have recently attracted considerable attention due to their novel optical properties and potential applications in future subwavelength optics, biosensing and data storage device. Here we demonstrate a free-standing chiral plasmonic film composed of entropy-driven self-co-assembly of gold nanoparticles (GNPs) and rod-like cellulose nanocrystals (CNCs). The CNCs-GNPs composite films not only preserve the photonic ordering of the CNCs matrix but also retain the plasmonic resonance of GNPs, leading to a distinct plasmon-induced chiroptical activity and a strong resonant plasmonic-photonic coupling that is confirmed by the stationary and ultrafast transient optical response. Switchable optical activity can be obtained by either varying the incidence angle of lights, or by taking advantage of the responsive feature of the CNCs matrix. Notably, an angle-dependent plasmon resonance in chiral nematic hybrid film has been observed for the first time, which differs drastically from that of the GNPs embed in three-dimensional photonic crystals, revealing a close relation with the structure of the host matrix. The current approach for fabricating device-scale, macroscopic chiral plasmonic materials from abundant CNCs with robust chiral nematic matrix may enable the mass production of functional optical metamaterials.

Effect of viscosity of a thermoplastic prepreg and matrix upon winding of rings

NASA Astrophysics Data System (ADS)

Stavrov, V. P.; Markov, A. V.; Zhernovskii, A. V.; Friedrich, K. F.

2000-05-01

The problem of compression of a unidirectional layer and shear of a polymer interlayer during winding of rings is considered. The equations determining the dependence of the layer thickness and stresses on the parameters entering into the power flow law for a prepreg and polymer matrix and on the basic parameters of the winding process—the initial tension of the prepreg, its placement rate, and the radius of a mandrel—are derived. The ring thickness measurements obtained at various temperatures and initial tension forces of plies confirm the adequacy of the model offered. It is found that the viscous properties of the prepreg and matrix upon winding affect the relative change in the layer thickness to a greater extent than the stresses in these layers. With increase in temperature and tension force upon winding, the effect of viscous deformations of the prepreg and matrix increases. A decrease in viscosity and an increase in the tension force of the tape lead to a higher strength of the ring in tension and interlaminar shear; however, the growing percolation of the polymer melt leads to a greater inhomogeneity of the structure of the composite in the ring and to a lower reinforcing effect of the factors mentioned.