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

Smallwood, D.O.

In a previous paper Smallwood and Paez (1991) showed how to generate realizations of partially coherent stationary normal time histories with a specified cross-spectral density matrix. This procedure is generalized for the case of multiple inputs with a specified cross-spectral density function and a specified marginal probability density function (pdf) for each of the inputs. The specified pdfs are not required to be Gaussian. A zero memory nonlinear (ZMNL) function is developed for each input to transform a Gaussian or normal time history into a time history with a specified non-Gaussian distribution. The transformation functions have the property that amore » transformed time history will have nearly the same auto spectral density as the original time history. A vector of Gaussian time histories are then generated with the specified cross-spectral density matrix. These waveforms are then transformed into the required time history realizations using the ZMNL function.« less

Joint refinement model for the spin resolved one-electron reduced density matrix of YTiO3 using magnetic structure factors and magnetic Compton profiles data.

PubMed

Gueddida, Saber; Yan, Zeyin; Kibalin, Iurii; Voufack, Ariste Bolivard; Claiser, Nicolas; Souhassou, Mohamed; Lecomte, Claude; Gillon, Béatrice; Gillet, Jean-Michel

2018-04-28

In this paper, we propose a simple cluster model with limited basis sets to reproduce the unpaired electron distributions in a YTiO 3 ferromagnetic crystal. The spin-resolved one-electron-reduced density matrix is reconstructed simultaneously from theoretical magnetic structure factors and directional magnetic Compton profiles using our joint refinement algorithm. This algorithm is guided by the rescaling of basis functions and the adjustment of the spin population matrix. The resulting spin electron density in both position and momentum spaces from the joint refinement model is in agreement with theoretical and experimental results. Benefits brought from magnetic Compton profiles to the entire spin density matrix are illustrated. We studied the magnetic properties of the YTiO 3 crystal along the Ti-O 1 -Ti bonding. We found that the basis functions are mostly rescaled by means of magnetic Compton profiles, while the molecular occupation numbers are mainly modified by the magnetic structure factors.

A well-scaling natural orbital theory

DOE PAGES

Gebauer, Ralph; Cohen, Morrel H.; Car, Roberto

2016-11-01

Here, we introduce an energy functional for ground-state electronic structure calculations. Its variables are the natural spin-orbitals of singlet many-body wave functions and their joint occupation probabilities deriving from controlled approximations to the two-particle density matrix that yield algebraic scaling in general, and Hartree–Fock scaling in its seniority-zero version. Results from the latter version for small molecular systems are compared with those of highly accurate quantum-chemical computations. The energies lie above full configuration interaction calculations, close to doubly occupied configuration interaction calculations. Their accuracy is considerably greater than that obtained from current density-functional theory approximations and from current functionals ofmore » the oneparticle density matrix.« less

A well-scaling natural orbital theory

PubMed Central

Gebauer, Ralph; Cohen, Morrel H.; Car, Roberto

2016-01-01

We introduce an energy functional for ground-state electronic structure calculations. Its variables are the natural spin-orbitals of singlet many-body wave functions and their joint occupation probabilities deriving from controlled approximations to the two-particle density matrix that yield algebraic scaling in general, and Hartree–Fock scaling in its seniority-zero version. Results from the latter version for small molecular systems are compared with those of highly accurate quantum-chemical computations. The energies lie above full configuration interaction calculations, close to doubly occupied configuration interaction calculations. Their accuracy is considerably greater than that obtained from current density-functional theory approximations and from current functionals of the one-particle density matrix. PMID:27803328

Exact and quasi-classical density matrix and Wigner functions for a particle in the box and half space

NASA Technical Reports Server (NTRS)

Akhundova, E. A.; Dodonov, V. V.; Manko, V. I.

1993-01-01

The exact expressions for density matrix and Wigner functions of quantum systems are known only in special cases. Corresponding Hamiltonians are quadratic forms of Euclidean coordinates and momenta. In this paper we consider the problem of one-dimensional free particle movement in the bounded region 0 is less than x is less than a (including the case a = infinity).

Performance of the density matrix functional theory in the quantum theory of atoms in molecules.

PubMed

García-Revilla, Marco; Francisco, E; Costales, A; Martín Pendás, A

2012-02-02

The generalization to arbitrary molecular geometries of the energetic partitioning provided by the atomic virial theorem of the quantum theory of atoms in molecules (QTAIM) leads to an exact and chemically intuitive energy partitioning scheme, the interacting quantum atoms (IQA) approach, that depends on the availability of second-order reduced density matrices (2-RDMs). This work explores the performance of this approach in particular and of the QTAIM in general with approximate 2-RDMs obtained from the density matrix functional theory (DMFT), which rests on the natural expansion (natural orbitals and their corresponding occupation numbers) of the first-order reduced density matrix (1-RDM). A number of these functionals have been implemented in the promolden code and used to perform QTAIM and IQA analyses on several representative molecules and model chemical reactions. Total energies, covalent intra- and interbasin exchange-correlation interactions, as well as localization and delocalization indices have been determined with these functionals from 1-RDMs obtained at different levels of theory. Results are compared to the values computed from the exact 2-RDMs, whenever possible.

A meta-GGA level screened range-separated hybrid functional by employing short range Hartree-Fock with a long range semilocal functional.

PubMed

Jana, Subrata; Samal, Prasanjit

2018-03-28

The range-separated hybrid density functionals are very successful in describing a wide range of molecular and solid-state properties accurately. In principle, such functionals are designed from spherically averaged or system averaged as well as reverse engineered exchange holes. In the present attempt, the screened range-separated hybrid functional scheme has been applied to the meta-GGA rung by using the density matrix expansion based semilocal exchange hole (or functional). The hybrid functional proposed here utilizes the spherically averaged density matrix expansion based exchange hole in the range separation scheme. For slowly varying density correction the range separation scheme is employed only through the local density approximation based exchange hole coupled with the corresponding fourth order gradient approximate Tao-Mo enhancement factor. The comprehensive testing and performance of the newly constructed functional indicates its applicability in describing several molecular properties. The most appealing feature of this present screened hybrid functional is that it will be practically very useful in describing solid-state properties at the meta-GGA level.

Coherent nonlinear optical studies of elementary processes in biological complexes: diagrammatic techniques based on the wave function versus the density matrix

PubMed Central

Biggs, Jason D.; Voll, Judith A.; Mukamel, Shaul

2012-01-01

Two types of diagrammatic approaches for the design and simulation of nonlinear optical experiments (closed-time path loops based on the wave function and double-sided Feynman diagrams for the density matrix) are presented and compared. We give guidelines for the assignment of relevant pathways and provide rules for the interpretation of existing nonlinear experiments in carotenoids. PMID:22753822

Variational Optimization of the Second-Order Density Matrix Corresponding to a Seniority-Zero Configuration Interaction Wave Function.

PubMed

Poelmans, Ward; Van Raemdonck, Mario; Verstichel, Brecht; De Baerdemacker, Stijn; Torre, Alicia; Lain, Luis; Massaccesi, Gustavo E; Alcoba, Diego R; Bultinck, Patrick; Van Neck, Dimitri

2015-09-08

We perform a direct variational determination of the second-order (two-particle) density matrix corresponding to a many-electron system, under a restricted set of the two-index N-representability P-, Q-, and G-conditions. In addition, we impose a set of necessary constraints that the two-particle density matrix must be derivable from a doubly occupied many-electron wave function, i.e., a singlet wave function for which the Slater determinant decomposition only contains determinants in which spatial orbitals are doubly occupied. We rederive the two-index N-representability conditions first found by Weinhold and Wilson and apply them to various benchmark systems (linear hydrogen chains, He, N2, and CN(-)). This work is motivated by the fact that a doubly occupied many-electron wave function captures in many cases the bulk of the static correlation. Compared to the general case, the structure of doubly occupied two-particle density matrices causes the associate semidefinite program to have a very favorable scaling as L(3), where L is the number of spatial orbitals. Since the doubly occupied Hilbert space depends on the choice of the orbitals, variational calculation steps of the two-particle density matrix are interspersed with orbital-optimization steps (based on Jacobi rotations in the space of the spatial orbitals). We also point to the importance of symmetry breaking of the orbitals when performing calculations in a doubly occupied framework.

Alternative dimensional reduction via the density matrix

NASA Astrophysics Data System (ADS)

de Carvalho, C. A.; Cornwall, J. M.; da Silva, A. J.

2001-07-01

We give graphical rules, based on earlier work for the functional Schrödinger equation, for constructing the density matrix for scalar and gauge fields in equilibrium at finite temperature T. More useful is a dimensionally reduced effective action (DREA) constructed from the density matrix by further functional integration over the arguments of the density matrix coupled to a source. The DREA is an effective action in one less dimension which may be computed order by order in perturbation theory or by dressed-loop expansions; it encodes all thermal matrix elements. We term the DREA procedure alternative dimensional reduction, to distinguish it from the conventional dimensionally reduced field theory (DRFT) which applies at infinite T. The DREA is useful because it gives a dimensionally reduced theory usable at any T including infinity, where it yields the DRFT, and because it does not and cannot have certain spurious infinities which sometimes occur in the density matrix itself or the conventional DRFT; these come from ln T factors at infinite temperature. The DREA can be constructed to all orders (in principle) and the only regularizations needed are those which control the ultraviolet behavior of the zero-T theory. An example of spurious divergences in the DRFT occurs in d=2+1φ4 theory dimensionally reduced to d=2. We study this theory and show that the rules for the DREA replace these ``wrong'' divergences in physical parameters by calculable powers of ln T; we also compute the phase transition temperature of this φ4 theory in one-loop order. Our density-matrix construction is equivalent to a construction of the Landau-Ginzburg ``coarse-grained free energy'' from a microscopic Hamiltonian.

Density-functional expansion methods: evaluation of LDA, GGA, and meta-GGA functionals and different integral approximations.

PubMed

Giese, Timothy J; York, Darrin M

2010-12-28

We extend the Kohn-Sham potential energy expansion (VE) to include variations of the kinetic energy density and use the VE formulation with a 6-31G* basis to perform a "Jacob's ladder" comparison of small molecule properties using density functionals classified as being either LDA, GGA, or meta-GGA. We show that the VE reproduces standard Kohn-Sham DFT results well if all integrals are performed without further approximation, and there is no substantial improvement in using meta-GGA functionals relative to GGA functionals. The advantages of using GGA versus LDA functionals becomes apparent when modeling hydrogen bonds. We furthermore examine the effect of using integral approximations to compute the zeroth-order energy and first-order matrix elements, and the results suggest that the origin of the short-range repulsive potential within self-consistent charge density-functional tight-binding methods mainly arises from the approximations made to the first-order matrix elements.

Nonorthogonal orbital based N-body reduced density matrices and their applications to valence bond theory. I. Hamiltonian matrix elements between internally contracted excited valence bond wave functions

NASA Astrophysics Data System (ADS)

Chen, Zhenhua; Chen, Xun; Wu, Wei

2013-04-01

In this series, the n-body reduced density matrix (n-RDM) approach for nonorthogonal orbitals and their applications to ab initio valence bond (VB) methods are presented. As the first paper of this series, Hamiltonian matrix elements between internally contracted VB wave functions are explicitly provided by means of nonorthogonal orbital based RDM approach. To this end, a more generalized Wick's theorem, called enhanced Wick's theorem, is presented both in arithmetical and in graphical forms, by which the deduction of expressions for the matrix elements between internally contracted VB wave functions is dramatically simplified, and the matrix elements are finally expressed in terms of tensor contractions of electronic integrals and n-RDMs of the reference VB self-consistent field wave function. A string-based algorithm is developed for the purpose of evaluating n-RDMs in an efficient way. Using the techniques presented in this paper, one is able to develop new methods and efficient algorithms for nonorthogonal orbital based many-electron theory much easier than by use of the first quantized formulism.

Generalization of the Kohn-Sham system that can represent arbitrary one-electron density matrices

DOE PAGES

Hubertus J. J. van Dam

2016-04-27

Density functional theory is currently the most widely applied method in electronic structure theory. The Kohn-Sham method, based on a fictitious system of noninteracting particles, is the workhorse of the theory. The particular form of the Kohn-Sham wave function admits only idempotent one-electron density matrices whereas wave functions of correlated electrons in post-Hartree-Fock methods invariably have fractional occupation numbers. Here we show that by generalizing the orbital concept and introducing a suitable dot product as well as a probability density, a noninteracting system can be chosen that can represent the one-electron density matrix of any system, even one with fractionalmore » occupation numbers. This fictitious system ensures that the exact electron density is accessible within density functional theory. It can also serve as the basis for reduced density matrix functional theory. Moreover, to aid the analysis of the results the orbitals may be assigned energies from a mean-field Hamiltonian. This produces energy levels that are akin to Hartree-Fock orbital energies such that conventional analyses based on Koopmans' theorem are available. Lastly, this system is convenient in formalisms that depend on creation and annihilation operators as they are trivially applied to single-determinant wave functions.« less

Invertibility of retarded response functions for Laplace transformable potentials: Application to one-body reduced density matrix functional theory.

PubMed

Giesbertz, K J H

2015-08-07

A theorem for the invertibility of arbitrary response functions is presented under the following conditions: the time dependence of the potentials should be Laplace transformable and the initial state should be a ground state, though it might be degenerate. This theorem provides a rigorous foundation for all density-functional-like theories in the time-dependent linear response regime. Especially for time-dependent one-body reduced density matrix (1RDM) functional theory, this is an important step forward, since a solid foundation has currently been lacking. The theorem is equally valid for static response functions in the non-degenerate case, so can be used to characterize the uniqueness of the potential in the ground state version of the corresponding density-functional-like theory. Such a classification of the uniqueness of the non-local potential in ground state 1RDM functional theory has been lacking for decades. With the aid of presented invertibility theorem presented here, a complete classification of the non-uniqueness of the non-local potential in 1RDM functional theory can be given for the first time.

Collagen Matrix Density Drives the Metabolic Shift in Breast Cancer Cells.

PubMed

Morris, Brett A; Burkel, Brian; Ponik, Suzanne M; Fan, Jing; Condeelis, John S; Aguirre-Ghiso, Julio A; Castracane, James; Denu, John M; Keely, Patricia J

2016-11-01

Increased breast density attributed to collagen I deposition is associated with a 4-6 fold increased risk of developing breast cancer. Here, we assessed cellular metabolic reprogramming of mammary carcinoma cells in response to increased collagen matrix density using an in vitro 3D model. Our initial observations demonstrated changes in functional metabolism in both normal mammary epithelial cells and mammary carcinoma cells in response to changes in matrix density. Further, mammary carcinoma cells grown in high density collagen matrices displayed decreased oxygen consumption and glucose metabolism via the tricarboxylic acid (TCA) cycle compared to cells cultured in low density matrices. Despite decreased glucose entry into the TCA cycle, levels of glucose uptake, cell viability, and ROS were not different between high and low density matrices. Interestingly, under high density conditions the contribution of glutamine as a fuel source to drive the TCA cycle was significantly enhanced. These alterations in functional metabolism mirrored significant changes in the expression of metabolic genes involved in glycolysis, oxidative phosphorylation, and the serine synthesis pathway. This study highlights the broad importance of the collagen microenvironment to cellular expression profiles, and shows that changes in density of the collagen microenvironment can modulate metabolic shifts of cancer cells. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Density matrix embedding in an antisymmetrized geminal power bath

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

Tsuchimochi, Takashi; Welborn, Matthew; Van Voorhis, Troy, E-mail: tvan@mit.edu

2015-07-14

Density matrix embedding theory (DMET) has emerged as a powerful tool for performing wave function-in-wave function embedding for strongly correlated systems. In traditional DMET, an accurate calculation is performed on a small impurity embedded in a mean field bath. Here, we extend the original DMET equations to account for correlation in the bath via an antisymmetrized geminal power (AGP) wave function. The resulting formalism has a number of advantages. First, it allows one to properly treat the weak correlation limit of independent pairs, which DMET is unable to do with a mean-field bath. Second, it associates a size extensive correlationmore » energy with a given density matrix (for the models tested), which AGP by itself is incapable of providing. Third, it provides a reasonable description of charge redistribution in strongly correlated but non-periodic systems. Thus, AGP-DMET appears to be a good starting point for describing electron correlation in molecules, which are aperiodic and possess both strong and weak electron correlation.« less

Partially coherent electron transport in terahertz quantum cascade lasers based on a Markovian master equation for the density matrix

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

Jonasson, O.; Karimi, F.; Knezevic, I.

2016-08-01

We derive a Markovian master equation for the single-electron density matrix, applicable to quantum cascade lasers (QCLs). The equation conserves the positivity of the density matrix, includes off-diagonal elements (coherences) as well as in-plane dynamics, and accounts for electron scattering with phonons and impurities. We use the model to simulate a terahertz-frequency QCL, and compare the results with both experiment and simulation via nonequilibrium Green's functions (NEGF). We obtain very good agreement with both experiment and NEGF when the QCL is biased for optimal lasing. For the considered device, we show that the magnitude of coherences can be a significantmore » fraction of the diagonal matrix elements, which demonstrates their importance when describing THz QCLs. We show that the in-plane energy distribution can deviate far from a heated Maxwellian distribution, which suggests that the assumption of thermalized subbands in simplified density-matrix models is inadequate. As a result, we also show that the current density and subband occupations relax towards their steady-state values on very different time scales.« less

Surface Snow Density of East Antarctica Derived from In-Situ Observations

NASA Astrophysics Data System (ADS)

Tian, Y.; Zhang, S.; Du, W.; Chen, J.; Xie, H.; Tong, X.; Li, R.

2018-04-01

Models based on physical principles or semi-empirical parameterizations have used to compute the firn density, which is essential for the study of surface processes in the Antarctic ice sheet. However, parameterization of surface snow density is often challenged by the description of detailed local characterization. In this study we propose to generate a surface density map for East Antarctica from all the filed observations that are available. Considering that the observations are non-uniformly distributed around East Antarctica, obtained by different methods, and temporally inhomogeneous, the field observations are used to establish an initial density map with a grid size of 30 × 30 km2 in which the observations are averaged at a temporal scale of five years. We then construct an observation matrix with its columns as the map grids and rows as the temporal scale. If a site has an unknown density value for a period, we will set it to 0 in the matrix. In order to construct the main spatial and temple information of surface snow density matrix we adopt Empirical Orthogonal Function (EOF) method to decompose the observation matrix and only take first several lower-order modes, because these modes already contain most information of the observation matrix. However, there are a lot of zeros in the matrix and we solve it by using matrix completion algorithm, and then we derive the time series of surface snow density at each observation site. Finally, we can obtain the surface snow density by multiplying the modes interpolated by kriging with the corresponding amplitude of the modes. Comparative analysis have done between our surface snow density map and model results. The above details will be introduced in the paper.

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.

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.

Microscopically based energy density functionals for nuclei using the density matrix expansion. II. Full optimization and validation

NASA Astrophysics Data System (ADS)

Navarro Pérez, R.; Schunck, N.; Dyhdalo, A.; Furnstahl, R. J.; Bogner, S. K.

2018-05-01

Background: Energy density functional methods provide a generic framework to compute properties of atomic nuclei starting from models of nuclear potentials and the rules of quantum mechanics. Until now, the overwhelming majority of functionals have been constructed either from empirical nuclear potentials such as the Skyrme or Gogny forces, or from systematic gradient-like expansions in the spirit of the density functional theory for atoms. Purpose: We seek to obtain a usable form of the nuclear energy density functional that is rooted in the modern theory of nuclear forces. We thus consider a functional obtained from the density matrix expansion of local nuclear potentials from chiral effective field theory. We propose a parametrization of this functional carefully calibrated and validated on selected ground-state properties that is suitable for large-scale calculations of nuclear properties. Methods: Our energy functional comprises two main components. The first component is a non-local functional of the density and corresponds to the direct part (Hartree term) of the expectation value of local chiral potentials on a Slater determinant. Contributions to the mean field and the energy of this term are computed by expanding the spatial, finite-range components of the chiral potential onto Gaussian functions. The second component is a local functional of the density and is obtained by applying the density matrix expansion to the exchange part (Fock term) of the expectation value of the local chiral potential. We apply the UNEDF2 optimization protocol to determine the coupling constants of this energy functional. Results: We obtain a set of microscopically constrained functionals for local chiral potentials from leading order up to next-to-next-to-leading order with and without three-body forces and contributions from Δ excitations. These functionals are validated on the calculation of nuclear and neutron matter, nuclear mass tables, single-particle shell structure in closed-shell nuclei, and the fission barrier of 240Pu. Quantitatively, they perform noticeably better than the more phenomenological Skyrme functionals. Conclusions: The inclusion of higher-order terms in the chiral perturbation expansion seems to produce a systematic improvement in predicting nuclear binding energies while the impact on other observables is not really significant. This result is especially promising since all the fits have been performed at the single-reference level of the energy density functional approach, where important collective correlations such as center-of-mass correction, rotational correction, or zero-point vibrational energies have not been taken into account yet.

Relative Contribution of Matrix Structure, Patch Resources and Management to the Local Densities of Two Large Blue Butterfly Species

PubMed Central

Skórka, Piotr; Nowicki, Piotr; Bonk, Maciej; Król, Wiesław; Szpiłyk, Damian; Woyciechowski, Michal

2016-01-01

The type of matrix, the landscape surrounding habitat patches, may determine the distribution and function of local populations. However, the matrix is often heterogeneous, and its various components may differentially contribute to metapopulation processes at different spatial scales, a phenomenon that has rarely been investigated. The aim of this study was to estimate the relative importance of matrix composition and spatial scale, habitat quality, and management intensity on the occurrence and density of local populations of two endangered large blue butterflies: Phengaris teleius and P. nausithous. Presence and abundance data were assessed over two years, 2011–12, in 100 local patches within two heterogeneous regions (near Kraków and Tarnów, southern Poland). The matrix composition was analyzed at eight spatial scales. We observed high occupancy rates in both species, regions and years. With the exception of area and isolation, almost all of the matrix components contributed to Phengaris sp. densities. The different matrix components acted at different spatial scales (grassland cover within 4 and 3 km, field cover within 0.4 and 0.3 km and water cover within 4 km radii for P. teleius and P. nausithous, respectively) and provided the highest independent contribution to the butterfly densities. Additionally, the effects of a 0.4 km radius of forest cover and a food plant cover on P. teleius, and a 1 km radius of settlement cover and management intensity on P. nausithous densities were observed. Contrary to former studies we conclude that the matrix heterogeneity and spatial scale rather than general matrix type are of relevance for densities of butterflies. Conservation strategies for these umbrella species should concentrate on maintaining habitat quality and managing matrix composition at the most appropriate spatial scales. PMID:28005942

Relative Contribution of Matrix Structure, Patch Resources and Management to the Local Densities of Two Large Blue Butterfly Species.

PubMed

Kajzer-Bonk, Joanna; Skórka, Piotr; Nowicki, Piotr; Bonk, Maciej; Król, Wiesław; Szpiłyk, Damian; Woyciechowski, Michal

2016-01-01

The type of matrix, the landscape surrounding habitat patches, may determine the distribution and function of local populations. However, the matrix is often heterogeneous, and its various components may differentially contribute to metapopulation processes at different spatial scales, a phenomenon that has rarely been investigated. The aim of this study was to estimate the relative importance of matrix composition and spatial scale, habitat quality, and management intensity on the occurrence and density of local populations of two endangered large blue butterflies: Phengaris teleius and P. nausithous. Presence and abundance data were assessed over two years, 2011-12, in 100 local patches within two heterogeneous regions (near Kraków and Tarnów, southern Poland). The matrix composition was analyzed at eight spatial scales. We observed high occupancy rates in both species, regions and years. With the exception of area and isolation, almost all of the matrix components contributed to Phengaris sp. densities. The different matrix components acted at different spatial scales (grassland cover within 4 and 3 km, field cover within 0.4 and 0.3 km and water cover within 4 km radii for P. teleius and P. nausithous, respectively) and provided the highest independent contribution to the butterfly densities. Additionally, the effects of a 0.4 km radius of forest cover and a food plant cover on P. teleius, and a 1 km radius of settlement cover and management intensity on P. nausithous densities were observed. Contrary to former studies we conclude that the matrix heterogeneity and spatial scale rather than general matrix type are of relevance for densities of butterflies. Conservation strategies for these umbrella species should concentrate on maintaining habitat quality and managing matrix composition at the most appropriate spatial scales.

Microscopically based energy density functionals for nuclei using the density matrix expansion: Implementation and pre-optimization

NASA Astrophysics Data System (ADS)

Stoitsov, M.; Kortelainen, M.; Bogner, S. K.; Duguet, T.; Furnstahl, R. J.; Gebremariam, B.; Schunck, N.

2010-11-01

In a recent series of articles, Gebremariam, Bogner, and Duguet derived a microscopically based nuclear energy density functional by applying the density matrix expansion (DME) to the Hartree-Fock energy obtained from chiral effective field theory two- and three-nucleon interactions. Owing to the structure of the chiral interactions, each coupling in the DME functional is given as the sum of a coupling constant arising from zero-range contact interactions and a coupling function of the density arising from the finite-range pion exchanges. Because the contact contributions have essentially the same structure as those entering empirical Skyrme functionals, a microscopically guided Skyrme phenomenology has been suggested in which the contact terms in the DME functional are released for optimization to finite-density observables to capture short-range correlation energy contributions from beyond Hartree-Fock. The present article is the first attempt to assess the ability of the newly suggested DME functional, which has a much richer set of density dependencies than traditional Skyrme functionals, to generate sensible and stable results for nuclear applications. The results of the first proof-of-principle calculations are given, and numerous practical issues related to the implementation of the new functional in existing Skyrme codes are discussed. Using a restricted singular value decomposition optimization procedure, it is found that the new DME functional gives numerically stable results and exhibits a small but systematic reduction of our test χ2 function compared to standard Skyrme functionals, thus justifying its suitability for future global optimizations and large-scale calculations.

Electronic coupling matrix elements from charge constrained density functional theory calculations using a plane wave basis set

NASA Astrophysics Data System (ADS)

Oberhofer, Harald; Blumberger, Jochen

2010-12-01

We present a plane wave basis set implementation for the calculation of electronic coupling matrix elements of electron transfer reactions within the framework of constrained density functional theory (CDFT). Following the work of Wu and Van Voorhis [J. Chem. Phys. 125, 164105 (2006)], the diabatic wavefunctions are approximated by the Kohn-Sham determinants obtained from CDFT calculations, and the coupling matrix element calculated by an efficient integration scheme. Our results for intermolecular electron transfer in small systems agree very well with high-level ab initio calculations based on generalized Mulliken-Hush theory, and with previous local basis set CDFT calculations. The effect of thermal fluctuations on the coupling matrix element is demonstrated for intramolecular electron transfer in the tetrathiafulvalene-diquinone (Q-TTF-Q-) anion. Sampling the electronic coupling along density functional based molecular dynamics trajectories, we find that thermal fluctuations, in particular the slow bending motion of the molecule, can lead to changes in the instantaneous electron transfer rate by more than an order of magnitude. The thermal average, ( {< {| {H_ab } |^2 } > } )^{1/2} = 6.7 {mH}, is significantly higher than the value obtained for the minimum energy structure, | {H_ab } | = 3.8 {mH}. While CDFT in combination with generalized gradient approximation (GGA) functionals describes the intermolecular electron transfer in the studied systems well, exact exchange is required for Q-TTF-Q- in order to obtain coupling matrix elements in agreement with experiment (3.9 mH). The implementation presented opens up the possibility to compute electronic coupling matrix elements for extended systems where donor, acceptor, and the environment are treated at the quantum mechanical (QM) level.

Local representation of the electronic dielectric response function

DOE PAGES

Lu, Deyu; Ge, Xiaochuan

2015-12-11

We present a local representation of the electronic dielectric response function, based on a spatial partition of the dielectric response into contributions from each occupied Wannier orbital using a generalized density functional perturbation theory. This procedure is fully ab initio, and therefore allows us to rigorously define local metrics, such as “bond polarizability,” on Wannier centers. We show that the locality of the bare response function is determined by the locality of three quantities: Wannier functions of the occupied manifold, the density matrix, and the Hamiltonian matrix. Furthermore, in systems with a gap, the bare dielectric response is exponentially localized,more » which supports the physical picture of the dielectric response function as a collection of interacting local responses that can be captured by a tight-binding model.« less

Increased extracellular matrix density decreases MCF10A breast cell acinus formation in 3D culture conditions.

PubMed

Lance, Amanda; Yang, Chih-Chao; Swamydas, Muthulekha; Dean, Delphine; Deitch, Sandy; Burg, Karen J L; Dréau, Didier

2016-01-01

The extracellular matrix (ECM) contributes to the generation and dynamic of normal breast tissue, in particular to the generation of polarized acinar and ductal structures. In vitro 3D culture conditions, including variations in the composition of the ECM, have been shown to directly influence the formation and organization of acinus-like and duct-like structures. Furthermore, the density of the ECM appears to also play a role in the normal mammary tissue and tumour formation. Here we show that the density of the ECM directly influences the number, organization and function of breast acini. Briefly, non-malignant human breast MCF10A cells were incubated in increasing densities of a Matrigel®-collagen I matrix. Elastic moduli near and distant to the acinus structures were measured by atomic force microscopy, and the number of acinus structures was determined. Immunochemistry was used to investigate the expression levels of E-cadherin, laminin, matrix metalloproteinase-14 and ß-casein in MCF10A cells. The modulus of the ECM was significantly increased near the acinus structures and the number of acinus structures decreased with the increase in Matrigel-collagen I density. As evaluated by the expression of laminin, the organization of the acinus structures present was altered as the density of the ECM increased. Increases in both E-cadherin and MMP14 expression by MCF10A cells as ECM density increased were also observed. In contrast, MCF10A cells expressed lower ß-casein levels as the ECM density increased. Taken together, these observations highlight the key role of ECM density in modulating the number, organization and function of breast acini. Copyright © 2013 John Wiley & Sons, Ltd.

Path Integrals for Electronic Densities, Reactivity Indices, and Localization Functions in Quantum Systems

PubMed Central

Putz, Mihai V.

2009-01-01

The density matrix theory, the ancestor of density functional theory, provides the immediate framework for Path Integral (PI) development, allowing the canonical density be extended for the many-electronic systems through the density functional closure relationship. Yet, the use of path integral formalism for electronic density prescription presents several advantages: assures the inner quantum mechanical description of the system by parameterized paths; averages the quantum fluctuations; behaves as the propagator for time-space evolution of quantum information; resembles Schrödinger equation; allows quantum statistical description of the system through partition function computing. In this framework, four levels of path integral formalism were presented: the Feynman quantum mechanical, the semiclassical, the Feynman-Kleinert effective classical, and the Fokker-Planck non-equilibrium ones. In each case the density matrix or/and the canonical density were rigorously defined and presented. The practical specializations for quantum free and harmonic motions, for statistical high and low temperature limits, the smearing justification for the Bohr’s quantum stability postulate with the paradigmatic Hydrogen atomic excursion, along the quantum chemical calculation of semiclassical electronegativity and hardness, of chemical action and Mulliken electronegativity, as well as by the Markovian generalizations of Becke-Edgecombe electronic focalization functions – all advocate for the reliability of assuming PI formalism of quantum mechanics as a versatile one, suited for analytically and/or computationally modeling of a variety of fundamental physical and chemical reactivity concepts characterizing the (density driving) many-electronic systems. PMID:20087467

Path integrals for electronic densities, reactivity indices, and localization functions in quantum systems.

PubMed

Putz, Mihai V

2009-11-10

The density matrix theory, the ancestor of density functional theory, provides the immediate framework for Path Integral (PI) development, allowing the canonical density be extended for the many-electronic systems through the density functional closure relationship. Yet, the use of path integral formalism for electronic density prescription presents several advantages: assures the inner quantum mechanical description of the system by parameterized paths; averages the quantum fluctuations; behaves as the propagator for time-space evolution of quantum information; resembles Schrödinger equation; allows quantum statistical description of the system through partition function computing. In this framework, four levels of path integral formalism were presented: the Feynman quantum mechanical, the semiclassical, the Feynman-Kleinert effective classical, and the Fokker-Planck non-equilibrium ones. In each case the density matrix or/and the canonical density were rigorously defined and presented. The practical specializations for quantum free and harmonic motions, for statistical high and low temperature limits, the smearing justification for the Bohr's quantum stability postulate with the paradigmatic Hydrogen atomic excursion, along the quantum chemical calculation of semiclassical electronegativity and hardness, of chemical action and Mulliken electronegativity, as well as by the Markovian generalizations of Becke-Edgecombe electronic focalization functions - all advocate for the reliability of assuming PI formalism of quantum mechanics as a versatile one, suited for analytically and/or computationally modeling of a variety of fundamental physical and chemical reactivity concepts characterizing the (density driving) many-electronic systems.

Multivariate Granger causality: an estimation framework based on factorization of the spectral density matrix

PubMed Central

Wen, Xiaotong; Rangarajan, Govindan; Ding, Mingzhou

2013-01-01

Granger causality is increasingly being applied to multi-electrode neurophysiological and functional imaging data to characterize directional interactions between neurons and brain regions. For a multivariate dataset, one might be interested in different subsets of the recorded neurons or brain regions. According to the current estimation framework, for each subset, one conducts a separate autoregressive model fitting process, introducing the potential for unwanted variability and uncertainty. In this paper, we propose a multivariate framework for estimating Granger causality. It is based on spectral density matrix factorization and offers the advantage that the estimation of such a matrix needs to be done only once for the entire multivariate dataset. For any subset of recorded data, Granger causality can be calculated through factorizing the appropriate submatrix of the overall spectral density matrix. PMID:23858479

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

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

Extension of many-body theory and approximate density functionals to fractional charges and fractional spins.

PubMed

Yang, Weitao; Mori-Sánchez, Paula; Cohen, Aron J

2013-09-14

The exact conditions for density functionals and density matrix functionals in terms of fractional charges and fractional spins are known, and their violation in commonly used functionals has been shown to be the root of many major failures in practical applications. However, approximate functionals are designed for physical systems with integer charges and spins, not in terms of the fractional variables. Here we develop a general framework for extending approximate density functionals and many-electron theory to fractional-charge and fractional-spin systems. Our development allows for the fractional extension of any approximate theory that is a functional of G(0), the one-electron Green's function of the non-interacting reference system. The extension to fractional charge and fractional spin systems is based on the ensemble average of the basic variable, G(0). We demonstrate the fractional extension for the following theories: (1) any explicit functional of the one-electron density, such as the local density approximation and generalized gradient approximations; (2) any explicit functional of the one-electron density matrix of the non-interacting reference system, such as the exact exchange functional (or Hartree-Fock theory) and hybrid functionals; (3) many-body perturbation theory; and (4) random-phase approximations. A general rule for such an extension has also been derived through scaling the orbitals and should be useful for functionals where the link to the Green's function is not obvious. The development thus enables the examination of approximate theories against known exact conditions on the fractional variables and the analysis of their failures in chemical and physical applications in terms of violations of exact conditions of the energy functionals. The present work should facilitate the calculation of chemical potentials and fundamental bandgaps with approximate functionals and many-electron theories through the energy derivatives with respect to the fractional charge. It should play an important role in developing accurate approximate density functionals and many-body theory.

Prediction of thermal cycling induced matrix cracking

NASA Technical Reports Server (NTRS)

Mcmanus, Hugh L.

1992-01-01

Thermal fatigue has been observed to cause matrix cracking in laminated composite materials. A method is presented to predict transverse matrix cracks in composite laminates subjected to cyclic thermal load. Shear lag stress approximations and a simple energy-based fracture criteria are used to predict crack densities as a function of temperature. Prediction of crack densities as a function of thermal cycling is accomplished by assuming that fatigue degrades the material's inherent resistance to cracking. The method is implemented as a computer program. A simple experiment provides data on progressive cracking of a laminate with decreasing temperature. Existing data on thermal fatigue is also used. Correlations of the analytical predictions to the data are very good. A parametric study using the analytical method is presented which provides insight into material behavior under cyclical thermal loads.

Spin-polarized density-matrix functional theory of the single-impurity Anderson model

NASA Astrophysics Data System (ADS)

Töws, W.; Pastor, G. M.

2012-12-01

Lattice density functional theory (LDFT) is used to investigate spin excitations in the single-impurity Anderson model. In this method, the single-particle density matrix γijσ with respect to the lattice sites replaces the wave function as the basic variable of the many-body problem. A recently developed two-level approximation (TLA) to the interaction-energy functional W[γ] is extended to systems having spin-polarized density distributions and bond orders. This allows us to investigate the effect of external magnetic fields and, in particular, the important singlet-triplet gap ΔE, which determines the Kondo temperature. Applications to finite Anderson rings and square lattices show that the gap ΔE as well as other ground-state and excited-state properties are very accurately reproduced. One concludes that the spin-polarized TLA is reliable in all interaction regimes, from weak to strong correlations, for different hybridization strengths and for all considered impurity valence states. In this way the efficiency of LDFT to account for challenging electron-correlation effects is demonstrated.

The difference between two random mixed quantum states: exact and asymptotic spectral analysis

NASA Astrophysics Data System (ADS)

Mejía, José; Zapata, Camilo; Botero, Alonso

2017-01-01

We investigate the spectral statistics of the difference of two density matrices, each of which is independently obtained by partially tracing a random bipartite pure quantum state. We first show how a closed-form expression for the exact joint eigenvalue probability density function for arbitrary dimensions can be obtained from the joint probability density function of the diagonal elements of the difference matrix, which is straightforward to compute. Subsequently, we use standard results from free probability theory to derive a relatively simple analytic expression for the asymptotic eigenvalue density (AED) of the difference matrix ensemble, and using Carlson’s theorem, we obtain an expression for its absolute moments. These results allow us to quantify the typical asymptotic distance between the two random mixed states using various distance measures; in particular, we obtain the almost sure asymptotic behavior of the operator norm distance and the trace distance.

Low-memory iterative density fitting.

PubMed

Grajciar, Lukáš

2015-07-30

A new low-memory modification of the density fitting approximation based on a combination of a continuous fast multipole method (CFMM) and a preconditioned conjugate gradient solver is presented. Iterative conjugate gradient solver uses preconditioners formed from blocks of the Coulomb metric matrix that decrease the number of iterations needed for convergence by up to one order of magnitude. The matrix-vector products needed within the iterative algorithm are calculated using CFMM, which evaluates them with the linear scaling memory requirements only. Compared with the standard density fitting implementation, up to 15-fold reduction of the memory requirements is achieved for the most efficient preconditioner at a cost of only 25% increase in computational time. The potential of the method is demonstrated by performing density functional theory calculations for zeolite fragment with 2592 atoms and 121,248 auxiliary basis functions on a single 12-core CPU workstation. © 2015 Wiley Periodicals, Inc.

Robust location and spread measures for nonparametric probability density function estimation.

PubMed

López-Rubio, Ezequiel

2009-10-01

Robustness against outliers is a desirable property of any unsupervised learning scheme. In particular, probability density estimators benefit from incorporating this feature. A possible strategy to achieve this goal is to substitute the sample mean and the sample covariance matrix by more robust location and spread estimators. Here we use the L1-median to develop a nonparametric probability density function (PDF) estimator. We prove its most relevant properties, and we show its performance in density estimation and classification applications.

Regional variations in the density and arrangement of elastic fibres in the anulus fibrosus of the human lumbar disc

PubMed Central

Smith, Lachlan J; Fazzalari, Nicola L

2006-01-01

Elastic fibres are critical components of the extracellular matrix in dynamic biological structures that undergo extension and recoil. Their presence has been demonstrated in the anulus fibrosus of the human lumbar intervertebral disc; however, a detailed regional analysis of their density and arrangement has not been undertaken, limiting our understanding of their structural and functional roles. In this investigation we have quantitatively described regional variations in elastic fibre density in the anulus fibrosus of the human L3–L4 intervertebral disc using histochemistry and light microscopy. Additionally, a multiplanar comparison of patterns of elastic fibre distribution in the intralamellar and interlamellar zones was undertaken. Novel imaging techniques were developed to facilitate the visualization of elastic fibres otherwise masked by dense surrounding matrix. Elastic fibre density was found to be significantly higher in the lamellae of the posterolateral region of the anulus than the anterolateral, and significantly higher in the outer regions than the inner, suggesting that elastic fibre density in each region of the anulus is commensurate with the magnitude of the tensile deformations experienced in bending and torsion. Elastic fibre arrangments in intralamellar and interlamellar zones were shown to be architecturally distinct, suggesting that they perform multiple functional roles within the anulus matrix structural hierarchy. PMID:16928204

Communication: A difference density picture for the self-consistent field ansatz.

PubMed

Parrish, Robert M; Liu, Fang; Martínez, Todd J

2016-04-07

We formulate self-consistent field (SCF) theory in terms of an interaction picture where the working variable is the difference density matrix between the true system and a corresponding superposition of atomic densities. As the difference density matrix directly represents the electronic deformations inherent in chemical bonding, this "difference self-consistent field (dSCF)" picture provides a number of significant conceptual and computational advantages. We show that this allows for a stable and efficient dSCF iterative procedure with wholly single-precision Coulomb and exchange matrix builds. We also show that the dSCF iterative procedure can be performed with aggressive screening of the pair space. These approximations are tested and found to be accurate for systems with up to 1860 atoms and >10 000 basis functions, providing for immediate overall speedups of up to 70% in the heavily optimized TeraChem SCF implementation.

Communication: A difference density picture for the self-consistent field ansatz

NASA Astrophysics Data System (ADS)

Parrish, Robert M.; Liu, Fang; Martínez, Todd J.

2016-04-01

We formulate self-consistent field (SCF) theory in terms of an interaction picture where the working variable is the difference density matrix between the true system and a corresponding superposition of atomic densities. As the difference density matrix directly represents the electronic deformations inherent in chemical bonding, this "difference self-consistent field (dSCF)" picture provides a number of significant conceptual and computational advantages. We show that this allows for a stable and efficient dSCF iterative procedure with wholly single-precision Coulomb and exchange matrix builds. We also show that the dSCF iterative procedure can be performed with aggressive screening of the pair space. These approximations are tested and found to be accurate for systems with up to 1860 atoms and >10 000 basis functions, providing for immediate overall speedups of up to 70% in the heavily optimized TeraChem SCF implementation.

Quantitative Tomography for Continuous Variable Quantum Systems

NASA Astrophysics Data System (ADS)

Landon-Cardinal, Olivier; Govia, Luke C. G.; Clerk, Aashish A.

2018-03-01

We present a continuous variable tomography scheme that reconstructs the Husimi Q function (Wigner function) by Lagrange interpolation, using measurements of the Q function (Wigner function) at the Padua points, conjectured to be optimal sampling points for two dimensional reconstruction. Our approach drastically reduces the number of measurements required compared to using equidistant points on a regular grid, although reanalysis of such experiments is possible. The reconstruction algorithm produces a reconstructed function with exponentially decreasing error and quasilinear runtime in the number of Padua points. Moreover, using the interpolating polynomial of the Q function, we present a technique to directly estimate the density matrix elements of the continuous variable state, with only a linear propagation of input measurement error. Furthermore, we derive a state-independent analytical bound on this error, such that our estimate of the density matrix is accompanied by a measure of its uncertainty.

Energy Dissipation of Rayleigh Waves due to Absorption Along the Path by the Use of Finite Element Method

DTIC Science & Technology

1979-07-31

3 x 3 t Strain vector a ij,j Space derivative of the stress tensor Fi Force vector per unit volume o Density x CHAPTER III F Total force K Stiffness...matrix 6Vector displacements M Mass matrix B Space operating matrix DO Matrix moduli 2 x 3 DZ Operating matrix in Z direction N Matrix of shape...dissipating medium the deformation of a solid is a function of time, temperature and space . Creep phenomenon is a deformation process in which there is

Watching excitons move: the time-dependent transition density matrix

NASA Astrophysics Data System (ADS)

Ullrich, Carsten

2012-02-01

Time-dependent density-functional theory allows one to calculate excitation energies and the associated transition densities in principle exactly. The transition density matrix (TDM) provides additional information on electron-hole localization and coherence of specific excitations of the many-body system. We have extended the TDM concept into the real-time domain in order to visualize the excited-state dynamics in conjugated molecules. The time-dependent TDM is defined as an implicit density functional, and can be approximately obtained from the time-dependent Kohn-Sham orbitals. The quality of this approximation is assessed in simple model systems. A computational scheme for real molecular systems is presented: the time-dependent Kohn-Sham equations are solved with the OCTOPUS code and the time-dependent Kohn-Sham TDM is calculated using a spatial partitioning scheme. The method is applied to show in real time how locally created electron-hole pairs spread out over neighboring conjugated molecular chains. The coupling mechanism, electron-hole coherence, and the possibility of charge separation are discussed.

Excitation energies of dissociating H2: A problematic case for the adiabatic approximation of time-dependent density functional theory

NASA Astrophysics Data System (ADS)

Gritsenko, O. V.; van Gisbergen, S. J. A.; Görling, A.; Baerends, E. J.

2000-11-01

Time-dependent density functional theory (TDDFT) is applied for calculation of the excitation energies of the dissociating H2 molecule. The standard TDDFT method of adiabatic local density approximation (ALDA) totally fails to reproduce the potential curve for the lowest excited singlet 1Σu+ state of H2. Analysis of the eigenvalue problem for the excitation energies as well as direct derivation of the exchange-correlation (xc) kernel fxc(r,r',ω) shows that ALDA fails due to breakdown of its simple spatially local approximation for the kernel. The analysis indicates a complex structure of the function fxc(r,r',ω), which is revealed in a different behavior of the various matrix elements K1c,1cxc (between the highest occupied Kohn-Sham molecular orbital ψ1 and virtual MOs ψc) as a function of the bond distance R(H-H). The effect of nonlocality of fxc(r,r') is modeled by using different expressions for the corresponding matrix elements of different orbitals. Asymptotically corrected ALDA (ALDA-AC) expressions for the matrix elements K12,12xc(στ) are proposed, while for other matrix elements the standard ALDA expressions are retained. This approach provides substantial improvement over the standard ALDA. In particular, the ALDA-AC curve for the lowest singlet excitation qualitatively reproduces the shape of the exact curve. It displays a minimum and approaches a relatively large positive energy at large R(H-H). ALDA-AC also produces a substantial improvement for the calculated lowest triplet excitation, which is known to suffer from the triplet instability problem of the restricted KS ground state. Failure of the ALDA for the excitation energies is related to the failure of the local density as well as generalized gradient approximations to reproduce correctly the polarizability of dissociating H2. The expression for the response function χ is derived to show the origin of the field-counteracting term in the xc potential, which is lacking in the local density and generalized gradient approximations and which is required to obtain a correct polarizability.

Extending density functional embedding theory for covalently bonded systems.

PubMed

Yu, Kuang; Carter, Emily A

2017-12-19

Quantum embedding theory aims to provide an efficient solution to obtain accurate electronic energies for systems too large for full-scale, high-level quantum calculations. It adopts a hierarchical approach that divides the total system into a small embedded region and a larger environment, using different levels of theory to describe each part. Previously, we developed a density-based quantum embedding theory called density functional embedding theory (DFET), which achieved considerable success in metals and semiconductors. In this work, we extend DFET into a density-matrix-based nonlocal form, enabling DFET to study the stronger quantum couplings between covalently bonded subsystems. We name this theory density-matrix functional embedding theory (DMFET), and we demonstrate its performance in several test examples that resemble various real applications in both chemistry and biochemistry. DMFET gives excellent results in all cases tested thus far, including predicting isomerization energies, proton transfer energies, and highest occupied molecular orbital-lowest unoccupied molecular orbital gaps for local chromophores. Here, we show that DMFET systematically improves the quality of the results compared with the widely used state-of-the-art methods, such as the simple capped cluster model or the widely used ONIOM method.

The trust-region self-consistent field method in Kohn-Sham density-functional theory.

PubMed

Thøgersen, Lea; Olsen, Jeppe; Köhn, Andreas; Jørgensen, Poul; Sałek, Paweł; Helgaker, Trygve

2005-08-15

The trust-region self-consistent field (TRSCF) method is extended to the optimization of the Kohn-Sham energy. In the TRSCF method, both the Roothaan-Hall step and the density-subspace minimization step are replaced by trust-region optimizations of local approximations to the Kohn-Sham energy, leading to a controlled, monotonic convergence towards the optimized energy. Previously the TRSCF method has been developed for optimization of the Hartree-Fock energy, which is a simple quadratic function in the density matrix. However, since the Kohn-Sham energy is a nonquadratic function of the density matrix, the local energy functions must be generalized for use with the Kohn-Sham model. Such a generalization, which contains the Hartree-Fock model as a special case, is presented here. For comparison, a rederivation of the popular direct inversion in the iterative subspace (DIIS) algorithm is performed, demonstrating that the DIIS method may be viewed as a quasi-Newton method, explaining its fast local convergence. In the global region the convergence behavior of DIIS is less predictable. The related energy DIIS technique is also discussed and shown to be inappropriate for the optimization of the Kohn-Sham energy.

Structure of the first order reduced density matrix in three electron systems: A generalized Pauli constraints assisted study.

PubMed

Theophilou, Iris; Lathiotakis, Nektarios N; Helbig, Nicole

2018-03-21

We investigate the structure of the one-body reduced density matrix of three electron systems, i.e., doublet and quadruplet spin configurations, corresponding to the smallest interacting system with an open-shell ground state. To this end, we use configuration interaction (CI) expansions of the exact wave function in Slater determinants built from natural orbitals in a finite dimensional Hilbert space. With the exception of maximally polarized systems, the natural orbitals of spin eigenstates are generally spin dependent, i.e., the spatial parts of the up and down natural orbitals form two different sets. A measure to quantify this spin dependence is introduced and it is shown that it varies by several orders of magnitude depending on the system. We also study the ordering issue of the spin-dependent occupation numbers which has practical implications in reduced density matrix functional theory minimization schemes, when generalized Pauli constraints (GPCs) are imposed and in the form of the CI expansion in terms of the natural orbitals. Finally, we discuss the aforementioned CI expansion when there are GPCs that are almost "pinned."

Dodecylamine functionalization of carbon nanotubes to improve dispersion, thermal and mechanical properties of polyethylene based nanocomposites

NASA Astrophysics Data System (ADS)

Ferreira, F. V.; Franceschi, W.; Menezes, B. R. C.; Brito, F. S.; Lozano, K.; Coutinho, A. R.; Cividanes, L. S.; Thim, G. P.

2017-07-01

This study presents the effect of dodecylamine (DDA) functionalization of carbon nanotubes (CNTs) on the thermo-physical and mechanical properties of high-density polyethylene (HDPE) based composites. Here, we showed that the functionalization with DDA improved the dispersion of the CNTs as well as the interfacial adhesion with the HDPE matrix via non-covalent interactions. The better dispersion and interaction of CNT in the HDPE matrix as a function of the surface chemistry was correlated with the improved thermo-physical and mechanical properties.

Probability density functions for CP-violating rephasing invariants

NASA Astrophysics Data System (ADS)

Fortin, Jean-François; Giasson, Nicolas; Marleau, Luc

2018-05-01

The implications of the anarchy principle on CP violation in the lepton sector are investigated. A systematic method is introduced to compute the probability density functions for the CP-violating rephasing invariants of the PMNS matrix from the Haar measure relevant to the anarchy principle. Contrary to the CKM matrix which is hierarchical, it is shown that the Haar measure, and hence the anarchy principle, are very likely to lead to the observed PMNS matrix. Predictions on the CP-violating Dirac rephasing invariant |jD | and Majorana rephasing invariant |j1 | are also obtained. They correspond to 〈 |jD | 〉 Haar = π / 105 ≈ 0.030 and 〈 |j1 | 〉 Haar = 1 / (6 π) ≈ 0.053 respectively, in agreement with the experimental hint from T2K of | jDexp | ≈ 0.032 ± 0.005 (or ≈ 0.033 ± 0.003) for the normal (or inverted) hierarchy.

Energy-density field approach for low- and medium-frequency vibroacoustic analysis of complex structures using a statistical computational model

NASA Astrophysics Data System (ADS)

Kassem, M.; Soize, C.; Gagliardini, L.

2009-06-01

In this paper, an energy-density field approach applied to the vibroacoustic analysis of complex industrial structures in the low- and medium-frequency ranges is presented. This approach uses a statistical computational model. The analyzed system consists of an automotive vehicle structure coupled with its internal acoustic cavity. The objective of this paper is to make use of the statistical properties of the frequency response functions of the vibroacoustic system observed from previous experimental and numerical work. The frequency response functions are expressed in terms of a dimensionless matrix which is estimated using the proposed energy approach. Using this dimensionless matrix, a simplified vibroacoustic model is proposed.

Time-dependent transition density matrix for visualizing charge-transfer excitations in photoexcited organic donor-acceptor systems

NASA Astrophysics Data System (ADS)

Li, Yonghui; Ullrich, Carsten

2013-03-01

The time-dependent transition density matrix (TDM) is a useful tool to visualize and interpret the induced charges and electron-hole coherences of excitonic processes in large molecules. Combined with time-dependent density functional theory on a real-space grid (as implemented in the octopus code), the TDM is a computationally viable visualization tool for optical excitation processes in molecules. It provides real-time maps of particles and holes which gives information on excitations, in particular those that have charge-transfer character, that cannot be obtained from the density alone. Some illustration of the TDM and comparison with standard density difference plots will be shown for photoexcited organic donor-acceptor molecules. This work is supported by NSF Grant DMR-1005651

Time-dependent quantum transport: An efficient method based on Liouville-von-Neumann equation for single-electron density matrix

NASA Astrophysics Data System (ADS)

Xie, Hang; Jiang, Feng; Tian, Heng; Zheng, Xiao; Kwok, Yanho; Chen, Shuguang; Yam, ChiYung; Yan, YiJing; Chen, Guanhua

2012-07-01

Basing on our hierarchical equations of motion for time-dependent quantum transport [X. Zheng, G. H. Chen, Y. Mo, S. K. Koo, H. Tian, C. Y. Yam, and Y. J. Yan, J. Chem. Phys. 133, 114101 (2010), 10.1063/1.3475566], we develop an efficient and accurate numerical algorithm to solve the Liouville-von-Neumann equation. We solve the real-time evolution of the reduced single-electron density matrix at the tight-binding level. Calculations are carried out to simulate the transient current through a linear chain of atoms, with each represented by a single orbital. The self-energy matrix is expanded in terms of multiple Lorentzian functions, and the Fermi distribution function is evaluated via the Padè spectrum decomposition. This Lorentzian-Padè decomposition scheme is employed to simulate the transient current. With sufficient Lorentzian functions used to fit the self-energy matrices, we show that the lead spectral function and the dynamics response can be treated accurately. Compared to the conventional master equation approaches, our method is much more efficient as the computational time scales cubically with the system size and linearly with the simulation time. As a result, the simulations of the transient currents through systems containing up to one hundred of atoms have been carried out. As density functional theory is also an effective one-particle theory, the Lorentzian-Padè decomposition scheme developed here can be generalized for first-principles simulation of realistic systems.

Spectral functions with the density matrix renormalization group: Krylov-space approach for correction vectors

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

None, None

Frequency-dependent correlations, such as the spectral function and the dynamical structure factor, help illustrate condensed matter experiments. Within the density matrix renormalization group (DMRG) framework, an accurate method for calculating spectral functions directly in frequency is the correction-vector method. The correction vector can be computed by solving a linear equation or by minimizing a functional. Our paper proposes an alternative to calculate the correction vector: to use the Krylov-space approach. This paper also studies the accuracy and performance of the Krylov-space approach, when applied to the Heisenberg, the t-J, and the Hubbard models. The cases we studied indicate that themore » Krylov-space approach can be more accurate and efficient than the conjugate gradient, and that the error of the former integrates best when a Krylov-space decomposition is also used for ground state DMRG.« less

Spectral functions with the density matrix renormalization group: Krylov-space approach for correction vectors

DOE PAGES

None, None

2016-11-21

Frequency-dependent correlations, such as the spectral function and the dynamical structure factor, help illustrate condensed matter experiments. Within the density matrix renormalization group (DMRG) framework, an accurate method for calculating spectral functions directly in frequency is the correction-vector method. The correction vector can be computed by solving a linear equation or by minimizing a functional. Our paper proposes an alternative to calculate the correction vector: to use the Krylov-space approach. This paper also studies the accuracy and performance of the Krylov-space approach, when applied to the Heisenberg, the t-J, and the Hubbard models. The cases we studied indicate that themore » Krylov-space approach can be more accurate and efficient than the conjugate gradient, and that the error of the former integrates best when a Krylov-space decomposition is also used for ground state DMRG.« less

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

Theophilou, Iris; Helbig, Nicole; Lathiotakis, Nektarios N.

Functionals of the one-body reduced density matrix (1-RDM) are routinely minimized under Coleman’s ensemble N-representability conditions. Recently, the topic of pure-state N-representability conditions, also known as generalized Pauli constraints, received increased attention following the discovery of a systematic way to derive them for any number of electrons and any finite dimensionality of the Hilbert space. The target of this work is to assess the potential impact of the enforcement of the pure-state conditions on the results of reduced density-matrix functional theory calculations. In particular, we examine whether the standard minimization of typical 1-RDM functionals under the ensemble N-representability conditions violatesmore » the pure-state conditions for prototype 3-electron systems. We also enforce the pure-state conditions, in addition to the ensemble ones, for the same systems and functionals and compare the correlation energies and optimal occupation numbers with those obtained by the enforcement of the ensemble conditions alone.« less

Linear-scaling method for calculating nuclear magnetic resonance chemical shifts using gauge-including atomic orbitals within Hartree-Fock and density-functional theory.

PubMed

Kussmann, Jörg; Ochsenfeld, Christian

2007-08-07

Details of a new density matrix-based formulation for calculating nuclear magnetic resonance chemical shifts at both Hartree-Fock and density functional theory levels are presented. For systems with a nonvanishing highest occupied molecular orbital-lowest unoccupied molecular orbital gap, the method allows us to reduce the asymptotic scaling order of the computational effort from cubic to linear, so that molecular systems with 1000 and more atoms can be tackled with today's computers. The key feature is a reformulation of the coupled-perturbed self-consistent field (CPSCF) theory in terms of the one-particle density matrix (D-CPSCF), which avoids entirely the use of canonical MOs. By means of a direct solution for the required perturbed density matrices and the adaptation of linear-scaling integral contraction schemes, the overall scaling of the computational effort is reduced to linear. A particular focus of our formulation is to ensure numerical stability when sparse-algebra routines are used to obtain an overall linear-scaling behavior.

Practical auxiliary basis implementation of Rung 3.5 functionals

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

Janesko, Benjamin G., E-mail: b.janesko@tcu.edu; Scalmani, Giovanni; Frisch, Michael J.

2014-07-21

Approximate exchange-correlation functionals for Kohn-Sham density functional theory often benefit from incorporating exact exchange. Exact exchange is constructed from the noninteracting reference system's nonlocal one-particle density matrix γ(r{sup -vector},r{sup -vector}′). Rung 3.5 functionals attempt to balance the strengths and limitations of exact exchange using a new ingredient, a projection of γ(r{sup -vector},r{sup -vector} ′) onto a semilocal model density matrix γ{sub SL}(ρ(r{sup -vector}),∇ρ(r{sup -vector}),r{sup -vector}−r{sup -vector} ′). γ{sub SL} depends on the electron density ρ(r{sup -vector}) at reference point r{sup -vector}, and is closely related to semilocal model exchange holes. We present a practical implementation of Rung 3.5 functionals, expandingmore » the r{sup -vector}−r{sup -vector} ′ dependence of γ{sub SL} in an auxiliary basis set. Energies and energy derivatives are obtained from 3D numerical integration as in standard semilocal functionals. We also present numerical tests of a range of properties, including molecular thermochemistry and kinetics, geometries and vibrational frequencies, and bandgaps and excitation energies. Rung 3.5 functionals typically provide accuracy intermediate between semilocal and hybrid approximations. Nonlocal potential contributions from γ{sub SL} yield interesting successes and failures for band structures and excitation energies. The results enable and motivate continued exploration of Rung 3.5 functional forms.« less

The supersymmetric method in random matrix theory and applications to QCD

NASA Astrophysics Data System (ADS)

Verbaarschot, Jacobus

2004-12-01

The supersymmetric method is a powerful method for the nonperturbative evaluation of quenched averages in disordered systems. Among others, this method has been applied to the statistical theory of S-matrix fluctuations, the theory of universal conductance fluctuations and the microscopic spectral density of the QCD Dirac operator. We start this series of lectures with a general review of Random Matrix Theory and the statistical theory of spectra. An elementary introduction of the supersymmetric method in Random Matrix Theory is given in the second and third lecture. We will show that a Random Matrix Theory can be rewritten as an integral over a supermanifold. This integral will be worked out in detail for the Gaussian Unitary Ensemble that describes level correlations in systems with broken time-reversal invariance. We especially emphasize the role of symmetries. As a second example of the application of the supersymmetric method we discuss the calculation of the microscopic spectral density of the QCD Dirac operator. This is the eigenvalue density near zero on the scale of the average level spacing which is known to be given by chiral Random Matrix Theory. Also in this case we use symmetry considerations to rewrite the generating function for the resolvent as an integral over a supermanifold. The main topic of the second last lecture is the recent developments on the relation between the supersymmetric partition function and integrable hierarchies (in our case the Toda lattice hierarchy). We will show that this relation is an efficient way to calculate superintegrals. Several examples that were given in previous lectures will be worked out by means of this new method. Finally, we will discuss the quenched QCD Dirac spectrum at nonzero chemical potential. Because of the nonhermiticity of the Dirac operator the usual supersymmetric method has not been successful in this case. However, we will show that the supersymmetric partition function can be evaluated by means of the replica limit of the Toda lattice equation.

Linear-scaling density-functional simulations of charged point defects in Al2O3 using hierarchical sparse matrix algebra.

PubMed

Hine, N D M; Haynes, P D; Mostofi, A A; Payne, M C

2010-09-21

We present calculations of formation energies of defects in an ionic solid (Al(2)O(3)) extrapolated to the dilute limit, corresponding to a simulation cell of infinite size. The large-scale calculations required for this extrapolation are enabled by developments in the approach to parallel sparse matrix algebra operations, which are central to linear-scaling density-functional theory calculations. The computational cost of manipulating sparse matrices, whose sizes are determined by the large number of basis functions present, is greatly improved with this new approach. We present details of the sparse algebra scheme implemented in the ONETEP code using hierarchical sparsity patterns, and demonstrate its use in calculations on a wide range of systems, involving thousands of atoms on hundreds to thousands of parallel processes.

Quasi-particle energy spectra in local reduced density matrix functional theory.

PubMed

Lathiotakis, Nektarios N; Helbig, Nicole; Rubio, Angel; Gidopoulos, Nikitas I

2014-10-28

Recently, we introduced [N. N. Lathiotakis, N. Helbig, A. Rubio, and N. I. Gidopoulos, Phys. Rev. A 90, 032511 (2014)] local reduced density matrix functional theory (local RDMFT), a theoretical scheme capable of incorporating static correlation effects in Kohn-Sham equations. Here, we apply local RDMFT to molecular systems of relatively large size, as a demonstration of its computational efficiency and its accuracy in predicting single-electron properties from the eigenvalue spectrum of the single-particle Hamiltonian with a local effective potential. We present encouraging results on the photoelectron spectrum of molecular systems and the relative stability of C20 isotopes. In addition, we propose a modelling of the fractional occupancies as functions of the orbital energies that further improves the efficiency of the method useful in applications to large systems and solids.

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

Parrish, Robert M.; Liu, Fang; Martínez, Todd J., E-mail: toddjmartinez@gmail.com

We formulate self-consistent field (SCF) theory in terms of an interaction picture where the working variable is the difference density matrix between the true system and a corresponding superposition of atomic densities. As the difference density matrix directly represents the electronic deformations inherent in chemical bonding, this “difference self-consistent field (dSCF)” picture provides a number of significant conceptual and computational advantages. We show that this allows for a stable and efficient dSCF iterative procedure with wholly single-precision Coulomb and exchange matrix builds. We also show that the dSCF iterative procedure can be performed with aggressive screening of the pair space.more » These approximations are tested and found to be accurate for systems with up to 1860 atoms and >10 000 basis functions, providing for immediate overall speedups of up to 70% in the heavily optimized TERACHEM SCF implementation.« less

Hybrid reconstruction of quantum density matrix: when low-rank meets sparsity

NASA Astrophysics Data System (ADS)

Li, Kezhi; Zheng, Kai; Yang, Jingbei; Cong, Shuang; Liu, Xiaomei; Li, Zhaokai

2017-12-01

Both the mathematical theory and experiments have verified that the quantum state tomography based on compressive sensing is an efficient framework for the reconstruction of quantum density states. In recent physical experiments, we found that many unknown density matrices in which people are interested in are low-rank as well as sparse. Bearing this information in mind, in this paper we propose a reconstruction algorithm that combines the low-rank and the sparsity property of density matrices and further theoretically prove that the solution of the optimization function can be, and only be, the true density matrix satisfying the model with overwhelming probability, as long as a necessary number of measurements are allowed. The solver leverages the fixed-point equation technique in which a step-by-step strategy is developed by utilizing an extended soft threshold operator that copes with complex values. Numerical experiments of the density matrix estimation for real nuclear magnetic resonance devices reveal that the proposed method achieves a better accuracy compared to some existing methods. We believe that the proposed method could be leveraged as a generalized approach and widely implemented in the quantum state estimation.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

PubMed

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

Partition-free approach to open quantum systems in harmonic environments: An exact stochastic Liouville equation

NASA Astrophysics Data System (ADS)

McCaul, G. M. G.; Lorenz, C. D.; Kantorovich, L.

2017-03-01

We present a partition-free approach to the evolution of density matrices for open quantum systems coupled to a harmonic environment. The influence functional formalism combined with a two-time Hubbard-Stratonovich transformation allows us to derive a set of exact differential equations for the reduced density matrix of an open system, termed the extended stochastic Liouville-von Neumann equation. Our approach generalizes previous work based on Caldeira-Leggett models and a partitioned initial density matrix. This provides a simple, yet exact, closed-form description for the evolution of open systems from equilibriated initial conditions. The applicability of this model and the potential for numerical implementations are also discussed.

A non-JKL density matrix functional for intergeminal correlation between closed-shell geminals from analysis of natural orbital configuration interaction expansions

NASA Astrophysics Data System (ADS)

van Meer, R.; Gritsenko, O. V.; Baerends, E. J.

2018-03-01

Almost all functionals that are currently used in density matrix functional theory have been created by some a priori ansatz that generates approximations to the second-order reduced density matrix (2RDM). In this paper, a more consistent approach is used: we analyze the 2RDMs (in the natural orbital basis) of rather accurate multi-reference configuration interaction expansions for several small molecules (CH4, NH3, H2O, FH, and N2) and use the knowledge gained to generate new functionals. The analysis shows that a geminal-like structure is present in the 2RDMs, even though no geminal theory has been applied from the onset. It is also shown that the leading non-geminal dynamical correlation contributions are generated by a specific set of double excitations. The corresponding determinants give rise to non-JKL (non Coulomb/Exchange like) multipole-multipole dispersive attractive terms between geminals. Due to the proximity of the geminals, these dispersion terms are large and cannot be omitted, proving pure JKL functionals to be essentially deficient. A second correction emerges from the observation that the "normal" geminal-like exchange between geminals breaks down when one breaks multiple bonds. This problem can be fixed by doubling the exchange between bond broken geminals, effectively restoring the often physically correct high-spin configurations on the bond broken fragments. Both of these corrections have been added to the commonly used antisymmetrized product of strongly orthogonal geminals functional. The resulting non-JKL functional Extended Löwdin-Shull Dynamical-Multibond is capable of reproducing complete active space self-consistent field curves, in which one active orbital is used for each valence electron.

Universality of quantum information in chaotic CFTs

NASA Astrophysics Data System (ADS)

Lashkari, Nima; Dymarsky, Anatoly; Liu, Hong

2018-03-01

We study the Eigenstate Thermalization Hypothesis (ETH) in chaotic conformal field theories (CFTs) of arbitrary dimensions. Assuming local ETH, we compute the reduced density matrix of a ball-shaped subsystem of finite size in the infinite volume limit when the full system is an energy eigenstate. This reduced density matrix is close in trace distance to a density matrix, to which we refer as the ETH density matrix, that is independent of all the details of an eigenstate except its energy and charges under global symmetries. In two dimensions, the ETH density matrix is universal for all theories with the same value of central charge. We argue that the ETH density matrix is close in trace distance to the reduced density matrix of the (micro)canonical ensemble. We support the argument in higher dimensions by comparing the Von Neumann entropy of the ETH density matrix with the entropy of a black hole in holographic systems in the low temperature limit. Finally, we generalize our analysis to the coherent states with energy density that varies slowly in space, and show that locally such states are well described by the ETH density matrix.

Time-Dependent Density Functional Theory for Open Systems and Its Applications.

PubMed

Chen, Shuguang; Kwok, YanHo; Chen, GuanHua

2018-02-20

Photovoltaic devices, electrochemical cells, catalysis processes, light emitting diodes, scanning tunneling microscopes, molecular electronics, and related devices have one thing in common: open quantum systems where energy and matter are not conserved. Traditionally quantum chemistry is confined to isolated and closed systems, while quantum dissipation theory studies open quantum systems. The key quantity in quantum dissipation theory is the reduced system density matrix. As the reduced system density matrix is an O(M! × M!) matrix, where M is the number of the particles of the system of interest, quantum dissipation theory can only be employed to simulate systems of a few particles or degrees of freedom. It is thus important to combine quantum chemistry and quantum dissipation theory so that realistic open quantum systems can be simulated from first-principles. We have developed a first-principles method to simulate the dynamics of open electronic systems, the time-dependent density functional theory for open systems (TDDFT-OS). Instead of the reduced system density matrix, the key quantity is the reduced single-electron density matrix, which is an N × N matrix where N is the number of the atomic bases of the system of interest. As the dimension of the key quantity is drastically reduced, the TDDFT-OS can thus be used to simulate the dynamics of realistic open electronic systems and efficient numerical algorithms have been developed. As an application, we apply the method to study how quantum interference develops in a molecular transistor in time domain. We include electron-phonon interaction in our simulation and show that quantum interference in the given system is robust against nuclear vibration not only in the steady state but also in the transient dynamics. As another application, by combining TDDFT-OS with Ehrenfest dynamics, we study current-induced dissociation of water molecules under scanning tunneling microscopy and follow its time dependent dynamics. Given the rapid development in ultrafast experiments with atomic resolution in recent years, time dependent simulation of open electronic systems will be useful to gain insight and understanding of such experiments. This Account will mainly focus on the practical aspects of the TDDFT-OS method, describing the numerical implementation and demonstrating the method with applications.

Accurate Semilocal Density Functional for Condensed-Matter Physics and Quantum Chemistry.

PubMed

Tao, Jianmin; Mo, Yuxiang

2016-08-12

Most density functionals have been developed by imposing the known exact constraints on the exchange-correlation energy, or by a fit to a set of properties of selected systems, or by both. However, accurate modeling of the conventional exchange hole presents a great challenge, due to the delocalization of the hole. Making use of the property that the hole can be made localized under a general coordinate transformation, here we derive an exchange hole from the density matrix expansion, while the correlation part is obtained by imposing the low-density limit constraint. From the hole, a semilocal exchange-correlation functional is calculated. Our comprehensive test shows that this functional can achieve remarkable accuracy for diverse properties of molecules, solids, and solid surfaces, substantially improving upon the nonempirical functionals proposed in recent years. Accurate semilocal functionals based on their associated holes are physically appealing and practically useful for developing nonlocal functionals.

QCD-inspired spectra from Blue's functions

NASA Astrophysics Data System (ADS)

Nowak, Maciej A.; Papp, Gábor; Zahed, Ismail

1996-02-01

We use the law of addition in random matrix theory to analyze the spectral distributions of a variety of chiral random matrix models as inspired from QCD whether through symmetries or models. In terms of the Blue's functions recently discussed by Zee, we show that most of the spectral distributions in the macroscopic limit and the quenched approximation, follow algebraically from the discontinuity of a pertinent solution to a cubic (Cardano) or a quartic (Ferrari) equation. We use the end-point equation of the energy spectra in chiral random matrix models to argue for novel phase structures, in which the Dirac density of states plays the role of an order parameter.

LFSPMC: Linear feature selection program using the probability of misclassification

NASA Technical Reports Server (NTRS)

Guseman, L. F., Jr.; Marion, B. P.

1975-01-01

The computational procedure and associated computer program for a linear feature selection technique are presented. The technique assumes that: a finite number, m, of classes exists; each class is described by an n-dimensional multivariate normal density function of its measurement vectors; the mean vector and covariance matrix for each density function are known (or can be estimated); and the a priori probability for each class is known. The technique produces a single linear combination of the original measurements which minimizes the one-dimensional probability of misclassification defined by the transformed densities.

Entanglement classification in the noninteracting Fermi gas

NASA Astrophysics Data System (ADS)

Jafarizadeh, M. A.; Eghbalifam, F.; Nami, S.; Yahyavi, M.

In this paper, entanglement classification shared among the spins of localized fermions in the noninteracting Fermi gas is studied. It is proven that the Fermi gas density matrix is block diagonal on the basis of the projection operators to the irreducible representations of symmetric group Sn. Every block of density matrix is in the form of the direct product of a matrix and identity matrix. Then it is useful to study entanglement in every block of density matrix separately. The basis of corresponding Hilbert space are identified from the Schur-Weyl duality theorem. Also, it can be shown that the symmetric part of the density matrix is fully separable. Then it has been shown that the entanglement measure which is introduced in Eltschka et al. [New J. Phys. 10, 043104 (2008)] and Guhne et al. [New J. Phys. 7, 229 (2005)], is zero for the even n qubit Fermi gas density matrix. Then by focusing on three spin reduced density matrix, the entanglement classes have been investigated. In three qubit states there is an entanglement measure which is called 3-tangle. It can be shown that 3-tangle is zero for three qubit density matrix, but the density matrix is not biseparable for all possible values of its parameters and its eigenvectors are in the form of W-states. Then an entanglement witness for detecting non-separable state and an entanglement witness for detecting nonbiseparable states, have been introduced for three qubit density matrix by using convex optimization problem. Finally, the four spin reduced density matrix has been investigated by restricting the density matrix to the irreducible representations of Sn. The restricted density matrix to the subspaces of the irreducible representations: Ssym, S3,1 and S2,2 are denoted by ρsym, ρ3,1 and ρ2,2, respectively. It has been shown that some highly entangled classes (by using the results of Miyake [Phys. Rev. A 67, 012108 (2003)] for entanglement classification) do not exist in the blocks of density matrix ρ3,1 and ρ2,2, so these classes do not exist in the total Fermi gas density matrix.

Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure.

PubMed

Hoy, Erik P; Mazziotti, David A

2015-08-14

Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

Absorption, scattering, and radiation force efficiencies in the longitudinal wave scattering by a small viscoelastic particle in an isotropic solid.

PubMed

Lopes, J H; Leão-Neto, J P; Silva, G T

2017-11-01

Analytical expressions of the absorption, scattering, and elastic radiation force efficiency factors are derived for the longitudinal plane wave scattering by a small viscoelastic particle in a lossless solid matrix. The particle is assumed to be much smaller than the incident wavelength, i.e., the so-called long-wavelength (Rayleigh) approximation. The efficiencies are dimensionless quantities that represent the absorbed and scattering powers and the elastic radiation force on the particle. In the quadrupole approximation, they are expressed in terms of contrast functions (bulk and shear moduli, and density) between the particle and solid matrix. The results for a high-density polyethylene particle embedded in an aluminum matrix agree with those obtained with the partial wave expansion method. Additionally, the connection between the elastic radiation force and forward scattering function is established through the optical theorem. The present results should be useful for ultrasound characterization of particulate composites, and the development of implanted devices activated by radiation force.

Metrics of cellular and vascular infiltration of human acellular dermal matrix in ventral hernia repairs.

PubMed

Campbell, Kristin Turza; Burns, Nadja K; Ensor, Joe; Butler, Charles E

2012-04-01

Human acellular dermal matrix is used for ventral hernia repair, as it resists infection and remodels by means of surrounding tissue. However, the tissue source and impact of basement membrane on cell and vessel infiltration have not been determined. The authors hypothesized that musculofascia would be the primary tissue source of cells and vessels infiltrating into human acellular dermal matrix and that the basement membrane would inhibit infiltration. Fifty-six guinea pigs underwent inlay human acellular dermal matrix ventral hernia repair with the basement membrane oriented toward or away from the peritoneum. At postoperative weeks 1, 2, or 4, repair sites were completely excised. Histologic and immunohistochemical analyses were performed to quantify cell and vessel density within repair-site zones, including interface (lateral, beneath musculofascia) and center (beneath subcutaneous fat) zones. Cell and vessel quantities were compared as functions of zone, basement membrane orientation, and time. Cellular and vascular infiltration increased over time universally. The interface demonstrated greater mean cell density than the center (weeks 1 and 2, p = 0.01 and p < 0.0001, respectively). Cell density was greater with the basement membrane oriented toward the peritoneum at week 4 (p = 0.02). The interface zone had greater mean vessel density than the center zone at week 4 (p < 0.0001). Orienting the basement membrane toward the peritoneum increased vessel density at week 4 (p = 0.0004). Cellular and vascular infiltration into human acellular dermal matrix for ventral hernia repairs was greater from musculofascia than from subcutaneous fat, and the basement membrane inhibited cellular and vascular infiltration. Human acellular dermal matrix should be placed adjacent to the best vascularizing tissue to improve fibrovascular incorporation.

Theoretical approach to embed nanocrystallites into a bulk crystalline matrix and the embedding influence on the electronic band structure and optical properties of the resulting heterostructures

NASA Astrophysics Data System (ADS)

Balagan, Semyon A.; Nazarov, Vladimir U.; Shevlyagin, Alexander V.; Goroshko, Dmitrii L.; Galkin, Nikolay G.

2018-06-01

We develop an approach and present results of the combined molecular dynamics and density functional theory calculations of the structural and optical properties of the nanometer-sized crystallites embedded in a bulk crystalline matrix. The method is designed and implemented for both compatible and incompatible lattices of the nanocrystallite (NC) and the host matrix, when determining the NC optimal orientation relative to the matrix constitutes a challenging problem. We suggest and substantiate an expression for the cost function of the search algorithm, which is the energy per supercell generalized for varying number of atoms in the latter. The epitaxial relationships at the Si/NC interfaces and the optical properties are obtained and found to be in a reasonable agreement with experimental data. Dielectric functions show significant sensitivity to the NC’s orientation relative to the matrix at energies below 0.5 eV.

Theoretical approach to embed nanocrystallites into a bulk crystalline matrix and the embedding influence on the electronic band structure and optical properties of the resulting heterostructures.

PubMed

Balagan, Semyon Anatolyevich; Nazarov, Vladimir U; Shevlyagin, Alexander Vladimirovich; Goroshko, Dmitrii L; Galkin, N G

2018-05-03

We develop an approach and present results of the combined molecular dynamics and density functional theory calculations of the structural and optical properties of the nanometer-sized crystallites embedded in a bulk crystalline matrix. The method is designed and implemented for both compatible and incompatible lattices of the nanocrystallite (NC) and the host matrix, when determining the NC optimal orientation relative to the matrix constitutes a challenging problem. We suggest and substantiate an expression for the cost function of the search algorithm, which is the energy per supercell generalized for varying number of atoms in the latter. The epitaxial relationships at the Si/NC interfaces and the optical properties are obtained and found to be in a reasonable agreement with experimental data. Dielectric functions show significant sensitivity to the NC's orientation relative to the matrix at energies below 0.5 eV. © 2018 IOP Publishing Ltd.

Hartree and Exchange in Ensemble Density Functional Theory: Avoiding the Nonuniqueness Disaster.

PubMed

Gould, Tim; Pittalis, Stefano

2017-12-15

Ensemble density functional theory is a promising method for the efficient and accurate calculation of excitations of quantum systems, at least if useful functionals can be developed to broaden its domain of practical applicability. Here, we introduce a guaranteed single-valued "Hartree-exchange" ensemble density functional, E_{Hx}[n], in terms of the right derivative of the universal ensemble density functional with respect to the coupling constant at vanishing interaction. We show that E_{Hx}[n] is straightforwardly expressible using block eigenvalues of a simple matrix [Eq. (14)]. Specialized expressions for E_{Hx}[n] from the literature, including those involving superpositions of Slater determinants, can now be regarded as originating from the unifying picture presented here. We thus establish a clear and practical description for Hartree and exchange in ensemble systems.

Development and application of a 2-electron reduced density matrix approach to electron transport via molecular junctions

NASA Astrophysics Data System (ADS)

Hoy, Erik P.; Mazziotti, David A.; Seideman, Tamar

2017-11-01

Can an electronic device be constructed using only a single molecule? Since this question was first asked by Aviram and Ratner in the 1970s [Chem. Phys. Lett. 29, 277 (1974)], the field of molecular electronics has exploded with significant experimental advancements in the understanding of the charge transport properties of single molecule devices. Efforts to explain the results of these experiments and identify promising new candidate molecules for molecular devices have led to the development of numerous new theoretical methods including the current standard theoretical approach for studying single molecule charge transport, i.e., the non-equilibrium Green's function formalism (NEGF). By pairing this formalism with density functional theory (DFT), a wide variety of transport problems in molecular junctions have been successfully treated. For some systems though, the conductance and current-voltage curves predicted by common DFT functionals can be several orders of magnitude above experimental results. In addition, since density functional theory relies on approximations to the exact exchange-correlation functional, the predicted transport properties can show significant variation depending on the functional chosen. As a first step to addressing this issue, the authors have replaced density functional theory in the NEGF formalism with a 2-electron reduced density matrix (2-RDM) method, creating a new approach known as the NEGF-RDM method. 2-RDM methods provide a more accurate description of electron correlation compared to density functional theory, and they have lower computational scaling compared to wavefunction based methods of similar accuracy. Additionally, 2-RDM methods are capable of capturing static electron correlation which is untreatable by existing NEGF-DFT methods. When studying dithiol alkane chains and dithiol benzene in model junctions, the authors found that the NEGF-RDM predicts conductances and currents that are 1-2 orders of magnitude below those of B3LYP and M06 DFT functionals. This suggests that the NEGF-RDM method could be a viable alternative to NEGF-DFT for molecular junction calculations.

Quantum Crystallography: Density Matrix-Density Functional Theory and the X-Ray Diffraction Experiment

NASA Astrophysics Data System (ADS)

Soirat, Arnaud J. A.

Density Matrix Theory is a Quantum Mechanical formalism in which the wavefunction is eliminated and its role taken over by reduced density matrices. The interest of this is that, it allows one, in principle, to calculate any electronic property of a physical system, without having to solve the Schrodinger equation, using only two entities much simpler than an N-body wavefunction: first and second -order reduced density matrices. In practice, though, this very promising possibility faces the tremendous theoretical problem of N-representability, which has been solved for the former, but, until now, voids any hope of theoretically determining the latter. However, it has been shown that single determinant reduced density matrices of any order may be recovered from coherent X-ray diffraction data, if one provides a proper Quantum Mechanical description of the Crystallography experiment. A deeper investigation of this method is the purpose of this work, where we, first, further study the calculation of X-ray reduced density matrices N-representable by a single Slater determinant. In this context, we independently derive necessary and sufficient conditions for the uniqueness of the method. We then show how to account for electron correlation in this model. For the first time, indeed, we derive highly accurate, yet practical, density matrices approximately N-representable by correlated-determinant wavefunctions. The interest of such a result lies in the Quantum Mechanical validity of these density matrices, their property of being entirely obtainable from X-ray coherent diffraction data, their very high accuracy conferred by this known property of the N-representing wavefunction, as well as their definition as explicit functionals of the density. All of these properties are finally used in both a theoretical and a numerical application: in the former, we show that these density matrices may be used in the context of Density Functional Theory to highly accurately determine the unknown HK functional, associated with the theorem of Hohenberg and Kohn. The latter is provided by the calculation of helium correlation energy, where we test approximating the second-order density function by the leading term of its McLaurin's series expansion.

Two-dimensional enzyme diffusion in laterally confined DNA monolayers.

PubMed

Castronovo, Matteo; Lucesoli, Agnese; Parisse, Pietro; Kurnikova, Anastasia; Malhotra, Aseem; Grassi, Mario; Grassi, Gabriele; Scaggiante, Bruna; Casalis, Loredana; Scoles, Giacinto

2011-01-01

Addressing the effects of confinement and crowding on biomolecular function may provide insight into molecular mechanisms within living organisms, and may promote the development of novel biotechnology tools. Here, using molecular manipulation methods, we investigate restriction enzyme reactions with double-stranded (ds)DNA oligomers confined in relatively large (and flat) brushy matrices of monolayer patches of controlled, variable density. We show that enzymes from the contacting solution cannot access the dsDNAs from the top-matrix interface, and instead enter at the matrix sides to diffuse two-dimensionally in the gap between top- and bottom-matrix interfaces. This is achieved by limiting lateral access with a barrier made of high-density molecules that arrest enzyme diffusion. We put forward, as a possible explanation, a simple and general model that relates these data to the steric hindrance in the matrix, and we briefly discuss the implications and applications of this strikingly new phenomenon.

Matching-pursuit/split-operator-Fourier-transform computations of thermal correlation functions.

PubMed

Chen, Xin; Wu, Yinghua; Batista, Victor S

2005-02-08

A rigorous and practical methodology for evaluating thermal-equilibrium density matrices, finite-temperature time-dependent expectation values, and time-correlation functions is described. The method involves an extension of the matching-pursuit/split-operator-Fourier-transform method to the solution of the Bloch equation via imaginary-time propagation of the density matrix and the evaluation of Heisenberg time-evolution operators through real-time propagation in dynamically adaptive coherent-state representations.

The tensor hypercontracted parametric reduced density matrix algorithm: coupled-cluster accuracy with O(r(4)) scaling.

PubMed

Shenvi, Neil; van Aggelen, Helen; Yang, Yang; Yang, Weitao; Schwerdtfeger, Christine; Mazziotti, David

2013-08-07

Tensor hypercontraction is a method that allows the representation of a high-rank tensor as a product of lower-rank tensors. In this paper, we show how tensor hypercontraction can be applied to both the electron repulsion integral tensor and the two-particle excitation amplitudes used in the parametric 2-electron reduced density matrix (p2RDM) algorithm. Because only O(r) auxiliary functions are needed in both of these approximations, our overall algorithm can be shown to scale as O(r(4)), where r is the number of single-particle basis functions. We apply our algorithm to several small molecules, hydrogen chains, and alkanes to demonstrate its low formal scaling and practical utility. Provided we use enough auxiliary functions, we obtain accuracy similar to that of the standard p2RDM algorithm, somewhere between that of CCSD and CCSD(T).

Generalized Reduction Formula for Discrete Wigner Functions of Multiqubit Systems

NASA Astrophysics Data System (ADS)

Srinivasan, K.; Raghavan, G.

2018-03-01

Density matrices and Discrete Wigner Functions are equally valid representations of multiqubit quantum states. For density matrices, the partial trace operation is used to obtain the quantum state of subsystems, but an analogous prescription is not available for discrete Wigner Functions. Further, the discrete Wigner function corresponding to a density matrix is not unique but depends on the choice of the quantum net used for its reconstruction. In the present work, we derive a reduction formula for discrete Wigner functions of a general multiqubit state which works for arbitrary quantum nets. These results would be useful for the analysis and classification of entangled states and the study of decoherence purely in a discrete phase space setting and also in applications to quantum computing.

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.

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

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

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

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

DOE PAGES

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

2015-06-26

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Low-density, high-strength intermetallic matrix composites by XD (trademark) synthesis

NASA Technical Reports Server (NTRS)

Kumar, K. S.; Dipietro, M. S.; Brown, S. A.; Whittenberger, J. D.

1991-01-01

A feasibility study was conducted to evaluate the potential of particulate composites based on low-density, L1(sub 2) trialuminide matrices for high-temperature applications. The compounds evaluated included Al22Fe3Ti8 (as a multiphase matrix), Al67Ti25Cr8, and Al66Ti25Mn9. The reinforcement consisted of TiB2 particulates. The TiB2 composites were processed by ingot and powder metallurgy techniques. Microstructural characterization and mechanical testing were performed in the hot-pressed and hot-isostatic-pressed condition. The casting were sectioned and isothermally forged into pancakes. All the materials were tested in compression as a function of temperature, and at high temperatures as a function of strain rate. The test results are discussed.

Random density matrices versus random evolution of open system

NASA Astrophysics Data System (ADS)

Pineda, Carlos; Seligman, Thomas H.

2015-10-01

We present and compare two families of ensembles of random density matrices. The first, static ensemble, is obtained foliating an unbiased ensemble of density matrices. As criterion we use fixed purity as the simplest example of a useful convex function. The second, dynamic ensemble, is inspired in random matrix models for decoherence where one evolves a separable pure state with a random Hamiltonian until a given value of purity in the central system is achieved. Several families of Hamiltonians, adequate for different physical situations, are studied. We focus on a two qubit central system, and obtain exact expressions for the static case. The ensemble displays a peak around Werner-like states, modulated by nodes on the degeneracies of the density matrices. For moderate and strong interactions good agreement between the static and the dynamic ensembles is found. Even in a model where one qubit does not interact with the environment excellent agreement is found, but only if there is maximal entanglement with the interacting one. The discussion is started recalling similar considerations for scattering theory. At the end, we comment on the reach of the results for other convex functions of the density matrix, and exemplify the situation with the von Neumann entropy.

Ground-state densities from the Rayleigh-Ritz variation principle and from density-functional theory.

PubMed

Kvaal, Simen; Helgaker, Trygve

2015-11-14

The relationship between the densities of ground-state wave functions (i.e., the minimizers of the Rayleigh-Ritz variation principle) and the ground-state densities in density-functional theory (i.e., the minimizers of the Hohenberg-Kohn variation principle) is studied within the framework of convex conjugation, in a generic setting covering molecular systems, solid-state systems, and more. Having introduced admissible density functionals as functionals that produce the exact ground-state energy for a given external potential by minimizing over densities in the Hohenberg-Kohn variation principle, necessary and sufficient conditions on such functionals are established to ensure that the Rayleigh-Ritz ground-state densities and the Hohenberg-Kohn ground-state densities are identical. We apply the results to molecular systems in the Born-Oppenheimer approximation. For any given potential v ∈ L(3/2)(ℝ(3)) + L(∞)(ℝ(3)), we establish a one-to-one correspondence between the mixed ground-state densities of the Rayleigh-Ritz variation principle and the mixed ground-state densities of the Hohenberg-Kohn variation principle when the Lieb density-matrix constrained-search universal density functional is taken as the admissible functional. A similar one-to-one correspondence is established between the pure ground-state densities of the Rayleigh-Ritz variation principle and the pure ground-state densities obtained using the Hohenberg-Kohn variation principle with the Levy-Lieb pure-state constrained-search functional. In other words, all physical ground-state densities (pure or mixed) are recovered with these functionals and no false densities (i.e., minimizing densities that are not physical) exist. The importance of topology (i.e., choice of Banach space of densities and potentials) is emphasized and illustrated. The relevance of these results for current-density-functional theory is examined.

Quadratic canonical transformation theory and higher order density matrices.

PubMed

Neuscamman, Eric; Yanai, Takeshi; Chan, Garnet Kin-Lic

2009-03-28

Canonical transformation (CT) theory provides a rigorously size-extensive description of dynamic correlation in multireference systems, with an accuracy superior to and cost scaling lower than complete active space second order perturbation theory. Here we expand our previous theory by investigating (i) a commutator approximation that is applied at quadratic, as opposed to linear, order in the effective Hamiltonian, and (ii) incorporation of the three-body reduced density matrix in the operator and density matrix decompositions. The quadratic commutator approximation improves CT's accuracy when used with a single-determinant reference, repairing the previous formal disadvantage of the single-reference linear CT theory relative to singles and doubles coupled cluster theory. Calculations on the BH and HF binding curves confirm this improvement. In multireference systems, the three-body reduced density matrix increases the overall accuracy of the CT theory. Tests on the H(2)O and N(2) binding curves yield results highly competitive with expensive state-of-the-art multireference methods, such as the multireference Davidson-corrected configuration interaction (MRCI+Q), averaged coupled pair functional, and averaged quadratic coupled cluster theories.

Raney Distributions and Random Matrix Theory

NASA Astrophysics Data System (ADS)

Forrester, Peter J.; Liu, Dang-Zheng

2015-03-01

Recent works have shown that the family of probability distributions with moments given by the Fuss-Catalan numbers permit a simple parameterized form for their density. We extend this result to the Raney distribution which by definition has its moments given by a generalization of the Fuss-Catalan numbers. Such computations begin with an algebraic equation satisfied by the Stieltjes transform, which we show can be derived from the linear differential equation satisfied by the characteristic polynomial of random matrix realizations of the Raney distribution. For the Fuss-Catalan distribution, an equilibrium problem characterizing the density is identified. The Stieltjes transform for the limiting spectral density of the singular values squared of the matrix product formed from inverse standard Gaussian matrices, and standard Gaussian matrices, is shown to satisfy a variant of the algebraic equation relating to the Raney distribution. Supported on , we show that it too permits a simple functional form upon the introduction of an appropriate choice of parameterization. As an application, the leading asymptotic form of the density as the endpoints of the support are approached is computed, and is shown to have some universal features.

Communication: Hilbert-space partitioning of the molecular one-electron density matrix with orthogonal projectors

NASA Astrophysics Data System (ADS)

Vanfleteren, Diederik; Van Neck, Dimitri; Bultinck, Patrick; Ayers, Paul W.; Waroquier, Michel

2010-12-01

A double-atom partitioning of the molecular one-electron density matrix is used to describe atoms and bonds. All calculations are performed in Hilbert space. The concept of atomic weight functions (familiar from Hirshfeld analysis of the electron density) is extended to atomic weight matrices. These are constructed to be orthogonal projection operators on atomic subspaces, which has significant advantages in the interpretation of the bond contributions. In close analogy to the iterative Hirshfeld procedure, self-consistency is built in at the level of atomic charges and occupancies. The method is applied to a test set of about 67 molecules, representing various types of chemical binding. A close correlation is observed between the atomic charges and the Hirshfeld-I atomic charges.

Combining Density Functional Theory and Green's Function Theory: Range-Separated, Nonlocal, Dynamic, and Orbital-Dependent Hybrid Functional.

PubMed

Kananenka, Alexei A; Zgid, Dominika

2017-11-14

We present a rigorous framework which combines single-particle Green's function theory with density functional theory based on a separation of electron-electron interactions into short- and long-range components. Short-range contribution to the total energy and exchange-correlation potential is provided by a density functional approximation, while the long-range contribution is calculated using an explicit many-body Green's function method. Such a hybrid results in a nonlocal, dynamic, and orbital-dependent exchange-correlation functional of a single-particle Green's function. In particular, we present a range-separated hybrid functional called srSVWN5-lrGF2 which combines the local-density approximation and the second-order Green's function theory. We illustrate that similarly to density functional approximations, the new functional is weakly basis-set dependent. Furthermore, it offers an improved description of the short-range dynamic correlation. The many-body contribution to the functional mitigates the many-electron self-interaction error present in many density functional approximations and provides a better description of molecular properties. Additionally, we illustrate that the new functional can be used to scale down the self-energy and, therefore, introduce an additional sparsity to the self-energy matrix that in the future can be exploited in calculations for large molecules or periodic systems.

Accurate Exchange-Correlation Energies for the Warm Dense Electron Gas.

PubMed

Malone, Fionn D; Blunt, N S; Brown, Ethan W; Lee, D K K; Spencer, J S; Foulkes, W M C; Shepherd, James J

2016-09-09

The density matrix quantum Monte Carlo (DMQMC) method is used to sample exact-on-average N-body density matrices for uniform electron gas systems of up to 10^{124} matrix elements via a stochastic solution of the Bloch equation. The results of these calculations resolve a current debate over the accuracy of the data used to parametrize finite-temperature density functionals. Exchange-correlation energies calculated using the real-space restricted path-integral formalism and the k-space configuration path-integral formalism disagree by up to ∼10% at certain reduced temperatures T/T_{F}≤0.5 and densities r_{s}≤1. Our calculations confirm the accuracy of the configuration path-integral Monte Carlo results available at high density and bridge the gap to lower densities, providing trustworthy data in the regime typical of planetary interiors and solids subject to laser irradiation. We demonstrate that the DMQMC method can calculate free energies directly and present exact free energies for T/T_{F}≥1 and r_{s}≤2.

Charge-transfer contributions to the excitonic coupling matrix element in BODIPY-based energy transfer cassettes

NASA Astrophysics Data System (ADS)

Spiegel, J. Dominik; Lyskov, Igor; Kleinschmidt, Martin; Marian, Christel M.

2017-01-01

BODIPY-based dyads serve as model systems for the investigation of excitation energy transfer (EET). Through-space EET is brought about by direct and exchange interactions between the transition densities of donor and acceptor localized states. The presence of a molecular linker gives rise to additional charge transfer (CT) contributions. Here, we present a novel approach for the calculation of the excitonic coupling matrix element (ECME) including CT contributions which is based on supermolecular one-electron transition density matrices (STD). The validity of the approach is assessed for a model system of two π -stacked ethylene molecules at varying intermolecular separation. Wave functions and electronic excitation energies of five EET cassettes comprising anthracene as exciton donor and BODIPY as exciton acceptor are obtained by the redesigned combined density functional theory and multireference configuration interaction (DFT/MRCI-R) method. CT contributions to the ECME are shown to be important in the covalently linked EET cassettes.

Shift-and-invert parallel spectral transformation eigensolver: Massively parallel performance for density-functional based tight-binding

DOE PAGES

Zhang, Hong; Zapol, Peter; Dixon, David A.; ...

2015-11-17

The Shift-and-invert parallel spectral transformations (SIPs), a computational approach to solve sparse eigenvalue problems, is developed for massively parallel architectures with exceptional parallel scalability and robustness. The capabilities of SIPs are demonstrated by diagonalization of density-functional based tight-binding (DFTB) Hamiltonian and overlap matrices for single-wall metallic carbon nanotubes, diamond nanowires, and bulk diamond crystals. The largest (smallest) example studied is a 128,000 (2000) atom nanotube for which ~330,000 (~5600) eigenvalues and eigenfunctions are obtained in ~190 (~5) seconds when parallelized over 266,144 (16,384) Blue Gene/Q cores. Weak scaling and strong scaling of SIPs are analyzed and the performance of SIPsmore » is compared with other novel methods. Different matrix ordering methods are investigated to reduce the cost of the factorization step, which dominates the time-to-solution at the strong scaling limit. As a result, a parallel implementation of assembling the density matrix from the distributed eigenvectors is demonstrated.« less

Shift-and-invert parallel spectral transformation eigensolver: Massively parallel performance for density-functional based tight-binding

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

Zhang, Hong; Zapol, Peter; Dixon, David A.

The Shift-and-invert parallel spectral transformations (SIPs), a computational approach to solve sparse eigenvalue problems, is developed for massively parallel architectures with exceptional parallel scalability and robustness. The capabilities of SIPs are demonstrated by diagonalization of density-functional based tight-binding (DFTB) Hamiltonian and overlap matrices for single-wall metallic carbon nanotubes, diamond nanowires, and bulk diamond crystals. The largest (smallest) example studied is a 128,000 (2000) atom nanotube for which ~330,000 (~5600) eigenvalues and eigenfunctions are obtained in ~190 (~5) seconds when parallelized over 266,144 (16,384) Blue Gene/Q cores. Weak scaling and strong scaling of SIPs are analyzed and the performance of SIPsmore » is compared with other novel methods. Different matrix ordering methods are investigated to reduce the cost of the factorization step, which dominates the time-to-solution at the strong scaling limit. As a result, a parallel implementation of assembling the density matrix from the distributed eigenvectors is demonstrated.« less

A frequency domain global parameter estimation method for multiple reference frequency response measurements

NASA Astrophysics Data System (ADS)

Shih, C. Y.; Tsuei, Y. G.; Allemang, R. J.; Brown, D. L.

1988-10-01

A method of using the matrix Auto-Regressive Moving Average (ARMA) model in the Laplace domain for multiple-reference global parameter identification is presented. This method is particularly applicable to the area of modal analysis where high modal density exists. The method is also applicable when multiple reference frequency response functions are used to characterise linear systems. In order to facilitate the mathematical solution, the Forsythe orthogonal polynomial is used to reduce the ill-conditioning of the formulated equations and to decouple the normal matrix into two reduced matrix blocks. A Complex Mode Indicator Function (CMIF) is introduced, which can be used to determine the proper order of the rational polynomials.

Density-functional expansion methods: Grand challenges.

PubMed

Giese, Timothy J; York, Darrin M

2012-03-01

We discuss the source of errors in semiempirical density functional expansion (VE) methods. In particular, we show that VE methods are capable of well-reproducing their standard Kohn-Sham density functional method counterparts, but suffer from large errors upon using one or more of these approximations: the limited size of the atomic orbital basis, the Slater monopole auxiliary basis description of the response density, and the one- and two-body treatment of the core-Hamiltonian matrix elements. In the process of discussing these approximations and highlighting their symptoms, we introduce a new model that supplements the second-order density-functional tight-binding model with a self-consistent charge-dependent chemical potential equalization correction; we review our recently reported method for generalizing the auxiliary basis description of the atomic orbital response density; and we decompose the first-order potential into a summation of additive atomic components and many-body corrections, and from this examination, we provide new insights and preliminary results that motivate and inspire new approximate treatments of the core-Hamiltonian.

Minkowski Tensors in Two Dimensions: Probing the Morphology and Isotropy of the Matter and Galaxy Density Fields

NASA Astrophysics Data System (ADS)

Appleby, Stephen; Chingangbam, Pravabati; Park, Changbom; Hong, Sungwook E.; Kim, Juhan; Ganesan, Vidhya

2018-05-01

We apply the Minkowski tensor statistics to two-dimensional slices of the three-dimensional matter density field. The Minkowski tensors are a set of functions that are sensitive to directionally dependent signals in the data and, furthermore, can be used to quantify the mean shape of density fields. We begin by reviewing the definition of Minkowski tensors and introducing a method of calculating them from a discretely sampled field. Focusing on the statistic {W}21,1—a 2 × 2 matrix—we calculate its value for both the entire excursion set and individual connected regions and holes within the set. To study the morphology of structures within the excursion set, we calculate the eigenvalues λ 1, λ 2 for the matrix {W}21,1 of each distinct connected region and hole and measure their mean shape using the ratio β \\equiv < {λ }2/{λ }1> . We compare both {W}21,1 and β for a Gaussian field and a smoothed density field generated from the latest Horizon Run 4 cosmological simulation to study the effect of gravitational collapse on these functions. The global statistic {W}21,1 is essentially independent of gravitational collapse, as the process maintains statistical isotropy. However, β is modified significantly, with overdensities becoming relatively more circular compared to underdensities at low redshifts. When applying the statistics to a redshift-space distorted density field, the matrix {W}21,1 is no longer proportional to the identity matrix, and measurements of its diagonal elements can be used to probe the large-scale velocity field.

Communication: Wigner functions in action-angle variables, Bohr-Sommerfeld quantization, the Heisenberg correspondence principle, and a symmetrical quasi-classical approach to the full electronic density matrix

DOE PAGES

Miller, William H.; Cotton, Stephen J.

2016-08-28

It is pointed out that the classical phase space distribution in action-angle (a-a) variables obtained from a Wigner function depends on how the calculation is carried out: if one computes the standard Wigner function in Cartesian variables (p, x), and then replaces p and x by their expressions in terms of a-a variables, one obtains a different result than if the Wigner function is computed directly in terms of the a-a variables. Furthermore, the latter procedure gives a result more consistent with classical and semiclassical theory - e.g., by incorporating the Bohr-Sommerfeld quantization condition (quantum states defined by integer valuesmore » of the action variable) as well as the Heisenberg correspondence principle for matrix elements of an operator between such states - and has also been shown to be more accurate when applied to electronically non-adiabatic applications as implemented within the recently developed symmetrical quasi-classical (SQC) Meyer-Miller (MM) approach. Moreover, use of the Wigner function (obtained directly) in a-a variables shows how our standard SQC/MM approach can be used to obtain off-diagonal elements of the electronic density matrix by processing in a different way the same set of trajectories already used (in the SQC/MM methodology) to obtain the diagonal elements.« less

Communication: Wigner functions in action-angle variables, Bohr-Sommerfeld quantization, the Heisenberg correspondence principle, and a symmetrical quasi-classical approach to the full electronic density matrix.

PubMed

Miller, William H; Cotton, Stephen J

2016-08-28

It is pointed out that the classical phase space distribution in action-angle (a-a) variables obtained from a Wigner function depends on how the calculation is carried out: if one computes the standard Wigner function in Cartesian variables (p, x), and then replaces p and x by their expressions in terms of a-a variables, one obtains a different result than if the Wigner function is computed directly in terms of the a-a variables. Furthermore, the latter procedure gives a result more consistent with classical and semiclassical theory-e.g., by incorporating the Bohr-Sommerfeld quantization condition (quantum states defined by integer values of the action variable) as well as the Heisenberg correspondence principle for matrix elements of an operator between such states-and has also been shown to be more accurate when applied to electronically non-adiabatic applications as implemented within the recently developed symmetrical quasi-classical (SQC) Meyer-Miller (MM) approach. Moreover, use of the Wigner function (obtained directly) in a-a variables shows how our standard SQC/MM approach can be used to obtain off-diagonal elements of the electronic density matrix by processing in a different way the same set of trajectories already used (in the SQC/MM methodology) to obtain the diagonal elements.

Phase dilemma in natural orbital functional theory from the N-representability perspective

NASA Astrophysics Data System (ADS)

Mitxelena, Ion; Rodriguez-Mayorga, Mauricio; Piris, Mario

2018-06-01

Any rigorous approach to first-order reduced density matrix ( Γ) functional theory faces the phase dilemma, that is, having to deal with a large number of possible combinations of signs in terms of the electron-electron interaction energy. This problem was discovered by reducing a ground-state energy generated from an approximate N-particle wavefunction into a functional of Γ, known as the top-down method. Here, we show that the phase dilemma also appears in the bottom-up method, in which the functional E[ Γ] is generated by progressive inclusion of N-representability conditions on the reconstructed two-particle reduced density matrix. It is shown that an adequate choice of signs is essential to accurately describe model systems with strong non-dynamic (static) electron correlation, specifically, the one-dimensional Hubbard model with periodic boundary conditions and hydrogen rings. For the latter, the Piris natural orbital functional 7 (PNOF7), with phases equal to -1 for the inter-pair energy terms containing the exchange-time-inversion integrals, agrees with exact diagonalization results.

Extending the range of real time density matrix renormalization group simulations

NASA Astrophysics Data System (ADS)

Kennes, D. M.; Karrasch, C.

2016-03-01

We discuss a few simple modifications to time-dependent density matrix renormalization group (DMRG) algorithms which allow to access larger time scales. We specifically aim at beginners and present practical aspects of how to implement these modifications within any standard matrix product state (MPS) based formulation of the method. Most importantly, we show how to 'combine' the Schrödinger and Heisenberg time evolutions of arbitrary pure states | ψ 〉 and operators A in the evaluation of 〈A〉ψ(t) = 〈 ψ | A(t) | ψ 〉 . This includes quantum quenches. The generalization to (non-)thermal mixed state dynamics 〈A〉ρ(t) =Tr [ ρA(t) ] induced by an initial density matrix ρ is straightforward. In the context of linear response (ground state or finite temperature T > 0) correlation functions, one can extend the simulation time by a factor of two by 'exploiting time translation invariance', which is efficiently implementable within MPS DMRG. We present a simple analytic argument for why a recently-introduced disentangler succeeds in reducing the effort of time-dependent simulations at T > 0. Finally, we advocate the python programming language as an elegant option for beginners to set up a DMRG code.

Dynamics of entanglement in expanding quantum fields

NASA Astrophysics Data System (ADS)

Berges, Jürgen; Floerchinger, Stefan; Venugopalan, Raju

2018-04-01

We develop a functional real-time approach to computing the entanglement between spatial regions for Gaussian states in quantum field theory. The entanglement entropy is characterized in terms of local correlation functions on space-like Cauchy hypersurfaces. The framework is applied to explore an expanding light cone geometry in the particular case of the Schwinger model for quantum electrodynamics in 1+1 space-time dimensions. We observe that the entanglement entropy becomes extensive in rapidity at early times and that the corresponding local reduced density matrix is a thermal density matrix for excitations around a coherent field with a time dependent temperature. Since the Schwinger model successfully describes many features of multiparticle production in e + e - collisions, our results provide an attractive explanation in this framework for the apparent thermal nature of multiparticle production even in the absence of significant final state scattering.

Electronic Absorption Spectra of Neutral Perylene (C20H12), Terrylene (C30H16), and Quaterrylene (C40H20) and their Positive and Negative Ions: Ne Matrix-Isolation Spectroscopy and Time Dependent Density Functional Theory Calculations

NASA Technical Reports Server (NTRS)

Halasinski, Thomas M.; Weisman, Jennifer L.; Lee, Timothy J.; Salama, Farid; Head-Gordon, Martin; Kwak, Dochan (Technical Monitor)

2002-01-01

We present a full experimental and theoretical study of an interesting series of polycyclic aromatic hydrocarbons, the oligorylenes. The absorption spectra of perylene, terrylene and quaterrylene in neutral, cationic and anionic charge states are obtained by matrix-isolation spectroscopy in Ne. The experimental spectra are dominated by a bright state that red shifts with growing molecular size. Excitation energies and state symmetry assignments are supported by calculations using time dependent density functional theory methods. These calculations also provide new insight into the observed trends in oscillator strength and excitation energy for the bright states: the oscillator strength per unit mass of carbon increases along the series.

Density functional theory study of defects in unalloyed δ-Pu

DOE PAGES

Hernandez, S. C.; Freibert, F. J.; Wills, J. M.

2017-03-19

Using density functional theory, we explore in this paper various classical point and complex defects within the face-centered cubic unalloyed δ-plutonium matrix that are potentially induced from self-irradiation. For plutonium only defects, the most energetically stable defect is a distorted split-interstitial. Gallium, the δ-phase stabilizer, is thermodynamically stable as a substitutional defect, but becomes unstable when participating in a complex defect configuration. Finally, complex uranium defects may thermodynamically exist as uranium substitutional with neighboring plutonium interstitial and stabilization of uranium within the lattice is shown via partial density of states and charge density difference plots to be 5f hybridization betweenmore » uranium and plutonium.« less

Density functional theory study of defects in unalloyed δ-Pu

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

Hernandez, S. C.; Freibert, F. J.; Wills, J. M.

Using density functional theory, we explore in this paper various classical point and complex defects within the face-centered cubic unalloyed δ-plutonium matrix that are potentially induced from self-irradiation. For plutonium only defects, the most energetically stable defect is a distorted split-interstitial. Gallium, the δ-phase stabilizer, is thermodynamically stable as a substitutional defect, but becomes unstable when participating in a complex defect configuration. Finally, complex uranium defects may thermodynamically exist as uranium substitutional with neighboring plutonium interstitial and stabilization of uranium within the lattice is shown via partial density of states and charge density difference plots to be 5f hybridization betweenmore » uranium and plutonium.« less

Symmetry properties of the electron density and following from it limits on the KS-DFT applications

NASA Astrophysics Data System (ADS)

Kaplan, Ilya G.

2018-03-01

At present, the Density Functional Theory (DFT) approach elaborated by Kohn with co-authors more than 50 years ago became the most widely used method for study molecules and solids. Using modern computation facilities, it can be applied to systems with million atoms. In the atmosphere of such great popularity, it is particularly important to know the limits of the applicability of DFT methods. In this report, I will discuss two cases when the conventional DFT approaches, using only electron density ρ and its gradients, cannot be applied (I will not consider the Ψ-versions of DFT). The first case is quite evident. In the degenerated states, the electron density may not be defined, since electronic and nuclear motions cannot be separated, the vibronic interaction mixed them. The second case is related to the spin of the state. As it was rigorously proved by group theoretical methods at the theorem level, the electron density does not depend on the total spin S of the arbitrary N-electron state. It means that the Kohn-Sham equations have the same form for states with different S. The critical survey of elaborated DFT procedures, taking into account spin, shows that they modified only exchange functionals, the correlation functionals do not correspond to the spin of the state. The point is that the conception of spin cannot be defined in the framework of the electron density formalism, which corresponds to the one-particle reduced density matrix. This is the main reason of the problems arising in the study by DFT of magnetic properties of the transition metals. The possible way of resolving these problems can be found in the two-particle reduced density matrix formulation of DFT.

Fourier-Legendre expansion of the one-electron density matrix of ground-state two-electron atoms.

PubMed

Ragot, Sébastien; Ruiz, María Belén

2008-09-28

The density matrix rho(r,r(')) of a spherically symmetric system can be expanded as a Fourier-Legendre series of Legendre polynomials P(l)(cos theta=rr(')rr(')). Application is here made to harmonically trapped electron pairs (i.e., Moshinsky's and Hooke's atoms), for which exact wavefunctions are known, and to the helium atom, using a near-exact wavefunction. In the present approach, generic closed form expressions are derived for the series coefficients of rho(r,r(')). The series expansions are shown to converge rapidly in each case, with respect to both the electron number and the kinetic energy. In practice, a two-term expansion accounts for most of the correlation effects, so that the correlated density matrices of the atoms at issue are essentially a linear functions of P(l)(cos theta)=cos theta. For example, in the case of Hooke's atom, a two-term expansion takes in 99.9% of the electrons and 99.6% of the kinetic energy. The correlated density matrices obtained are finally compared to their determinantal counterparts, using a simplified representation of the density matrix rho(r,r(')), suggested by the Legendre expansion. Interestingly, two-particle correlation is shown to impact the angular delocalization of each electron, in the one-particle space spanned by the r and r(') variables.

Site-occupation embedding theory using Bethe ansatz local density approximations

NASA Astrophysics Data System (ADS)

Senjean, Bruno; Nakatani, Naoki; Tsuchiizu, Masahisa; Fromager, Emmanuel

2018-06-01

Site-occupation embedding theory (SOET) is an alternative formulation of density functional theory (DFT) for model Hamiltonians where the fully interacting Hubbard problem is mapped, in principle exactly, onto an impurity-interacting (rather than a noninteracting) one. It provides a rigorous framework for combining wave-function (or Green function)-based methods with DFT. In this work, exact expressions for the per-site energy and double occupation of the uniform Hubbard model are derived in the context of SOET. As readily seen from these derivations, the so-called bath contribution to the per-site correlation energy is, in addition to the latter, the key density functional quantity to model in SOET. Various approximations based on Bethe ansatz and perturbative solutions to the Hubbard and single-impurity Anderson models are constructed and tested on a one-dimensional ring. The self-consistent calculation of the embedded impurity wave function has been performed with the density-matrix renormalization group method. It has been shown that promising results are obtained in specific regimes of correlation and density. Possible further developments have been proposed in order to provide reliable embedding functionals and potentials.

Probabilistic homogenization of random composite with ellipsoidal particle reinforcement by the iterative stochastic finite element method

NASA Astrophysics Data System (ADS)

Sokołowski, Damian; Kamiński, Marcin

2018-01-01

This study proposes a framework for determination of basic probabilistic characteristics of the orthotropic homogenized elastic properties of the periodic composite reinforced with ellipsoidal particles and a high stiffness contrast between the reinforcement and the matrix. Homogenization problem, solved by the Iterative Stochastic Finite Element Method (ISFEM) is implemented according to the stochastic perturbation, Monte Carlo simulation and semi-analytical techniques with the use of cubic Representative Volume Element (RVE) of this composite containing single particle. The given input Gaussian random variable is Young modulus of the matrix, while 3D homogenization scheme is based on numerical determination of the strain energy of the RVE under uniform unit stretches carried out in the FEM system ABAQUS. The entire series of several deterministic solutions with varying Young modulus of the matrix serves for the Weighted Least Squares Method (WLSM) recovery of polynomial response functions finally used in stochastic Taylor expansions inherent for the ISFEM. A numerical example consists of the High Density Polyurethane (HDPU) reinforced with the Carbon Black particle. It is numerically investigated (1) if the resulting homogenized characteristics are also Gaussian and (2) how the uncertainty in matrix Young modulus affects the effective stiffness tensor components and their PDF (Probability Density Function).

Evolution equation of population genetics: Relation to the density-matrix theory of quasiparticles with general dispersion laws

NASA Astrophysics Data System (ADS)

Bezák, V.

2003-02-01

The Waxman-Peck theory of population genetics is discussed in regard of soil bacteria. Each bacterium is understood as a carrier of a phenotypic parameter p. The central objective is the calculation of the probability density with respect to p, Φ(p,t;p0), of the carriers living at time t>0, provided that initially at t0=0, all bacteria carried the phenotypic parameter p0=0. The theory involves two small parameters: the mutation probability μ and a parameter γ involved in a function w(p) defining the fitness of the bacteria to survive the generation time τ and give birth to an offspring. The mutation from a state p to a state q is defined by a Gaussian with a dispersion σ2m. The author focuses our attention on a function φ(p,t) which determines uniquely the function Φ(p,t;p0) and satisfies a linear equation (Waxman’s equation). The Green function of this equation is mathematically identical with the one-particle Bloch density matrix, where μ characterizes the order of magnitude of the potential energy. (In the x representation, the potential energy is proportional to the inverted Gaussian with the dispersion σ2m). The author solves Waxman’s equation in the standard style of a perturbation theory and discusses how the solution depends on the choice of the fitness function w(p). In a sense, the function c(p)=1-w(p)/w(0) is analogous to the dispersion function E(p) of fictitious quasiparticles. In contrast to Waxman’s approximation, where c(p) was taken as a quadratic function, c(p)≈γp2, the author exemplifies the problem with another function, c(p)=γ[1-exp(-ap2)], where γ is small but a may be large. The author shows that the use of this function in the theory of the population genetics is the same as the use of a nonparabolic dispersion law E=E(p) in the density-matrix theory. With a general function c(p), the distribution function Φ(p,t;0) is composed of a δ-function component, N(t)δ(p), and a blurred component. When discussing the limiting transition for t→∞, the author shows that his function c(p) implies that N(t)→N(∞)≠0 in contrast with the asymptotics N(t)→0 resulting from the use of Waxman’s function c(p)˜p2.

Multiconfiguration Pair-Density Functional Theory.

PubMed

Li Manni, Giovanni; Carlson, Rebecca K; Luo, Sijie; Ma, Dongxia; Olsen, Jeppe; Truhlar, Donald G; Gagliardi, Laura

2014-09-09

We present a new theoretical framework, called Multiconfiguration Pair-Density Functional Theory (MC-PDFT), which combines multiconfigurational wave functions with a generalization of density functional theory (DFT). A multiconfigurational self-consistent-field (MCSCF) wave function with correct spin and space symmetry is used to compute the total electronic density, its gradient, the on-top pair density, and the kinetic and Coulomb contributions to the total electronic energy. We then use a functional of the total density, its gradient, and the on-top pair density to calculate the remaining part of the energy, which we call the on-top-density-functional energy in contrast to the exchange-correlation energy of Kohn-Sham DFT. Because the on-top pair density is an element of the two-particle density matrix, this goes beyond the Hohenberg-Kohn theorem that refers only to the one-particle density. To illustrate the theory, we obtain first approximations to the required new type of density functionals by translating conventional density functionals of the spin densities using a simple prescription, and we perform post-SCF density functional calculations using the total density, density gradient, and on-top pair density from the MCSCF calculations. Double counting of dynamic correlation or exchange does not occur because the MCSCF energy is not used. The theory is illustrated by applications to the bond energies and potential energy curves of H2, N2, F2, CaO, Cr2, and NiCl and the electronic excitation energies of Be, C, N, N(+), O, O(+), Sc(+), Mn, Co, Mo, Ru, N2, HCHO, C4H6, c-C5H6, and pyrazine. The method presented has a computational cost and scaling similar to MCSCF, but a quantitative accuracy, even with the present first approximations to the new types of density functionals, that is comparable to much more expensive multireference perturbation theory methods.

Grid-free density functional calculations on periodic systems.

PubMed

Varga, Stefan

2007-09-21

Density fitting scheme is applied to the exchange part of the Kohn-Sham potential matrix in a grid-free local density approximation for infinite systems with translational periodicity. It is shown that within this approach the computational demands for the exchange part scale in the same way as for the Coulomb part. The efficiency of the scheme is demonstrated on a model infinite polymer chain. For simplicity, the implementation with Dirac-Slater Xalpha exchange functional is presented only. Several choices of auxiliary basis set expansion coefficients were tested with both Coulomb and overlap metric. Their effectiveness is discussed also in terms of robustness and norm preservation.

Grid-free density functional calculations on periodic systems

NASA Astrophysics Data System (ADS)

Varga, Štefan

2007-09-01

Density fitting scheme is applied to the exchange part of the Kohn-Sham potential matrix in a grid-free local density approximation for infinite systems with translational periodicity. It is shown that within this approach the computational demands for the exchange part scale in the same way as for the Coulomb part. The efficiency of the scheme is demonstrated on a model infinite polymer chain. For simplicity, the implementation with Dirac-Slater Xα exchange functional is presented only. Several choices of auxiliary basis set expansion coefficients were tested with both Coulomb and overlap metric. Their effectiveness is discussed also in terms of robustness and norm preservation.

Theory of time-resolved photoelectron imaging. Comparison of a density functional with a time-dependent density functional approach

NASA Astrophysics Data System (ADS)

Suzuki, Yoshi-ichi; Seideman, Tamar; Stener, Mauro

2004-01-01

Time-resolved photoelectron differential cross sections are computed within a quantum dynamical theory that combines a formally exact solution of the nuclear dynamics with density functional theory (DFT)-based approximations of the electronic dynamics. Various observables of time-resolved photoelectron imaging techniques are computed at the Kohn-Sham and at the time-dependent DFT levels. Comparison of the results serves to assess the reliability of the former method and hence its usefulness as an economic approach for time-domain photoelectron cross section calculations, that is applicable to complex polyatomic systems. Analysis of the matrix elements that contain the electronic dynamics provides insight into a previously unexplored aspect of femtosecond-resolved photoelectron imaging.

Silver metal nano-matrixes as high efficiency and versatile catalytic reactors for environmental remediation

NASA Astrophysics Data System (ADS)

Dumée, Ludovic F.; Yi, Zhifeng; Tardy, Blaise; Merenda, Andrea; Des Ligneris, Elise; Dagastine, Ray R.; Kong, Lingxue

2017-03-01

Nano-porous metallic matrixes (NMMs) offer superior surface to volume ratios as well as enhanced optical, photonic, and electronic properties to bulk metallic materials. Such behaviours are correlated to the nano-scale inter-grain metal domains that favour the presence of electronic vacancies. In this work, continuous 3D NMMs were synthesized for the first time through a simple diffusion-reduction process whereby the aerogel matrix was functionalized with (3-Mercaptopropyl)trimethoxysilane. The surface energy of the silica monolith templates was tuned to improve the homogeneity of the reduction process while thiol functionalization facilitated the formation of a high density of seeding points for metal ions to reduce. The diameter of NMMs was between 2 and 1000 nm, corresponding to a silver loading between 1.23 and 41.16 at.%. A rates of catalytic degradation kinetics of these NMMS which is three orders of magnitude higher than those of the non-functionalized silver-silica structures. Furthermore, the enhancement in mechanical stability at nanoscale which was evaluated by Atomic Force Microscopy force measurements, electronic density and chemical inertness was assessed and critically correlated to their catalytic potential. This strategy opens up new avenues for design of complex architectures of either single or multi-metal alloy NMMs with enhanced surface properties for various applications.

Silver metal nano-matrixes as high efficiency and versatile catalytic reactors for environmental remediation

PubMed Central

Dumée, Ludovic F.; Yi, Zhifeng; Tardy, Blaise; Merenda, Andrea; des Ligneris, Elise; Dagastine, Ray R.; Kong, Lingxue

2017-01-01

Nano-porous metallic matrixes (NMMs) offer superior surface to volume ratios as well as enhanced optical, photonic, and electronic properties to bulk metallic materials. Such behaviours are correlated to the nano-scale inter-grain metal domains that favour the presence of electronic vacancies. In this work, continuous 3D NMMs were synthesized for the first time through a simple diffusion-reduction process whereby the aerogel matrix was functionalized with (3-Mercaptopropyl)trimethoxysilane. The surface energy of the silica monolith templates was tuned to improve the homogeneity of the reduction process while thiol functionalization facilitated the formation of a high density of seeding points for metal ions to reduce. The diameter of NMMs was between 2 and 1000 nm, corresponding to a silver loading between 1.23 and 41.16 at.%. A rates of catalytic degradation kinetics of these NMMS which is three orders of magnitude higher than those of the non-functionalized silver-silica structures. Furthermore, the enhancement in mechanical stability at nanoscale which was evaluated by Atomic Force Microscopy force measurements, electronic density and chemical inertness was assessed and critically correlated to their catalytic potential. This strategy opens up new avenues for design of complex architectures of either single or multi-metal alloy NMMs with enhanced surface properties for various applications. PMID:28332602

Cross-linked κ-carrageenan polymer/zinc nanoporous composite matrix for expanded bed application: Fabrication and hydrodynamic characterization.

PubMed

Mohsenkhani, Sadaf; Jahanshahi, Mohsen; Rahimpour, Ahmad

2015-08-21

Expanded bed adsorption (EBA) is a reliable separation technique for the purification of bioproducts from complex feedstocks. The specifically designed adsorbent is necessary to form a stable expanded bed. In the present work, a novel custom-designed composite matrix has been prepared through the method of water-in-oil emulsification. In order to develop an adsorbent with desirable qualities and reduce the costs, κ-carrageenan and zinc powder were used as the polymeric skeleton and the densifier, respectively. The prepared composite matrix was named as KC-Zn. Optical microscope (OM) and scanning electron microscope (SEM) were applied to characterize the morphology and structure of prepared composite matrix. These analyses approved good spherical shape and porous structure with nano-scale pores in the range of about 60-180nm. The results from the particle size analyzer (PSA) revealed that all the KC-Zn beads followed logarithmic normal size distribution with the range of 50-350μm and average diameter of 160-230μm, respectively. Main physical properties of KC-Zn matrices were measured as a function of zinc powder ratio to κ-carrageenan slurry, which showed an appropriate wet density in the range of 1.39-2.27g/ml, water content of 72.67-36.41% and porosity of 98.07-80.24%, respectively. The effects of matrix density and liquid phase viscosity on hydrodynamic behavior of prepared matrix have been investigated by residence time distribution (RTD) experiments in an expanded bed. The results indicated that in a constant liquid velocity as the matrix density was increased, the expansion factor of bed decreased and the axial mixing coefficient increased. Moreover, an enhancement in the fluid viscosity led to an increase in the bed expansion and a decrease in the stability of expanded bed. Therefore using a matrix with higher density seems necessary to face viscous feedstocks. All the results demonstrated that proper physical properties and hydrodynamic characteristics of KC-Zn matrix confirm good potential for possible use in high flow rate expanded bed operations. Copyright © 2015 Elsevier B.V. All rights reserved.

Inner Space Perturbation Theory in Matrix Product States: Replacing Expensive Iterative Diagonalization.

PubMed

Ren, Jiajun; Yi, Yuanping; Shuai, Zhigang

2016-10-11

We propose an inner space perturbation theory (isPT) to replace the expensive iterative diagonalization in the standard density matrix renormalization group theory (DMRG). The retained reduced density matrix eigenstates are partitioned into the active and secondary space. The first-order wave function and the second- and third-order energies are easily computed by using one step Davidson iteration. Our formulation has several advantages including (i) keeping a balance between the efficiency and accuracy, (ii) capturing more entanglement with the same amount of computational time, (iii) recovery of the standard DMRG when all the basis states belong to the active space. Numerical examples for the polyacenes and periacene show that the efficiency gain is considerable and the accuracy loss due to the perturbation treatment is very small, when half of the total basis states belong to the active space. Moreover, the perturbation calculations converge in all our numerical examples.

Matrix Density-induced Mechanoregulation of Breast Cell Phenotype, Signaling, and Gene Expression through a FAK ERK Linkage

DTIC Science & Technology

2009-12-10

sites of integrin-clustering that link the actin cytoskeleton to the extracellular matrix (ECM; (Burridge et al., 1988)). The primary functions of...Hall, 1992). Furthermore, in fibroblasts, focal adhesion kinase (FAK), a key FA signaling molecule, is necessary for mechanosensing (Geiger et al...promotes FAK activation through phosphorylation on Y397 and Y925, followed by FAK- dependent extracellular signal-regulated kinase (ERK) phosphorylation

A matrix contraction process

NASA Astrophysics Data System (ADS)

Wilkinson, Michael; Grant, John

2018-03-01

We consider a stochastic process in which independent identically distributed random matrices are multiplied and where the Lyapunov exponent of the product is positive. We continue multiplying the random matrices as long as the norm, ɛ, of the product is less than unity. If the norm is greater than unity we reset the matrix to a multiple of the identity and then continue the multiplication. We address the problem of determining the probability density function of the norm, \

Modulation of hematopoietic progenitor cell fate in vitro by varying collagen oligomer matrix stiffness in the presence or absence of osteoblasts.

PubMed

Chitteti, Brahmananda Reddy; Kacena, Melissa A; Voytik-Harbin, Sherry L; Srour, Edward F

2015-10-01

To recreate the in vivo hematopoietic cell microenvironment or niche and to study the impact of extracellular matrix (ECM) biophysical properties on hematopoietic progenitor cell (HPC) proliferation and function, mouse bone-marrow derived HPC (Lin-Sca1+cKit+/(LSK) were cultured within three-dimensional (3D) type I collagen oligomer matrices. To generate a more physiologic milieu, 3D cultures were established in both the presence and absence of calvariae-derived osteoblasts (OB). Collagen oligomers were polymerized at varying concentration to give rise to matrices of different fibril densities and therefore matrix stiffness (shear storage modulus, 50-800 Pa). Decreased proliferation and increased clonogenicity of LSK cells was associated with increase of matrix stiffness regardless of whether OB were present or absent from the 3D culture system. Also, regardless of whether OB were or were not added to the 3D co-culture system, LSK within 800 Pa collagen oligomer matrices maintained the highest percentage of Lin-Sca1+ cells as well as higher percentage of cells in quiescent state (G0/G1) compared to 50 Pa or 200Pa matrices. Collectively, these data illustrate that biophysical features of collagen oligomer matrices, specifically fibril density-induced modulation of matrix stiffness, provide important guidance cues in terms of LSK expansion and differentiation and therefore maintenance of progenitor cell function. Copyright © 2015. Published by Elsevier B.V.

Fibromodulin deficiency reduces collagen structural network but not glycosaminoglycan content in a syngeneic model of colon carcinoma.

PubMed

Olsson, P Olof; Kalamajski, Sebastian; Maccarana, Marco; Oldberg, Åke; Rubin, Kristofer

2017-01-01

Tumor barrier function in carcinoma represents a major challenge to treatment and is therefore an attractive target for increasing drug delivery. Variables related to tumor barrier include aberrant blood vessels, high interstitial fluid pressure, and the composition and structure of the extracellular matrix. One of the proteins associated with dense extracellular matrices is fibromodulin, a collagen fibrillogenesis modulator expressed in tumor stroma but scarce in normal loose connective tissues. Here, we investigated the effects of fibromodulin on stroma ECM in a syngeneic murine colon carcinoma model. We show that fibromodulin deficiency decreased collagen fibril thickness but glycosaminoglycan content and composition were unchanged. Furthermore, vascular density, pericyte coverage and macrophage amount were unaffected. Fibromodulin can therefore be a unique effector of dense collagen matrix assembly in tumor stroma and, without affecting other major matrix components or the cellular composition, can function as a main agent in tumor barrier function.

Time-dependent density-functional tight-binding method with the third-order expansion of electron density

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

Nishimoto, Yoshio, E-mail: nishimoto.yoshio@fukui.kyoto-u.ac.jp

2015-09-07

We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of themore » third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well.« less

Time-dependent density-functional tight-binding method with the third-order expansion of electron density.

PubMed

Nishimoto, Yoshio

2015-09-07

We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of the third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well.

Unveiling the nature of post-linear response Z-vector method for time-dependent density functional theory.

PubMed

Pastore, Mariachiara; Assfeld, Xavier; Mosconi, Edoardo; Monari, Antonio; Etienne, Thibaud

2017-07-14

We report a theoretical study on the analysis of the relaxed one-particle difference density matrix characterizing the passage from the ground to the excited state of a molecular system, as obtained from time-dependent density functional theory. In particular, this work aims at using the physics contained in the so-called Z-vector, which differentiates between unrelaxed and relaxed difference density matrices to analyze excited states' nature. For this purpose, we introduce novel quantum-mechanical quantities, based on the detachment/attachment methodology, for analysing the Z-vector transformation for different molecules and density functional theory functionals. A derivation pathway of these novel descriptors is reported, involving a numerical integration to be performed in the Euclidean space on the density functions. This topological analysis is then applied to two sets of chromophores, and the correlation between the level of theory and the behavior of our descriptors is properly rationalized. In particular, the effect of range-separation on the relaxation amplitude is discussed. The relaxation term is finally shown to be system-specific (for a given level of theory) and independent of the number of electrons (i.e., the relaxation amplitude is not simply the result of a collective phenomenon).

Theory of Tunneling Spectroscopy in a Mn12 Single-Electron Transistor by Density-Functional Theory Methods

NASA Astrophysics Data System (ADS)

Michalak, Ł.; Canali, C. M.; Pederson, M. R.; Paulsson, M.; Benza, V. G.

2010-01-01

We consider tunneling transport through a Mn12 molecular magnet using spin density functional theory. A tractable methodology for constructing many-body wave functions from Kohn-Sham orbitals allows for the determination of spin-dependent matrix elements for use in transport calculations. The tunneling conductance at finite bias is characterized by peaks representing transitions between spin multiplets, separated by an energy on the order of the magnetic anisotropy. The energy splitting of the spin multiplets and the spatial part of their many-body wave functions, describing the orbital degrees of freedom of the excess charge, strongly affect the electronic transport, and can lead to negative differential conductance.

Theory of tunneling spectroscopy in a Mn12 single-electron transistor by density-functional theory methods.

PubMed

Michalak, Ł; Canali, C M; Pederson, M R; Paulsson, M; Benza, V G

2010-01-08

We consider tunneling transport through a Mn12 molecular magnet using spin density functional theory. A tractable methodology for constructing many-body wave functions from Kohn-Sham orbitals allows for the determination of spin-dependent matrix elements for use in transport calculations. The tunneling conductance at finite bias is characterized by peaks representing transitions between spin multiplets, separated by an energy on the order of the magnetic anisotropy. The energy splitting of the spin multiplets and the spatial part of their many-body wave functions, describing the orbital degrees of freedom of the excess charge, strongly affect the electronic transport, and can lead to negative differential conductance.

Random matrix theory for transition strengths: Applications and open questions

NASA Astrophysics Data System (ADS)

Kota, V. K. B.

2017-12-01

Embedded random matrix ensembles are generic models for describing statistical properties of finite isolated interacting quantum many-particle systems. A finite quantum system, induced by a transition operator, makes transitions from its states to the states of the same system or to those of another system. Examples are electromagnetic transitions (then the initial and final systems are same), nuclear beta and double beta decay (then the initial and final systems are different) and so on. Using embedded ensembles (EE), there are efforts to derive a good statistical theory for transition strengths. With m fermions (or bosons) in N mean-field single particle levels and interacting via two-body forces, we have with GOE embedding, the so called EGOE(1+2). Now, the transition strength density (transition strength multiplied by the density of states at the initial and final energies) is a convolution of the density generated by the mean-field one-body part with a bivariate spreading function due to the two-body interaction. Using the embedding U(N) algebra, it is established, for a variety of transition operators, that the spreading function, for sufficiently strong interactions, is close to a bivariate Gaussian. Also, as the interaction strength increases, the spreading function exhibits a transition from bivariate Breit-Wigner to bivariate Gaussian form. In appropriate limits, this EE theory reduces to the polynomial theory of Draayer, French and Wong on one hand and to the theory due to Flambaum and Izrailev for one-body transition operators on the other. Using spin-cutoff factors for projecting angular momentum, the theory is applied to nuclear matrix elements for neutrinoless double beta decay (NDBD). In this paper we will describe: (i) various developments in the EE theory for transition strengths; (ii) results for nuclear matrix elements for 130Te and 136Xe NDBD; (iii) important open questions in the current form of the EE theory.

Modeling Transverse Cracking in Laminates With a Single Layer of Elements Per Ply

NASA Technical Reports Server (NTRS)

Van Der Meer, Frans P.; Davila, Carlos G.

2012-01-01

The objective of the present paper is to investigate the ability of mesolevel X-FEM models with a single layer of elements per ply to capture accurately all aspects of matrix cracking. In particular, we examine whether the model can predict the insitu ply thickness effect on crack initiation and propagation, the crack density as a function of strain, the strain for crack saturation, and the interaction between delamination and transverse cracks. Results reveal that the simplified model does not capture correctly the shear-lag relaxation of the stress field on either side of a crack, which leads to an overprediction of the crack density. It is also shown, however, that after onset of delamination many of the inserted matrix cracks close again, and that the density of open cracks becomes similar to the density predicted by the detailed model. The degree to which the spurious cracks affect the global response is quantified and the reliability of the mesolevel approach with a single layer of elements per ply is discussed.

Stability and Physical Accuracy Analysis of the Numerical Solutions to Wigner-Poisson Modeling of Resonant Tunneling Diodes

DTIC Science & Technology

2013-03-22

discrete Wigner function is periodic in momentum space. The periodicity follows from the Fourier transform of the density matrix. The inverse...resonant-tunneling diode . The Green function method has been one of alternatives. Another alternative was to utilize the Wigner function . The Wigner ... function approach to the simulation of a resonant-tunneling diode offers many advantages. In the limit of the classical physics the Wigner equation

Structured block copolymer thin film composites for ultra-high energy density capacitors

NASA Astrophysics Data System (ADS)

Samant, Saumil; Hailu, Shimelis; Grabowski, Christopher; Durstock, Michael; Raghavan, Dharmaraj; Karim, Alamgir

2014-03-01

Development of high energy density capacitors is essential for future applications like hybrid vehicles and directed energy weaponry. Fundamentally, energy density is governed by product of dielectric permittivity ɛ and breakdown strength Vbd. Hence, improvements in energy density are greatly reliant on improving either ɛ or Vbd or a combination of both. Polymer films are widely used in capacitors due to high Vbd and low loss but they suffer from very low permittivities. Composite dielectrics offer a unique opportunity to combine the high ɛ of inorganic fillers with the high Vbd of a polymer matrix. For enhancement of dielectric properties, it is essential to improve matrix-filler interaction and control the spatial distribution of fillers for which nanostructured block copolymers BCP act as ideal templates. We use Directed Self-assembly of block copolymers to rapidly fabricate highly aligned BCP-TiO2 composite nanostructures in thin films under dynamic thermal gradient field to synergistically combine the high ɛ of functionalized TiO2 and high Vbd of BCP matrix. The results of impact of BCP morphology, processing conditions and concentration of TiO2 on capacitor performance will be reported. U.S. Air Force of Scientific Research under contract FA9550-12-1-0306

Balancing Cell Migration with Matrix Degradation Enhances Gene Delivery to Cells Cultured Three-Dimensionally Within Hydrogels

PubMed Central

Shepard, Jaclyn A.; Huang, Alyssa; Shikanova, Ariella; Shea, Lonnie D.

2010-01-01

In regenerative medicine, hydrogels are employed to fill defects and support the infiltration of cells that can ultimately regenerate tissue. Gene delivery within hydrogels targeting infiltrating cells has the potential to promote tissue formation, but the delivery efficiency of nonviral vectors within hydrogels is low hindering their applicability in tissue regeneration. To improve their functionality, we have conducted a mechanistic study to investigate the contribution of cell migration and matrix degradation on gene delivery. In this report, lipoplexes were entrapped within hydrogels based on poly(ethylene glycol) (PEG) crosslinked with peptides containing matrix metalloproteinase degradable sequences. The mesh size of these hydrogels is substantially less than the size of the entrapped lipoplexes, which can function to retain vectors. Cell migration and transfection were simultaneously measured within hydrogels with varying density of cell adhesion sites (Arg-Gly-Asp peptides) and solids content. Increasing RGD density increased expression levels up to 100-fold, while greater solids content sustained expression levels for 16 days. Increasing RGD density and decreasing solids content increased cell migration, which indicates expression levels increase with increased cell migration. Initially exposing cells to vector resulted in transient expression that declined after 2 days, verifying the requirement of migration to sustain expression. Transfected cells were predominantly located within the population of migrating cells for hydrogels that supported cell migration. Although the small mesh size retained at least 70% of the lipoplexes in the absence of cells after 32 days, the presence of cells decreased retention to 10% after 16 days. These results indicate that vectors retained within hydrogels contact migrating cells, and that persistent cell migration can maintain elevated expression levels. Thus matrix degradation and cell migration are fundamental design parameters for maximizing gene delivery from hydrogels. PMID:20450944

A molecular dynamics study on Young's modulus and tribology of carbon nanotube reinforced styrene-butadiene rubber.

PubMed

Chawla, Raj; Sharma, Sumit

2018-03-18

Styrene-butadiene rubber is a copolymer widely used in making car tires and has excellent abrasion resistance. The Young's modulus and tribology of pure styrene butadiene rubber (SBR) polymer and carbon nanotube reinforced polymer composites have been investigated using molecular dynamics simulations. The mechanism of enhanced tribology properties using carbon nanotube has been studied and discussed. The obtained Young's modulus shows the enhancement in mechanical properties of SBR polymer when carbon nanotubes are used as reinforcement. The concentration, temperature and velocity profiles, radial distribution function, frictional stresses, and cohesive energy density are calculated and analyzed in detail. The Young's modulus of SBR matrix increases about 29.16% in the presence of the 5% CNT. The atom movement velocity and average cohesive energy density in the friction area of pure SBR matrix was found to be more than that of the CNT/SBR composite. Graphical abstract Initial and final conditions of (a) pure SBR matrix and (b) CNT/SBR matrix subjected toshear loading and frictional stresses of top Fe layers of both pure SBR and CNT/SBR composite.

Interacting hadron resonance gas model in the K -matrix formalism

NASA Astrophysics Data System (ADS)

Dash, Ashutosh; Samanta, Subhasis; Mohanty, Bedangadas

2018-05-01

An extension of hadron resonance gas (HRG) model is constructed to include interactions using relativistic virial expansion of partition function. The noninteracting part of the expansion contains all the stable baryons and mesons and the interacting part contains all the higher mass resonances which decay into two stable hadrons. The virial coefficients are related to the phase shifts which are calculated using K -matrix formalism in the present work. We have calculated various thermodynamics quantities like pressure, energy density, and entropy density of the system. A comparison of thermodynamic quantities with noninteracting HRG model, calculated using the same number of hadrons, shows that the results of the above formalism are larger. A good agreement between equation of state calculated in K -matrix formalism and lattice QCD simulations is observed. Specifically, the lattice QCD calculated interaction measure is well described in our formalism. We have also calculated second-order fluctuations and correlations of conserved charges in K -matrix formalism. We observe a good agreement of second-order fluctuations and baryon-strangeness correlation with lattice data below the crossover temperature.

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

PubMed

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

2016-10-30

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

A Comparative Study of Collagen Matrix Density Effect on Endothelial Sprout Formation Using Experimental and Computational Approaches.

PubMed

Shamloo, Amir; Mohammadaliha, Negar; Heilshorn, Sarah C; Bauer, Amy L

2016-04-01

A thorough understanding of determining factors in angiogenesis is a necessary step to control the development of new blood vessels. Extracellular matrix density is known to have a significant influence on cellular behaviors and consequently can regulate vessel formation. The utilization of experimental platforms in combination with numerical models can be a powerful method to explore the mechanisms of new capillary sprout formation. In this study, using an integrative method, the interplay between the matrix density and angiogenesis was investigated. Owing the fact that the extracellular matrix density is a global parameter that can affect other parameters such as pore size, stiffness, cell-matrix adhesion and cross-linking, deeper understanding of the most important biomechanical or biochemical properties of the ECM causing changes in sprout morphogenesis is crucial. Here, we implemented both computational and experimental methods to analyze the mechanisms responsible for the influence of ECM density on the sprout formation that is difficult to be investigated comprehensively using each of these single methods. For this purpose, we first utilized an innovative approach to quantify the correspondence of the simulated collagen fibril density to the collagen density in the experimental part. Comparing the results of the experimental study and computational model led to some considerable achievements. First, we verified the results of the computational model using the experimental results. Then, we reported parameters such as the ratio of proliferating cells to migrating cells that was difficult to obtain from experimental study. Finally, this integrative system led to gain an understanding of the possible mechanisms responsible for the effect of ECM density on angiogenesis. The results showed that stable and long sprouts were observed at an intermediate collagen matrix density of 1.2 and 1.9 mg/ml due to a balance between the number of migrating and proliferating cells. As a result of weaker connections between the cells and matrix, a lower collagen matrix density (0.7 mg/ml) led to unstable and broken sprouts. However, higher matrix density (2.7 mg/ml) suppressed sprout formation due to the high level of matrix entanglement, which inhibited cell migration. This study also showed that extracellular matrix density can influence sprout branching. Our experimental results support this finding.

Inhomogeneity induced and appropriately parameterized semilocal exchange and correlation energy functionals in two-dimensions.

PubMed

Patra, Abhilash; Jana, Subrata; Samal, Prasanjit

2018-04-07

The construction of meta generalized gradient approximations based on the density matrix expansion (DME) is considered as one of the most accurate techniques to design semilocal exchange energy functionals in two-dimensional density functional formalism. The exchange holes modeled using DME possess unique features that make it a superior entity. Parameterized semilocal exchange energy functionals based on the DME are proposed. The use of different forms of the momentum and flexible parameters is to subsume the non-uniform effects of the density in the newly constructed semilocal functionals. In addition to the exchange functionals, a suitable correlation functional is also constructed by working upon the local correlation functional developed for 2D homogeneous electron gas. The non-local effects are induced into the correlation functional by a parametric form of one of the newly constructed exchange energy functionals. The proposed functionals are applied to the parabolic quantum dots with a varying number of confined electrons and the confinement strength. The results obtained with the aforementioned functionals are quite satisfactory, which indicates why these are suitable for two-dimensional quantum systems.

Inhomogeneity induced and appropriately parameterized semilocal exchange and correlation energy functionals in two-dimensions

NASA Astrophysics Data System (ADS)

Patra, Abhilash; Jana, Subrata; Samal, Prasanjit

2018-04-01

The construction of meta generalized gradient approximations based on the density matrix expansion (DME) is considered as one of the most accurate techniques to design semilocal exchange energy functionals in two-dimensional density functional formalism. The exchange holes modeled using DME possess unique features that make it a superior entity. Parameterized semilocal exchange energy functionals based on the DME are proposed. The use of different forms of the momentum and flexible parameters is to subsume the non-uniform effects of the density in the newly constructed semilocal functionals. In addition to the exchange functionals, a suitable correlation functional is also constructed by working upon the local correlation functional developed for 2D homogeneous electron gas. The non-local effects are induced into the correlation functional by a parametric form of one of the newly constructed exchange energy functionals. The proposed functionals are applied to the parabolic quantum dots with a varying number of confined electrons and the confinement strength. The results obtained with the aforementioned functionals are quite satisfactory, which indicates why these are suitable for two-dimensional quantum systems.

Enhanced Constraints for Accurate Lower Bounds on Many-Electron Quantum Energies from Variational Two-Electron Reduced Density Matrix Theory.

PubMed

Mazziotti, David A

2016-10-07

A central challenge of physics is the computation of strongly correlated quantum systems. The past ten years have witnessed the development and application of the variational calculation of the two-electron reduced density matrix (2-RDM) without the wave function. In this Letter we present an orders-of-magnitude improvement in the accuracy of 2-RDM calculations without an increase in their computational cost. The advance is based on a low-rank, dual formulation of an important constraint on the 2-RDM, the T2 condition. Calculations are presented for metallic chains and a cadmium-selenide dimer. The low-scaling T2 condition will have significant applications in atomic and molecular, condensed-matter, and nuclear physics.

Enhanced Constraints for Accurate Lower Bounds on Many-Electron Quantum Energies from Variational Two-Electron Reduced Density Matrix Theory

NASA Astrophysics Data System (ADS)

Mazziotti, David A.

2016-10-01

A central challenge of physics is the computation of strongly correlated quantum systems. The past ten years have witnessed the development and application of the variational calculation of the two-electron reduced density matrix (2-RDM) without the wave function. In this Letter we present an orders-of-magnitude improvement in the accuracy of 2-RDM calculations without an increase in their computational cost. The advance is based on a low-rank, dual formulation of an important constraint on the 2-RDM, the T 2 condition. Calculations are presented for metallic chains and a cadmium-selenide dimer. The low-scaling T 2 condition will have significant applications in atomic and molecular, condensed-matter, and nuclear physics.

Real time evolution at finite temperatures with operator space matrix product states

NASA Astrophysics Data System (ADS)

Pižorn, Iztok; Eisler, Viktor; Andergassen, Sabine; Troyer, Matthias

2014-07-01

We propose a method to simulate the real time evolution of one-dimensional quantum many-body systems at finite temperature by expressing both the density matrices and the observables as matrix product states. This allows the calculation of expectation values and correlation functions as scalar products in operator space. The simulations of density matrices in inverse temperature and the local operators in the Heisenberg picture are independent and result in a grid of expectation values for all intermediate temperatures and times. Simulations can be performed using real arithmetics with only polynomial growth of computational resources in inverse temperature and time for integrable systems. The method is illustrated for the XXZ model and the single impurity Anderson model.

Gravitational collapse and Hawking-like radiation of a shell in AdS spacetime

NASA Astrophysics Data System (ADS)

Saini, Anshul; Stojkovic, Dejan

2018-01-01

In this paper, we study the collapse of a massive shell in 2 +1 and 3 +1 dimensional gravity with anti-de Sitter asymptotics. Using the Gauss-Codazzi method, we derive gravitational equations of motion of the shell. We then use the functional Schrödinger formalism to calculate the spectrum of particles produced during the collapse. At the late time, radiation agrees very well with the standard Hawking results. In 3 +1 dimensions, we reproduce the Hawking-Page transition. We then construct the density matrix of this collapsing system and analyze the information content in the emitted radiation. We find that the off-diagonal elements of the density matrix are very important in preserving the unitarity of the system.

Principles of Quantum Mechanics

NASA Astrophysics Data System (ADS)

Landé, Alfred

2013-10-01

Preface; Introduction: 1. Observation and interpretation; 2. Difficulties of the classical theories; 3. The purpose of quantum theory; Part I. Elementary Theory of Observation (Principle of Complementarity): 4. Refraction in inhomogeneous media (force fields); 5. Scattering of charged rays; 6. Refraction and reflection at a plane; 7. Absolute values of momentum and wave length; 8. Double ray of matter diffracting light waves; 9. Double ray of matter diffracting photons; 10. Microscopic observation of ρ (x) and σ (p); 11. Complementarity; 12. Mathematical relation between ρ (x) and σ (p) for free particles; 13. General relation between ρ (q) and σ (p); 14. Crystals; 15. Transition density and transition probability; 16. Resultant values of physical functions; matrix elements; 17. Pulsating density; 18. General relation between ρ (t) and σ (є); 19. Transition density; matrix elements; Part II. The Principle of Uncertainty: 20. Optical observation of density in matter packets; 21. Distribution of momenta in matter packets; 22. Mathematical relation between ρ and σ; 23. Causality; 24. Uncertainty; 25. Uncertainty due to optical observation; 26. Dissipation of matter packets; rays in Wilson Chamber; 27. Density maximum in time; 28. Uncertainty of energy and time; 29. Compton effect; 30. Bothe-Geiger and Compton-Simon experiments; 31. Doppler effect; Raman effect; 32. Elementary bundles of rays; 33. Jeans' number of degrees of freedom; 34. Uncertainty of electromagnetic field components; Part III. The Principle of Interference and Schrödinger's equation: 35. Physical functions; 36. Interference of probabilities for p and q; 37. General interference of probabilities; 38. Differential equations for Ψp (q) and Xq (p); 39. Differential equation for фβ (q); 40. The general probability amplitude Φβ' (Q); 41. Point transformations; 42. General theorem of interference; 43. Conjugate variables; 44. Schrödinger's equation for conservative systems; 45. Schrödinger's equation for non-conservative systems; 46. Pertubation theory; 47. Orthogonality, normalization and Hermitian conjugacy; 48. General matrix elements; Part IV. The Principle of Correspondence: 49. Contact transformations in classical mechanics; 50. Point transformations; 51. Contact transformations in quantum mechanics; 52. Constants of motion and angular co-ordinates; 53. Periodic orbits; 54. De Broglie and Schrödinger function; correspondence to classical mechanics; 55. Packets of probability; 56. Correspondence to hydrodynamics; 57. Motion and scattering of wave packets; 58. Formal correspondence between classical and quantum mechanics; Part V. Mathematical Appendix: Principle of Invariance: 59. The general theorem of transformation; 60. Operator calculus; 61. Exchange relations; three criteria for conjugacy; 62. First method of canonical transformation; 63. Second method of canonical transformation; 64. Proof of the transformation theorem; 65. Invariance of the matrix elements against unitary transformations; 66. Matrix mechanics; Index of literature; Index of names and subjects.

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.

Anisotropy of the elastic properties of crystalline cellulose Iß from first principles density functional theory with Van der Waals interactions

Treesearch

Fernando L. Dri; Louis G. Jr. Hector; Robert J. Moon; Pablo D. Zavattieri

2013-01-01

In spite of the significant potential of cellulose nanocrystals as functional nanoparticles for numerous applications, a fundamental understanding of the mechanical properties of defect-free, crystalline cellulose is still lacking. In this paper, the elasticity matrix for cellulose Iß with hydrogen bonding network A was calculated using ab initio...

Matrix cracking in laminated composites under monotonic and cyclic loadings

NASA Technical Reports Server (NTRS)

Allen, David H.; Lee, Jong-Won

1991-01-01

An analytical model based on the internal state variable (ISV) concept and the strain energy method is proposed for characterizing the monotonic and cyclic response of laminated composites containing matrix cracks. A modified constitution is formulated for angle-ply laminates under general in-plane mechanical loading and constant temperature change. A monotonic matrix cracking criterion is developed for predicting the crack density in cross-ply laminates as a function of the applied laminate axial stress. An initial formulation for a cyclic matrix cracking criterion for cross-ply laminates is also discussed. For the monotonic loading case, a number of experimental data and well-known models are compared with the present study for validating the practical applicability of the ISV approach.

Symmetry Transition Preserving Chirality in QCD: A Versatile Random Matrix Model

NASA Astrophysics Data System (ADS)

Kanazawa, Takuya; Kieburg, Mario

2018-06-01

We consider a random matrix model which interpolates between the chiral Gaussian unitary ensemble and the Gaussian unitary ensemble while preserving chiral symmetry. This ensemble describes flavor symmetry breaking for staggered fermions in 3D QCD as well as in 4D QCD at high temperature or in 3D QCD at a finite isospin chemical potential. Our model is an Osborn-type two-matrix model which is equivalent to the elliptic ensemble but we consider the singular value statistics rather than the complex eigenvalue statistics. We report on exact results for the partition function and the microscopic level density of the Dirac operator in the ɛ regime of QCD. We compare these analytical results with Monte Carlo simulations of the matrix model.

Assessment of a Three-Dimensional Line-of-Response Probability Density Function System Matrix for PET

PubMed Central

Yao, Rutao; Ramachandra, Ranjith M.; Mahajan, Neeraj; Rathod, Vinay; Gunasekar, Noel; Panse, Ashish; Ma, Tianyu; Jian, Yiqiang; Yan, Jianhua; Carson, Richard E.

2012-01-01

To achieve optimal PET image reconstruction through better system modeling, we developed a system matrix that is based on the probability density function for each line of response (LOR-PDF). The LOR-PDFs are grouped by LOR-to-detector incident angles to form a highly compact system matrix. The system matrix was implemented in the MOLAR list mode reconstruction algorithm for a small animal PET scanner. The impact of LOR-PDF on reconstructed image quality was assessed qualitatively as well as quantitatively in terms of contrast recovery coefficient (CRC) and coefficient of variance (COV), and its performance was compared with a fixed Gaussian (iso-Gaussian) line spread function. The LOR-PDFs of 3 coincidence signal emitting sources, 1) ideal positron emitter that emits perfect back-to-back γ rays (γγ) in air; 2) fluorine-18 (18F) nuclide in water; and 3) oxygen-15 (15O) nuclide in water, were derived, and assessed with simulated and experimental phantom data. The derived LOR-PDFs showed anisotropic and asymmetric characteristics dependent on LOR-detector angle, coincidence emitting source, and the medium, consistent with common PET physical principles. The comparison of the iso-Gaussian function and LOR-PDF showed that: 1) without positron range and acolinearity effects, the LOR-PDF achieved better or similar trade-offs of contrast recovery and noise for objects of 4-mm radius or larger, and this advantage extended to smaller objects (e.g. 2-mm radius sphere, 0.6-mm radius hot-rods) at higher iteration numbers; and 2) with positron range and acolinearity effects, the iso-Gaussian achieved similar or better resolution recovery depending on the significance of positron range effect. We conclude that the 3-D LOR-PDF approach is an effective method to generate an accurate and compact system matrix. However, when used directly in expectation-maximization based list-mode iterative reconstruction algorithms such as MOLAR, its superiority is not clear. For this application, using an iso-Gaussian function in MOLAR is a simple but effective technique for PET reconstruction. PMID:23032702

Separability and Entanglement in the Hilbert Space Reference Frames Related Through the Generic Unitary Transform for Four Level System

NASA Astrophysics Data System (ADS)

Man'ko, V. I.; Markovich, L. A.

2018-02-01

Quantum correlations in the state of four-level atom are investigated by using generic unitary transforms of the classical (diagonal) density matrix. Partial cases of pure state, X-state, Werner state are studied in details. The geometrical meaning of unitary Hilbert reference-frame rotations generating entanglement in the initially separable state is discussed. Characteristics of the entanglement in terms of concurrence, entropy and negativity are obtained as functions of the unitary matrix rotating the reference frame.

Lanczos algorithm with matrix product states for dynamical correlation functions

NASA Astrophysics Data System (ADS)

Dargel, P. E.; Wöllert, A.; Honecker, A.; McCulloch, I. P.; Schollwöck, U.; Pruschke, T.

2012-05-01

The density-matrix renormalization group (DMRG) algorithm can be adapted to the calculation of dynamical correlation functions in various ways which all represent compromises between computational efficiency and physical accuracy. In this paper we reconsider the oldest approach based on a suitable Lanczos-generated approximate basis and implement it using matrix product states (MPS) for the representation of the basis states. The direct use of matrix product states combined with an ex post reorthogonalization method allows us to avoid several shortcomings of the original approach, namely the multitargeting and the approximate representation of the Hamiltonian inherent in earlier Lanczos-method implementations in the DMRG framework, and to deal with the ghost problem of Lanczos methods, leading to a much better convergence of the spectral weights and poles. We present results for the dynamic spin structure factor of the spin-1/2 antiferromagnetic Heisenberg chain. A comparison to Bethe ansatz results in the thermodynamic limit reveals that the MPS-based Lanczos approach is much more accurate than earlier approaches at minor additional numerical cost.

Detection of Matrix Crack Density of CFRP using an Electrical Potential Change Method with Multiple Probes

NASA Astrophysics Data System (ADS)

Todoroki, Akira; Omagari, Kazuomi

Carbon Fiber Reinforced Plastic (CFRP) laminates are adopted for fuel tank structures of next generation space rockets or automobiles. Matrix cracks may cause fuel leak or trigger fatigue damage. A monitoring system of the matrix crack density is required. The authors have developed an electrical resistance change method for the monitoring of delamination cracks in CFRP laminates. Reinforcement fibers are used as a self-sensing system. In the present study, the electric potential method is adopted for matrix crack density monitoring. Finite element analysis (FEA) was performed to investigate the possibility of monitoring matrix crack density using multiple electrodes mounted on a single surface of a specimen. The FEA reveals the matrix crack density increases electrical resistance for a target segment between electrodes. Experimental confirmation was also performed using cross-ply laminates. Eight electrodes were mounted on a single surface of a specimen using silver paste after polishing of the specimen surface with sandpaper. The two outermost electrodes applied electrical current, and the inner electrodes measured electric voltage changes. The slope of electrical resistance during reloading is revealed to be an appropriate index for the detection of matrix crack density.

Semiconductor spintronics: The full matrix approach

NASA Astrophysics Data System (ADS)

Rossani, A.

2015-12-01

A new model, based on an asymptotic procedure for solving the spinor kinetic equations of electrons and phonons is proposed, which gives naturally the displaced Fermi-Dirac distribution function at the leading order. The balance equations for the electron number, energy density and momentum, plus the Poisson’s equation, constitute now a system of six equations. Moreover, two equations for the evolution of the spin densities are added, which account for a general dispersion relation.

Fragmentation and matrix contrast favor understory plants through negative cascading effects on a strong competitor palm.

PubMed

Hernández-Ruedas, Manuel A; Arroyo-Rodríguez, Víctor; Morante-Filho, José Carlos; Meave, Jorge A; Martínez-Ramos, Miguel

2018-05-04

Understanding the patterns and processes driving biodiversity maintenance in fragmented tropical forests is urgently needed for conservation planning, especially in species-rich forest reserves. Of particular concern are the effects that habitat modifications at the landscape scale may have on forest regeneration and ecosystem functioning: a topic that has received limited attention. Here, we assessed the effects of landscape structure (i.e., forest cover, open area matrices, forest fragmentation, and mean inter-patch isolation distance) on understory plant assemblages in the Los Tuxtlas Biosphere Reserve, Mexico. Previous studies suggest that the demographic burst of the strong competitor palm Astrocaryum mexicanum in the core area of this reserve limits plant recruitment and imperils biodiversity conservation within this protected area. Yet, the local and landscape predictors of this palm, and its impact on tree recruitment at a regional scale are unknown. Thus, we used structural equation modeling to assess the direct and cascading effects of landscape structure on stem and species density in the understory of 20 forest sites distributed across this biodiversity hotspot. Indirect paths included the effect of landscape structure on tree basal area (a proxy of local disturbance), and the effects of these variables on A. mexicanum. Density of A. mexicanum mainly increased with decreasing both fragmentation and open areas in the matrix (matrix contrast, hereafter), and such an increase in palm density negatively affected stem and species density in the understory. The negative direct effect of matrix contrast on stem density was overridden by the indirect positive effects (i.e., through negative cascading effects on A. mexicanum), resulting in a weak effect of matrix contrast on stem density. These findings suggest that dispersal limitation and negative edge effects in more fragmented landscapes dominated by open areas prevent the proliferation of this palm species, enhancing the diversity and abundance of understory trees. This "positive" news adds to an increasing line of evidence suggesting that fragmentation may have some positive effects on biodiversity, in this case by preventing the proliferation of species that can jeopardize biodiversity conservation within tropical reserves. © 2018 by the Ecological Society of America.

Very high cell density perfusion of CHO cells anchored in a non-woven matrix-based bioreactor.

PubMed

Zhang, Ye; Stobbe, Per; Silvander, Christian Orrego; Chotteau, Véronique

2015-11-10

Recombinant Chinese Hamster Ovary (CHO) cells producing IgG monoclonal antibody were cultivated in a novel perfusion culture system CellTank, integrating the bioreactor and the cell retention function. In this system, the cells were harbored in a non-woven polyester matrix perfused by the culture medium and immersed in a reservoir. Although adapted to suspension, the CHO cells stayed entrapped in the matrix. The cell-free medium was efficiently circulated from the reservoir into- and through the matrix by a centrifugal pump placed at the bottom of the bioreactor resulting in highly homogenous concentrations of the nutrients and metabolites in the whole system as confirmed by measurements from different sampling locations. A real-time biomass sensor using the dielectric properties of living cells was used to measure the cell density. The performances of the CellTank were studied in three perfusion runs. A very high cell density measured as 200 pF/cm (where 1 pF/cm is equivalent to 1 × 10(6)viable cells/mL) was achieved at a perfusion rate of 10 reactor volumes per day (RV/day) in the first run. In the second run, the effect of cell growth arrest by hypothermia at temperatures lowered gradually from 37 °C to 29 °C was studied during 13 days at cell densities above 100 pF/cm. Finally a production run was performed at high cell densities, where a temperature shift to 31 °C was applied at cell density 100 pF/cm during a production period of 14 days in minimized feeding conditions. The IgG concentrations were comparable in the matrix and in the harvest line in all the runs, indicating no retention of the product of interest. The cell specific productivity was comparable or higher than in Erlenmeyer flask batch culture. During the production run, the final harvested IgG production was 35 times higher in the CellTank compared to a repeated batch culture in the same vessel volume during the same time period. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Quantitative Study of Interface/Interphase in Epoxy/Graphene-Based Nanocomposites by Combining STEM and EELS.

PubMed

Liu, Yu; Hamon, Ann-Lenaig; Haghi-Ashtiani, Paul; Reiss, Thomas; Fan, Benhui; He, Delong; Bai, Jinbo

2016-12-14

A quantitative study of the interphase and interface of graphene nanoplatelets (GNPs)/epoxy and graphene oxide (GO)/epoxy was carried out by combining scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy (EELS). The interphase regions between GNPs and epoxy matrix were clearly identified by the discrepancy of the plasmon peak positions in the low energy-loss spectra due to different valence electron densities. The spectrum acquisitions were carried out along lines across the interface. An interphase thickness of 13 and 12.5 nm was measured for GNPs/epoxy and GO/epoxy, respectively. The density of the GNPs/epoxy interphase was 2.89% higher than that of the epoxy matrix. However, the density of the GO/epoxy interphase was 1.37% lower than that of the epoxy matrix. The interphase layer thickness measured in this work is in good agreement with the transition layer theory, which proposed an area with modulus linearly varying across a finite width. The results provide an insight into the interphase for carbon-based polymer composites that can help to design the functionalization of nanofillers to improve the composite properties.

Optoelectronics of inverted type-I CdS/CdSe core/crown quantum ring

NASA Astrophysics Data System (ADS)

Bose, Sumanta; Fan, Weijun; Zhang, Dao Hua

2017-10-01

Inverted type-I heterostructure core/crown quantum rings (QRs) are quantum-efficient luminophores, whose spectral characteristics are highly tunable. Here, we study the optoelectronic properties of type-I core/crown CdS/CdSe QRs in the zincblende phase—over contrasting lateral size and crown width. For this, we inspect their strain profiles, transition energies, transition matrix elements, spatial charge densities, electronic bandstructures, band-mixing probabilities, optical gain spectra, maximum optical gains, and differential optical gains. Our framework uses an effective-mass envelope function theory based on the 8-band k ṡ p method employing the valence force field model for calculating the atomic strain distributions. The gain calculations are based on the density-matrix equation and take into consideration the excitonic effects with intraband scattering. Variations in the QR lateral size and relative widths of core and crown (ergo the composition) affect their energy levels, band-mixing probabilities, optical transition matrix elements, emission wavelengths/intensities, etc. The optical gain of QRs is also strongly dimension and composition dependent with further dependency on the injection carrier density causing the band-filling effect. They also affect the maximum and differential gain at varying dimensions and compositions.

Quantum Jeffreys prior for displaced squeezed thermal states

NASA Astrophysics Data System (ADS)

Kwek, L. C.; Oh, C. H.; Wang, Xiang-Bin

1999-09-01

It is known that, by extending the equivalence of the Fisher information matrix to its quantum version, the Bures metric, the quantum Jeffreys prior can be determined from the volume element of the Bures metric. We compute the Bures metric for the displaced squeezed thermal state and analyse the quantum Jeffreys prior and its marginal probability distributions. To normalize the marginal probability density function, it is necessary to provide a range of values of the squeezing parameter or the inverse temperature. We find that if the range of the squeezing parameter is kept narrow, there are significant differences in the marginal probability density functions in terms of the squeezing parameters for the displaced and undisplaced situations. However, these differences disappear as the range increases. Furthermore, marginal probability density functions against temperature are very different in the two cases.

Efficient evaluation of Coulomb integrals in a mixed Gaussian and plane-wave basis using the density fitting and Cholesky decomposition.

PubMed

Čársky, Petr; Čurík, Roman; Varga, Štefan

2012-03-21

The objective of this paper is to show that the density fitting (resolution of the identity approximation) can also be applied to Coulomb integrals of the type (k(1)(1)k(2)(1)|g(1)(2)g(2)(2)), where k and g symbols refer to plane-wave functions and gaussians, respectively. We have shown how to achieve the accuracy of these integrals that is needed in wave-function MO and density functional theory-type calculations using mixed Gaussian and plane-wave basis sets. The crucial issues for achieving such a high accuracy are application of constraints for conservation of the number electrons and components of the dipole moment, optimization of the auxiliary basis set, and elimination of round-off errors in the matrix inversion. © 2012 American Institute of Physics

Multireference Density Functional Theory with Generalized Auxiliary Systems for Ground and Excited States.

PubMed

Chen, Zehua; Zhang, Du; Jin, Ye; Yang, Yang; Su, Neil Qiang; Yang, Weitao

2017-09-21

To describe static correlation, we develop a new approach to density functional theory (DFT), which uses a generalized auxiliary system that is of a different symmetry, such as particle number or spin, from that of the physical system. The total energy of the physical system consists of two parts: the energy of the auxiliary system, which is determined with a chosen density functional approximation (DFA), and the excitation energy from an approximate linear response theory that restores the symmetry to that of the physical system, thus rigorously leading to a multideterminant description of the physical system. The electron density of the physical system is different from that of the auxiliary system and is uniquely determined from the functional derivative of the total energy with respect to the external potential. Our energy functional is thus an implicit functional of the physical system density, but an explicit functional of the auxiliary system density. We show that the total energy minimum and stationary states, describing the ground and excited states of the physical system, can be obtained by a self-consistent optimization with respect to the explicit variable, the generalized Kohn-Sham noninteracting density matrix. We have developed the generalized optimized effective potential method for the self-consistent optimization. Among options of the auxiliary system and the associated linear response theory, reformulated versions of the particle-particle random phase approximation (pp-RPA) and the spin-flip time-dependent density functional theory (SF-TDDFT) are selected for illustration of principle. Numerical results show that our multireference DFT successfully describes static correlation in bond dissociation and double bond rotation.

Kibble Zurek mechanism of topological defect formation in quantum field theory with matrix product states

NASA Astrophysics Data System (ADS)

Gillman, Edward; Rajantie, Arttu

2018-05-01

The Kibble Zurek mechanism in a relativistic ϕ4 scalar field theory in D =(1 +1 ) is studied using uniform matrix product states. The equal time two point function in momentum space G2(k ) is approximated as the system is driven through a quantum phase transition at a variety of different quench rates τQ. We focus on looking for signatures of topological defect formation in the system and demonstrate the consistency of the picture that the two point function G2(k ) displays two characteristic scales, the defect density n and the kink width dK. Consequently, G2(k ) provides a clear signature for the formation of defects and a well defined measure of the defect density in the system. These results provide a benchmark for the use of tensor networks as powerful nonperturbative nonequilibrium methods for relativistic quantum field theory, providing a promising technique for the future study of high energy physics and cosmology.

Leucine/Pd-loaded (5,5) single-walled carbon nanotube matrix as a novel nanobiosensors for in silico detection of protein.

PubMed

Yoosefian, Mehdi; Etminan, Nazanin

2018-06-01

We have designed a novel nanobiosensor for in silico detecting proteins based on leucine/Pd-loaded single-walled carbon nanotube matrix. Density functional theory at the B3LYP/6-31G (d) level of theory was realized to analyze the geometrical and electronic structure of the proposed nanobiosensor. The solvent effects were investigated using the Tomasi's polarized continuum model. Atoms-in-molecules theory was used to study the nature of interactions by calculating the electron density ρ(r) and Laplacian at the bond critical points. Natural bond orbital analysis was performed to achieve a deep understanding of the nature of the interactions. The biosensor has potential application for high sensitive and rapid response to protein due to the chemical adsorption of L-leucine amino acid onto Pd-loaded single-walled carbon nanotube and reactive functional groups that can incorporate in hydrogen binding, hydrophobic interactions and van der Waals forces with the protein surface in detection process.

Thermal and active fluctuations of a compressible bilayer vesicle

NASA Astrophysics Data System (ADS)

Sachin Krishnan, T. V.; Yasuda, Kento; Okamoto, Ryuichi; Komura, Shigeyuki

2018-05-01

We discuss thermal and active fluctuations of a compressible bilayer vesicle by using the results of hydrodynamic theory for vesicles. Coupled Langevin equations for the membrane deformation and the density fields are employed to calculate the power spectral density matrix of membrane fluctuations. Thermal contribution is obtained by means of the fluctuation dissipation theorem, whereas active contribution is calculated from exponentially decaying time correlation functions of active random forces. We obtain the total power spectral density as a sum of thermal and active contributions. An apparent response function is further calculated in order to compare with the recent microrheology experiment on red blood cells. An enhanced response is predicted in the low-frequency regime for non-thermal active fluctuations.

Reexamination of relaxation of spins due to a magnetic field gradient: Identity of the Redfield and Torrey theories

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

Golub, R.; Rohm, Ryan M.; Swank, C. M.

2011-02-15

There is an extensive literature on magnetic-gradient-induced spin relaxation. Cates, Schaefer, and Happer, in a seminal publication, have solved the problem in the regime where diffusion theory (the Torrey equation) is applicable using an expansion of the density matrix in diffusion equation eigenfunctions and angular momentum tensors. McGregor has solved the problem in the same regime using a slightly more general formulation using the Redfield theory formulated in terms of the autocorrelation function of the fluctuating field seen by the spins and calculating the correlation functions using the diffusion-theory Green's function. The results of both calculations were shown to agreemore » for a special case. In the present work, we show that the eigenfunction expansion of the Torrey equation yields the expansion of the Green's function for the diffusion equation, thus showing the identity of this approach with that of the Redfield theory. The general solution can also be obtained directly from the Torrey equation for the density matrix. Thus, the physical content of the Redfield and Torrey approaches are identical. We then introduce a more general expression for the position autocorrelation function of particles moving in a closed cell, extending the range of applicability of the theory.« less

Phase space explorations in time dependent density functional theory

NASA Astrophysics Data System (ADS)

Rajam, Aruna K.

Time dependent density functional theory (TDDFT) is one of the useful tools for the study of the dynamic behavior of correlated electronic systems under the influence of external potentials. The success of this formally exact theory practically relies on approximations for the exchange-correlation potential which is a complicated functional of the co-ordinate density, non-local in space and time. Adiabatic approximations (such as ALDA), which are local in time, are most commonly used in the increasing applications of the field. Going beyond ALDA, has been proved difficult leading to mathematical inconsistencies. We explore the regions where the theory faces challenges, and try to answer some of them via the insights from two electron model systems. In this thesis work we propose a phase-space extension of the TDDFT. We want to answer the challenges the theory is facing currently by exploring the one-body phase-space. We give a general introduction to this theory and its mathematical background in the first chapter. In second chapter, we carryout a detailed study of instantaneous phase-space densities and argue that the functionals of distributions can be a better alternative to the nonlocality issue of the exchange-correlation potentials. For this we study in detail the interacting and the non-interacting phase-space distributions for Hookes atom model. The applicability of ALDA-based TDDFT for the dynamics in strongfields can become severely problematic due to the failure of single-Slater determinant picture.. In the third chapter, we analyze how the phase-space distributions can shine some light into this problem. We do a comparative study of Kohn-Sham and interacting phase-space and momentum distributions for single ionization and double ionization systems. Using a simple model of two-electron systems, we have showed that the momentum distribution computed directly from the exact KS system contains spurious oscillations: a non-classical description of the essentially classical two-electron dynamics. In Time dependent density matrix functional theory (TDDMFT), the evolution scheme of the 1RDM (first order reduced density matrix) contains second-order reduced density matrix (2RDM), which has to be expressed in terms of 1RDMs. Any non-correlated approximations (Hartree-Fock) for 2RDM would fail to capture the natural occupations of the system. In our fourth chapter, we show that by applying the quasi-classical and semi-classical approximations one can capture the natural occupations of the excited systems. We study a time-dependent Moshinsky atom model for this. The fifth chapter contains a comparative work on the existing non-local exchange-correlation kernels that are based on current density response frame work and the co-moving frame work. We show that the two approaches though coinciding with each other in linear response regime, actually turn out to be different in non-linear regime.

Gradient-based stochastic estimation of the density matrix

NASA Astrophysics Data System (ADS)

Wang, Zhentao; Chern, Gia-Wei; Batista, Cristian D.; Barros, Kipton

2018-03-01

Fast estimation of the single-particle density matrix is key to many applications in quantum chemistry and condensed matter physics. The best numerical methods leverage the fact that the density matrix elements f(H)ij decay rapidly with distance rij between orbitals. This decay is usually exponential. However, for the special case of metals at zero temperature, algebraic decay of the density matrix appears and poses a significant numerical challenge. We introduce a gradient-based probing method to estimate all local density matrix elements at a computational cost that scales linearly with system size. For zero-temperature metals, the stochastic error scales like S-(d+2)/2d, where d is the dimension and S is a prefactor to the computational cost. The convergence becomes exponential if the system is at finite temperature or is insulating.

Robust validation of approximate 1-matrix functionals with few-electron harmonium atoms

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

Cioslowski, Jerzy, E-mail: jerzy@wmf.univ.szczecin.pl; Piris, Mario; Matito, Eduard

2015-12-07

A simple comparison between the exact and approximate correlation components U of the electron-electron repulsion energy of several states of few-electron harmonium atoms with varying confinement strengths provides a stringent validation tool for 1-matrix functionals. The robustness of this tool is clearly demonstrated in a survey of 14 known functionals, which reveals their substandard performance within different electron correlation regimes. Unlike spot-testing that employs dissociation curves of diatomic molecules or more extensive benchmarking against experimental atomization energies of molecules comprising some standard set, the present approach not only uncovers the flaws and patent failures of the functionals but, even moremore » importantly, also allows for pinpointing their root causes. Since the approximate values of U are computed at exact 1-densities, the testing requires minimal programming and thus is particularly suitable for rapid screening of new functionals.« less

Multireference configuration interaction theory using cumulant reconstruction with internal contraction of density matrix renormalization group wave function.

PubMed

Saitow, Masaaki; Kurashige, Yuki; Yanai, Takeshi

2013-07-28

We report development of the multireference configuration interaction (MRCI) method that can use active space scalable to much larger size references than has previously been possible. The recent development of the density matrix renormalization group (DMRG) method in multireference quantum chemistry offers the ability to describe static correlation in a large active space. The present MRCI method provides a critical correction to the DMRG reference by including high-level dynamic correlation through the CI treatment. When the DMRG and MRCI theories are combined (DMRG-MRCI), the full internal contraction of the reference in the MRCI ansatz, including contraction of semi-internal states, plays a central role. However, it is thought to involve formidable complexity because of the presence of the five-particle rank reduced-density matrix (RDM) in the Hamiltonian matrix elements. To address this complexity, we express the Hamiltonian matrix using commutators, which allows the five-particle rank RDM to be canceled out without any approximation. Then we introduce an approximation to the four-particle rank RDM by using a cumulant reconstruction from lower-particle rank RDMs. A computer-aided approach is employed to derive the exceedingly complex equations of the MRCI in tensor-contracted form and to implement them into an efficient parallel computer code. This approach extends to the size-consistency-corrected variants of MRCI, such as the MRCI+Q, MR-ACPF, and MR-AQCC methods. We demonstrate the capability of the DMRG-MRCI method in several benchmark applications, including the evaluation of single-triplet gap of free-base porphyrin using 24 active orbitals.

Effects of increased collagen-matrix density on the mechanical properties and in vivo absorbability of hydroxyapatite-collagen composites as artificial bone materials.

PubMed

Yunoki, Shunji; Sugiura, Hiroaki; Ikoma, Toshiyuki; Kondo, Eiji; Yasuda, Kazunori; Tanaka, Junzo

2011-02-01

The aim of this study was to evaluate the effects of increased collagen-matrix density on the mechanical properties and in vivo absorbability of porous hydroxyapatite (HAp)-collagen composites as artificial bone materials. Seven types of porous HAp-collagen composites were prepared from HAp nanocrystals and dense collagen fibrils. Their densities and HAp/collagen weight ratios ranged from 122 to 331 mg cm⁻³ and from 20/80 to 80/20, respectively. The flexural modulus and strength increased with an increase in density, reaching 2.46 ± 0.48 and 0.651 ± 0.103 MPa, respectively. The porous composites with a higher collagen-matrix density exhibited much higher mechanical properties at the same densities, suggesting that increasing the collagen-matrix density is an effective way of improving the mechanical properties. It was also suggested that other structural factors in addition to collagen-matrix density are required to achieve bone-like mechanical properties. The in vivo absorbability of the composites was investigated in bone defects of rabbit femurs, demonstrating that the absorption rate decreased with increases in the composite density. An exhaustive increase in density is probably limited by decreases in absorbability as artificial bones.

Enhanced Electro-Static Modulation of Ionic Diffusion through Carbon Nanotube Membranes by Diazonium Grafting Chemistry

PubMed Central

Majumder, Mainak; Keis, Karin; Zhan, Xin; Meadows, Corey; Cole, Jeggan

2013-01-01

A membrane structure consisting of an aligned array of open ended carbon nanotubes (~ 7 nm i.d.) spanning across an inert polymer matrix allows the diffusive transport of aqueous ionic species through CNT cores. The plasma oxidation process that opens CNTs tips inherently introduces carboxylic acid groups at the CNT tips, which allows for a limited amount of chemical functional at the CNT pore entrance. However for numerous applications, it is important to increase the density of carboxylic acid groups at the pore entrance for effective separation processes. Aqueous diazonium based electro-chemistry significantly increases the functional density of carboxylic acid groups. pH dependent dye adsorption-desorption and interfacial capacitance measurements indicate ~ 5–6 times increase in functional density. To further control the spatial location of the functional chemistry, a fast flowing inert liquid column inside the CNT core is found to restrict the diazonium grafting to the CNT tips only. This is confirmed by the increased flux of positively charged Ru(bi-py)3+2 with anionic functionality. The electrostatic enhancement of ion diffusion is readily screened in 0.1(M) electrolyte solution consistent with the membrane pore geometry and increased functional density. PMID:25132719

Direct Measurement of the Density Matrix of a Quantum System

NASA Astrophysics Data System (ADS)

Thekkadath, G. S.; Giner, L.; Chalich, Y.; Horton, M. J.; Banker, J.; Lundeen, J. S.

2016-09-01

One drawback of conventional quantum state tomography is that it does not readily provide access to single density matrix elements since it requires a global reconstruction. Here, we experimentally demonstrate a scheme that can be used to directly measure individual density matrix elements of general quantum states. The scheme relies on measuring a sequence of three observables, each complementary to the last. The first two measurements are made weak to minimize the disturbance they cause to the state, while the final measurement is strong. We perform this joint measurement on polarized photons in pure and mixed states to directly measure their density matrix. The weak measurements are achieved using two walk-off crystals, each inducing a polarization-dependent spatial shift that couples the spatial and polarization degrees of freedom of the photons. This direct measurement method provides an operational meaning to the density matrix and promises to be especially useful for large dimensional states.

Direct Measurement of the Density Matrix of a Quantum System.

PubMed

Thekkadath, G S; Giner, L; Chalich, Y; Horton, M J; Banker, J; Lundeen, J S

2016-09-16

One drawback of conventional quantum state tomography is that it does not readily provide access to single density matrix elements since it requires a global reconstruction. Here, we experimentally demonstrate a scheme that can be used to directly measure individual density matrix elements of general quantum states. The scheme relies on measuring a sequence of three observables, each complementary to the last. The first two measurements are made weak to minimize the disturbance they cause to the state, while the final measurement is strong. We perform this joint measurement on polarized photons in pure and mixed states to directly measure their density matrix. The weak measurements are achieved using two walk-off crystals, each inducing a polarization-dependent spatial shift that couples the spatial and polarization degrees of freedom of the photons. This direct measurement method provides an operational meaning to the density matrix and promises to be especially useful for large dimensional states.

Matrix-product-operator approach to the nonequilibrium steady state of driven-dissipative quantum arrays

NASA Astrophysics Data System (ADS)

Mascarenhas, Eduardo; Flayac, Hugo; Savona, Vincenzo

2015-08-01

We develop a numerical procedure to efficiently model the nonequilibrium steady state of one-dimensional arrays of open quantum systems based on a matrix-product operator ansatz for the density matrix. The procedure searches for the null eigenvalue of the Liouvillian superoperator by sweeping along the system while carrying out a partial diagonalization of the single-site stationary problem. It bears full analogy to the density-matrix renormalization-group approach to the ground state of isolated systems, and its numerical complexity scales as a power law with the bond dimension. The method brings considerable advantage when compared to the integration of the time-dependent problem via Trotter decomposition, as it can address arbitrarily long-ranged couplings. Additionally, it ensures numerical stability in the case of weakly dissipative systems thanks to a slow tuning of the dissipation rates along the sweeps. We have tested the method on a driven-dissipative spin chain, under various assumptions for the Hamiltonian, drive, and dissipation parameters, and compared the results to those obtained both by Trotter dynamics and Monte Carlo wave function methods. Accurate and numerically stable convergence was always achieved when applying the method to systems with a gapped Liouvillian and a nondegenerate steady state.

Dissolution behavior of MgO based inert matrix fuel for the transmutation of minor actinides

NASA Astrophysics Data System (ADS)

Mühr-Ebert, E. L.; Lichte, E.; Bukaemskiy, A.; Finkeldei, S.; Klinkenberg, M.; Brandt, F.; Bosbach, D.; Modolo, G.

2018-07-01

This study explores the dissolution properties of magnesia-based inert matrix nuclear fuel (IMF) containing transuranium elements (TRU). Pure MgO pellets as well as MgO pellets containing CeO2, as surrogate for TRU oxides, and are considered as model systems for genuine magnesia based inert matrix fuel were fabricated. The aim of this study is to identify conditions at which the matrix material can be selectively dissolved during the head-end reprocessing step, allowing a separation of MgO from the actinides, whereas the actinides remain undissolved. The dissolution behavior was studied in macroscopic batch experiments as a function of nitric acid concentration, dissolution medium volume, temperature, stirring velocity, and pellet density (85, 90, 96, and 99%TD). To mimic pellets with various burn-ups the density of the here fabricated pellets was varied. MgO is soluble even under mild conditions (RT, 2.5 mol/L HNO3). The dissolution rates of MgO at different acid concentrations are rather similar, whereas the dissolution rate is strongly dependent on the temperature. Via a microscopic approach, a model was developed to describe the evolution of the pellet surface area during dissolution and determine a surface normalized dissolution rate. Moreover, dissolution rates of the inert matrix fuel containing CeO2 were determined as a function of the acid concentration and temperature. During the dissolution of MgO/CeO2 pellets the MgO dissolves completely, while CeO2 (>99%) remains undissolved. This study intends to provide a profound understanding of the chemical performance of magnesia based IMF containing fissile material. The feasibility of the dissolution of magnesia based IMF with nitric acid is discussed.

A Parameter-Free Semilocal Exchange Energy Functional for Two-Dimensional Quantum Systems.

PubMed

Patra, Abhilash; Jana, Subrata; Samal, Prasanjit

2018-04-05

The method of constructing semilocal density functional for exchange in two dimensions using one of the premier approaches, i.e., density matrix expansion, is revisited, and an accurate functional is constructed. The form of the functional is quite simple and includes no adjustable semiempirical parameters. In it, the kinetic energy dependent momentum is used to compensate nonlocal effects of the system. The functional is then examined by considering the very well-known semiconductor quantum dot systems. And despite its very simple form, the results obtained for quantum dots containing a higher number of electrons agrees pretty well with that of the standard exact exchange theory. Some of the desired properties relevant for the two-dimensional exchange functional and the lower bound associated with it are also discussed. It is observed that the above parameter-free semilocal exchange functional satisfies most of the discussed conditions.

Derivation of an eigenvalue probability density function relating to the Poincaré disk

NASA Astrophysics Data System (ADS)

Forrester, Peter J.; Krishnapur, Manjunath

2009-09-01

A result of Zyczkowski and Sommers (2000 J. Phys. A: Math. Gen. 33 2045-57) gives the eigenvalue probability density function for the top N × N sub-block of a Haar distributed matrix from U(N + n). In the case n >= N, we rederive this result, starting from knowledge of the distribution of the sub-blocks, introducing the Schur decomposition and integrating over all variables except the eigenvalues. The integration is done by identifying a recursive structure which reduces the dimension. This approach is inspired by an analogous approach which has been recently applied to determine the eigenvalue probability density function for random matrices A-1B, where A and B are random matrices with entries standard complex normals. We relate the eigenvalue distribution of the sub-blocks to a many-body quantum state, and to the one-component plasma, on the pseudosphere.

Open-Ended Recursive Approach for the Calculation of Multiphoton Absorption Matrix Elements

PubMed Central

2015-01-01

We present an implementation of single residues for response functions to arbitrary order using a recursive approach. Explicit expressions in terms of density-matrix-based response theory for the single residues of the linear, quadratic, cubic, and quartic response functions are also presented. These residues correspond to one-, two-, three- and four-photon transition matrix elements. The newly developed code is used to calculate the one-, two-, three- and four-photon absorption cross sections of para-nitroaniline and para-nitroaminostilbene, making this the first treatment of four-photon absorption in the framework of response theory. We find that the calculated multiphoton absorption cross sections are not very sensitive to the size of the basis set as long as a reasonably large basis set with diffuse functions is used. The choice of exchange–correlation functional, however, significantly affects the calculated cross sections of both charge-transfer transitions and other transitions, in particular, for the larger para-nitroaminostilbene molecule. We therefore recommend the use of a range-separated exchange–correlation functional in combination with the augmented correlation-consistent double-ζ basis set aug-cc-pVDZ for the calculation of multiphoton absorption properties. PMID:25821415

Polymer Composite and Nanocomposite Dielectric Materials for Pulse Power Energy Storage †

PubMed Central

Barber, Peter; Balasubramanian, Shiva; Anguchamy, Yogesh; Gong, Shushan; Wibowo, Arief; Gao, Hongsheng; Ploehn, Harry J.; zur Loye, Hans-Conrad

2009-01-01

This review summarizes the current state of polymer composites used as dielectric materials for energy storage. The particular focus is on materials: polymers serving as the matrix, inorganic fillers used to increase the effective dielectric constant, and various recent investigations of functionalization of metal oxide fillers to improve compatibility with polymers. We review the recent literature focused on the dielectric characterization of composites, specifically the measurement of dielectric permittivity and breakdown field strength. Special attention is given to the analysis of the energy density of polymer composite materials and how the functionalization of the inorganic filler affects the energy density of polymer composite dielectric materials.

Path-integral approach to the Wigner-Kirkwood expansion.

PubMed

Jizba, Petr; Zatloukal, Václav

2014-01-01

We study the high-temperature behavior of quantum-mechanical path integrals. Starting from the Feynman-Kac formula, we derive a functional representation of the Wigner-Kirkwood perturbation expansion for quantum Boltzmann densities. As shown by its applications to different potentials, the presented expansion turns out to be quite efficient in generating analytic form of the higher-order expansion coefficients. To put some flesh on the bare bones, we apply the expansion to obtain basic thermodynamic functions of the one-dimensional anharmonic oscillator. Further salient issues, such as generalization to the Bloch density matrix and comparison with the more customary world-line formulation, are discussed.

Continuum Level Density of a Coupled-Channel System in the Complex Scaling Method

NASA Astrophysics Data System (ADS)

Suzuki, R.; Kruppa, A. T.; Giraud, B. G.; Katō, K.

2008-06-01

We study the continuum level density (CLD) in the formalism of the complex scaling method (CSM) for coupled-channel systems. We apply the formalism to the ^{4}He = [^{3}H + p] + [^3{He} + n] coupled-channel cluster model where there are resonances at low energy. Numerical calculations of the CLD in the CSM with a finite number of L^{2} basis functions are consistent with the exact result calculated from the S-matrix by solving coupled-channel equations. We also study channel densities. In this framework, the extended completeness relation (ECR) plays an important role.

Energy density functional on a microscopic basis

NASA Astrophysics Data System (ADS)

Baldo, M.; Robledo, L.; Schuck, P.; Viñas, X.

2010-06-01

In recent years impressive progress has been made in the development of highly accurate energy density functionals, which allow us to treat medium-heavy nuclei. In this approach one tries to describe not only the ground state but also the first relevant excited states. In general, higher accuracy requires a larger set of parameters, which must be carefully chosen to avoid redundancy. Following this line of development, it is unavoidable that the connection of the functional with the bare nucleon-nucleon interaction becomes more and more elusive. In principle, the construction of a density functional from a density matrix expansion based on the effective nucleon-nucleon interaction is possible, and indeed the approach has been followed by few authors. However, to what extent a density functional based on such a microscopic approach can reach the accuracy of the fully phenomenological ones remains an open question. A related question is to establish which part of a functional can be actually derived by a microscopic approach and which part, in contrast, must be left as purely phenomenological. In this paper we discuss the main problems that are encountered when the microscopic approach is followed. To this purpose we will use the method we have recently introduced to illustrate the different aspects of these problems. In particular we will discuss the possible connection of the density functional with the nuclear matter equation of state and the distinct features of finite-size effect typical of nuclei.

Anisotropy-driven transition from the Moore-Read state to quantum Hall stripes

NASA Astrophysics Data System (ADS)

Zhu, Zheng; Sodemann, Inti; Sheng, D. N.; Fu, Liang

2017-05-01

We investigate the nature of the quantum Hall liquid in a half-filled second Landau level (n =1 ) as a function of band mass anisotropy using numerical exact diagonalization and density matrix renormalization group methods. We find increasing the mass anisotropy induces a quantum phase transition from the Moore-Read state to a charge density wave state. By analyzing the energy spectrum, guiding center structure factors, and by adding weak pinning potentials, we show that this charge density wave is a unidirectional quantum Hall stripe, which has a periodicity of a few magnetic lengths and survives in the thermodynamic limit. We find smooth profiles for the guiding center occupation function that reveal the strong coupling nature of the array of chiral Luttinger liquids residing at the stripe edges.

Projected quasiparticle theory for molecular electronic structure

NASA Astrophysics Data System (ADS)

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

2011-09-01

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

Symbolic computation of the Hartree-Fock energy from a chiral EFT three-nucleon interaction at N 2LO

NASA Astrophysics Data System (ADS)

Gebremariam, B.; Bogner, S. K.; Duguet, T.

2010-06-01

We present the first of a two-part Mathematica notebook collection that implements a symbolic approach for the application of the density matrix expansion (DME) to the Hartree-Fock (HF) energy from a chiral effective field theory (EFT) three-nucleon interaction at N 2LO. The final output from the notebooks is a Skyrme-like energy density functional that provides a quasi-local approximation to the non-local HF energy. In this paper, we discuss the derivation of the HF energy and its simplification in terms of the scalar/vector-isoscalar/isovector parts of the one-body density matrix. Furthermore, a set of steps is described and illustrated on how to extend the approach to other three-nucleon interactions. Program summaryProgram title: SymbHFNNN Catalogue identifier: AEGC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 96 666 No. of bytes in distributed program, including test data, etc.: 378 083 Distribution format: tar.gz Programming language: Mathematica 7.1 Computer: Any computer running Mathematica 6.0 and later versions Operating system: Windows Xp, Linux/Unix RAM: 256 Mb Classification: 5, 17.16, 17.22 Nature of problem: The calculation of the HF energy from the chiral EFT three-nucleon interaction at N 2LO involves tremendous spin-isospin algebra. The problem is compounded by the need to eventually obtain a quasi-local approximation to the HF energy, which requires the HF energy to be expressed in terms of scalar/vector-isoscalar/isovector parts of the one-body density matrix. The Mathematica notebooks discussed in this paper solve the latter issue. Solution method: The HF energy from the chiral EFT three-nucleon interaction at N 2LO is cast into a form suitable for an automatic simplification of the spin-isospin traces. Several Mathematica functions and symbolic manipulation techniques are used to obtain the result in terms of the scalar/vector-isoscalar/isovector parts of the one-body density matrix. Running time: Several hours

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

Aaltonen, T.; Brucken, E.; Devoto, F.

We search for resonant production of tt pairs in 4.8 fb{sup -1} integrated luminosity of pp collision data at {radical}(s)=1.96 TeV in the lepton+jets decay channel, where one top quark decays leptonically and the other hadronically. A matrix-element reconstruction technique is used; for each event a probability density function of the tt candidate invariant mass is sampled. These probability density functions are used to construct a likelihood function, whereby the cross section for resonant tt production is estimated, given a hypothetical resonance mass and width. The data indicate no evidence of resonant production of tt pairs. A benchmark model ofmore » leptophobic Z{sup '}{yields}tt is excluded with m{sub Z}{sup '}<900 GeV/c{sup 2} at 95% confidence level.« less

Spectroscopic accuracy directly from quantum chemistry: application to ground and excited states of beryllium dimer.

PubMed

Sharma, Sandeep; Yanai, Takeshi; Booth, George H; Umrigar, C J; Chan, Garnet Kin-Lic

2014-03-14

We combine explicit correlation via the canonical transcorrelation approach with the density matrix renormalization group and initiator full configuration interaction quantum Monte Carlo methods to compute a near-exact beryllium dimer curve, without the use of composite methods. In particular, our direct density matrix renormalization group calculations produce a well-depth of D(e) = 931.2 cm(-1) which agrees very well with recent experimentally derived estimates D(e) = 929.7±2 cm(-1) [J. M. Merritt, V. E. Bondybey, and M. C. Heaven, Science 324, 1548 (2009)] and D(e) = 934.6 cm(-1) [K. Patkowski, V. Špirko, and K. Szalewicz, Science 326, 1382 (2009)], as well the best composite theoretical estimates, D(e) = 938±15 cm(-1) [K. Patkowski, R. Podeszwa, and K. Szalewicz, J. Phys. Chem. A 111, 12822 (2007)] and D(e) = 935.1±10 cm(-1) [J. Koput, Phys. Chem. Chem. Phys. 13, 20311 (2011)]. Our results suggest possible inaccuracies in the functional form of the potential used at shorter bond lengths to fit the experimental data [J. M. Merritt, V. E. Bondybey, and M. C. Heaven, Science 324, 1548 (2009)]. With the density matrix renormalization group we also compute near-exact vertical excitation energies at the equilibrium geometry. These provide non-trivial benchmarks for quantum chemical methods for excited states, and illustrate the surprisingly large error that remains for 1 ¹Σ(g)⁻ state with approximate multi-reference configuration interaction and equation-of-motion coupled cluster methods. Overall, we demonstrate that explicitly correlated density matrix renormalization group and initiator full configuration interaction quantum Monte Carlo methods allow us to fully converge to the basis set and correlation limit of the non-relativistic Schrödinger equation in small molecules.

On the non-linear spectroscopy including saturated absorption and four-wave mixing in two and multi-level atoms: a computational study

NASA Astrophysics Data System (ADS)

Patel, M.; De Jager, G.; Nkosi, Z.; Wyngaard, A.; Govender, K.

2017-10-01

In this paper we report on the study of two and multi-level atoms interacting with multiple laser beams. The semi-classical approach is used to describe the system in which the atoms are treated quantum mechanically via the density matrix operator, while the laser beams are treated classically using Maxwells equations. We present results of a two level atom interacting with single and multiple laser beams and demonstrate Rabi oscillations between the levels. The effects of laser modulation on the dynamics of the atom (atomic populations and coherences) are examined by solving the optical Bloch equations. Plots of the density matrix elements as a function of time are presented for various parameters such as laser intensity, detuning, modulation etc. In addition, phase-space plots and Fourier analysis of the density matrix elements are provided. The atomic polarization, estimated from the coherence terms of the density matrix elements, is used in the numerical solution of Maxwells equations to determine the behaviour of the laser beams as they propagate through the atomic ensemble. The effects of saturation and hole-burning are demonstrated in the case of two counter propagating beams with one being a strong beam and the other being very weak. The above work is extended to include four-wave mixing in four level atoms in a diamond configuration. Two co-propagating beams of different wavelengths drive the atoms from a ground state |1〉 to an excited state |3〉 via an intermediate state |2〉. The atoms then move back to the ground state via another intermediate state |4〉, resulting in the generation of two additional correlated photon beams. The characteristics of these additional photons are studied.

Co-regulation of Primary Mouse Hepatocyte Viability and Function by Oxygen and Matrix

PubMed Central

Buck, Lorenna D.; Inman, S. Walker; Rusyn, Ivan; Griffith, Linda G.

2014-01-01

Although oxygen and extracellular matrix cues both influence differentiation state and metabolic function of primary rat and human hepatocytes, relatively little is known about how these factors together regulate behaviors of primary mouse hepatocytes in culture. To determine the effects of pericellular oxygen tension on hepatocellular function, we employed 2 methods of altering oxygen concentration in the local cellular microenvironment of cells cultured in the presence or absence of an extracellular matrix (Matrigel) supplement. By systematically altering medium depth and gas phase oxygen tension, we created multiple oxygen regimes (hypoxic, normoxic, and hyperoxic) and measured the local oxygen concentrations in the pericellular environment using custom-designed oxygen microprobes. From these measurements of oxygen concentrations, we derived values of oxygen consumption rates under a spectrum of environmental contexts, thus providing the first reported estimates of these values for primary mouse hepatocytes. Oxygen tension and matrix microenvironment were found to synergistically regulate hepatocellular survival and function as assessed using quantitative image analysis for cells stained with vital dyes, and assessment of secretion of albumin. Hepatocellular viability was affected only at strongly hypoxic conditions. Surprisingly, albumin secretion rates were greatest at a moderately supra-physiological oxygen concentration, and this effect was mitigated at still greater supra-physiological concentrations. Matrigel enhanced the effects of oxygen on retention of function. This study underscores the importance of carefully controlling cell density, medium depth and gas phase oxygen, as the effects of these parameters on local pericellular oxygen tension and subsequent hepatocellular function are profound. PMID:24222008

Topological entanglement Rényi entropy and reduced density matrix structure.

PubMed

Flammia, Steven T; Hamma, Alioscia; Hughes, Taylor L; Wen, Xiao-Gang

2009-12-31

We generalize the topological entanglement entropy to a family of topological Rényi entropies parametrized by a parameter alpha, in an attempt to find new invariants for distinguishing topologically ordered phases. We show that, surprisingly, all topological Rényi entropies are the same, independent of alpha for all nonchiral topological phases. This independence shows that topologically ordered ground-state wave functions have reduced density matrices with a certain simple structure, and no additional universal information can be extracted from the entanglement spectrum.

Topological Entanglement Rényi Entropy and Reduced Density Matrix Structure

NASA Astrophysics Data System (ADS)

Flammia, Steven T.; Hamma, Alioscia; Hughes, Taylor L.; Wen, Xiao-Gang

2009-12-01

We generalize the topological entanglement entropy to a family of topological Rényi entropies parametrized by a parameter α, in an attempt to find new invariants for distinguishing topologically ordered phases. We show that, surprisingly, all topological Rényi entropies are the same, independent of α for all nonchiral topological phases. This independence shows that topologically ordered ground-state wave functions have reduced density matrices with a certain simple structure, and no additional universal information can be extracted from the entanglement spectrum.

Natural occupation numbers: when do they vanish?

PubMed

Giesbertz, K J H; van Leeuwen, R

2013-09-14

The non-vanishing of the natural orbital (NO) occupation numbers of the one-particle density matrix of many-body systems has important consequences for the existence of a density matrix-potential mapping for nonlocal potentials in reduced density matrix functional theory and for the validity of the extended Koopmans' theorem. On the basis of Weyl's theorem we give a connection between the differentiability properties of the ground state wavefunction and the rate at which the natural occupations approach zero when ordered as a descending series. We show, in particular, that the presence of a Coulomb cusp in the wavefunction leads, in general, to a power law decay of the natural occupations, whereas infinitely differentiable wavefunctions typically have natural occupations that decay exponentially. We analyze for a number of explicit examples of two-particle systems that in case the wavefunction is non-analytic at its spatial diagonal (for instance, due to the presence of a Coulomb cusp) the natural orbital occupations are non-vanishing. We further derive a more general criterium for the non-vanishing of NO occupations for two-particle wavefunctions with a certain separability structure. On the basis of this criterium we show that for a two-particle system of harmonically confined electrons with a Coulombic interaction (the so-called Hookium) the natural orbital occupations never vanish.

Matrix Structure Evolution and Nanoreinforcement Distribution in Mechanically Milled and Spark Plasma Sintered Al-SiC Nanocomposites.

PubMed

Saheb, Nouari; Aliyu, Ismaila Kayode; Hassan, Syed Fida; Al-Aqeeli, Nasser

2014-09-19

Development of homogenous metal matrix nanocomposites with uniform distribution of nanoreinforcement, preserved matrix nanostructure features, and improved properties, was possible by means of innovative processing techniques. In this work, Al-SiC nanocomposites were synthesized by mechanical milling and consolidated through spark plasma sintering. Field Emission Scanning Electron Microscope (FE-SEM) with Energy Dispersive X-ray Spectroscopy (EDS) facility was used for the characterization of the extent of SiC particles' distribution in the mechanically milled powders and spark plasma sintered samples. The change of the matrix crystallite size and lattice strain during milling and sintering was followed through X-ray diffraction (XRD). The density and hardness of the developed materials were evaluated as function of SiC content at fixed sintering conditions using a densimeter and a digital microhardness tester, respectively. It was found that milling for 24 h led to uniform distribution of SiC nanoreinforcement, reduced particle size and crystallite size of the aluminum matrix, and increased lattice strain. The presence and amount of SiC reinforcement enhanced the milling effect. The uniform distribution of SiC achieved by mechanical milling was maintained in sintered samples. Sintering led to the increase in the crystallite size of the aluminum matrix; however, it remained less than 100 nm in the composite containing 10 wt.% SiC. Density and hardness of sintered nanocomposites were reported and compared with those published in the literature.

On Schrödinger's bridge problem

NASA Astrophysics Data System (ADS)

Friedland, S.

2017-11-01

In the first part of this paper we generalize Georgiou-Pavon's result that a positive square matrix can be scaled uniquely to a column stochastic matrix which maps a given positive probability vector to another given positive probability vector. In the second part we prove that a positive quantum channel can be scaled to another positive quantum channel which maps a given positive definite density matrix to another given positive definite density matrix using Brouwer's fixed point theorem. This result proves the Georgiou-Pavon conjecture for two positive definite density matrices, made in their recent paper. We show that the fixed points are unique for certain pairs of positive definite density matrices. Bibliography: 15 titles.

Analysis of the progressive failure of brittle matrix composites

NASA Technical Reports Server (NTRS)

Thomas, David J.

1995-01-01

This report investigates two of the most common modes of localized failures, namely, periodic fiber-bridged matrix cracks and transverse matrix cracks. A modification of Daniels' bundle theory is combined with Weibull's weakest link theory to model the statistical distribution of the periodic matrix cracking strength for an individual layer. Results of the model predictions are compared with experimental data from the open literature. Extensions to the model are made to account for possible imperfections within the layer (i.e., nonuniform fiber lengths, irregular crack spacing, and degraded in-situ fiber properties), and the results of these studies are presented. A generalized shear-lag analysis is derived which is capable of modeling the development of transverse matrix cracks in material systems having a general multilayer configuration and under states of full in-plane load. A method for computing the effective elastic properties for the damaged layer at the global level is detailed based upon the solution for the effects of the damage at the local level. This methodology is general in nature and is therefore also applicable to (0(sub m)/90(sub n))(sub s) systems. The characteristic stress-strain response for more general cases is shown to be qualitatively correct (experimental data is not available for a quantitative evaluation), and the damage evolution is recorded in terms of the matrix crack density as a function of the applied strain. Probabilistic effects are introduced to account for the statistical nature of the material strengths, thus allowing cumulative distribution curves for the probability of failure to be generated for each of the example laminates. Additionally, Oh and Finney's classic work on fracture location in brittle materials is extended and combined with the shear-lag analysis. The result is an analytical form for predicting the probability density function for the location of the next transverse crack occurrence within a crack bounded region. The results of this study verified qualitatively the validity of assuming a uniform crack spacing (as was done in the shear-lag model).

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

Liu, Siqi; Senses, Erkan; Jiao, Yang

Nanoparticles functionalized with long polymer chains at low graft density are interesting systems to study structure–dynamic relationships in polymer nanocomposites since they are shown to aggregate into strings in both solution and melts and also into spheres and branched aggregates in the presence of free polymer chains. Our work investigates structure and entanglement effects in composites of polystyrene-grafted iron oxide nanoparticles by measuring particle relaxations using X-ray photon correlation spectroscopy. And for particles within highly ordered strings and aggregated systems, they experience a dynamically heterogeneous environment displaying hyperdiffusive relaxation commonly observed in jammed soft glassy systems. Furthermore, particle dynamics ismore » diffusive for branched aggregated structures which could be caused by less penetration of long matrix chains into brushes. These results suggest that particle motion is dictated by the strong interactions of chains grafted at low density with the host matrix polymer.« less

Semiclassical propagation: Hilbert space vs. Wigner representation

NASA Astrophysics Data System (ADS)

Gottwald, Fabian; Ivanov, Sergei D.

2018-03-01

A unified viewpoint on the van Vleck and Herman-Kluk propagators in Hilbert space and their recently developed counterparts in Wigner representation is presented. Based on this viewpoint, the Wigner Herman-Kluk propagator is conceptually the most general one. Nonetheless, the respective semiclassical expressions for expectation values in terms of the density matrix and the Wigner function are mathematically proven here to coincide. The only remaining difference is a mere technical flexibility of the Wigner version in choosing the Gaussians' width for the underlying coherent states beyond minimal uncertainty. This flexibility is investigated numerically on prototypical potentials and it turns out to provide neither qualitative nor quantitative improvements. Given the aforementioned generality, utilizing the Wigner representation for semiclassical propagation thus leads to the same performance as employing the respective most-developed (Hilbert-space) methods for the density matrix.

Fluids in porous media. IV. Quench effect on chemical potential.

PubMed

Qiao, C Z; Zhao, S L; Liu, H L; Dong, W

2017-06-21

It appears to be a common sense to measure the crowdedness of a fluid system by the densities of the species constituting it. In the present work, we show that this ceases to be valid for confined fluids under some conditions. A quite thorough investigation is made for a hard sphere (HS) fluid adsorbed in a hard sphere matrix (a quench-annealed system) and its corresponding equilibrium binary mixture. When fluid particles are larger than matrix particles, the quench-annealed system can appear much more crowded than its corresponding equilibrium binary mixture, i.e., having a much higher fluid chemical potential, even when the density of each species is strictly the same in both systems, respectively. We believe that the insight gained from this study should be useful for the design of functionalized porous materials.

Intersubband Transitions in InAs/AlSb Quantum Wells

NASA Technical Reports Server (NTRS)

Li, J.; Koloklov, K.; Ning, C. Z.; Larraber, D. C.; Khodaparast, G. A.; Kono, J.; Ueda, K.; Nakajima, Y.; Sasa, S.; Inoue, M.

2003-01-01

We have studied intersubband transitions in InAs/AlSb quantum wells experimentally and theoretically. Experimentally, we performed polarization-resolved infrared absorption spectroscopy to measure intersubband absorption peak frequencies and linewidths as functions of temperature (from 4 K to room temperature) and quantum well width (from a few nm to 10 nm). To understand experimental results, we performed a self-consistent 8-band k-p band-structure calculation including spatial charge separation. Based on the calculated band structure, we developed a set of density matrix equations to compute TE and TM optical transitions self-consistently, including both interband and intersubband channels. This density matrix formalism is also ideal for the inclusion of various many-body effects, which are known to be important for intersubband transitions. Detailed comparison between experimental data and theoretical simulations is presented.

Information loss in effective field theory: Entanglement and thermal entropies

NASA Astrophysics Data System (ADS)

Boyanovsky, Daniel

2018-03-01

Integrating out high energy degrees of freedom to yield a low energy effective field theory leads to a loss of information with a concomitant increase in entropy. We obtain the effective field theory of a light scalar field interacting with heavy fields after tracing out the heavy degrees of freedom from the time evolved density matrix. The initial density matrix describes the light field in its ground state and the heavy fields in equilibrium at a common temperature T . For T =0 , we obtain the reduced density matrix in a perturbative expansion; it reveals an emergent mixed state as a consequence of the entanglement between light and heavy fields. We obtain the effective action that determines the time evolution of the reduced density matrix for the light field in a nonperturbative Dyson resummation of one-loop correlations of the heavy fields. The Von-Neumann entanglement entropy associated with the reduced density matrix is obtained for the nonresonant and resonant cases in the asymptotic long time limit. In the nonresonant case the reduced density matrix displays an incipient thermalization albeit with a wave-vector, time and coupling dependent effective temperature as a consequence of memory of initial conditions. The entanglement entropy is time independent and is the thermal entropy for this effective, nonequilibrium temperature. In the resonant case the light field fully thermalizes with the heavy fields, the reduced density matrix loses memory of the initial conditions and the entanglement entropy becomes the thermal entropy of the light field. We discuss the relation between the entanglement entropy ultraviolet divergences and renormalization.

The influence of hyaluronic acid hydrogel crosslinking density and macromolecular diffusivity on human MSC chondrogenesis and hypertrophy.

PubMed

Bian, Liming; Hou, Chieh; Tous, Elena; Rai, Reena; Mauck, Robert L; Burdick, Jason A

2013-01-01

Hyaluronic acid (HA) hydrogels formed via photocrosslinking provide stable 3D hydrogel environments that support the chondrogenesis of mesenchymal stem cells (MSCs). Crosslinking density has a significant impact on the physical properties of hydrogels, including their mechanical stiffness and macromolecular diffusivity. Variations in the HA hydrogel crosslinking density can be obtained by either changes in the HA macromer concentration (1, 3, or 5% w/v at 15 min exposure) or the extent of reaction through light exposure time (5% w/v at 5, 10, or 15 min). In this work, increased crosslinking by either method resulted in an overall decrease in cartilage matrix content and more restricted matrix distribution. Increased crosslinking also promoted hypertrophic differentiation of the chondrogenically induced MSCs, resulting in more matrix calcification in vitro. For example, type X collagen expression in the high crosslinking density 5% 15 min group was ~156 and 285% higher when compared to the low crosslinking density 1% 15 min and 5% 5 min groups on day 42, respectively. Supplementation with inhibitors of the small GTPase pathway involved in cytoskeletal tension or myosin II had no effect on hypertrophic differentiation and matrix calcification, indicating that the differential response is unlikely to be related to force-sensing mechanotransduction mechanisms. When implanted subcutaneously in nude mice, higher crosslinking density again resulted in reduced cartilage matrix content, restricted matrix distribution, and increased matrix calcification. This study demonstrates that hydrogel properties mediated through alterations in crosslinking density must be considered in the context of the hypertrophic differentiation of chondrogenically induced MSCs. Copyright © 2012 Elsevier Ltd. All rights reserved.

Matrix isolation infrared spectroscopic studies and density functional theory calculations of the MNN, (MN)2 (M = Y and La), and Y3NN molecules.

PubMed

Teng, Yun-Lei; Xu, Qiang

2008-04-24

The reactions of yttrium and lanthanum with dinitrogen were reinvestigated. Laser-ablated yttrium and lanthanum atoms were co-deposited at 4 K with dinitrogen in excess argon, and the low-temperature reactions of Y and La with N2 in solid argon were studied using infrared spectroscopy. The reaction products YNN, (YN)2, LaNN, and (LaN)2 were formed in the present experiments and characterized on the basis of 14N/15N isotopic shifts, mixed isotope splitting patterns, stepwise annealing, change of reagent concentration and laser energy, and comparison with theoretical predictions. Some assignments were made based on a previous report. Density functional theory calculations were performed on these systems to identify possible reaction products. The agreement between experimental and calculated vibrational frequencies, relative absorption intensities, and isotopic shifts of the MNN and (MN)2 (M = Y and La) molecules supports the identification of these molecules from the matrix infrared spectra. Plausible reaction mechanisms were proposed for the formation of these molecules along with tentative identification of the Y3NN molecule.

Block matrix based LU decomposition to analyze kinetic damping in active plasma resonance spectroscopy

NASA Astrophysics Data System (ADS)

Roehl, Jan Hendrik; Oberrath, Jens

2016-09-01

``Active plasma resonance spectroscopy'' (APRS) is a widely used diagnostic method to measure plasma parameter like electron density. Measurements with APRS probes in plasmas of a few Pa typically show a broadening of the spectrum due to kinetic effects. To analyze the broadening a general kinetic model in electrostatic approximation based on functional analytic methods has been presented [ 1 ] . One of the main results is, that the system response function Y(ω) is given in terms of the matrix elements of the resolvent of the dynamic operator evaluated for values on the imaginary axis. To determine the response function of a specific probe the resolvent has to be approximated by a huge matrix which is given by a banded block structure. Due to this structure a block based LU decomposition can be implemented. It leads to a solution of Y(ω) which is given only by products of matrices of the inner block size. This LU decomposition allows to analyze the influence of kinetic effects on the broadening and saves memory and calculation time. Gratitude is expressed to the internal funding of Leuphana University.

Spin-memory loss due to spin-orbit coupling at ferromagnet/heavy-metal interfaces: Ab initio spin-density matrix approach

NASA Astrophysics Data System (ADS)

Dolui, Kapildeb; Nikolić, Branislav K.

2017-12-01

Spin-memory loss (SML) of electrons traversing ferromagnetic-metal/heavy-metal (FM/HM), FM/normal-metal (FM/NM), and HM/NM interfaces is a fundamental phenomenon that must be invoked to explain consistently large numbers of spintronic experiments. However, its strength extracted by fitting experimental data to phenomenological semiclassical theory, which replaces each interface by a fictitious bulk diffusive layer, is poorly understood from a microscopic quantum framework and/or materials properties. Here we describe an ensemble of flowing spin quantum states using spin-density matrix, so that SML is measured like any decoherence process by the decay of its off-diagonal elements or, equivalently, by the reduction of the magnitude of polarization vector. By combining this framework with density functional theory, we examine how all three components of the polarization vector change at Co/Ta, Co/Pt, Co/Cu, Pt/Cu, and Pt/Au interfaces embedded within Cu/FM/HM/Cu vertical heterostructures. In addition, we use ab initio Green's functions to compute spectral functions and spin textures over FM, HM, and NM monolayers around these interfaces which quantify interfacial spin-orbit coupling and explain the microscopic origin of SML in long-standing puzzles, such as why it is nonzero at the Co/Cu interface; why it is very large at the Pt/Cu interface; and why it occurs even in the absence of disorder, intermixing and magnons at the interface.

Semilocal Exchange Energy Functional for Two-Dimensional Quantum Systems: A Step Beyond Generalized Gradient Approximations.

PubMed

Jana, Subrata; Samal, Prasanjit

2017-06-29

Semilocal density functionals for the exchange-correlation energy of electrons are extensively used as they produce realistic and accurate results for finite and extended systems. The choice of techniques plays a crucial role in constructing such functionals of improved accuracy and efficiency. An accurate and efficient semilocal exchange energy functional in two dimensions is constructed by making use of the corresponding hole which is derived based on the density matrix expansion. The exchange hole involved is localized under the generalized coordinate transformation and satisfies all the relevant constraints. Comprehensive testing and excellent performance of the functional is demonstrated versus exact exchange results. The accuracy of results obtained by using the newly constructed functional is quite remarkable as it substantially reduces the errors present in the local and nonempirical exchange functionals proposed so far for two-dimensional quantum systems. The underlying principles involved in the functional construction are physically appealing and hold promise for developing range separated and nonlocal exchange functionals in two dimensions.

The effect of matrix stiffness of injectable hydrogels on the preservation of cardiac function after a heart attack.

PubMed

Plotkin, Marian; Vaibavi, Srirangam Ramanujam; Rufaihah, Abdul Jalil; Nithya, Venkateswaran; Wang, Jing; Shachaf, Yonatan; Kofidis, Theo; Seliktar, Dror

2014-02-01

This study compares the effect of four injectable hydrogels with different mechanical properties on the post-myocardial infarction left ventricle (LV) remodeling process. The bioactive hydrogels were synthesized from Tetronic-fibrinogen (TF) and PEG-fibrinogen (PF) conjugates; each hydrogel was supplemented with two levels of additional cross-linker to increase the matrix stiffness as measured by the shear storage modulus (G'). Infarcts created by ligating the left anterior descending coronary artery in a rodent model were treated with the hydrogels, and all four treatment groups showed an increase in wall thickness, arterial density, and viable cardiac tissue in the peri-infarct areas of the LV. Echocardiography and hemodynamics data of the PF/TF treated groups showed significant improvement of heart function associated with the attenuated effects of the remodeling process. Multi-factorial regression analysis indicated that the group with the highest modulus exhibited the best rescue of heart function and highest neovascularization. The results of this study demonstrate that multiple properties of an injectable bioactive biomaterial, and notably the matrix stiffness, provide the multifaceted stimulation necessary to preserve cardiac function and prevent adverse remodeling following a heart attack. Copyright © 2013 Elsevier Ltd. All rights reserved.

Comment on "Generalization of the Kohn-Sham system that can represent arbitrary one-electron density matrices"

NASA Astrophysics Data System (ADS)

Piris, Mario; Pernal, Katarzyna

2017-10-01

van Dam [Phys. Rev. A 93, 052512 (2016), 10.1103/PhysRevA.93.052512] claims that the one-particle reduced density matrix (1RDM) of an interacting system can be represented by means of a single-determinant wave function of fictitious noninteracting particles. van Dam [Phys. Rev. A 93, 052512 (2016), 10.1103/PhysRevA.93.052512] introduced orbitals within a mean-field framework that produce energy levels similar to Hartree-Fock orbital energies, therefore he also claims that conventional analyses based on Koopmans' theorem are possible in 1RDM functional theory. In this Comment, we demonstrate that both claims are unfounded.

Ising tricriticality in the extended Hubbard model with bond dimerization

NASA Astrophysics Data System (ADS)

Fehske, Holger; Ejima, Satoshi; Lange, Florian; Essler, Fabian H. L.

We explore the quantum phase transition between Peierls and charge-density-wave insulating states in the one-dimensional, half-filled, extended Hubbard model with explicit bond dimerization. We show that the critical line of the continuous Ising transition terminates at a tricritical point, belonging to the universality class of the tricritical Ising model with central charge c=7/10. Above this point, the quantum phase transition becomes first order. Employing a numerical matrix-product-state based (infinite) density-matrix renormalization group method we determine the ground-state phase diagram, the spin and two-particle charge excitations gaps, and the entanglement properties of the model with high precision. Performing a bosonization analysis we can derive a field description of the transition region in terms of a triple sine-Gordon model. This allows us to derive field theory predictions for the power-law (exponential) decay of the density-density (spin-spin) and bond-order-wave correlation functions, which are found to be in excellent agreement with our numerical results. This work was supported by Deutsche Forschungsgemeinschaft (Germany), SFB 652, project B5, and by the EPSRC under Grant No. EP/N01930X/1 (FHLE).

Cell density and N-cadherin interactions regulate cell proliferation in the sensory epithelia of the inner ear.

PubMed

Warchol, Mark E

2002-04-01

Sensory hair cells in the inner ears of nonmammalian vertebrates can regenerate after injury. In many species, replacement hair cells are produced by the proliferation of epithelial supporting cells. Thus, the ability of supporting cells to undergo renewed proliferation is a key determinant of regenerative ability. The present study used cultures of isolated inner ear sensory epithelia to identify cellular signals that regulate supporting cell proliferation. Small pieces of sensory epithelia from the chicken utricle were cultured in glass microwells. Under those conditions, cell proliferation was inversely related to local cell density. The signaling molecules N-cadherin, beta-catenin, and focal adhesion kinase were immunolocalized in the cultured epithelial cells, and high levels of phosphotyrosine immunoreactivity were present at cell-cell junctions and focal contacts of proliferating cells. Binding of microbeads coated with a function-blocking antibody to N-cadherin inhibited ongoing proliferation. The growth of epithelial cells was also affected by the density of extracellular matrix molecules. The results suggest that cell density, cell-cell contact, and the composition of the extracellular matrix may be critical influences on the regulation of sensory regeneration in the inner ear.

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.

Stochastic Optimally Tuned Range-Separated Hybrid Density Functional Theory.

PubMed

Neuhauser, Daniel; Rabani, Eran; Cytter, Yael; Baer, Roi

2016-05-19

We develop a stochastic formulation of the optimally tuned range-separated hybrid density functional theory that enables significant reduction of the computational effort and scaling of the nonlocal exchange operator at the price of introducing a controllable statistical error. Our method is based on stochastic representations of the Coulomb convolution integral and of the generalized Kohn-Sham density matrix. The computational cost of the approach is similar to that of usual Kohn-Sham density functional theory, yet it provides a much more accurate description of the quasiparticle energies for the frontier orbitals. This is illustrated for a series of silicon nanocrystals up to sizes exceeding 3000 electrons. Comparison with the stochastic GW many-body perturbation technique indicates excellent agreement for the fundamental band gap energies, good agreement for the band edge quasiparticle excitations, and very low statistical errors in the total energy for large systems. The present approach has a major advantage over one-shot GW by providing a self-consistent Hamiltonian that is central for additional postprocessing, for example, in the stochastic Bethe-Salpeter approach.

A new time dependent density functional algorithm for large systems and plasmons in metal clusters

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

Baseggio, Oscar; Fronzoni, Giovanna; Stener, Mauro, E-mail: stener@univ.trieste.it

2015-07-14

A new algorithm to solve the Time Dependent Density Functional Theory (TDDFT) equations in the space of the density fitting auxiliary basis set has been developed and implemented. The method extracts the spectrum from the imaginary part of the polarizability at any given photon energy, avoiding the bottleneck of Davidson diagonalization. The original idea which made the present scheme very efficient consists in the simplification of the double sum over occupied-virtual pairs in the definition of the dielectric susceptibility, allowing an easy calculation of such matrix as a linear combination of constant matrices with photon energy dependent coefficients. The methodmore » has been applied to very different systems in nature and size (from H{sub 2} to [Au{sub 147}]{sup −}). In all cases, the maximum deviations found for the excitation energies with respect to the Amsterdam density functional code are below 0.2 eV. The new algorithm has the merit not only to calculate the spectrum at whichever photon energy but also to allow a deep analysis of the results, in terms of transition contribution maps, Jacob plasmon scaling factor, and induced density analysis, which have been all implemented.« less

Harnessing molecular excited states with Lanczos chains.

PubMed

Baroni, Stefano; Gebauer, Ralph; Bariş Malcioğlu, O; Saad, Yousef; Umari, Paolo; Xian, Jiawei

2010-02-24

The recursion method of Haydock, Heine and Kelly is a powerful tool for calculating diagonal matrix elements of the resolvent of quantum-mechanical Hamiltonian operators by elegantly expressing them in terms of continued fractions. In this paper we extend the recursion method to off-diagonal matrix elements of general (possibly non-Hermitian) operators and apply it to the simulation of molecular optical absorption and photoemission spectra within time-dependent density-functional and many-body perturbation theories, respectively. This method is demonstrated with a couple of applications to the optical absorption and photoemission spectra of the caffeine molecule.

Harnessing molecular excited states with Lanczos chains

NASA Astrophysics Data System (ADS)

Baroni, Stefano; Gebauer, Ralph; Bariş Malcioğlu, O.; Saad, Yousef; Umari, Paolo; Xian, Jiawei

2010-02-01

The recursion method of Haydock, Heine and Kelly is a powerful tool for calculating diagonal matrix elements of the resolvent of quantum-mechanical Hamiltonian operators by elegantly expressing them in terms of continued fractions. In this paper we extend the recursion method to off-diagonal matrix elements of general (possibly non-Hermitian) operators and apply it to the simulation of molecular optical absorption and photoemission spectra within time-dependent density-functional and many-body perturbation theories, respectively. This method is demonstrated with a couple of applications to the optical absorption and photoemission spectra of the caffeine molecule.

Co-regulation of primary mouse hepatocyte viability and function by oxygen and matrix.

PubMed

Buck, Lorenna D; Inman, S Walker; Rusyn, Ivan; Griffith, Linda G

2014-05-01

Although oxygen and extracellular matrix cues both influence differentiation state and metabolic function of primary rat and human hepatocytes, relatively little is known about how these factors together regulate behaviors of primary mouse hepatocytes in culture. To determine the effects of pericellular oxygen tension on hepatocellular function, we employed two methods of altering oxygen concentration in the local cellular microenvironment of cells cultured in the presence or absence of an extracellular matrix (Matrigel) supplement. By systematically altering medium depth and gas phase oxygen tension, we created multiple oxygen regimes (hypoxic, normoxic, and hyperoxic) and measured the local oxygen concentrations in the pericellular environment using custom-designed oxygen microprobes. From these measurements of oxygen concentrations, we derived values of oxygen consumption rates under a spectrum of environmental contexts, thus providing the first reported estimates of these values for primary mouse hepatocytes. Oxygen tension and matrix microenvironment were found to synergistically regulate hepatocellular survival and function as assessed using quantitative image analysis for cells stained with vital dyes, and assessment of secretion of albumin. Hepatocellular viability was affected only at strongly hypoxic conditions. Surprisingly, albumin secretion rates were greatest at a moderately supra-physiological oxygen concentration, and this effect was mitigated at still greater supra-physiological concentrations. Matrigel enhanced the effects of oxygen on retention of function. This study underscores the importance of carefully controlling cell density, medium depth, and gas phase oxygen, as the effects of these parameters on local pericellular oxygen tension and subsequent hepatocellular function are profound. © 2014 Wiley Periodicals, Inc.

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

NASA Astrophysics Data System (ADS)

Pekker, David; Clark, Bryan K.

2017-01-01

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

Linear scaling computation of the Fock matrix. II. Rigorous bounds on exchange integrals and incremental Fock build

NASA Astrophysics Data System (ADS)

Schwegler, Eric; Challacombe, Matt; Head-Gordon, Martin

1997-06-01

A new linear scaling method for computation of the Cartesian Gaussian-based Hartree-Fock exchange matrix is described, which employs a method numerically equivalent to standard direct SCF, and which does not enforce locality of the density matrix. With a previously described method for computing the Coulomb matrix [J. Chem. Phys. 106, 5526 (1997)], linear scaling incremental Fock builds are demonstrated for the first time. Microhartree accuracy and linear scaling are achieved for restricted Hartree-Fock calculations on sequences of water clusters and polyglycine α-helices with the 3-21G and 6-31G basis sets. Eightfold speedups are found relative to our previous method. For systems with a small ionization potential, such as graphitic sheets, the method naturally reverts to the expected quadratic behavior. Also, benchmark 3-21G calculations attaining microhartree accuracy are reported for the P53 tetramerization monomer involving 698 atoms and 3836 basis functions.

Conceptual DFT analysis of the fragility spectra of atoms along the minimum energy reaction coordinate.

PubMed

Ordon, Piotr; Komorowski, Ludwik; Jedrzejewski, Mateusz

2017-10-07

Theoretical justification has been provided to the method for monitoring the sequence of chemical bonds' rearrangement along a reaction path, by tracing the evolution of the diagonal elements of the Hessian matrix. Relations between the divergences of Hellman-Feynman forces and the energy and electron density derivatives have been demonstrated. By the proof presented on the grounds of the conceptual density functional theory formalism, the spectral amplitude observed on the atomic fragility spectra [L. Komorowski et al., Phys. Chem. Chem. Phys. 18, 32658 (2016)] reflects selectively the electron density modifications in bonds of an atom. In fact the spectral peaks for an atom reveal changes of the electron density occurring with bonds creation, breaking, or varying with the reaction progress.

Conceptual DFT analysis of the fragility spectra of atoms along the minimum energy reaction coordinate

NASA Astrophysics Data System (ADS)

Ordon, Piotr; Komorowski, Ludwik; Jedrzejewski, Mateusz

2017-10-01

Theoretical justification has been provided to the method for monitoring the sequence of chemical bonds' rearrangement along a reaction path, by tracing the evolution of the diagonal elements of the Hessian matrix. Relations between the divergences of Hellman-Feynman forces and the energy and electron density derivatives have been demonstrated. By the proof presented on the grounds of the conceptual density functional theory formalism, the spectral amplitude observed on the atomic fragility spectra [L. Komorowski et al., Phys. Chem. Chem. Phys. 18, 32658 (2016)] reflects selectively the electron density modifications in bonds of an atom. In fact the spectral peaks for an atom reveal changes of the electron density occurring with bonds creation, breaking, or varying with the reaction progress.

Structure and Entanglement Factors on Dynamics of Polymer-Grafted Nanoparticles

DOE PAGES

Liu, Siqi; Senses, Erkan; Jiao, Yang; ...

2016-04-15

Nanoparticles functionalized with long polymer chains at low graft density are interesting systems to study structure–dynamic relationships in polymer nanocomposites since they are shown to aggregate into strings in both solution and melts and also into spheres and branched aggregates in the presence of free polymer chains. Our work investigates structure and entanglement effects in composites of polystyrene-grafted iron oxide nanoparticles by measuring particle relaxations using X-ray photon correlation spectroscopy. And for particles within highly ordered strings and aggregated systems, they experience a dynamically heterogeneous environment displaying hyperdiffusive relaxation commonly observed in jammed soft glassy systems. Furthermore, particle dynamics ismore » diffusive for branched aggregated structures which could be caused by less penetration of long matrix chains into brushes. These results suggest that particle motion is dictated by the strong interactions of chains grafted at low density with the host matrix polymer.« less

Drude weight of the spin-(1)/(2) XXZ chain: Density matrix renormalization group versus exact diagonalization

NASA Astrophysics Data System (ADS)

Karrasch, C.; Hauschild, J.; Langer, S.; Heidrich-Meisner, F.

2013-06-01

We revisit the problem of the spin Drude weight D of the integrable spin-1/2 XXZ chain using two complementary approaches, exact diagonalization (ED) and the time-dependent density-matrix renormalization group (tDMRG). We pursue two main goals. First, we present extensive results for the temperature dependence of D. By exploiting time translation invariance within tDMRG, one can extract D for significantly lower temperatures than in previous tDMRG studies. Second, we discuss the numerical quality of the tDMRG data and elaborate on details of the finite-size scaling of the ED results, comparing calculations carried out in the canonical and grand-canonical ensembles. Furthermore, we analyze the behavior of the Drude weight as the point with SU(2)-symmetric exchange is approached and discuss the relative contribution of the Drude weight to the sum rule as a function of temperature.

Advancing X-ray scattering metrology using inverse genetic algorithms.

PubMed

Hannon, Adam F; Sunday, Daniel F; Windover, Donald; Kline, R Joseph

2016-01-01

We compare the speed and effectiveness of two genetic optimization algorithms to the results of statistical sampling via a Markov chain Monte Carlo algorithm to find which is the most robust method for determining real space structure in periodic gratings measured using critical dimension small angle X-ray scattering. Both a covariance matrix adaptation evolutionary strategy and differential evolution algorithm are implemented and compared using various objective functions. The algorithms and objective functions are used to minimize differences between diffraction simulations and measured diffraction data. These simulations are parameterized with an electron density model known to roughly correspond to the real space structure of our nanogratings. The study shows that for X-ray scattering data, the covariance matrix adaptation coupled with a mean-absolute error log objective function is the most efficient combination of algorithm and goodness of fit criterion for finding structures with little foreknowledge about the underlying fine scale structure features of the nanograting.

An efficient implementation of a high-order filter for a cubed-sphere spectral element model

NASA Astrophysics Data System (ADS)

Kang, Hyun-Gyu; Cheong, Hyeong-Bin

2017-03-01

A parallel-scalable, isotropic, scale-selective spatial filter was developed for the cubed-sphere spectral element model on the sphere. The filter equation is a high-order elliptic (Helmholtz) equation based on the spherical Laplacian operator, which is transformed into cubed-sphere local coordinates. The Laplacian operator is discretized on the computational domain, i.e., on each cell, by the spectral element method with Gauss-Lobatto Lagrange interpolating polynomials (GLLIPs) as the orthogonal basis functions. On the global domain, the discrete filter equation yielded a linear system represented by a highly sparse matrix. The density of this matrix increases quadratically (linearly) with the order of GLLIP (order of the filter), and the linear system is solved in only O (Ng) operations, where Ng is the total number of grid points. The solution, obtained by a row reduction method, demonstrated the typical accuracy and convergence rate of the cubed-sphere spectral element method. To achieve computational efficiency on parallel computers, the linear system was treated by an inverse matrix method (a sparse matrix-vector multiplication). The density of the inverse matrix was lowered to only a few times of the original sparse matrix without degrading the accuracy of the solution. For better computational efficiency, a local-domain high-order filter was introduced: The filter equation is applied to multiple cells, and then the central cell was only used to reconstruct the filtered field. The parallel efficiency of applying the inverse matrix method to the global- and local-domain filter was evaluated by the scalability on a distributed-memory parallel computer. The scale-selective performance of the filter was demonstrated on Earth topography. The usefulness of the filter as a hyper-viscosity for the vorticity equation was also demonstrated.

Shrink Wrapping Cells in a Defined Extracellular Matrix to Modulate the Chemo-Mechanical Microenvironment.

PubMed

Palchesko, Rachelle N; Szymanski, John M; Sahu, Amrita; Feinberg, Adam W

2014-09-01

Cell-matrix interactions are important for the physical integration of cells into tissues and the function of insoluble, mechanosensitive signaling networks. Studying these interactions in vitro can be difficult because the extracellular matrix (ECM) proteins that adsorb to in vitro cell culture surfaces do not fully recapitulate the ECM-dense basement membranes to which cells such as cardiomyocytes and endothelial cells adhere to in vivo . Towards addressing this limitation, we have developed a surface-initiated assembly process to engineer ECM proteins into nanostructured, microscale sheets that can be shrink wrapped around single cells and small cell ensembles to provide a functional and instructive matrix niche. Unlike current cell encapsulation technology using alginate, fibrin or other hydrogels, our engineered ECM is similar in density and thickness to native basal lamina and can be tailored in structure and composition using the proteins fibronectin, laminin, fibrinogen, and/or collagen type IV. A range of cells including C2C12 myoblasts, bovine corneal endothelial cells and cardiomyocytes survive the shrink wrapping process with high viability. Further, we demonstrate that, compared to non-encapsulated controls, the engineered ECM modulates cytoskeletal structure, stability of cell-matrix adhesions and cell behavior in 2D and 3D microenvironments.

Shrink Wrapping Cells in a Defined Extracellular Matrix to Modulate the Chemo-Mechanical Microenvironment

PubMed Central

Palchesko, Rachelle N.; Szymanski, John M.; Sahu, Amrita; Feinberg, Adam W.

2014-01-01

Cell-matrix interactions are important for the physical integration of cells into tissues and the function of insoluble, mechanosensitive signaling networks. Studying these interactions in vitro can be difficult because the extracellular matrix (ECM) proteins that adsorb to in vitro cell culture surfaces do not fully recapitulate the ECM-dense basement membranes to which cells such as cardiomyocytes and endothelial cells adhere to in vivo. Towards addressing this limitation, we have developed a surface-initiated assembly process to engineer ECM proteins into nanostructured, microscale sheets that can be shrink wrapped around single cells and small cell ensembles to provide a functional and instructive matrix niche. Unlike current cell encapsulation technology using alginate, fibrin or other hydrogels, our engineered ECM is similar in density and thickness to native basal lamina and can be tailored in structure and composition using the proteins fibronectin, laminin, fibrinogen, and/or collagen type IV. A range of cells including C2C12 myoblasts, bovine corneal endothelial cells and cardiomyocytes survive the shrink wrapping process with high viability. Further, we demonstrate that, compared to non-encapsulated controls, the engineered ECM modulates cytoskeletal structure, stability of cell-matrix adhesions and cell behavior in 2D and 3D microenvironments. PMID:25530816

MEPE Localization in the Craniofacial Complex and Function in Tooth Dentin Formation.

PubMed

Gullard, Angela; Gluhak-Heinrich, Jelica; Papagerakis, Silvana; Sohn, Philip; Unterbrink, Aaron; Chen, Shuo; MacDougall, Mary

2016-04-01

Matrix extracellular phosphoglycoprotein (MEPE) is an extracellular matrix protein found in dental and skeletal tissues. Although information regarding the role of MEPE in bone and disorders of phosphate metabolism is emerging, the role of MEPE in dental tissues remains unclear. We performed RNA in situ hybridization and immunohistochemistry analyses to delineate the expression pattern of MEPE during embryonic and postnatal development in craniofacial mineralizing tissues. Mepe RNA expression was seen within teeth from cap through root formation in association with odontoblasts and cellular cementoblasts. More intense expression was seen in the alveolar bone within the osteoblasts and osteocytes. MEPE immunohistochemistry showed biphasic dentin staining in incisors and more intense staining in alveolar bone matrix and in forming cartilage. Analysis of Mepe null mouse molars showed overall mineralized tooth volume and density of enamel and dentin comparable with that of wild-type samples. However, Mepe(-/-) molars exhibited increased thickness of predentin, dentin, and enamel over controls and decreased gene expression of Enam, Bsp, Dmp1, Dspp, and Opnby RT-PCR. In vitro Mepe overexpression in odontoblasts led to significant reductions in Dspp reporter activity. These data suggest MEPE may be instrumental in craniofacial and dental matrix maturation, potentially functioning in the maintenance of non-mineralized matrix. © 2016 The Histochemical Society.

The ab-initio density matrix renormalization group in practice.

PubMed

Olivares-Amaya, Roberto; Hu, Weifeng; Nakatani, Naoki; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic

2015-01-21

The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.

Development of edge effects around experimental ecosystem hotspots is affected by edge density and matrix type

USDA-ARS?s Scientific Manuscript database

Ecological edge effects are sensitive to landscape context. In particular, edge effects can be altered by matrix type and by the presence of other nearby edges. We experimentally altered patch configurations in an African savanna to determine how edge density and matrix type influence edge effect de...

Industrial entrepreneurial network: Structural and functional analysis

NASA Astrophysics Data System (ADS)

Medvedeva, M. A.; Davletbaev, R. H.; Berg, D. B.; Nazarova, J. J.; Parusheva, S. S.

2016-12-01

Structure and functioning of two model industrial entrepreneurial networks are investigated in the present paper. One of these networks is forming when implementing an integrated project and consists of eight agents, which interact with each other and external environment. The other one is obtained from the municipal economy and is based on the set of the 12 real business entities. Analysis of the networks is carried out on the basis of the matrix of mutual payments aggregated over the certain time period. The matrix is created by the methods of experimental economics. Social Network Analysis (SNA) methods and instruments were used in the present research. The set of basic structural characteristics was investigated: set of quantitative parameters such as density, diameter, clustering coefficient, different kinds of centrality, and etc. They were compared with the random Bernoulli graphs of the corresponding size and density. Discovered variations of random and entrepreneurial networks structure are explained by the peculiarities of agents functioning in production network. Separately, were identified the closed exchange circuits (cyclically closed contours of graph) forming an autopoietic (self-replicating) network pattern. The purpose of the functional analysis was to identify the contribution of the autopoietic network pattern in its gross product. It was found that the magnitude of this contribution is more than 20%. Such value allows using of the complementary currency in order to stimulate economic activity of network agents.

Estimation of proportions in mixed pixels through their region characterization

NASA Technical Reports Server (NTRS)

Chittineni, C. B. (Principal Investigator)

1981-01-01

A region of mixed pixels can be characterized through the probability density function of proportions of classes in the pixels. Using information from the spectral vectors of a given set of pixels from the mixed pixel region, expressions are developed for obtaining the maximum likelihood estimates of the parameters of probability density functions of proportions. The proportions of classes in the mixed pixels can then be estimated. If the mixed pixels contain objects of two classes, the computation can be reduced by transforming the spectral vectors using a transformation matrix that simultaneously diagonalizes the covariance matrices of the two classes. If the proportions of the classes of a set of mixed pixels from the region are given, then expressions are developed for obtaining the estmates of the parameters of the probability density function of the proportions of mixed pixels. Development of these expressions is based on the criterion of the minimum sum of squares of errors. Experimental results from the processing of remotely sensed agricultural multispectral imagery data are presented.

Collision cross sections of N2 by H+ impact at keV energies within time-dependent density-functional theory

NASA Astrophysics Data System (ADS)

Yu, W.; Gao, C.-Z.; Zhang, Y.; Zhang, F. S.; Hutton, R.; Zou, Y.; Wei, B.

2018-03-01

We calculate electron capture and ionization cross sections of N2 impacted by the H+ projectile at keV energies. To this end, we employ the time-dependent density-functional theory coupled nonadiabatically to molecular dynamics. To avoid the explicit treatment of the complex density matrix in the calculation of cross sections, we propose an approximate method based on the assumption of constant ionization rate over the period of the projectile passing the absorbing boundary. Our results agree reasonably well with experimental data and semi-empirical results within the measurement uncertainties in the considered energy range. The discrepancies are mainly attributed to the inadequate description of exchange-correlation functional and the crude approximation for constant ionization rate. Although the present approach does not predict the experiments quantitatively for collision energies below 10 keV, it is still helpful to calculate total cross sections of ion-molecule collisions within a certain energy range.

Finite-temperature dynamics of the Mott insulating Hubbard chain

NASA Astrophysics Data System (ADS)

Nocera, Alberto; Essler, Fabian H. L.; Feiguin, Adrian E.

2018-01-01

We study the dynamical response of the half-filled one-dimensional Hubbard model for a range of interaction strengths U and temperatures T by a combination of numerical and analytical techniques. Using time-dependent density matrix renormalization group computations we find that the single-particle spectral function undergoes a crossover to a spin-incoherent Luttinger liquid regime at temperatures T ˜J =4 t2/U for sufficiently large U >4 t . At smaller values of U and elevated temperatures the spectral function is found to exhibit two thermally broadened bands of excitations, reminiscent of what is found in the Hubbard-I approximation. The dynamical density-density response function is shown to exhibit a finite-temperature resonance at low frequencies inside the Mott gap, with a physical origin similar to the Villain mode in gapped quantum spin chains. We complement our numerical computations by developing an analytic strong-coupling approach to the low-temperature dynamics in the spin-incoherent regime.

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.

Perturbation theory corrections to the two-particle reduced density matrix variational method.

PubMed

Juhasz, Tamas; Mazziotti, David A

2004-07-15

In the variational 2-particle-reduced-density-matrix (2-RDM) method, the ground-state energy is minimized with respect to the 2-particle reduced density matrix, constrained by N-representability conditions. Consider the N-electron Hamiltonian H(lambda) as a function of the parameter lambda where we recover the Fock Hamiltonian at lambda=0 and we recover the fully correlated Hamiltonian at lambda=1. We explore using the accuracy of perturbation theory at small lambda to correct the 2-RDM variational energies at lambda=1 where the Hamiltonian represents correlated atoms and molecules. A key assumption in the correction is that the 2-RDM method will capture a fairly constant percentage of the correlation energy for lambda in (0,1] because the nonperturbative 2-RDM approach depends more significantly upon the nature rather than the strength of the two-body Hamiltonian interaction. For a variety of molecules we observe that this correction improves the 2-RDM energies in the equilibrium bonding region, while the 2-RDM energies at stretched or nearly dissociated geometries, already highly accurate, are not significantly changed. At equilibrium geometries the corrected 2-RDM energies are similar in accuracy to those from coupled-cluster singles and doubles (CCSD), but at nonequilibrium geometries the 2-RDM energies are often dramatically more accurate as shown in the bond stretching and dissociation data for water and nitrogen. (c) 2004 American Institute of Physics.

A study of optical, mechanical and electrical properties of poly(methacrylic acid)/TiO2 nanocomposite

NASA Astrophysics Data System (ADS)

AL-Baradi, Ateyyah M.; Al-Shehri, Samar F.; Badawi, Ali; Merazga, Amar; Atta, A. A.

2018-06-01

This work is concerned with the study of the effect of titanium dioxide (TiO2) nanofillers on the optical, mechanical and electrical properties of poly(methacrylic acid) (PMAA) networks as a function of TiO2 concentration and crosslink density. The structure of the prepared samples was investigated by X-ray diffractometry (XRD) and Transmittance Electron Microscope (TEM). XRD results showed a single phase for the nanocomposites indicating that no large TiO2 aggregates in the polymer matrix. The optical properties of the prepared samples including the absorption, transmittance, energy band gap and refractive index were explored using Spectrophotometer. These measurements showed that there is a red-shift in the absorption caused by the increase of TiO2 concentration. However, the crosslink density in the polymer plays no role in changing the absorption. The energy band gap (Eg) decreases with increasing the concentration of TiO2 in the polymer matrix; whereas Eg increases with increasing the crosslink density. Moreover, the mechanical properties of PMAA/TiO2 nanocomposites by Dynamic Mechanical Analysis (DMA) showed that the viscoelasticity of PMAA decreases with adding TiO2 nanoparticles and the glass transition temperature (Tg) was also found to drop from 130 °C to 114 °C. Finally, the DC conductivity of the obtained systems was found to increase with increasing TiO2 nanoparticles in the matrix.

One-electron reduced density matrices of strongly correlated harmonium atoms.

PubMed

Cioslowski, Jerzy

2015-03-21

Explicit asymptotic expressions are derived for the reduced one-electron density matrices (the 1-matrices) of strongly correlated two- and three-electron harmonium atoms in the ground and first excited states. These expressions, which are valid at the limit of small confinement strength ω, yield electron densities and kinetic energies in agreement with the published values. In addition, they reveal the ω(5/6) asymptotic scaling of the exchange components of the electron-electron repulsion energies that differs from the ω(2/3) scaling of their Coulomb and correlation counterparts. The natural orbitals of the totally symmetric ground state of the two-electron harmonium atom are found to possess collective occupancies that follow a mixed power/Gaussian dependence on the angular momentum in variance with the simple power-law prediction of Hill's asymptotics. Providing rigorous constraints on energies as functionals of 1-matrices, these results are expected to facilitate development of approximate implementations of the density matrix functional theory and ensure their proper description of strongly correlated systems.

Fast Time-Dependent Density Functional Theory Calculations of the X-ray Absorption Spectroscopy of Large Systems.

PubMed

Besley, Nicholas A

2016-10-11

The computational cost of calculations of K-edge X-ray absorption spectra using time-dependent density functional (TDDFT) within the Tamm-Dancoff approximation is significantly reduced through the introduction of a severe integral screening procedure that includes only integrals that involve the core s basis function of the absorbing atom(s) coupled with a reduced quality numerical quadrature for integrals associated with the exchange and correlation functionals. The memory required for the calculations is reduced through construction of the TDDFT matrix within the absorbing core orbitals excitation space and exploiting further truncation of the virtual orbital space. The resulting method, denoted fTDDFTs, leads to much faster calculations and makes the study of large systems tractable. The capability of the method is demonstrated through calculations of the X-ray absorption spectra at the carbon K-edge of chlorophyll a, C 60 and C 70 .

Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory.

PubMed

Sissay, Adonay; Abanador, Paul; Mauger, François; Gaarde, Mette; Schafer, Kenneth J; Lopata, Kenneth

2016-09-07

Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.

Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory

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

Sissay, Adonay; Abanador, Paul; Mauger, François

2016-09-07

Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagatingmore » the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.« less

Parallel scalability of Hartree-Fock calculations

NASA Astrophysics Data System (ADS)

Chow, Edmond; Liu, Xing; Smelyanskiy, Mikhail; Hammond, Jeff R.

2015-03-01

Quantum chemistry is increasingly performed using large cluster computers consisting of multiple interconnected nodes. For a fixed molecular problem, the efficiency of a calculation usually decreases as more nodes are used, due to the cost of communication between the nodes. This paper empirically investigates the parallel scalability of Hartree-Fock calculations. The construction of the Fock matrix and the density matrix calculation are analyzed separately. For the former, we use a parallelization of Fock matrix construction based on a static partitioning of work followed by a work stealing phase. For the latter, we use density matrix purification from the linear scaling methods literature, but without using sparsity. When using large numbers of nodes for moderately sized problems, density matrix computations are network-bandwidth bound, making purification methods potentially faster than eigendecomposition methods.

The Structures of Fibronectin Adsorbed on Polyelectrolyte Thin Films

NASA Astrophysics Data System (ADS)

Shin, Kwanwoo; Satija, Sushil; Fang, Xiao-Hua; Li, Bin-Quan; Nadine, Pernodet; Miriam, Rafailovich; Sokolov, Jonathan; Arach, Goldar; Roser, Steve

2002-03-01

We have shown that it is possible to form a fibrilar network of fibronectin on a polyelectrolyte polymer film whose dimensions are similar to those reported on the extra cellular matrix. The fibronectin network was observed to form only when the charge density of the polymer was in excess of the natural charge density of the cell wall. Furthermore, the self-organized fibronectin layer was much thicker than the polymer film, indicating that long ranged interaction may play a key role in the assembly process. It is therefore important to understand the structure of the polymer layer/protein interface. Here we report on a neutron reflectivity study where we explore the structure of the polyelectrolyte layer, in this case sulfonated polystyrene (PSS_x.), with varying degree of sulfonation (x<30%), as a function of sulfur content and counter ion concentration. These results are then correlated with systemic study of the adsorption and the multilayer formation of fibronectin as a function of incubation time for various sulfonation levels of PSS_x. Furthermore, the surface charge on the substrates can be strongly influenced by the presence of salt ions, it is important to understand changes due to electrostatic interactions occurring in the various salt conditions. Complementary X-ray reflection was used to determine the salt density profile associating with the internal ionic polymer matrix. This work was funded in part of the NSF-MRSEC program.

Geometric multiaxial representation of N -qubit mixed symmetric separable states

NASA Astrophysics Data System (ADS)

SP, Suma; Sirsi, Swarnamala; Hegde, Subramanya; Bharath, Karthik

2017-08-01

The study of N -qubit mixed symmetric separable states is a longstanding challenging problem as no unique separability criterion exists. In this regard, we take up the N -qubit mixed symmetric separable states for a detailed study as these states are of experimental importance and offer an elegant mathematical analysis since the dimension of the Hilbert space is reduced from 2N to N +1 . Since there exists a one-to-one correspondence between the spin-j system and an N -qubit symmetric state, we employ Fano statistical tensor parameters for the parametrization of the spin-density matrix. Further, we use a geometric multiaxial representation (MAR) of the density matrix to characterize the mixed symmetric separable states. Since the separability problem is NP-hard, we choose to study it in the continuum limit where mixed symmetric separable states are characterized by the P -distribution function λ (θ ,ϕ ) . We show that the N -qubit mixed symmetric separable states can be visualized as a uniaxial system if the distribution function is independent of θ and ϕ . We further choose a distribution function to be the most general positive function on a sphere and observe that the statistical tensor parameters characterizing the N -qubit symmetric system are the expansion coefficients of the distribution function. As an example for the discrete case, we investigate the MAR of a uniformly weighted two-qubit mixed symmetric separable state. We also observe that there exists a correspondence between the separability and classicality of states.

Fabrication and evaluation of low-cost agarose-zinc nanoporous composite matrix: influence of adsorbent density and size distribution on the performance of expanded beds.

PubMed

Asghari, Fateme; Jahanshahi, Mohsen

2012-09-28

Expanded bed adsorption (EBA), a promising and practical separation technique for adsorption of nanobioproduct/bioproduct, has been widely studied in the past two decades. The development of adsorbent with the special design for expanded bed process is a challenging course. To reduce the costs of adsorbent preparation, fine zinc powder was used as the inexpensive densifier. A series of matrices named Ag-Zn were prepared by water-in-oil emulsification method. The structure and morphology of the prepared matrix were studied by the optical microscope (OM) and scanning electron microscopy (SEM). The physical properties as a function of zinc powder ratio to agarose slurry were measured. The prepared matrices had regular spherical shape, and followed logarithmic normal size distribution with the range of 75-330 μm, mean diameter of 140.54-191.11 μm, wet density of 1.33-2.01 g/ml, water content of 0.45-0.75, porosity of 0.86-0.97 and pore size of about 40-90 nm. The bed expansion factor at the range of 2-3 was examined. The obtained results indicated that the expansion factor was decreased with increasing of matrix density. In addition, it was found that matrices with large particle size were suitable for high operation flow rate. The hydrodynamic properties were determined in expanded bed by the residence time distribution method (RTD). The effects of flow velocity, expansion factor and density of matrix on the hydrodynamic properties were also investigated. Moreover, the influence of particle size distribution on the performance of expanded bed has been studied. Therefore, three different particle size fractions (65-140, 215-280 and 65-280 μm) were assessed. The results indicated that dispersion in liquid-solid expanded beds increased with increasing flow rate and expansion factor; and matrix with a wide particle size distribution leaded to a reduced axial dispersion compared to matrices with a narrow size distribution. The axial dispersion coefficient also enhanced with the increasing of matrix density. It was found that flow rate was the most essential factor to effect on the hydrodynamic characteristics in the bed. For all the prepared matrices, the values of axial mixing coefficients (D(axl)) were smaller than 1.0 × 10⁻⁵ m²/s when flow velocities in expanded bed were less than 700 cm/h. All the results indicate that the prepared matrix show good expansion and stability in expanded bed; and it is suitable for expanded bed processes as an economical adsorbent. Copyright © 2012 Elsevier B.V. All rights reserved.

An efficient method for quantum transport simulations in the time domain

NASA Astrophysics Data System (ADS)

Wang, Y.; Yam, C.-Y.; Frauenheim, Th.; Chen, G. H.; Niehaus, T. A.

2011-11-01

An approximate method based on adiabatic time dependent density functional theory (TDDFT) is presented, that allows for the description of the electron dynamics in nanoscale junctions under arbitrary time dependent external potentials. The density matrix of the device region is propagated according to the Liouville-von Neumann equation. The semi-infinite leads give rise to dissipative terms in the equation of motion which are calculated from first principles in the wide band limit. In contrast to earlier ab initio implementations of this formalism, the Hamiltonian is here approximated in the spirit of the density functional based tight-binding (DFTB) method. Results are presented for two prototypical molecular devices and compared to full TDDFT calculations. The temporal profile of the current traces is qualitatively well captured by the DFTB scheme. Steady state currents show considerable variations, both in comparison of approximate and full TDDFT, but also among TDDFT calculations with different basis sets.

A physical model study of scattering of waves by aligned cracks: Comparison between experiment and theory

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

Ass'ad, J.M.; McDonald, J.A.; Kusky, T.M.

1993-04-01

An approximation to plane-wave propagation through a composite material is examined using a physical model with oriented but randomly distributed penny-shaped rubber inclusions within an isotropic epoxy resin matrix. A pulse transmission method is used to determine velocities of shear and compressional waves as a function of angle of incidence and crack density. The experimental and theoretical results of Hudson were compared and limitations within the crack parameters used in this study have been determined. Results from both polarized shear waves (S1, S2) compare favorably with the theory for a composite with up to 7% crack density, but theory andmore » experiment diverge at higher crack densities. On the other hand, compressional-wave velocities at low crack densities (1% and 3%) compare favorably with the theory. It is also shown that the velocity ratio V[sub p]/V[sub s] for two extreme cases, i.e. propagation normal and parallel to the cracks, as a function of crack density and porosity, has a strong directional dependence.« less

Five- and six-electron harmonium atoms: Highly accurate electronic properties and their application to benchmarking of approximate 1-matrix functionals

NASA Astrophysics Data System (ADS)

Cioslowski, Jerzy; Strasburger, Krzysztof

2018-04-01

Electronic properties of several states of the five- and six-electron harmonium atoms are obtained from large-scale calculations employing explicitly correlated basis functions. The high accuracy of the computed energies (including their components), natural spinorbitals, and their occupation numbers makes them suitable for testing, calibration, and benchmarking of approximate formalisms of quantum chemistry and solid state physics. In the case of the five-electron species, the availability of the new data for a wide range of the confinement strengths ω allows for confirmation and generalization of the previously reached conclusions concerning the performance of the presently known approximations for the electron-electron repulsion energy in terms of the 1-matrix that are at heart of the density matrix functional theory (DMFT). On the other hand, the properties of the three low-lying states of the six-electron harmonium atom, computed at ω = 500 and ω = 1000, uncover deficiencies of the 1-matrix functionals not revealed by previous studies. In general, the previously published assessment of the present implementations of DMFT being of poor accuracy is found to hold. Extending the present work to harmonically confined systems with even more electrons is most likely counterproductive as the steep increase in computational cost required to maintain sufficient accuracy of the calculated properties is not expected to be matched by the benefits of additional information gathered from the resulting benchmarks.

Polystyrene Foam EOS as a Function of Porosity and Fill Gas

NASA Astrophysics Data System (ADS)

Mulford, Roberta; Swift, Damian

2009-06-01

An accurate EOS for polystyrene foam is necessary for analysis of numerous experiments in shock compression, inertial confinement fusion, and astrophysics. Plastic to gas ratios vary between various samples of foam, according to the density and cell-size of the foam. A matrix of compositions has been investigated, allowing prediction of foam response as a function of the plastic-to-air ratio. The EOS code CHEETAH allows participation of the air in the decomposition reaction of the foam, Differences between air-filled, nitrogen-blown, and CO2-blown foams are investigated, to estimate the importance of allowing air to react with plastic products during decomposition. Results differ somewhat from the conventional EOS, which are generated from values for plastic extrapolated to low densities.

Local entanglement entropy of fermions as a marker of quantum phase transition in the one-dimensional Hubbard model

NASA Astrophysics Data System (ADS)

Cha, Min-Chul; Chung, Myung-Hoon

2018-05-01

We study quantum phase transition of interacting fermions by measuring the local entanglement entropy in the one-dimensional Hubbard model. The reduced density matrices for blocks of a few sites are constructed from the ground state wave function in infinite systems by adopting the matrix product state representation where time-evolving block decimations are performed to obtain the lowest energy states. The local entanglement entropy, constructed from the reduced density matrices, as a function of the chemical potential shows clear signatures of the Mott transition. The value of the central charge, numerically determined from the universal properties of the local entanglement entropy, confirms that the transition is caused by the suppression of the charge degrees of freedom.

Modified Hartree-Fock-Bogoliubov theory at finite temperature

NASA Astrophysics Data System (ADS)

Dinh Dang, Nguyen; Arima, Akito

2003-07-01

The modified Hartree-Fock-Bogoliubov (MHFB) theory at finite temperature is derived, which conserves the unitarity relation of the particle-density matrix. This is achieved by constructing a modified-quasiparticle-density matrix, where the fluctuation of the quasiparticle number is microscopically built in. This matrix can be directly obtained from the usual quasiparticle-density matrix by applying the secondary Bogoliubov transformation, which includes the quasiparticle-occupation number. It is shown that, in the limit of constant pairing parameter, the MHFB theory yields the previously obtained modified BCS (MBCS) equations. It is also proved that the modified quasiparticle-random-phase approximation, which is based on the MBCS quasiparticle excitations, conserves the Ikeda sum rule. The numerical calculations of the pairing gap, heat capacity, level density, and level-density parameter within the MBCS theory are carried out for 120Sn. The results show that the superfluid-normal phase transition is completely washed out. The applicability of the MBCS up to a temperature as high as T˜5 MeV is analyzed in detail.

The spatial-temporal characteristics of type I collagen-based extracellular matrix.

PubMed

Jones, Christopher Allen Rucksack; Liang, Long; Lin, Daniel; Jiao, Yang; Sun, Bo

2014-11-28

Type I collagen abounds in mammalian extracellular matrix (ECM) and is crucial to many biophysical processes. While previous studies have mostly focused on bulk averaged properties, here we provide a comprehensive and quantitative spatial-temporal characterization of the microstructure of type I collagen-based ECM as the gelation temperature varies. The structural characteristics including the density and nematic correlation functions are obtained by analyzing confocal images of collagen gels prepared at a wide range of gelation temperatures (from 16 °C to 36 °C). As temperature increases, the gel microstructure varies from a "bundled" network with strong orientational correlation between the fibers to an isotropic homogeneous network with no significant orientational correlation, as manifested by the decaying of length scales in the correlation functions. We develop a kinetic Monte-Carlo collagen growth model to better understand how ECM microstructure depends on various environmental or kinetic factors. We show that the nucleation rate, growth rate, and an effective hydrodynamic alignment of collagen fibers fully determines the spatiotemporal fluctuations of the density and orientational order of collagen gel microstructure. Also the temperature dependence of the growth rate and nucleation rate follow the prediction of classical nucleation theory.

A micromechanical approach for homogenization of elastic metamaterials with dynamic microstructure.

PubMed

Muhlestein, Michael B; Haberman, Michael R

2016-08-01

An approximate homogenization technique is presented for generally anisotropic elastic metamaterials consisting of an elastic host material containing randomly distributed heterogeneities displaying frequency-dependent material properties. The dynamic response may arise from relaxation processes such as viscoelasticity or from dynamic microstructure. A Green's function approach is used to model elastic inhomogeneities embedded within a uniform elastic matrix as force sources that are excited by a time-varying, spatially uniform displacement field. Assuming dynamic subwavelength inhomogeneities only interact through their volume-averaged fields implies the macroscopic stress and momentum density fields are functions of both the microscopic strain and velocity fields, and may be related to the macroscopic strain and velocity fields through localization tensors. The macroscopic and microscopic fields are combined to yield a homogenization scheme that predicts the local effective stiffness, density and coupling tensors for an effective Willis-type constitutive equation. It is shown that when internal degrees of freedom of the inhomogeneities are present, Willis-type coupling becomes necessary on the macroscale. To demonstrate the utility of the homogenization technique, the effective properties of an isotropic elastic matrix material containing isotropic and anisotropic spherical inhomogeneities, isotropic spheroidal inhomogeneities and isotropic dynamic spherical inhomogeneities are presented and discussed.

A micromechanical approach for homogenization of elastic metamaterials with dynamic microstructure

PubMed Central

Haberman, Michael R.

2016-01-01

An approximate homogenization technique is presented for generally anisotropic elastic metamaterials consisting of an elastic host material containing randomly distributed heterogeneities displaying frequency-dependent material properties. The dynamic response may arise from relaxation processes such as viscoelasticity or from dynamic microstructure. A Green's function approach is used to model elastic inhomogeneities embedded within a uniform elastic matrix as force sources that are excited by a time-varying, spatially uniform displacement field. Assuming dynamic subwavelength inhomogeneities only interact through their volume-averaged fields implies the macroscopic stress and momentum density fields are functions of both the microscopic strain and velocity fields, and may be related to the macroscopic strain and velocity fields through localization tensors. The macroscopic and microscopic fields are combined to yield a homogenization scheme that predicts the local effective stiffness, density and coupling tensors for an effective Willis-type constitutive equation. It is shown that when internal degrees of freedom of the inhomogeneities are present, Willis-type coupling becomes necessary on the macroscale. To demonstrate the utility of the homogenization technique, the effective properties of an isotropic elastic matrix material containing isotropic and anisotropic spherical inhomogeneities, isotropic spheroidal inhomogeneities and isotropic dynamic spherical inhomogeneities are presented and discussed. PMID:27616932

A micromechanical approach for homogenization of elastic metamaterials with dynamic microstructure

NASA Astrophysics Data System (ADS)

Muhlestein, Michael B.; Haberman, Michael R.

2016-08-01

An approximate homogenization technique is presented for generally anisotropic elastic metamaterials consisting of an elastic host material containing randomly distributed heterogeneities displaying frequency-dependent material properties. The dynamic response may arise from relaxation processes such as viscoelasticity or from dynamic microstructure. A Green's function approach is used to model elastic inhomogeneities embedded within a uniform elastic matrix as force sources that are excited by a time-varying, spatially uniform displacement field. Assuming dynamic subwavelength inhomogeneities only interact through their volume-averaged fields implies the macroscopic stress and momentum density fields are functions of both the microscopic strain and velocity fields, and may be related to the macroscopic strain and velocity fields through localization tensors. The macroscopic and microscopic fields are combined to yield a homogenization scheme that predicts the local effective stiffness, density and coupling tensors for an effective Willis-type constitutive equation. It is shown that when internal degrees of freedom of the inhomogeneities are present, Willis-type coupling becomes necessary on the macroscale. To demonstrate the utility of the homogenization technique, the effective properties of an isotropic elastic matrix material containing isotropic and anisotropic spherical inhomogeneities, isotropic spheroidal inhomogeneities and isotropic dynamic spherical inhomogeneities are presented and discussed.

Application of Semi-Definite Programming for Many-Fermion Systems

NASA Astrophysics Data System (ADS)

Zhao, Zhengji; Braams, Bastiaan; Fukuda, Mituhiro; Overton, Michael

2003-03-01

The ground state energy and other important observables of a many-fermion system with one- and two-body interactions only can all be obtained from the first order and second order Reduced Density Matrices (RDM's) of the system. Using these density matrices and a family of associated representability conditions one may obtain an approximation method for electronic structure theory that is in the mathematical form of Semi-Definite Programming (SDP): minimize a linear matrix functional over a space of positive semidefinite matrices subject to linear constraints. The representability conditions are some known necessary conditions, starting with the well-known P, Q, and G conditions [Claude Garrod and Jerome K. Percus, Reducation of the N-Particle Variational Problem, J. Math. Phys. 5 (1964) 1756-1776]. The RDM method with SDP has great potential advantages over the wave function method when the particle number N is large. The dimension of the full configuration space increases exponentially with N, but in RDM method with SDP the dimension of the objective matrix (which includes RDM's) increases only polynomially with N. We will report on the effect of adding the generalized three-index conditions proposed in [R. M. Erdahl, Representability, Int. J. Quantum Chem. 13 (1978) 697-718].

Characterization and reproducibility of HepG2 hanging drop spheroids toxicology in vitro.

PubMed

Hurrell, Tracey; Ellero, Andrea Antonio; Masso, Zelie Flavienne; Cromarty, Allan Duncan

2018-02-21

Hepatotoxicity remains a major challenge in drug development despite preclinical toxicity screening using hepatocytes of human origin. To overcome some limitations of reproducing the hepatic phenotype, more structurally and functionally authentic cultures in vitro can be introduced by growing cells in 3D spheroid cultures. Characterisation and reproducibility of HepG2 spheroid cultures using a high-throughput hanging drop technique was performed and features contributing to potential phenotypic variation highlighted. Cultured HepG2 cells were seeded into Perfecta 3D® 96-well hanging drop plates and assessed over time for morphology, viability, cell cycle distribution, protein content and protein-mass profiles. Divergent aspects which were assessed included cell stocks, seeding density, volume of culture medium and use of extracellular matrix additives. Hanging drops are advantageous due to no complex culture matrix being present, enabling background free extractions for downstream experimentation. Varying characteristics were observed across cell stocks and batches, seeding density, culture medium volume and extracellular matrix when using immortalized HepG2 cells. These factors contribute to wide-ranging cellular responses and highlights concerns with respect to generating a reproducible phenotype in HepG2 hanging drop spheroids. Copyright © 2018 Elsevier Ltd. All rights reserved.

Crosslink Density and Molecular Weight Effects on the Viscoelastic Response of a Glassy High-Performance Polyimide

NASA Technical Reports Server (NTRS)

Nicholson, Lee M.; Whitley, Karen S.; Gates, Thomas S.

2001-01-01

Durability and long-term performance are among the primary concerns for the use of advanced polymer matrix composites (PMCs) in modern aerospace structural applications. For a PMC subJected to long-term exposure at elevated temperatures. the viscoelastic nature of the polymer matrix will contribute to macroscopic changes in composite stiffness, strength and fatigue life. Over time. changes in the polymer due to physical aging will have profound effects on tile viscoelastic compliance of the material, hence affecting its long-term durability. Thus, the ability to predict material performance using intrinsic properties, such as crosslink density and molecular weight, would greatly enhance the efficiency of design and development of PMCs. The objective of this paper is to discuss and present the results of an experimental study that considers the effects of crosslink density, molecular weight and temperature on the viscoelastic behavior including physical aging of an advanced polymer. Five distinct variations in crosslink density were used to evaluate the differences in mechanical performance of an advanced polyimide. The physical aging behavior was isolated by conducting sequenced, short-term isothermal creep compliance tests in tension. These tests were performed over a range of sub-glass transition temperatures. The material constants, material master curves and physical aging-related parameters were evaluated as a function of temperature crosslink density and molecular weight using time-temperature and time-aging time superposition techniques.

Nogo-66 Receptor Antagonist Peptide (NEP1-40) Administration Promotes Functional Recovery and Axonal Growth After Lateral Funiculus Injury in the Adult Rat

PubMed Central

Cao, Y.; Shumsky, J. S.; Sabol, M. A.; Kushner, R. A.; Strittmatter, S.; Hamers, F. P. T.; Lee, D. H. S.; Rabacchi, S. A.; Murray, M.

2010-01-01

Objective The myelin protein Nogo inhibits axon regeneration by binding to its receptor (NgR) on axons. Intrathecal delivery of an NgR antagonist (NEP1-40) promotes growth of injured corticospinal axons and recovery of motor function following a dorsal hemisection. The authors used a similar design to examine recovery and repair after a lesion that interrupts the rubrospinal tract (RST). Methods Rats received a lateral funiculotomy at C4 and NEP1-40 or vehicle was delivered to the cervical spinal cord for 4 weeks. Outcome measures included motor and sensory tests and immunohistochemistry. Results Gait analysis showed recovery in the NEP1-40-treated group compared to operated controls, and a test of forelimb usage also showed a beneficial effect. The density of labeled RST axons increased ipsilaterally in the NEP1-40 group in the lateral funiculus rostral to the lesion and contralaterally in both gray and white matter. Thus, rubrospinal axons exhibited diminished dieback and/or growth up to the lesion site. This was accompanied by greater density of 5 HT and calcitonin gene-related peptide axons adjacent to and into the lesion/matrix site in the NEP1-40 group. Conclusions NgR blockade after RST injury is associated with axonal growth and/or diminished dieback of severed RST axons up to but not into or beyond the lesion/matrix site, and growth of serotonergic and dorsal root axons adjacent to and into the lesion/matrix site. NgR blockade also supported partial recovery of function. The authors’ results indicate that severed rubrospinal axons respond to NEP1-40 treatment but less robustly than corticospinal, raphe-spinal, or dorsal root axons. PMID:18056009

Interaction effects in Aharonov-Bohm-Kondo rings

NASA Astrophysics Data System (ADS)

Komijani, Yashar; Yoshii, Ryosuke; Affleck, Ian

2013-12-01

We study the conductance through an Aharonov-Bohm ring, containing a quantum dot in the Kondo regime in one arm, at finite temperature and arbitrary electronic density. We develop a general method for this calculation based on changing the basis to the screening and nonscreening channels. We show that an unusual term appears in the conductance, involving the connected four-point Green's function of the conduction electrons. However, this term and the terms quadratic in the T matrix can be eliminated at sufficiently low temperatures, leading to an expression for the conductance linear in the Kondo T matrix. Explicit results are given for temperatures that are high compared to the Kondo temperature.

Quantifying Complexity in Quantum Phase Transitions via Mutual Information Complex Networks

NASA Astrophysics Data System (ADS)

Valdez, Marc Andrew; Jaschke, Daniel; Vargas, David L.; Carr, Lincoln D.

2017-12-01

We quantify the emergent complexity of quantum states near quantum critical points on regular 1D lattices, via complex network measures based on quantum mutual information as the adjacency matrix, in direct analogy to quantifying the complexity of electroencephalogram or functional magnetic resonance imaging measurements of the brain. Using matrix product state methods, we show that network density, clustering, disparity, and Pearson's correlation obtain the critical point for both quantum Ising and Bose-Hubbard models to a high degree of accuracy in finite-size scaling for three classes of quantum phase transitions, Z2, mean field superfluid to Mott insulator, and a Berzinskii-Kosterlitz-Thouless crossover.

A feedforward artificial neural network based on quantum effect vector-matrix multipliers.

PubMed

Levy, H J; McGill, T C

1993-01-01

The vector-matrix multiplier is the engine of many artificial neural network implementations because it can simulate the way in which neurons collect weighted input signals from a dendritic arbor. A new technology for building analog weighting elements that is theoretically capable of densities and speeds far beyond anything that conventional VLSI in silicon could ever offer is presented. To illustrate the feasibility of such a technology, a small three-layer feedforward prototype network with five binary neurons and six tri-state synapses was built and used to perform all of the fundamental logic functions: XOR, AND, OR, and NOT.

Matrix stiffness modulates formation and activity of neuronal networks of controlled architectures.

PubMed

Lantoine, Joséphine; Grevesse, Thomas; Villers, Agnès; Delhaye, Geoffrey; Mestdagh, Camille; Versaevel, Marie; Mohammed, Danahe; Bruyère, Céline; Alaimo, Laura; Lacour, Stéphanie P; Ris, Laurence; Gabriele, Sylvain

2016-05-01

The ability to construct easily in vitro networks of primary neurons organized with imposed topologies is required for neural tissue engineering as well as for the development of neuronal interfaces with desirable characteristics. However, accumulating evidence suggests that the mechanical properties of the culture matrix can modulate important neuronal functions such as growth, extension, branching and activity. Here we designed robust and reproducible laminin-polylysine grid micropatterns on cell culture substrates that have similar biochemical properties but a 100-fold difference in Young's modulus to investigate the role of the matrix rigidity on the formation and activity of cortical neuronal networks. We found that cell bodies of primary cortical neurons gradually accumulate in circular islands, whereas axonal extensions spread on linear tracks to connect circular islands. Our findings indicate that migration of cortical neurons is enhanced on soft substrates, leading to a faster formation of neuronal networks. Furthermore, the pre-synaptic density was two times higher on stiff substrates and consistently the number of action potentials and miniature synaptic currents was enhanced on stiff substrates. Taken together, our results provide compelling evidence to indicate that matrix stiffness is a key parameter to modulate the growth dynamics, synaptic density and electrophysiological activity of cortical neuronal networks, thus providing useful information on scaffold design for neural tissue engineering. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Products of random matrices from fixed trace and induced Ginibre ensembles

NASA Astrophysics Data System (ADS)

Akemann, Gernot; Cikovic, Milan

2018-05-01

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

Recombinant human type II collagen hydrogel provides a xeno-free 3D micro-environment for chondrogenesis of human bone marrow-derived mesenchymal stromal cells.

PubMed

Muhonen, Virpi; Narcisi, Roberto; Nystedt, Johanna; Korhonen, Matti; van Osch, Gerjo J V M; Kiviranta, Ilkka

2017-03-01

Recombinant human type II collagen (rhCII) hydrogel was tested as a xeno-free micro-environment for the chondrogenesis of human bone marrow-derived mesenchymal stromal cells (BM-MSCs). The rhCII hydrogels were seeded with BM-MSCs and cultured in a xeno-free chondro-inductive medium for 14, 28 and 84 days. High-density pellet cultures served as controls. The samples were subjected to biochemical, histological and gene expression analyses. Although the cells deposited glycosaminoglycans into the extracellular space significantly more slowly in the rhCII hydrogels compared to the high-density pellets, a similar potential of matrix deposition was reached by the end of the 84-day culture. At day 28 of culture, the gene expression level for cartilage marker genes (i.e. genes encoding for Sox9 transcription factor, Collagen type II and Aggrecan) were considerably lower in the rhCII hydrogels than in the high-density pellets, but at the end of the 84-day culture period, all the cartilage marker genes analysed were expressed at a similar level. Interestingly, the expression of the matrix metallopeptidases (MMP)-13, MMP-14 and MMP-8, i.e. extracellular collagen network-degrading enzymes, were transiently upregulated in the rhCII hydrogel, indicating active matrix reorganization. This study demonstrated that the rhCII hydrogel functions as a xeno-free platform for BM-MSC chondrogenesis, although the process is delayed. The reversible catabolic reaction evoked by the rhCII hydrogel might be beneficial in graft integration in vivo and pinpoints the need to further explore the use of hydrogels containing recombinant extracellular matrix (ECM) proteins to induce the chondrogenesis of MSCs. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Surface modification of carbon nanotubes using 3-aminopropyltriethoxysilane to improve mechanical properties of nanocomposite based polymer matrix: Experimental and Density functional theory study

NASA Astrophysics Data System (ADS)

Hamed Mashhadzadeh, A.; Fereidoon, Ab.; Ghorbanzadeh Ahangari, M.

2017-10-01

In current study we combined theoretical and experimental studies to evaluate the effect of functionalization and silanization on mechanical behavior of polymer-based/CNT nanocomposites. Epoxy was selected as thermoset polymer, polypropylene and poly vinyl chloride were selected as thermoplastic polymers. The whole procedure is divided to two sections . At first we applied density functional theory (DFT) to analyze the effect of functionalization on equilibrium distance and adsorption energy of unmodified, functionalized by sbnd OH group and silanized epoxy/CNT, PP/CNT and PVC/CNT nanocomposites and the results showed that functionalization increased adsorption energy and reduced the equilibrium distance in all studied nanocomposites and silanization had higher effect comparing to OH functionalizing. Then we prepared experimental samples of all mentioned nanocomposites and tested their tensile and flexural strength properties. The obtained results showed that functionalization increased the studied mechanical properties in all evaluated nanocomposites. Finally we compared the results of experimental and theoretical sections with each other and estimated a suitable agreement between these parts.

The ameloblastin extracellular matrix molecule enhances bone fracture resistance and promotes rapid bone fracture healing.

PubMed

Lu, Xuanyu; Li, Wenjin; Fukumoto, Satoshi; Yamada, Yoshihiko; Evans, Carla A; Diekwisch, Tom; Luan, Xianghong

2016-01-01

The extracellular matrix (ECM) provides structural support, cell migration anchorage, cell differentiation cues, and fine-tuned cell proliferation signals during all stages of bone fracture healing, including cartilaginous callus formation, callus remodeling, and bony bridging of the fracture gap. In the present study we have defined the role of the extracellular matrix protein ameloblastin (AMBN) in fracture resistance and fracture healing of mouse long bones. To this end, long bones from WT and AMBN(Δ5-6) truncation model mice were subjected to biomechanical analysis, fracture healing assays, and stem cell colony formation comparisons. The effect of exogenous AMBN addition to fracture sites was also determined. Our data indicate that lack of a functional AMBN in the bone matrix resulted in 31% decreased femur bone mass and 40% reduced energy to failure. On a cellular level, AMBN function inhibition diminished the proliferative capacity of fracture repair callus cells, as evidenced by a 58% reduction in PCNA and a 40% reduction in Cyclin D1 gene expression, as well as PCNA immunohistochemistry. In terms of fracture healing, AMBN truncation was associated with an enhanced and prolonged chondrogenic phase, resulting in delayed mineralized tissue gene expression and delayed ossification of the fracture repair callus. Underscoring a role of AMBN in fracture healing, there was a 6.9-fold increase in AMBN expression at the fracture site one week after fracture, and distinct AMBN immunolabeling in the fracture gap. Finally, application of exogenous AMBN protein to bone fracture sites accelerated callus formation and bone fracture healing (33% increase in bone volume and 19% increase in bone mineral density), validating the findings of our AMBN loss of function studies. Together, these data demonstrate the functional importance of the AMBN extracellular matrix protein in bone fracture prevention and rapid fracture healing. Copyright © 2016 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

Typical entanglement

NASA Astrophysics Data System (ADS)

Deelan Cunden, Fabio; Facchi, Paolo; Florio, Giuseppe; Pascazio, Saverio

2013-05-01

Let a pure state | ψ> be chosen randomly in an NM-dimensional Hilbert space, and consider the reduced density matrix ρ A of an N-dimensional subsystem. The bipartite entanglement properties of | ψ> are encoded in the spectrum of ρ A . By means of a saddle point method and using a "Coulomb gas" model for the eigenvalues, we obtain the typical spectrum of reduced density matrices. We consider the cases of an unbiased ensemble of pure states and of a fixed value of the purity. We finally obtain the eigenvalue distribution by using a statistical mechanics approach based on the introduction of a partition function.

Towards a formal definition of static and dynamic electronic correlations.

PubMed

Benavides-Riveros, Carlos L; Lathiotakis, Nektarios N; Marques, Miguel A L

2017-05-24

Some of the most spectacular failures of density-functional and Hartree-Fock theories are related to an incorrect description of the so-called static electron correlation. Motivated by recent progress in the N-representability problem of the one-body density matrix for pure states, we propose a method to quantify the static contribution to the electronic correlation. By studying several molecular systems we show that our proposal correlates well with our intuition of static and dynamic electron correlation. Our results bring out the paramount importance of the occupancy of the highest occupied natural spin-orbital in such quantification.

The phonon-coupling model for Skyrme forces

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

Lyutorovich, N.; Tselyaev, V.; Speth, J., E-mail: J.Speth@fz-juelich.de

2016-11-15

A short review on the self-consistent RPA based on the energy-density functional of the Skyrme type is given. We also present an extension of the RPA where the coupling of phonons to the single-particle states is considered. Within this approach we present numerical results which are compared with data. The self-consistent approach is compared with the Landau–Migdal theory. Here we derive from the self-consistent ph interaction, the Landau–Migdal parameters as well as their density dependence. In the Appendix a new derivation of the reduced matrix elements of the ph interaction is presented.

Quantitative (31)P NMR spectroscopy and (1)H MRI measurements of bone mineral and matrix density differentiate metabolic bone diseases in rat models.

PubMed

Cao, Haihui; Nazarian, Ara; Ackerman, Jerome L; Snyder, Brian D; Rosenberg, Andrew E; Nazarian, Rosalynn M; Hrovat, Mirko I; Dai, Guangping; Mintzopoulos, Dionyssios; Wu, Yaotang

2010-06-01

In this study, bone mineral density (BMD) of normal (CON), ovariectomized (OVX), and partially nephrectomized (NFR) rats was measured by (31)P NMR spectroscopy; bone matrix density was measured by (1)H water- and fat-suppressed projection imaging (WASPI); and the extent of bone mineralization (EBM) was obtained by the ratio of BMD/bone matrix density. The capability of these MR methods to distinguish the bone composition of the CON, OVX, and NFR groups was evaluated against chemical analysis (gravimetry). For cortical bone specimens, BMD of the CON and OVX groups was not significantly different; BMD of the NFR group was 22.1% (by (31)P NMR) and 17.5% (by gravimetry) lower than CON. For trabecular bone specimens, BMD of the OVX group was 40.5% (by (31)P NMR) and 24.6% (by gravimetry) lower than CON; BMD of the NFR group was 26.8% (by (31)P NMR) and 21.5% (by gravimetry) lower than CON. No significant change of cortical bone matrix density between CON and OVX was observed by WASPI or gravimetry; NFR cortical bone matrix density was 10.3% (by WASPI) and 13.9% (by gravimetry) lower than CON. OVX trabecular bone matrix density was 38.0% (by WASPI) and 30.8% (by gravimetry) lower than CON, while no significant change in NFR trabecular bone matrix density was observed by either method. The EBMs of OVX cortical and trabecular specimens were slightly higher than CON but not significantly different from CON. Importantly, EBMs of NFR cortical and trabecular specimens were 12.4% and 26.3% lower than CON by (31)P NMR/WASPI, respectively, and 4.0% and 11.9% lower by gravimetry. Histopathology showed evidence of osteoporosis in the OVX group and severe secondary hyperparathyroidism (renal osteodystrophy) in the NFR group. These results demonstrate that the combined (31)P NMR/WASPI method is capable of discerning the difference in EBM between animals with osteoporosis and those with impaired bone mineralization. Copyright 2010 Elsevier Inc. All rights reserved.

Detecting Damage in Ceramic Matrix Composites Using Electrical Resistance

NASA Technical Reports Server (NTRS)

Smith, Craig E.; Gyekenyesi, Andrew

2011-01-01

The majority of damage in SiC/SiC ceramic matrix composites subjected to monotonic tensile loads is in the form of distributed matrix cracks. These cracks initiate near stress concentrations, such as 90 deg fiber tows or large matrix pores and continue to accumulate with additional stress until matrix crack saturation is achieved. Such damage is difficult to detect with conventional nondestructive evaluation techniques (immersion ultrasonics, x-ray, etc.). Monitoring a specimen.s electrical resistance change provides an indirect approach for monitoring matrix crack density. Sylramic-iBN fiber- reinforced SiC composites with a melt infiltrated (MI) matrix were tensile tested at room temperature. Results showed an increase in resistance of more than 500% prior to fracture, which can be detected either in situ or post-damage. A relationship between resistance change and matrix crack density was also determined.

Detecting Cracks in Ceramic Matrix Composites by Electrical Resistance

NASA Technical Reports Server (NTRS)

Smith, Craig; Gyekenyesi, Andrew

2011-01-01

The majority of damage in SiC/SiC ceramic matrix composites subjected to monotonic tensile loads is in the form of distributed matrix cracks. These cracks initiate near stress concentrations, such as 90o fiber tows or large matrix pores and continue to accumulate with additional stress until matrix crack saturation is achieved. Such damage is difficult to detect with conventional nondestructive evaluation techniques (immersion ultrasonics, x-ray, etc.). Monitoring a specimen.s electrical resistance change provides an indirect approach for monitoring matrix crack density. Sylramic-iBN fiber- reinforced SiC composites with a melt infiltrated (MI) matrix were tensile tested at room temperature. Results showed an increase in resistance of more than 500% prior to fracture, which can be detected either in situ or post-damage. A relationship between resistance change and matrix crack density was also determined.

Quasiclassical description of a superconductor with a spin density wave

NASA Astrophysics Data System (ADS)

Moor, A.; Volkov, A. F.; Efetov, K. B.

2011-04-01

We derive equations for the quasiclassical Green’s functions ǧ within a simple model of a two-band superconductor with a spin density wave (SDW). The elements of the matrix ǧ are the retarded, advanced, and Keldysh functions, each of which is an 8×8 matrix in the Gor’kov-Nambu, the spin, and the band space. In equilibrium, these equations are a generalization of the Eilenberger equation. On the basis of the derived equations, we analyze the Knight shift, the proximity, and the dc Josephson effects in the superconductors under consideration. The Knight shift is shown to depend on the orientation of the external magnetic field with respect to the direction of the vector of the magnetization of the SDW. The proximity effect is analyzed for an interface between a superconductor with the SDW and a normal metal. The function describing both superconducting and magnetic correlations is shown to penetrate the normal metal or a metal with the SDW due to the proximity effect. The dc Josephson current in an SSDW/N/SSDW junction is also calculated as a function of the phase difference φ. It is shown that in our model, the Josephson current does not depend on the mutual orientation of the magnetic moments in the superconductors SSDW and is proportional to sinφ. The dissipationless spin current jsp depends on the angle α between the magnetization vectors in the same way (jsp~sinα) and is not zero above the superconducting transition temperature.

A study of parameter identification

NASA Technical Reports Server (NTRS)

Herget, C. J.; Patterson, R. E., III

1978-01-01

A set of definitions for deterministic parameter identification ability were proposed. Deterministic parameter identificability properties are presented based on four system characteristics: direct parameter recoverability, properties of the system transfer function, properties of output distinguishability, and uniqueness properties of a quadratic cost functional. Stochastic parameter identifiability was defined in terms of the existence of an estimation sequence for the unknown parameters which is consistent in probability. Stochastic parameter identifiability properties are presented based on the following characteristics: convergence properties of the maximum likelihood estimate, properties of the joint probability density functions of the observations, and properties of the information matrix.

Coherent mode decomposition using mixed Wigner functions of Hermite-Gaussian beams.

PubMed

Tanaka, Takashi

2017-04-15

A new method of coherent mode decomposition (CMD) is proposed that is based on a Wigner-function representation of Hermite-Gaussian beams. In contrast to the well-known method using the cross spectral density (CSD), it directly determines the mode functions and their weights without solving the eigenvalue problem. This facilitates the CMD of partially coherent light whose Wigner functions (and thus CSDs) are not separable, in which case the conventional CMD requires solving an eigenvalue problem with a large matrix and thus is numerically formidable. An example is shown regarding the CMD of synchrotron radiation, one of the most important applications of the proposed method.

Unifying model for random matrix theory in arbitrary space dimensions

NASA Astrophysics Data System (ADS)

Cicuta, Giovanni M.; Krausser, Johannes; Milkus, Rico; Zaccone, Alessio

2018-03-01

A sparse random block matrix model suggested by the Hessian matrix used in the study of elastic vibrational modes of amorphous solids is presented and analyzed. By evaluating some moments, benchmarked against numerics, differences in the eigenvalue spectrum of this model in different limits of space dimension d , and for arbitrary values of the lattice coordination number Z , are shown and discussed. As a function of these two parameters (and their ratio Z /d ), the most studied models in random matrix theory (Erdos-Renyi graphs, effective medium, and replicas) can be reproduced in the various limits of block dimensionality d . Remarkably, the Marchenko-Pastur spectral density (which is recovered by replica calculations for the Laplacian matrix) is reproduced exactly in the limit of infinite size of the blocks, or d →∞ , which clarifies the physical meaning of space dimension in these models. We feel that the approximate results for d =3 provided by our method may have many potential applications in the future, from the vibrational spectrum of glasses and elastic networks to wave localization, disordered conductors, random resistor networks, and random walks.

Neutrinoless ββ decay mediated by the exchange of light and heavy neutrinos: the role of nuclear structure correlations

NASA Astrophysics Data System (ADS)

Menéndez, J.

2018-01-01

Neutrinoless β β decay nuclear matrix elements calculated with the shell model and energy-density functional theory typically disagree by more than a factor of two in the standard scenario of light-neutrino exchange. In contrast, for a decay mediated by sterile heavy neutrinos the deviations are reduced to about 50%, an uncertainty similar to the one due to short-range effects. We compare matrix elements in the light- and heavy-neutrino-exchange channels, exploring the radial, momentum transfer and angular momentum-parity matrix element distributions, and considering transitions that involve correlated and uncorrelated nuclear states. We argue that the shorter-range heavy-neutrino exchange is less sensitive to collective nuclear correlations, and that discrepancies in matrix elements are mostly due to the treatment of long-range correlations in many-body calculations. Our analysis supports previous studies suggesting that isoscalar pairing correlations, which affect mostly the longer-range part of the neutrinoless β β decay operator, are partially responsible for the differences between nuclear matrix elements in the standard light-neutrino-exchange mechanism.

Exact and approximate many-body dynamics with stochastic one-body density matrix evolution

NASA Astrophysics Data System (ADS)

Lacroix, Denis

2005-06-01

We show that the dynamics of interacting fermions can be exactly replaced by a quantum jump theory in the many-body density matrix space. In this theory, jumps occur between densities formed of pairs of Slater determinants, Dab=|Φa><Φb|, where each state evolves according to the stochastic Schrödinger equation given by O. Juillet and Ph. Chomaz [Phys. Rev. Lett. 88, 142503 (2002)]. A stochastic Liouville-von Neumann equation is derived as well as the associated. Bogolyubov-Born-Green-Kirwood-Yvon hierarchy. Due to the specific form of the many-body density along the path, the presented theory is equivalent to a stochastic theory in one-body density matrix space, in which each density matrix evolves according to its own mean-field augmented by a one-body noise. Guided by the exact reformulation, a stochastic mean-field dynamics valid in the weak coupling approximation is proposed. This theory leads to an approximate treatment of two-body effects similar to the extended time-dependent Hartree-Fock scheme. In this stochastic mean-field dynamics, statistical mixing can be directly considered and jumps occur on a coarse-grained time scale. Accordingly, numerical effort is expected to be significantly reduced for applications.

Second-order perturbation theory with a density matrix renormalization group self-consistent field reference function: theory and application to the study of chromium dimer.

PubMed

Kurashige, Yuki; Yanai, Takeshi

2011-09-07

We present a second-order perturbation theory based on a density matrix renormalization group self-consistent field (DMRG-SCF) reference function. The method reproduces the solution of the complete active space with second-order perturbation theory (CASPT2) when the DMRG reference function is represented by a sufficiently large number of renormalized many-body basis, thereby being named DMRG-CASPT2 method. The DMRG-SCF is able to describe non-dynamical correlation with large active space that is insurmountable to the conventional CASSCF method, while the second-order perturbation theory provides an efficient description of dynamical correlation effects. The capability of our implementation is demonstrated for an application to the potential energy curve of the chromium dimer, which is one of the most demanding multireference systems that require best electronic structure treatment for non-dynamical and dynamical correlation as well as large basis sets. The DMRG-CASPT2/cc-pwCV5Z calculations were performed with a large (3d double-shell) active space consisting of 28 orbitals. Our approach using large-size DMRG reference addressed the problems of why the dissociation energy is largely overestimated by CASPT2 with the small active space consisting of 12 orbitals (3d4s), and also is oversensitive to the choice of the zeroth-order Hamiltonian. © 2011 American Institute of Physics

Low-Density Parity-Check Code Design Techniques to Simplify Encoding

NASA Astrophysics Data System (ADS)

Perez, J. M.; Andrews, K.

2007-11-01

This work describes a method for encoding low-density parity-check (LDPC) codes based on the accumulate-repeat-4-jagged-accumulate (AR4JA) scheme, using the low-density parity-check matrix H instead of the dense generator matrix G. The use of the H matrix to encode allows a significant reduction in memory consumption and provides the encoder design a great flexibility. Also described are new hardware-efficient codes, based on the same kind of protographs, which require less memory storage and area, allowing at the same time a reduction in the encoding delay.

Infrared spectra and density functional calculations for SMO2 molecules (M = Cr, Mo, W).

PubMed

Wang, Xuefeng; Andrews, Lester

2009-08-06

Infrared absorptions of the matrix isolated SMO2 (M = Cr, Mo, W) molecules were observed following laser-ablated metal atom reactions with SO2 during condensation in solid argon and neon. The symmetric and antisymmetric M-O stretching mode assignments were confirmed by appropriate S18O2 and S(16,18)O2 isotopic shifts. The much weaker Cr-S stretching mode was identified through its 34S shift. Density functional (B3LYP and BPW91) calculations were performed to obtain molecular structures and to reproduce the infrared spectra. Computed pyramidal structures for the SMO2 molecules are very similar to those for the analogous trioxides and this functional group in [MO2S(bdt)]2- complexes. Additional weaker absorptions are assigned to the (SO2)(SMO2) adducts, which are stabilized by a four-membered ring.

Time-dependent density functional theory for open systems with a positivity-preserving decomposition scheme for environment spectral functions

NASA Astrophysics Data System (ADS)

Wang, RuLin; Zheng, Xiao; Kwok, YanHo; Xie, Hang; Chen, GuanHua; Yam, ChiYung

2015-04-01

Understanding electronic dynamics on material surfaces is fundamentally important for applications including nanoelectronics, inhomogeneous catalysis, and photovoltaics. Practical approaches based on time-dependent density functional theory for open systems have been developed to characterize the dissipative dynamics of electrons in bulk materials. The accuracy and reliability of such approaches depend critically on how the electronic structure and memory effects of surrounding material environment are accounted for. In this work, we develop a novel squared-Lorentzian decomposition scheme, which preserves the positive semi-definiteness of the environment spectral matrix. The resulting electronic dynamics is guaranteed to be both accurate and convergent even in the long-time limit. The long-time stability of electronic dynamics simulation is thus greatly improved within the current decomposition scheme. The validity and usefulness of our new approach are exemplified via two prototypical model systems: quasi-one-dimensional atomic chains and two-dimensional bilayer graphene.

Variational optimization algorithms for uniform matrix product states

NASA Astrophysics Data System (ADS)

Zauner-Stauber, V.; Vanderstraeten, L.; Fishman, M. T.; Verstraete, F.; Haegeman, J.

2018-01-01

We combine the density matrix renormalization group (DMRG) with matrix product state tangent space concepts to construct a variational algorithm for finding ground states of one-dimensional quantum lattices in the thermodynamic limit. A careful comparison of this variational uniform matrix product state algorithm (VUMPS) with infinite density matrix renormalization group (IDMRG) and with infinite time evolving block decimation (ITEBD) reveals substantial gains in convergence speed and precision. We also demonstrate that VUMPS works very efficiently for Hamiltonians with long-range interactions and also for the simulation of two-dimensional models on infinite cylinders. The new algorithm can be conveniently implemented as an extension of an already existing DMRG implementation.

Organic Light Emitting Devices and Materials Integrated with Active Matrix Backplanes for Flexible Displays

DTIC Science & Technology

2006-11-01

fabricated. Of the molecules, the fac- Ir(dfppy)(dfppz)2 compound had the blue-est emission with the highest quantum efficiency . Phosphorescent...phosphorescent lifetimes, high quantum efficiencies and good stability. The emission color can be readily tuned from blue/green to red by judicious... electroluminescent efficiency as a function of current density plotted against the luminance. Fig. 3 Illustration of an

A parallel computer implementation of fast low-rank QR approximation of the Biot-Savart law

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

White, D A; Fasenfest, B J; Stowell, M L

2005-11-07

In this paper we present a low-rank QR method for evaluating the discrete Biot-Savart law on parallel computers. It is assumed that the known current density and the unknown magnetic field are both expressed in a finite element expansion, and we wish to compute the degrees-of-freedom (DOF) in the basis function expansion of the magnetic field. The matrix that maps the current DOF to the field DOF is full, but if the spatial domain is properly partitioned the matrix can be written as a block matrix, with blocks representing distant interactions being low rank and having a compressed QR representation.more » The matrix partitioning is determined by the number of processors, the rank of each block (i.e. the compression) is determined by the specific geometry and is computed dynamically. In this paper we provide the algorithmic details and present computational results for large-scale computations.« less

Tailoring of physical properties in highly filled experimental nanohybrid resin composites.

PubMed

Pick, Bárbara; Pelka, Matthias; Belli, Renan; Braga, Roberto R; Lohbauer, Ulrich

2011-07-01

To assess the elastic modulus (EM), volumetric shrinkage (VS), and polymerization shrinkage stress (PSS) of experimental highly filled nanohybrid composites as a function of matrix composition, filler distribution, and density. One regular viscosity nanohybrid composite (Grandio, VOCO, Germany) and one flowable nanohybrid composite (Grandio Flow, VOCO) were tested as references along with six highly filled experimental nanohybrid composites (four Bis-GMA-based, one UDMA-based, and one Ormocer®-based). The experimental composites varied in filler size and density. EM values were obtained from the "three-point bending" load-displacement curve. VS was calculated with Archimedes' buoyancy principle. PSS was determined in 1-mm thick specimens placed between two (poly)methyl methacrylate rods (Ø=6mm) attached to an universal testing machine. Data were analyzed using oneway ANOVA, Tukey's test (α=0.05), and linear regression analyses. The flowable composite exhibited the highest VS and PSS but lowest EM. The PSS was significantly lower with Ormocer. The EM was significantly higher among experimental composites with highest filler levels. No significant differences were found between all other experimental composites regarding VS and PSS. Filler density and size did not influence EM, VS, or PSS. Neither the filler configuration nor matrix composition in the investigated materials significantly influenced composite shrinkage and mechanical properties. The highest filled experimental composite seemed to increase EM by keeping VS and PSS low; however, matrix composition seemed to be the determinant factor for shrinkage and stress development. The Ormocer, with reduced PSS, deserves further investigation. Filler size and density did not influence the tested parameters. Copyright © 2011 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Liquid-gas phase transitions and C K symmetry in quantum field theories

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

Nishimura, Hiromichi; Ogilvie, Michael C.; Pangeni, Kamal

A general field-theoretic framework for the treatment of liquid-gas phase transitions is developed. Starting from a fundamental four-dimensional field theory at nonzero temperature and density, an effective three-dimensional field theory is derived. The effective field theory has a sign problem at finite density. Although finite density explicitly breaks charge conjugation C , there remains a symmetry under C K , where K is complex conjugation. Here, we consider four models: relativistic fermions, nonrelativistic fermions, static fermions and classical particles. The interactions are via an attractive potential due to scalar field exchange and a repulsive potential due to massive vector exchange.more » The field-theoretic representation of the partition function is closely related to the equivalence of the sine-Gordon field theory with a classical gas. The thermodynamic behavior is extracted from C K -symmetric complex saddle points of the effective field theory at tree level. In the cases of nonrelativistic fermions and classical particles, we find complex saddle point solutions but no first-order transitions, and neither model has a ground state at tree level. The relativistic and static fermions show a liquid-gas transition at tree level in the effective field theory. The liquid-gas transition, when it occurs, manifests as a first-order line at low temperature and high density, terminated by a critical end point. The mass matrix controlling the behavior of correlation functions is obtained from fluctuations around the saddle points. Due to the C K symmetry of the models, the eigenvalues of the mass matrix are not always real but can be complex. This then leads to the existence of disorder lines, which mark the boundaries where the eigenvalues go from purely real to complex. The regions where the mass matrix eigenvalues are complex are associated with the critical line. In the case of static fermions, a powerful duality between particles and holes allows for the analytic determination of both the critical line and the disorder lines. Depending on the values of the parameters, either zero, one, or two disorder lines are found. Our numerical results for relativistic fermions give a very similar picture.« less

Liquid-gas phase transitions and C K symmetry in quantum field theories

DOE PAGES

Nishimura, Hiromichi; Ogilvie, Michael C.; Pangeni, Kamal

2017-04-04

A general field-theoretic framework for the treatment of liquid-gas phase transitions is developed. Starting from a fundamental four-dimensional field theory at nonzero temperature and density, an effective three-dimensional field theory is derived. The effective field theory has a sign problem at finite density. Although finite density explicitly breaks charge conjugation C , there remains a symmetry under C K , where K is complex conjugation. Here, we consider four models: relativistic fermions, nonrelativistic fermions, static fermions and classical particles. The interactions are via an attractive potential due to scalar field exchange and a repulsive potential due to massive vector exchange.more » The field-theoretic representation of the partition function is closely related to the equivalence of the sine-Gordon field theory with a classical gas. The thermodynamic behavior is extracted from C K -symmetric complex saddle points of the effective field theory at tree level. In the cases of nonrelativistic fermions and classical particles, we find complex saddle point solutions but no first-order transitions, and neither model has a ground state at tree level. The relativistic and static fermions show a liquid-gas transition at tree level in the effective field theory. The liquid-gas transition, when it occurs, manifests as a first-order line at low temperature and high density, terminated by a critical end point. The mass matrix controlling the behavior of correlation functions is obtained from fluctuations around the saddle points. Due to the C K symmetry of the models, the eigenvalues of the mass matrix are not always real but can be complex. This then leads to the existence of disorder lines, which mark the boundaries where the eigenvalues go from purely real to complex. The regions where the mass matrix eigenvalues are complex are associated with the critical line. In the case of static fermions, a powerful duality between particles and holes allows for the analytic determination of both the critical line and the disorder lines. Depending on the values of the parameters, either zero, one, or two disorder lines are found. Our numerical results for relativistic fermions give a very similar picture.« less

Flavin Charge Transfer Transitions Assist DNA Photolyase Electron Transfer

NASA Astrophysics Data System (ADS)

Skourtis, Spiros S.; Prytkova, Tatiana; Beratan, David N.

2007-12-01

This contribution describes molecular dynamics, semi-empirical and ab-initio studies of the primary photo-induced electron transfer reaction in DNA photolyase. DNA photolyases are FADH--containing proteins that repair UV-damaged DNA by photo-induced electron transfer. A DNA photolyase recognizes and binds to cyclobutatne pyrimidine dimer lesions of DNA. The protein repairs a bound lesion by transferring an electron to the lesion from FADH-, upon photo-excitation of FADH- with 350-450 nm light. We compute the lowest singlet excited states of FADH- in DNA photolyase using INDO/S configuration interaction, time-dependent density-functional, and time-dependent Hartree-Fock methods. The calculations identify the lowest singlet excited state of FADH- that is populated after photo-excitation and that acts as the electron donor. For this donor state we compute conformationally-averaged tunneling matrix elements to empty electron-acceptor states of a thymine dimer bound to photolyase. The conformational averaging involves different FADH--thymine dimer confromations obtained from molecular dynamics simulations of the solvated protein with a thymine dimer docked in its active site. The tunneling matrix element computations use INDO/S-level Green's function, energy splitting, and Generalized Mulliken-Hush methods. These calculations indicate that photo-excitation of FADH- causes a π→π* charge-transfer transition that shifts electron density to the side of the flavin isoalloxazine ring that is adjacent to the docked thymine dimer. This shift in electron density enhances the FADH--to-dimer electronic coupling, thus inducing rapid electron transfer.

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

Bezák, Viktor, E-mail: bezak@fmph.uniba.sk

Quantum theory of the non-harmonic oscillator defined by the energy operator proposed by Yurke and Buks (2006) is presented. Although these authors considered a specific problem related to a model of transmission lines in a Kerr medium, our ambition is not to discuss the physical substantiation of their model. Instead, we consider the problem from an abstract, logically deductive, viewpoint. Using the Yurke–Buks energy operator, we focus attention on the imaginary-time propagator. We derive it as a functional of the Mehler kernel and, alternatively, as an exact series involving Hermite polynomials. For a statistical ensemble of identical oscillators defined bymore » the Yurke–Buks energy operator, we calculate the partition function, average energy, free energy and entropy. Using the diagonal element of the canonical density matrix of this ensemble in the coordinate representation, we define a probability density, which appears to be a deformed Gaussian distribution. A peculiarity of this probability density is that it may reveal, when plotted as a function of the position variable, a shape with two peaks located symmetrically with respect to the central point.« less

A Sparse Self-Consistent Field Algorithm and Its Parallel Implementation: Application to Density-Functional-Based Tight Binding.

PubMed

Scemama, Anthony; Renon, Nicolas; Rapacioli, Mathias

2014-06-10

We present an algorithm and its parallel implementation for solving a self-consistent problem as encountered in Hartree-Fock or density functional theory. The algorithm takes advantage of the sparsity of matrices through the use of local molecular orbitals. The implementation allows one to exploit efficiently modern symmetric multiprocessing (SMP) computer architectures. As a first application, the algorithm is used within the density-functional-based tight binding method, for which most of the computational time is spent in the linear algebra routines (diagonalization of the Fock/Kohn-Sham matrix). We show that with this algorithm (i) single point calculations on very large systems (millions of atoms) can be performed on large SMP machines, (ii) calculations involving intermediate size systems (1000-100 000 atoms) are also strongly accelerated and can run efficiently on standard servers, and (iii) the error on the total energy due to the use of a cutoff in the molecular orbital coefficients can be controlled such that it remains smaller than the SCF convergence criterion.

Periodic orbit spectrum in terms of Ruelle-Pollicott resonances

NASA Astrophysics Data System (ADS)

Leboeuf, P.

2004-02-01

Fully chaotic Hamiltonian systems possess an infinite number of classical solutions which are periodic, e.g., a trajectory “p” returns to its initial conditions after some fixed time τp. Our aim is to investigate the spectrum {τ1,τ2,…} of periods of the periodic orbits. An explicit formula for the density ρ(τ)=∑pδ(τ-τp) is derived in terms of the eigenvalues of the classical evolution operator. The density is naturally decomposed into a smooth part plus an interferent sum over oscillatory terms. The frequencies of the oscillatory terms are given by the imaginary part of the complex eigenvalues (Ruelle-Pollicott resonances). For large periods, corrections to the well-known exponential growth of the smooth part of the density are obtained. An alternative formula for ρ(τ) in terms of the zeros and poles of the Ruelle ζ function is also discussed. The results are illustrated with the geodesic motion in billiards of constant negative curvature. Connections with the statistical properties of the corresponding quantum eigenvalues, random-matrix theory, and discrete maps are also considered. In particular, a random-matrix conjecture is proposed for the eigenvalues of the classical evolution operator of chaotic billiards.

Multipolar Ewald methods, 1: theory, accuracy, and performance.

PubMed

Giese, Timothy J; Panteva, Maria T; Chen, Haoyuan; York, Darrin M

2015-02-10

The Ewald, Particle Mesh Ewald (PME), and Fast Fourier–Poisson (FFP) methods are developed for systems composed of spherical multipole moment expansions. A unified set of equations is derived that takes advantage of a spherical tensor gradient operator formalism in both real space and reciprocal space to allow extension to arbitrary multipole order. The implementation of these methods into a novel linear-scaling modified “divide-and-conquer” (mDC) quantum mechanical force field is discussed. The evaluation times and relative force errors are compared between the three methods, as a function of multipole expansion order. Timings and errors are also compared within the context of the quantum mechanical force field, which encounters primary errors related to the quality of reproducing electrostatic forces for a given density matrix and secondary errors resulting from the propagation of the approximate electrostatics into the self-consistent field procedure, which yields a converged, variational, but nonetheless approximate density matrix. Condensed-phase simulations of an mDC water model are performed with the multipolar PME method and compared to an electrostatic cutoff method, which is shown to artificially increase the density of water and heat of vaporization relative to full electrostatic treatment.

Pairing of one-dimensional Bose-Fermi mixtures with unequal masses

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

Rizzi, Matteo; Max Planck Institut fuer QuantenOptik, Hans Kopfermann Strasse 1, D-85748 Garching; Imambekov, Adilet

We have considered one-dimensional Bose-Fermi mixture with equal densities and unequal masses using numerical density matrix renormalization group. For the mass ratio of K-Rb mixture and attraction between bosons and fermions, we determined the phase diagram. For weak boson-boson interactions, there is a direct transition between two-component Luttinger liquid and collapsed phases as the boson-fermion attraction is increased. For strong enough boson-boson interactions, we find an intermediate 'paired' phase, which is a single-component Luttinger liquid of composite particles. We investigated correlation functions of such a 'paired' phase, studied the stability of 'paired' phase to density imbalance, and discussed various experimentalmore » techniques which can be used to detect it.« less

Polymer-mediated tunneling transport between carbon nanotubes in nanocomposites.

PubMed

Derosa, Pedro A; Michalak, Tyler

2014-05-01

Electron transport in nanocomposites has attracted a good deal of attention for some time now; furthermore, the ability to control its characteristics is a necessary step in the design of multifunctional materials. When conductive nanostructures (for example carbon nanotubes) are inserted in a non-conductive matrix, electron transport below the percolation threshold is dominated by tunneling and thus the conductive characteristics of the composite depends heavily on the characteristics of the tunneling currents between nanoinserts. A parameter-free approach to study tunneling transport between carbon nanotubes across a polymer matrix is presented. The calculation is done with a combination of Density Functional Theory and Green functions (an approach heavily used in molecular electronics) which is shown here to be effective in this non-resonant transport condition. The results show that the method can effectively capture the effect of a dielectric layer in tunneling transport. The current is found to exponentially decrease with the size of the gap for both vacuum and polymer, and that the polymer layer lowers the tunneling barrier enhancing tunneling conduction. For a polyacrylonitrile matrix, a four-fold decrease in the tunneling constant, compared to tunneling in vacuum, is observed, a result that is consistent with available information. The method is very versatile as any DFT functional (or any other quantum mechanics method) can be used and thus the most accurate method for each particular system can be chosen. Furthermore as more methods become available, the calculations can be revised and improved. This approach can be used to design functional materials for fine-tunning the tunneling transport, for instance, the effect of modifying the nanoinsert-matrix interface (for example, by adding functional groups to carbon nanotubes) can be captured and the comparative performance of each interface predicted by simulation.

Many-body expansion of the Fock matrix in the fragment molecular orbital method

NASA Astrophysics Data System (ADS)

Fedorov, Dmitri G.; Kitaura, Kazuo

2017-09-01

A many-body expansion of the Fock matrix in the fragment molecular orbital method is derived up to three-body terms for restricted Hartree-Fock and density functional theory in the atomic orbital basis and compared to the expansion in the basis of fragment molecular orbitals (MOs). The physical nature of many-body corrections is revealed in terms of charge transfer terms. An improvement of the fragment MO expansion is proposed by adding exchange to the embedding. The accuracy of all developed methods is demonstrated in comparison to unfragmented results for polyalanines, a water cluster, Trp-cage (PDB: 1L2Y) and crambin (PDB: 1CRN) proteins, a zeolite cluster, a Si nano-wire, and a boron nitride ribbon. The physical nature of metallicity is discussed, and it is shown what kinds of metallic systems can be treated by fragment-based methods. The density of states is calculated for a fully closed and a partially open nano-ring of boron nitride with a diameter of 105 nm.

Electrospun Carbon Nanofibers with in Situ Encapsulated Co₃O₄ Nanoparticles as Electrodes for High-Performance Supercapacitors.

PubMed

Abouali, Sara; Garakani, Mohammad Akbari; Zhang, Biao; Xu, Zheng-Long; Heidari, Elham Kamali; Huang, Jian-qiu; Huang, Jiaqiang; Kim, Jang-Kyo

2015-06-24

A facile electrospinning method with subsequent heat treatments is employed to prepare carbon nanofibers (CNFs) containing uniformly dispersed Co3O4 nanoparticles as electrodes for supercapacitors. The Co3O4/CNF electrodes with ∼68 wt % active particles deliver a remarkable capacitance of 586 F g(-1) at a current density of 1 A g(-1). When the current density is increased to 50 A g(-1), ∼66% of the original capacitance is retained. The electrodes also present excellent cyclic stability of 74% capacity retention after 2000 cycles at 2 A g(-1). These superior electrochemical properties are attributed to the uniform dispersion of active particles in the CNF matrix, which functions as a conductive support. The onionlike graphitic layers formed around the Co3O4 nanoparticles not only improve the electrical conductivity of the electrode but also prevent the separation of the nanoparticles from the carbon matrix.

Beyond the single-file fluid limit using transfer matrix method: Exact results for confined parallel hard squares

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

Gurin, Péter; Varga, Szabolcs

2015-06-14

We extend the transfer matrix method of one-dimensional hard core fluids placed between confining walls for that case where the particles can pass each other and at most two layers can form. We derive an eigenvalue equation for a quasi-one-dimensional system of hard squares confined between two parallel walls, where the pore width is between σ and 3σ (σ is the side length of the square). The exact equation of state and the nearest neighbor distribution functions show three different structures: a fluid phase with one layer, a fluid phase with two layers, and a solid-like structure where the fluidmore » layers are strongly correlated. The structural transition between differently ordered fluids develops continuously with increasing density, i.e., no thermodynamic phase transition occurs. The high density structure of the system consists of clusters with two layers which are broken with particles staying in the middle of the pore.« less

Low-density resin impregnated ceramic article and method for making the same

NASA Technical Reports Server (NTRS)

Tran, Huy K. (Inventor); Henline, William D. (Inventor); Hsu, Ming-ta S. (Inventor); Rasky, Daniel J. (Inventor); Riccitiello, Salvatore R. (Inventor)

1997-01-01

A low-density resin impregnated ceramic article advantageously employed as a structural ceramic ablator comprising a matrix of ceramic fibers. The fibers of the ceramic matrix are coated with an organic resin film. The organic resin can be a thermoplastic resin or a cured thermosetting resin. In one embodiment, the resin is uniformly distributed within the ceramic article. In a second embodiment, the resin is distributed so as to provide a density gradient along at least one direction of the ceramic article. The resin impregnated ceramic article is prepared by providing a matrix of ceramic fibers; immersing the matrix of ceramic fibers in a solution of a solvent and an organic resin infiltrant; and removing the solvent to form a resin film on the ceramic fibers.

Entanglement and magnetism in high-spin graphene nanodisks

NASA Astrophysics Data System (ADS)

Hagymási, I.; Legeza, Ö.

2018-01-01

We investigate the ground-state properties of triangular graphene nanoflakes with zigzag edge configurations. The description of zero-dimensional nanostructures requires accurate many-body techniques since the widely used density-functional theory with local density approximation or Hartree-Fock methods cannot handle the strong quantum fluctuations. Applying the unbiased density-matrix renormalization group algorithm we calculate the magnetization and entanglement patterns with high accuracy for different interaction strengths and compare them to the mean-field results. With the help of quantum information analysis and subsystem density matrices we reveal that the edges are strongly entangled with each other. We also address the effect of electron and hole doping and demonstrate that the magnetic properties of triangular nanoflakes can be controlled by an electric field, which reveals features of flat-band ferromagnetism. This may open up new avenues in graphene based spintronics.

Bone formation by three-dimensional stromal osteoblast culture in biodegradable polymer scaffolds

NASA Technical Reports Server (NTRS)

Ishaug, S. L.; Crane, G. M.; Miller, M. J.; Yasko, A. W.; Yaszemski, M. J.; Mikos, A. G.; McIntire, L. V. (Principal Investigator)

1997-01-01

Bone formation was investigated in vitro by culturing stromal osteoblasts in three-dimensional (3-D), biodegradable poly(DL-lactic-co-glycolic acid) foams. Three polymer foam pore sizes, ranging from 150-300, 300-500, and 500-710 microns, and two different cell seeding densities, 6.83 x 10(5) cells/cm2 and 22.1 x 10(5) cells/cm2, were examined over a 56-day culture period. The polymer foams supported the proliferation of seeded osteoblasts as well as their differentiated function, as demonstrated by high alkaline phosphatase activity and deposition of a mineralized matrix by the cells. Cell number, alkaline phosphatase activity, and mineral deposition increased significantly over time for all the polymer foams. Osteoblast foam constructs created by seeding 6.83 x 10(5) cells/cm2 on foams with 300-500 microns pores resulted in a cell density of 4.63 x 10(5) cells/cm2 after 1 day in culture; they had alkaline phosphatase activities of 4.28 x 10(-7) and 2.91 x 10(-6) mumol/cell/min on Days 7 and 28, respectively; and they had a cell density that increased to 18.7 x 10(5) cells/cm2 by Day 56. For the same constructs, the mineralized matrix reached a maximum penetration depth of 240 microns from the top surface of the foam and a value of 0.083 mm for mineralized tissue volume per unit of cross sectional area. Seeding density was an important parameter for the constructs, but pore size over the range tested did not affect cell proliferation or function. This study suggests the feasibility of using poly(alpha-hydroxy ester) foams as scaffolding materials for the transplantation of autogenous osteoblasts to regenerate bone tissue.

Development of a poly(dimethylacrylamide) based matrix material for solid phase high density peptide array synthesis employing a laser based material transfer

NASA Astrophysics Data System (ADS)

Ridder, Barbara; Foertsch, Tobias C.; Welle, Alexander; Mattes, Daniela S.; von Bojnicic-Kninski, Clemens M.; Loeffler, Felix F.; Nesterov-Mueller, Alexander; Meier, Michael A. R.; Breitling, Frank

2016-12-01

Poly(dimethylacrylamide) (PDMA) based matrix materials were developed for laser-based in situ solid phase peptide synthesis to produce high density arrays. In this specific array synthesis approach, amino acid derivatives are embedded into a matrix material, serving as a ;solid; solvent material at room temperature. Then, a laser pulse transfers this mixture to the target position on a synthesis slide, where the peptide array is synthesized. Upon heating above the glass transition temperature of the matrix material, it softens, allowing diffusion of the amino acid derivatives to the synthesis surface and serving as a solvent for peptide bond formation. Here, we synthesized PDMA six-arm star polymers, offering the desired matrix material properties, using atom transfer radical polymerization. With the synthesized polymers as matrix material, we structured and synthesized arrays with combinatorial laser transfer. With densities of up to 20,000 peptide spots per cm2, the resolution could be increased compared to the commercially available standard matrix material. Time-of-Flight Secondary Ion Mass Spectrometry experiments revealed the penetration behavior of an amino acid derivative into the prepared acceptor synthesis surface and the effectiveness of the washing protocols.

Decay of correlations between cross-polarized electromagnetic waves in a two-dimensional random medium.

PubMed

Gorodnichev, E E

2018-04-01

The problem of multiple scattering of polarized light in a two-dimensional medium composed of fiberlike inhomogeneities is studied. The attenuation lengths for the density matrix elements are calculated. For a highly absorbing medium it is found that, as the sample thickness increases, the intensity of waves polarized along the fibers decays faster than the other density matrix elements. With further increase in the sample thickness, the off-diagonal elements which are responsible for correlations between the cross-polarized waves disappear. In the asymptotic limit of very thick samples the scattered light proves to be polarized perpendicular to the fibers. The difference in the attenuation lengths between the density matrix elements results in a nonmonotonic depth dependence of the degree of polarization. In the opposite case of a weakly absorbing medium, the off-diagonal element of the density matrix and, correspondingly, the correlations between the cross-polarized fields are shown to decay faster than the intensity of waves polarized along and perpendicular to the fibers.

A Patch Density Recommendation based on Convergence Studies for Vehicle Panel Vibration Response resulting from Excitation by a Diffuse Acoustic Field

NASA Technical Reports Server (NTRS)

Smith, Andrew; LaVerde, Bruce; Jones, Douglas; Towner, Robert; Waldon, James; Hunt, Ron

2013-01-01

Producing fluid structural interaction estimates of panel vibration from an applied pressure field excitation are quite dependent on the spatial correlation of the pressure field. There is a danger of either over estimating a low frequency response or under predicting broad band panel response in the more modally dense bands if the pressure field spatial correlation is not accounted for adequately. It is a useful practice to simulate the spatial correlation of the applied pressure field over a 2d surface using a matrix of small patch area regions on a finite element model (FEM). Use of a fitted function for the spatial correlation between patch centers can result in an error if the choice of patch density is not fine enough to represent the more continuous spatial correlation function throughout the intended frequency range of interest. Several patch density assumptions to approximate the fitted spatial correlation function are first evaluated using both qualitative and quantitative illustrations. The actual response of a typical vehicle panel system FEM is then examined in a convergence study where the patch density assumptions are varied over the same model. The convergence study results illustrate the impacts possible from a poor choice of patch density on the analytical response estimate. The fitted correlation function used in this study represents a diffuse acoustic field (DAF) excitation of the panel to produce vibration response.

Interaction between a circular inclusion and an arbitrarily oriented crack

NASA Technical Reports Server (NTRS)

Erdogan, F.; Gupta, G. D.; Ratwani, M.

1975-01-01

The plane interaction problem for a circular elastic inclusion embedded in an elastic matrix which contains an arbitrarily oriented crack is considered. Using the existing solutions for the edge dislocations as Green's functions, first the general problem of a through crack in the form of an arbitrary smooth arc located in the matrix in the vicinity of the inclusion is formulated. The integral equations for the line crack are then obtained as a system of singular integral equations with simple Cauchy kernels. The singular behavior of the stresses around the crack tips is examined and the expressions for the stress-intensity factors representing the strength of the stress singularities are obtained in terms of the asymptotic values of the density functions of the integral equations. The problem is solved for various typical crack orientations and the corresponding stress-intensity factors are given.

Thermodynamics of fission products in UO(2 ± x).

PubMed

Nerikar, P V; Liu, X-Y; Uberuaga, B P; Stanek, C R; Phillpot, S R; Sinnott, S B

2009-10-28

The stabilities of selected fission products-Xe, Cs, and Sr-are investigated as a function of non-stoichiometry x in UO(2 ± x). In particular, density functional theory (DFT) is used to calculate the incorporation and solution energies of these fission products at the anion and cation vacancy sites, at the divacancy, and at the bound Schottky defect. In order to reproduce the correct insulating state of UO(2), the DFT calculations are performed using spin polarization and with the Hubbard U term. In general, higher charge defects are more soluble in the fuel matrix and the solubility of fission products increases as the hyperstoichiometry increases. The solubility of fission product oxides is also explored. Cs(2)O is observed as a second stable phase and SrO is found to be soluble in the UO(2) matrix for all stoichiometries. These observations mirror experimentally observed phenomena.

Modeling of Interfacial Modification Effects on Thermal Conductivity of Carbon Nanotube Composites

NASA Technical Reports Server (NTRS)

Clancy, Thomas C.; Gates, Thomas S.

2006-01-01

The effect of functionalization of carbon nanotubes on the thermal conductivity of nanocomposites has been studied using a multi-scale modeling approach. These results predict that grafting linear hydrocarbon chains to the surface of a single wall carbon nanotube with covalent chemical bonds should result in a significant increase in the thermal conductivity of these nanocomposites. This is due to the decrease in the interfacial thermal (Kapitza) resistance between the single wall carbon nanotube and the surrounding polymer matrix upon chemical functionalization. The nanocomposites studied here consist of single wall carbon nanotubes in a bulk poly(ethylene vinyl acetate) matrix. The nanotubes are functionalized by end-grafting linear hydrocarbon chains of varying length to the surface of the nanotube. The effect which this functionalization has on the interfacial thermal resistance is studied by molecular dynamics simulation. Interfacial thermal resistance values are calculated for a range of chemical grafting densities and with several chain lengths. These results are subsequently used in an analytical model to predict the resulting effect on the bulk thermal conductivity of the nanocomposite.

Effect of bidispersity in grafted chain length on grafted chain conformations and potential of mean force between polymer grafted nanoparticles in a homopolymer matrix.

PubMed

Nair, Nitish; Wentzel, Nathaniel; Jayaraman, Arthi

2011-05-21

In efforts to produce polymeric materials with tailored physical properties, significant interest has grown around the ability to control the spatial organization of nanoparticles in polymer nanocomposites. One way to achieve controlled particle arrangement is by grafting the nanoparticle surface with polymers that are compatible with the matrix, thus manipulating the interfacial interactions between the nanoparticles and the polymer matrix. Previous work has shown that the molecular weight of the grafted polymer, both at high grafting density and low grafting density, plays a key role in dictating the effective inter-particle interactions in a polymer matrix. At high grafting density nanoparticles disperse (aggregate) if the graft molecular weight is higher (lower) than the matrix molecular weight. At low grafting density the longer grafts can better shield the nanoparticle surface from direct particle-particle contacts than the shorter grafts and lead to the dispersion of the grafted particles in the matrix. Despite the importance of graft molecular weight, and evidence of non-trivial effects of polydispersity of chains grafted on flat surfaces, most theoretical work on polymer grafted nanoparticles has only focused on monodisperse grafted chains. In this paper, we focus on how bidispersity in grafted chain lengths affects the grafted chain conformations and inter-particle interactions in an implicit solvent and in a dense homopolymer polymer matrix. We first present the effects of bidispersity on grafted chain conformations in a single polymer grafted particle using purely Monte Carlo (MC) simulations. This is followed by calculations of the potential of mean force (PMF) between two grafted particles in a polymer matrix using a self-consistent Polymer Reference Interaction Site Model theory-Monte Carlo simulation approach. Monte Carlo simulations of a single polymer grafted particle in an implicit solvent show that in the bidisperse polymer grafted particles with an equal number of short and long grafts at low to medium grafting density, the short grafts are in a more coiled up conformation (lower radius of gyration) than their monodisperse counterparts to provide a larger free volume to the longer grafts so they can gain conformational entropy. The longer grafts do not show much difference in conformation from their monodisperse counterparts at low grafting density, but at medium grafting density the longer grafts exhibit less stretched conformations (lower radius of gyration) as compared to their monodisperse counterparts. In the presence of an explicit homopolymer matrix, the longer grafts are more compressed by the matrix homopolymer chains than the short grafts. We observe that the potential of mean force between bidisperse grafted particles has features of the PMF of monodisperse grafted particles with short grafts and monodisperse grafted particles with long grafts. The value of the PMF at contact is governed by the short grafts and values at large inter-particle distances are governed by the longer grafts. Further comparison of the PMF for bidisperse and monodisperse polymer grafted particles in a homopolymer matrix at varying parameters shows that the effects of matrix chain length, matrix packing fraction, grafting density, and particle curvature on the PMF between bidisperse polymer grafted particles are similar to those seen between monodisperse polymer grafted particles. © 2011 American Institute of Physics.

Infrared Spectroscopy of Matrix-Isolated Polycyclic Aromatic Nitrogen Heterocycles (PANHs)

NASA Technical Reports Server (NTRS)

Mattioda, A. L.; Hudgins, D. M.; Bauschlicher, C. W.; Allamandola, L. J.; Biemesderfer, C. D.; Rosi, M.

2002-01-01

The mid-infrared spectra of the nitrogen-containing heterocyclic polycyclic aromatic compounds 1-azabenz[a]-anthracene; 2-azabenz[a]anthracene; 1-azachrysene; 2-azachrysene; 4-azachrysene; 2-azapyrene, and 7,8 benzoquinoline in their neutral and cation forms were investigated. The spectra of these species isolated in an argon matrix have been measured. Band frequencies and intensities were tabulated and these data compared with spectra computed using density functional theory at the B3LYP level. The overall agreement between experiment and theory is quite good, in keeping with earlier results on homonuclear polycyclic aromatic hydrocarbons. The differences between the spectral properties of nitrogen bearing aromatics and non-substituted, neutral polycyclic aromatic hydrocarbons will be discussed.

The time-dependent density matrix renormalisation group method

NASA Astrophysics Data System (ADS)

Ma, Haibo; Luo, Zhen; Yao, Yao

2018-04-01

Substantial progress of the time-dependent density matrix renormalisation group (t-DMRG) method in the recent 15 years is reviewed in this paper. By integrating the time evolution with the sweep procedures in density matrix renormalisation group (DMRG), t-DMRG provides an efficient tool for real-time simulations of the quantum dynamics for one-dimensional (1D) or quasi-1D strongly correlated systems with a large number of degrees of freedom. In the illustrative applications, the t-DMRG approach is applied to investigate the nonadiabatic processes in realistic chemical systems, including exciton dissociation and triplet fission in polymers and molecular aggregates as well as internal conversion in pyrazine molecule.

Petrophysical analysis of geophysical logs of the National Drilling Company-U.S. Geological Survey ground-water research project for Abu Dhabi Emirate, United Arab Emirates

USGS Publications Warehouse

Jorgensen, Donald G.; Petricola, Mario

1994-01-01

A program of borehole-geophysical logging was implemented to supply geologic and geohydrologic information for a regional ground-water investigation of Abu Dhabi Emirate. Analysis of geophysical logs was essential to provide information on geohydrologic properties because drill cuttings were not always adequate to define lithologic boundaries. The standard suite of logs obtained at most project test holes consisted of caliper, spontaneous potential, gamma ray, dual induction, microresistivity, compensated neutron, compensated density, and compensated sonic. Ophiolitic detritus from the nearby Oman Mountains has unusual petrophysical properties that complicated the interpretation of geophysical logs. The density of coarse ophiolitic detritus is typically greater than 3.0 grams per cubic centimeter, porosity values are large, often exceeding 45 percent, and the clay fraction included unusual clays, such as lizardite. Neither the spontaneous-potential log nor the natural gamma-ray log were useable clay indicators. Because intrinsic permeability is a function of clay content, additional research in determining clay content was critical. A research program of geophysical logging was conducted to determine the petrophysical properties of the shallow subsurface formations. The logging included spectral-gamma and thermal-decay-time logs. These logs, along with the standard geophysical logs, were correlated to mineralogy and whole-rock chemistry as determined from sidewall cores. Thus, interpretation of lithology and fluids was accomplished. Permeability and specific yield were calculated from geophysical-log data and correlated to results from an aquifer test. On the basis of results from the research logging, a method of lithologic and water-resistivity interpretation was developed for the test holes at which the standard suite of logs were obtained. In addition, a computer program was developed to assist in the analysis of log data. Geohydrologic properties were estimated, including volume of clay matrix, volume of matrix other than clay, density of matrix other than clay, density of matrix, intrinsic permeability, specific yield, and specific storage. Geophysical logs were used to (1) determine lithology, (2) correlate lithologic and permeable zones, (3) calibrate seismic reprocessing, (4) calibrate transient-electromagnetic surveys, and (5) calibrate uphole-survey interpretations. Logs were used at the drill site to (1) determine permeability zones, (2) determine dissolved-solids content, which is a function of water resistivity, and (3) design wells accordingly. Data and properties derived from logs were used to determine transmissivity and specific yield of aquifer materials.

Ising antiferromagnet on a finite triangular lattice with free boundary conditions

NASA Astrophysics Data System (ADS)

Kim, Seung-Yeon

2015-11-01

The exact integer values for the density of states of the Ising model on an equilateral triangular lattice with free boundary conditions are evaluated up to L = 24 spins on a side for the first time by using the microcanonical transfer matrix. The total number of states is 2 N s = 2300 ≈ 2.037 × 1090 for L = 24, where N s = L( L+1)/2 is the number of spins. Classifying all 2300 spin states according to their energy values is an enormous work. From the density of states, the exact partition function zeros in the complex temperature plane of the triangular-lattice Ising model are evaluated. Using the density of states and the partition function zeros, we investigate the properties of the triangularlattice Ising antiferromagnet. The scaling behavior of the ground-state entropy and the form of the correlation length at T = 0 are studied for the triangular-lattice Ising antiferromagnet with free boundary conditions. Also, the scaling behavior of the Fisher edge singularity is investigated.

Experiment and density functional theory analyses of GdTaO4 single crystal

NASA Astrophysics Data System (ADS)

Ding, Shoujun; Kinross, Ashlie; Wang, Xiaofei; Yang, Huajun; Zhang, Qingli; Liu, Wenpeng; Sun, Dunlu

2018-05-01

GdTaO4 is a type of excellent materials that can be used as scintillation, laser matrix as well as self-activated phosphor has generated significant interest. Whereas its band structure, electronic structure and optical properties are still need elucidation. To solve this intriguing problem, high-quality GdTaO4 single crystal (M-type) was grown successfully using Czochralski method. Its structure as well as optical properties was determined in experiment. Moreover, a systematic theoretical calculation based on the density function theory methods were performed on M-type and M‧-type GdTaO4 and their band structure, density of state as well as optical properties were obtained. Combine with the performed experiment results, the calculated results were proved with high reliability. Hence, the calculated results obtained in this work could provide a deep understanding of GdTaO4 material, which also useful for the further investigation on GdTaO4 material.

Atomic Cholesky decompositions: a route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency.

PubMed

Aquilante, Francesco; Gagliardi, Laura; Pedersen, Thomas Bondo; Lindh, Roland

2009-04-21

Cholesky decomposition of the atomic two-electron integral matrix has recently been proposed as a procedure for automated generation of auxiliary basis sets for the density fitting approximation [F. Aquilante et al., J. Chem. Phys. 127, 114107 (2007)]. In order to increase computational performance while maintaining accuracy, we propose here to reduce the number of primitive Gaussian functions of the contracted auxiliary basis functions by means of a second Cholesky decomposition. Test calculations show that this procedure is most beneficial in conjunction with highly contracted atomic orbital basis sets such as atomic natural orbitals, and that the error resulting from the second decomposition is negligible. We also demonstrate theoretically as well as computationally that the locality of the fitting coefficients can be controlled by means of the decomposition threshold even with the long-ranged Coulomb metric. Cholesky decomposition-based auxiliary basis sets are thus ideally suited for local density fitting approximations.

Atomic Cholesky decompositions: A route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency

NASA Astrophysics Data System (ADS)

Aquilante, Francesco; Gagliardi, Laura; Pedersen, Thomas Bondo; Lindh, Roland

2009-04-01

Cholesky decomposition of the atomic two-electron integral matrix has recently been proposed as a procedure for automated generation of auxiliary basis sets for the density fitting approximation [F. Aquilante et al., J. Chem. Phys. 127, 114107 (2007)]. In order to increase computational performance while maintaining accuracy, we propose here to reduce the number of primitive Gaussian functions of the contracted auxiliary basis functions by means of a second Cholesky decomposition. Test calculations show that this procedure is most beneficial in conjunction with highly contracted atomic orbital basis sets such as atomic natural orbitals, and that the error resulting from the second decomposition is negligible. We also demonstrate theoretically as well as computationally that the locality of the fitting coefficients can be controlled by means of the decomposition threshold even with the long-ranged Coulomb metric. Cholesky decomposition-based auxiliary basis sets are thus ideally suited for local density fitting approximations.

Fragment approach to constrained density functional theory calculations using Daubechies wavelets

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

Ratcliff, Laura E.; Genovese, Luigi; Mohr, Stephan

2015-06-21

In a recent paper, we presented a linear scaling Kohn-Sham density functional theory (DFT) code based on Daubechies wavelets, where a minimal set of localized support functions are optimized in situ and therefore adapted to the chemical properties of the molecular system. Thanks to the systematically controllable accuracy of the underlying basis set, this approach is able to provide an optimal contracted basis for a given system: accuracies for ground state energies and atomic forces are of the same quality as an uncontracted, cubic scaling approach. This basis set offers, by construction, a natural subset where the density matrix ofmore » the system can be projected. In this paper, we demonstrate the flexibility of this minimal basis formalism in providing a basis set that can be reused as-is, i.e., without reoptimization, for charge-constrained DFT calculations within a fragment approach. Support functions, represented in the underlying wavelet grid, of the template fragments are roto-translated with high numerical precision to the required positions and used as projectors for the charge weight function. We demonstrate the interest of this approach to express highly precise and efficient calculations for preparing diabatic states and for the computational setup of systems in complex environments.« less

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

Pratap, Surender; Sarkar, Niladri, E-mail: niladri@pilani.bits-pilani.ac.in

Self-Consistent Quantum Method using Schrodinger-Poisson equations have been used for determining the Channel electron density of Nano-Scale MOSFETs for 6nm and 9nm thick channels. The 6nm thick MOSFET show the peak of the electron density at the middle where as the 9nm thick MOSFET shows the accumulation of the electrons at the oxide/semiconductor interface. The electron density in the channel is obtained from the diagonal elements of the density matrix; [ρ]=[1/(1+exp(β(H − μ)))] A Tridiagonal Hamiltonian Matrix [H] is constructed for the oxide/channel/oxide 1D structure for the dual gate MOSFET. This structure is discretized and Finite-Difference method is used formore » constructing the matrix equation. The comparison of these results which are obtained by Quantum methods are done with Semi-Classical methods.« less

Simple expression for the quantum Fisher information matrix

NASA Astrophysics Data System (ADS)

Šafránek, Dominik

2018-04-01

Quantum Fisher information matrix (QFIM) is a cornerstone of modern quantum metrology and quantum information geometry. Apart from optimal estimation, it finds applications in description of quantum speed limits, quantum criticality, quantum phase transitions, coherence, entanglement, and irreversibility. We derive a surprisingly simple formula for this quantity, which, unlike previously known general expression, does not require diagonalization of the density matrix, and is provably at least as efficient. With a minor modification, this formula can be used to compute QFIM for any finite-dimensional density matrix. Because of its simplicity, it could also shed more light on the quantum information geometry in general.

Anomalous dynamics of intruders in a crowded environment of mobile obstacles

PubMed Central

Sentjabrskaja, Tatjana; Zaccarelli, Emanuela; De Michele, Cristiano; Sciortino, Francesco; Tartaglia, Piero; Voigtmann, Thomas; Egelhaaf, Stefan U.; Laurati, Marco

2016-01-01

Many natural and industrial processes rely on constrained transport, such as proteins moving through cells, particles confined in nanocomposite materials or gels, individuals in highly dense collectives and vehicular traffic conditions. These are examples of motion through crowded environments, in which the host matrix may retain some glass-like dynamics. Here we investigate constrained transport in a colloidal model system, in which dilute small spheres move in a slowly rearranging, glassy matrix of large spheres. Using confocal differential dynamic microscopy and simulations, here we discover a critical size asymmetry, at which anomalous collective transport of the small particles appears, manifested as a logarithmic decay of the density autocorrelation functions. We demonstrate that the matrix mobility is central for the observed anomalous behaviour. These results, crucially depending on size-induced dynamic asymmetry, are of relevance for a wide range of phenomena ranging from glassy systems to cell biology. PMID:27041068

Cytoskeletal filament assembly and the control of cell spreading and function by extracellular matrix

NASA Technical Reports Server (NTRS)

Mooney, D. J.; Langer, R.; Ingber, D. E.

1995-01-01

This study was undertaken to analyze how cell binding to extracellular matrix produces changes in cell shape. We focused on the initial process of cell spreading that follows cell attachment to matrix and, thus, cell 'shape' changes are defined here in terms of alterations in projected cell areas, as determined by computerized image analysis. Cell spreading kinetics and changes in microtubule and actin microfilament mass were simultaneously quantitated in hepatocytes plated on different extracellular matrix substrata. The initial rate of cell spreading was highly dependent on the matrix coating density and decreased from 740 microns 2/h to 50 microns 2/h as the coating density was lowered from 1000 to 1 ng/cm2. At approximately 4 to 6 hours after plating, this initial rapid spreading rate slowed and became independent of the matrix density regardless of whether laminin, fibronectin, type I collagen or type IV collagen was used for cell attachment. Analysis of F-actin mass revealed that cell adhesion to extracellular matrix resulted in a 20-fold increase in polymerized actin within 30 minutes after plating, before any significant change in cell shape was observed. This was followed by a phase of actin microfilament disassembly which correlated with the most rapid phase of cell extension and ended at about 6 hours; F-actin mass remained relatively constant during the slow matrix-independent spreading phase. Microtubule mass increased more slowly in spreading cells, peaking at 4 hours, the time at which the transition between rapid and slow spreading rates was observed. However, inhibition of this early rise in microtubule mass using either nocodazole or cycloheximide did not prevent this transition. Use of cytochalasin D revealed that microfilament integrity was absolutely required for hepatocyte spreading whereas interference with microtubule assembly (using nocodazole or taxol) or protein synthesis (using cycloheximide) only partially suppressed cell extension. In contrast, cell spreading could be completely inhibited by combining suboptimal doses of cytochalasin D and nocodazole, suggesting that intact microtubules can stabilize cell form when the microfilament lattice is partially compromised. The physiological relevance of the cytoskeleton and cell shape in hepatocyte physiology was highlighted by the finding that a short exposure (6 hour) of cells to nocodazole resulted in production of smaller cells 42 hours later that exhibited enhanced production of a liver-specific product (albumin). These data demonstrate that spreading and flattening of the entire cell body is not driven directly by net polymerization of either microfilaments or microtubules.(ABSTRACT TRUNCATED AT 400 WORDS).

Processing and properties of SiC whisker reinforced Si sub 3 N sub 4 ceramic matrix composites

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

Nunn, S.D.

1991-01-01

Silicon carbide whiskers reinforced silicon nitride ceramic matrix composites were pressureless sintered to high density by liquid phase sintering. Important processing parameters included: whisker dispersion by ultrasonic shear homogenization, particle refinement by attrition milling, pressure slip casting to obtain high greed densities, and sintering in a protective powder bed to limit decomposition. Composites with a {beta}20-Si{sub 3}N{sub 4} solid solution matrix containing 20 vol.% SiC whiskers were sintered to 98-100% theoretical density; composites having a Si{sub 3}N{sub 4} matrix containing YAG sintering aid were sintered to 98% of the theoretical density with 20 vol.% SiC whiskers, and 94% density withmore » 30 vol.% SiC whiskers. Analysis of the pressureless sintered composites revealed orientation of the SiC whiskers and the Si{sub 3}N{sub 4} matrix grains. The mechanical properties of hot pressed Si{sub 3}N{sub 4} composites reinforced with 20 vol.% SiC whiskers were shown to depend on the characteristics of the intergranular phase. Variations in the properties of the composites were analyzed in terms of the amount and morphology of the secondary phase, and the development of internal residual stresses due to the thermal expansion mismatch between the sintering aid phase at the grain boundaries.« less

Matrix product state representation of quasielectron wave functions

NASA Astrophysics Data System (ADS)

Kjäll, J.; Ardonne, E.; Dwivedi, V.; Hermanns, M.; Hansson, T. H.

2018-05-01

Matrix product state techniques provide a very efficient way to numerically evaluate certain classes of quantum Hall wave functions that can be written as correlators in two-dimensional conformal field theories. Important examples are the Laughlin and Moore-Read ground states and their quasihole excitations. In this paper, we extend the matrix product state techniques to evaluate quasielectron wave functions, a more complex task because the corresponding conformal field theory operator is not local. We use our method to obtain density profiles for states with multiple quasielectrons and quasiholes, and to calculate the (mutual) statistical phases of the excitations with high precision. The wave functions we study are subject to a known difficulty: the position of a quasielectron depends on the presence of other quasiparticles, even when their separation is large compared to the magnetic length. Quasielectron wave functions constructed using the composite fermion picture, which are topologically equivalent to the quasielectrons we study, have the same problem. This flaw is serious in that it gives wrong results for the statistical phases obtained by braiding distant quasiparticles. We analyze this problem in detail and show that it originates from an incomplete screening of the topological charges, which invalidates the plasma analogy. We demonstrate that this can be remedied in the case when the separation between the quasiparticles is large, which allows us to obtain the correct statistical phases. Finally, we propose that a modification of the Laughlin state, that allows for local quasielectron operators, should have good topological properties for arbitrary configurations of excitations.

Dynamical Epidemic Suppression Using Stochastic Prediction and Control

DTIC Science & Technology

2004-10-28

initial probability density function (PDF), p: D C R2 -- R, is defined by the stochastic Frobenius - Perron For deterministic systems, normal methods of...induced chaos. To analyze the qualitative change, we apply the technique of the stochastic Frobenius - Perron operator [L. Billings et al., Phys. Rev. Lett...transition matrix describing the probability of transport from one region of phase space to another, which approximates the stochastic Frobenius - Perron

Communication: Symmetrical quasi-classical analysis of linear optical spectroscopy

NASA Astrophysics Data System (ADS)

Provazza, Justin; Coker, David F.

2018-05-01

The symmetrical quasi-classical approach for propagation of a many degree of freedom density matrix is explored in the context of computing linear spectra. Calculations on a simple two state model for which exact results are available suggest that the approach gives a qualitative description of peak positions, relative amplitudes, and line broadening. Short time details in the computed dipole autocorrelation function result in exaggerated tails in the spectrum.

Computer simulation of the matrix-inclusion interphase in bulk metallic glass based nanocomposites

NASA Astrophysics Data System (ADS)

Kokotin, V.; Hermann, H.; Eckert, J.

2011-10-01

Atomistic models for matrix-inclusion systems are generated. Analyses of the systems show that interphase layers of finite thickness appear interlinking the surface of the nanocrystalline inclusion and the embedding amorphous matrix. In a first approximation, the interphase is characterized as an amorphous structure with a density slightly reduced compared to that of the matrix. This result holds for both monatomic hard sphere systems and a Cu47.5Zr47.5Al5 alloy simulated by molecular dynamics (MD). The elastic shear and bulk modulus of the interphase are calculated by simulated deformation of the MD systems. Both moduli diminish with decreasing density but the shear modulus is more sensitive against density reduction by one order of magnitude. This result explains recent observations of shear band initiation at the amorphous-crystalline interface during plastic deformation.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Unconventional field induced phases in a quantum magnet formed by free radical tetramers

NASA Astrophysics Data System (ADS)

Saúl, Andrés; Gauthier, Nicolas; Askari, Reza Moosavi; Côté, Michel; Maris, Thierry; Reber, Christian; Lannes, Anthony; Luneau, Dominique; Nicklas, Michael; Law, Joseph M.; Green, Elizabeth Lauren; Wosnitza, Jochen; Bianchi, Andrea Daniele; Feiguin, Adrian

2018-02-01

We report experimental and theoretical studies on the magnetic and thermodynamic properties of NIT-2Py, a free radical based organic magnet. From magnetization and specific-heat measurements we establish the temperature versus magnetic field phase diagram which includes two Bose-Einstein condensates (BEC) and an infrequent half-magnetization plateau. Calculations based on density functional theory demonstrate that magnetically this system can be mapped to a quasi-two-dimensional structure of weakly coupled tetramers. Density matrix renormalization group calculations show the unusual characteristics of the BECs where the spins forming the low-field condensate are different than those participating in the high-field one.

Simple Derivation of the Lindblad Equation

ERIC Educational Resources Information Center

Pearle, Philip

2012-01-01

The Lindblad equation is an evolution equation for the density matrix in quantum theory. It is the general linear, Markovian, form which ensures that the density matrix is Hermitian, trace 1, positive and completely positive. Some elementary examples of the Lindblad equation are given. The derivation of the Lindblad equation presented here is…

Resolution-of-identity stochastic time-dependent configuration interaction for dissipative electron dynamics in strong fields.

PubMed

Klinkusch, Stefan; Tremblay, Jean Christophe

2016-05-14

In this contribution, we introduce a method for simulating dissipative, ultrafast many-electron dynamics in intense laser fields. The method is based on the norm-conserving stochastic unraveling of the dissipative Liouville-von Neumann equation in its Lindblad form. The N-electron wave functions sampling the density matrix are represented in the basis of singly excited configuration state functions. The interaction with an external laser field is treated variationally and the response of the electronic density is included to all orders in this basis. The coupling to an external environment is included via relaxation operators inducing transition between the configuration state functions. Single electron ionization is represented by irreversible transition operators from the ionizing states to an auxiliary continuum state. The method finds its efficiency in the representation of the operators in the interaction picture, where the resolution-of-identity is used to reduce the size of the Hamiltonian eigenstate basis. The zeroth-order eigenstates can be obtained either at the configuration interaction singles level or from a time-dependent density functional theory reference calculation. The latter offers an alternative to explicitly time-dependent density functional theory which has the advantage of remaining strictly valid for strong field excitations while improving the description of the correlation as compared to configuration interaction singles. The method is tested on a well-characterized toy system, the excitation of the low-lying charge transfer state in LiCN.

Resolution-of-identity stochastic time-dependent configuration interaction for dissipative electron dynamics in strong fields

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

Klinkusch, Stefan; Tremblay, Jean Christophe

In this contribution, we introduce a method for simulating dissipative, ultrafast many-electron dynamics in intense laser fields. The method is based on the norm-conserving stochastic unraveling of the dissipative Liouville-von Neumann equation in its Lindblad form. The N-electron wave functions sampling the density matrix are represented in the basis of singly excited configuration state functions. The interaction with an external laser field is treated variationally and the response of the electronic density is included to all orders in this basis. The coupling to an external environment is included via relaxation operators inducing transition between the configuration state functions. Single electronmore » ionization is represented by irreversible transition operators from the ionizing states to an auxiliary continuum state. The method finds its efficiency in the representation of the operators in the interaction picture, where the resolution-of-identity is used to reduce the size of the Hamiltonian eigenstate basis. The zeroth-order eigenstates can be obtained either at the configuration interaction singles level or from a time-dependent density functional theory reference calculation. The latter offers an alternative to explicitly time-dependent density functional theory which has the advantage of remaining strictly valid for strong field excitations while improving the description of the correlation as compared to configuration interaction singles. The method is tested on a well-characterized toy system, the excitation of the low-lying charge transfer state in LiCN.« less

Uncertainty in dual permeability model parameters for structured soils.

PubMed

Arora, B; Mohanty, B P; McGuire, J T

2012-01-01

Successful application of dual permeability models (DPM) to predict contaminant transport is contingent upon measured or inversely estimated soil hydraulic and solute transport parameters. The difficulty in unique identification of parameters for the additional macropore- and matrix-macropore interface regions, and knowledge about requisite experimental data for DPM has not been resolved to date. Therefore, this study quantifies uncertainty in dual permeability model parameters of experimental soil columns with different macropore distributions (single macropore, and low- and high-density multiple macropores). Uncertainty evaluation is conducted using adaptive Markov chain Monte Carlo (AMCMC) and conventional Metropolis-Hastings (MH) algorithms while assuming 10 out of 17 parameters to be uncertain or random. Results indicate that AMCMC resolves parameter correlations and exhibits fast convergence for all DPM parameters while MH displays large posterior correlations for various parameters. This study demonstrates that the choice of parameter sampling algorithms is paramount in obtaining unique DPM parameters when information on covariance structure is lacking, or else additional information on parameter correlations must be supplied to resolve the problem of equifinality of DPM parameters. This study also highlights the placement and significance of matrix-macropore interface in flow experiments of soil columns with different macropore densities. Histograms for certain soil hydraulic parameters display tri-modal characteristics implying that macropores are drained first followed by the interface region and then by pores of the matrix domain in drainage experiments. Results indicate that hydraulic properties and behavior of the matrix-macropore interface is not only a function of saturated hydraulic conductivity of the macroporematrix interface ( K sa ) and macropore tortuosity ( l f ) but also of other parameters of the matrix and macropore domains.

Uncertainty in dual permeability model parameters for structured soils

NASA Astrophysics Data System (ADS)

Arora, B.; Mohanty, B. P.; McGuire, J. T.

2012-01-01

Successful application of dual permeability models (DPM) to predict contaminant transport is contingent upon measured or inversely estimated soil hydraulic and solute transport parameters. The difficulty in unique identification of parameters for the additional macropore- and matrix-macropore interface regions, and knowledge about requisite experimental data for DPM has not been resolved to date. Therefore, this study quantifies uncertainty in dual permeability model parameters of experimental soil columns with different macropore distributions (single macropore, and low- and high-density multiple macropores). Uncertainty evaluation is conducted using adaptive Markov chain Monte Carlo (AMCMC) and conventional Metropolis-Hastings (MH) algorithms while assuming 10 out of 17 parameters to be uncertain or random. Results indicate that AMCMC resolves parameter correlations and exhibits fast convergence for all DPM parameters while MH displays large posterior correlations for various parameters. This study demonstrates that the choice of parameter sampling algorithms is paramount in obtaining unique DPM parameters when information on covariance structure is lacking, or else additional information on parameter correlations must be supplied to resolve the problem of equifinality of DPM parameters. This study also highlights the placement and significance of matrix-macropore interface in flow experiments of soil columns with different macropore densities. Histograms for certain soil hydraulic parameters display tri-modal characteristics implying that macropores are drained first followed by the interface region and then by pores of the matrix domain in drainage experiments. Results indicate that hydraulic properties and behavior of the matrix-macropore interface is not only a function of saturated hydraulic conductivity of the macroporematrix interface (Ksa) and macropore tortuosity (lf) but also of other parameters of the matrix and macropore domains.

BinTree Seeking: A Novel Approach to Mine Both Bi-Sparse and Cohesive Modules in Protein Interaction Networks

PubMed Central

Shen, Hong-Bin

2011-01-01

Modern science of networks has brought significant advances to our understanding of complex systems biology. As a representative model of systems biology, Protein Interaction Networks (PINs) are characterized by a remarkable modular structures, reflecting functional associations between their components. Many methods were proposed to capture cohesive modules so that there is a higher density of edges within modules than those across them. Recent studies reveal that cohesively interacting modules of proteins is not a universal organizing principle in PINs, which has opened up new avenues for revisiting functional modules in PINs. In this paper, functional clusters in PINs are found to be able to form unorthodox structures defined as bi-sparse module. In contrast to the traditional cohesive module, the nodes in the bi-sparse module are sparsely connected internally and densely connected with other bi-sparse or cohesive modules. We present a novel protocol called the BinTree Seeking (BTS) for mining both bi-sparse and cohesive modules in PINs based on Edge Density of Module (EDM) and matrix theory. BTS detects modules by depicting links and nodes rather than nodes alone and its derivation procedure is totally performed on adjacency matrix of networks. The number of modules in a PIN can be automatically determined in the proposed BTS approach. BTS is tested on three real PINs and the results demonstrate that functional modules in PINs are not dominantly cohesive but can be sparse. BTS software and the supporting information are available at: www.csbio.sjtu.edu.cn/bioinf/BTS/. PMID:22140454

Breast cancer cell cyclooxygenase-2 expression alters extracellular matrix structure and function and numbers of cancer associated fibroblasts.

PubMed

Krishnamachary, Balaji; Stasinopoulos, Ioannis; Kakkad, Samata; Penet, Marie-France; Jacob, Desmond; Wildes, Flonne; Mironchik, Yelena; Pathak, Arvind P; Solaiyappan, Meiyappan; Bhujwalla, Zaver M

2017-03-14

Cyclooxygenase-2 (COX-2) is a critically important mediator of inflammation that significantly influences tumor angiogenesis, invasion, and metastasis. We investigated the role of COX-2 expressed by triple negative breast cancer cells in altering the structure and function of the extracellular matrix (ECM). COX-2 downregulation effects on ECM structure and function were investigated using magnetic resonance imaging (MRI) and second harmonic generation (SHG) microscopy of tumors derived from triple negative MDA-MB-231 breast cancer cells, and a derived clone stably expressing a short hairpin (shRNA) molecule downregulating COX-2. MRI of albumin-GdDTPA was used to characterize macromolecular fluid transport in vivo and SHG microscopy was used to quantify collagen 1 (Col1) fiber morphology. COX-2 downregulation decreased Col1 fiber density and altered macromolecular fluid transport. Immunohistochemistry identified significantly fewer activated cancer associated fibroblasts (CAFs) in low COX-2 expressing tumors. Metastatic lung nodules established by COX-2 downregulated cells were infrequent, smaller, and contained fewer Col1 fibers.COX-2 overexpression studies were performed with tumors derived from triple negative SUM-149 breast cancer cells lentivirally transduced to overexpress COX-2. SHG microscopy identified significantly higher Col1 fiber density in COX-2 overexpressing tumors with an increase of CAFs. These data expand upon the roles of COX-2 in shaping the structure and function of the ECM in primary and metastatic tumors, and identify the potential role of COX-2 in modifying the number of CAFs in tumors that may have contributed to the altered ECM.

Reelin, an extracellular matrix protein linked to early onset psychiatric diseases, drives postnatal development of the prefrontal cortex via GluN2B-NMDARs and the mTOR pathway

PubMed Central

Iafrati, J; Orejarena, M J; Lassalle, O; Bouamrane, L; Chavis, P

2014-01-01

Defective brain extracellular matrix (ECM) is a factor of vulnerability in various psychiatric diseases such as schizophrenia, depression and autism. The glycoprotein reelin is an essential building block of the brain ECM that modulates neuronal development and participates to the functions of adult central synapses. The reelin gene (RELN) is a strong candidate in psychiatric diseases of early onset, but its synaptic and behavioral functions in juvenile brain circuits remain unresolved. Here, we found that in juvenile reelin-haploinsufficient heterozygous reeler mice (HRM), abnormal fear memory erasure is concomitant to reduced dendritic spine density and anomalous long-term potentiation in the prefrontal cortex. In juvenile HRM, a single in vivo injection with ketamine or Ro25-6981 to inhibit GluN2B-N-methyl-𝒟-aspartate receptors (NMDARs) restored normal spine density, synaptic plasticity and converted fear memory to an erasure-resilient state typical of adult rodents. The functional and behavioral rescue by ketamine was prevented by rapamycin, an inhibitor of the mammalian target of rapamycin pathway. Finally, we show that fear memory erasure persists until adolescence in HRM and that a single exposure to ketamine during the juvenile period reinstates normal fear memory in adolescent mice. Our results show that reelin is essential for successful structural, functional and behavioral development of juvenile prefrontal circuits and that this developmental period provides a critical window for therapeutic rehabilitation with GluN2B-NMDAR antagonists. PMID:23752244

Exact steady state of a Kerr resonator with one- and two-photon driving and dissipation: Controllable Wigner-function multimodality and dissipative phase transitions

NASA Astrophysics Data System (ADS)

Bartolo, Nicola; Minganti, Fabrizio; Casteels, Wim; Ciuti, Cristiano

2016-09-01

We present exact results for the steady-state density matrix of a general class of driven-dissipative systems consisting of a nonlinear Kerr resonator in the presence of both coherent (one-photon) and parametric (two-photon) driving and dissipation. Thanks to the analytical solution, obtained via the complex P -representation formalism, we are able to explore any regime, including photon blockade, multiphoton resonant effects, and a mesoscopic regime with large photon density and quantum correlations. We show how the interplay between one- and two-photon driving provides a way to control the multimodality of the Wigner function in regimes where the semiclassical theory exhibits multistability. We also study the emergence of dissipative phase transitions in the thermodynamic limit of large photon numbers.

Truncated Calogero-Sutherland models

NASA Astrophysics Data System (ADS)

Pittman, S. M.; Beau, M.; Olshanii, M.; del Campo, A.

2017-05-01

A one-dimensional quantum many-body system consisting of particles confined in a harmonic potential and subject to finite-range two-body and three-body inverse-square interactions is introduced. The range of the interactions is set by truncation beyond a number of neighbors and can be tuned to interpolate between the Calogero-Sutherland model and a system with nearest and next-nearest neighbors interactions discussed by Jain and Khare. The model also includes the Tonks-Girardeau gas describing impenetrable bosons as well as an extension with truncated interactions. While the ground state wave function takes a truncated Bijl-Jastrow form, collective modes of the system are found in terms of multivariable symmetric polynomials. We numerically compute the density profile, one-body reduced density matrix, and momentum distribution of the ground state as a function of the range r and the interaction strength.

Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

NASA Astrophysics Data System (ADS)

Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.

2016-07-01

Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms.

PubMed

Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R

2016-07-07

Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

Validation and application of auxiliary density perturbation theory and non-iterative approximation to coupled-perturbed Kohn-Sham approach for calculation of dipole-quadrupole polarizability

NASA Astrophysics Data System (ADS)

Shedge, Sapana V.; Pal, Sourav; Köster, Andreas M.

2011-07-01

Recently, two non-iterative approaches have been proposed to calculate response properties within density functional theory (DFT). These approaches are auxiliary density perturbation theory (ADPT) and the non-iterative approach to the coupled-perturbed Kohn-Sham (NIA-CPKS) method. Though both methods are non-iterative, they use different techniques to obtain the perturbed Kohn-Sham matrix. In this Letter, for the first time, both of these two independent methods have been used for the calculation of dipole-quadrupole polarizabilities. To validate these methods, three tetrahedral molecules viz., P4,CH4 and adamantane (C10H16) have been used as examples. The comparison with MP2 and CCSD proves the reliability of the methodology.

Stress fluctuations in fracture networks from theoretical and numerical models

NASA Astrophysics Data System (ADS)

Davy, P.; Darcel, C.; Mas Ivars, D.; Le Goc, R.

2017-12-01

We analyze the spatial fluctuations of stress in a simple tridimensional model constituted by a population of disc-shaped fractures embedded in an elastic matrix with uniform and isotropic properties. The fluctuations arise from the classical stress enhancement at fracture tips and stress shadowing around fracture centers that are amplified or decreased by the interactions between close-by fractures. The distribution of local stresses is calculated at the elementary mesh scale with the 3DEC numerical program based on the distinct element method. As expected, the stress distributions vary with fracture density, the larger is the density, the wider is the distribution. For freely slipping fractures, it is mainly controlled by the percolation parameter p (i.e., the total volume of spheres surrounding fractures). For stresses smaller than the remote deviatoric stress, the distribution depends only on for the range of density that has been studied. For large stresses, the distribution decreases exponentially when increasing stress, with a characteristic stress that increases with entailing a widening of the stress distribution. We extend the analysis to fractures with plane resistance defined by an elastic shear stiffness ks and a slip Coulomb threshold. A consequence of the fracture plane resistance is to lower the stress perturbation in the surrounding matrix by a factor that depends on the ratio between ks and a fracture-matrix stiffness km mainly dependent on the ratio between Young modulus and fracture size. km is also the ratio between the remote shear stress and the displacement across the fracture plane in the case of freely slipping fractures. A complete analytical derivation of the expressions of the stress perturbations and of the fracture displacements is obtained and checked with numerical simulations. In the limit ks >> km, the stress perturbation tends to 0 and the stress state is spatially uniform. The analysis allows us to quantify the intensity of the stress fluctuations in fractured rocks as a function of both the fracture network characteristics (density and size distribution), and the mechanical properties (fracture shear stiffness vs matrix elastic properties).

A density functional theory study of the role of functionalized graphene particles as effective additives in power cable insulation

PubMed Central

Song, Shuwei; Zhao, Hong; Zheng, Xiaonan; Zhang, Hui; Wang, Ying; Han, Baozhong

2018-01-01

The role of a series of functionalized graphene additives in power cable insulation in suppressing the growth of electrical treeing and preventing the degradation of the polymer matrix has been investigated by density functional theory calculations. Bader charge analysis indicates that pristine, doped or defect graphene could effectively capture hot electrons to block their attack on cross-linked polyethylene (XLPE) because of the π–π conjugated unsaturated structures. Further exploration of the electronic properties in the interfacial region between the additives and XLPE shows that N-doped single-vacancy graphene, graphene oxide and B-, N-, Si- or P-doped graphene oxide have relatively strong physical interaction with XLPE to restrict its mobility and rather weak chemical activity to prevent the cleavage of the C–H or C–C bond, suggesting that they are all potential candidates as effective additives. The understanding of the features of functionalized graphene additives in trapping electrons and interfacial interaction will assist in the screening of promising additives as voltage stabilizers in power cables. PMID:29515821

A density functional theory study of the role of functionalized graphene particles as effective additives in power cable insulation.

PubMed

Song, Shuwei; Zhao, Hong; Zheng, Xiaonan; Zhang, Hui; Liu, Yang; Wang, Ying; Han, Baozhong

2018-02-01

The role of a series of functionalized graphene additives in power cable insulation in suppressing the growth of electrical treeing and preventing the degradation of the polymer matrix has been investigated by density functional theory calculations. Bader charge analysis indicates that pristine, doped or defect graphene could effectively capture hot electrons to block their attack on cross-linked polyethylene (XLPE) because of the π-π conjugated unsaturated structures. Further exploration of the electronic properties in the interfacial region between the additives and XLPE shows that N-doped single-vacancy graphene, graphene oxide and B-, N-, Si- or P-doped graphene oxide have relatively strong physical interaction with XLPE to restrict its mobility and rather weak chemical activity to prevent the cleavage of the C-H or C-C bond, suggesting that they are all potential candidates as effective additives. The understanding of the features of functionalized graphene additives in trapping electrons and interfacial interaction will assist in the screening of promising additives as voltage stabilizers in power cables.

Daubechies wavelets for linear scaling density functional theory.

PubMed

Mohr, Stephan; Ratcliff, Laura E; Boulanger, Paul; Genovese, Luigi; Caliste, Damien; Deutsch, Thierry; Goedecker, Stefan

2014-05-28

We demonstrate that Daubechies wavelets can be used to construct a minimal set of optimized localized adaptively contracted basis functions in which the Kohn-Sham orbitals can be represented with an arbitrarily high, controllable precision. Ground state energies and the forces acting on the ions can be calculated in this basis with the same accuracy as if they were calculated directly in a Daubechies wavelets basis, provided that the amplitude of these adaptively contracted basis functions is sufficiently small on the surface of the localization region, which is guaranteed by the optimization procedure described in this work. This approach reduces the computational costs of density functional theory calculations, and can be combined with sparse matrix algebra to obtain linear scaling with respect to the number of electrons in the system. Calculations on systems of 10,000 atoms or more thus become feasible in a systematic basis set with moderate computational resources. Further computational savings can be achieved by exploiting the similarity of the adaptively contracted basis functions for closely related environments, e.g., in geometry optimizations or combined calculations of neutral and charged systems.

Variational Two-Particle Density Matrix Calculation for the Hubbard Model Below Half Filling Using Spin-Adapted Lifting Conditions

NASA Astrophysics Data System (ADS)

Verstichel, Brecht; van Aggelen, Helen; Poelmans, Ward; Van Neck, Dimitri

2012-05-01

The variational determination of the two-particle density matrix is an interesting, but not yet fully explored technique that allows us to obtain ground-state properties of a quantum many-body system without reference to an N-particle wave function. The one-dimensional fermionic Hubbard model has been studied before with this method, using standard two- and three-index conditions on the density matrix [J. R. Hammond , Phys. Rev. A 73, 062505 (2006)PLRAAN1050-294710.1103/PhysRevA.73.062505], while a more recent study explored so-called subsystem constraints [N. Shenvi , Phys. Rev. Lett. 105, 213003 (2010)PRLTAO0031-900710.1103/PhysRevLett.105.213003]. These studies reported good results even with only standard two-index conditions, but have always been limited to the half-filled lattice. In this Letter, we establish the fact that the two-index approach fails for other fillings. In this case, a subset of three-index conditions is absolutely needed to describe the correct physics in the strong-repulsion limit. We show that applying lifting conditions [J. R. Hammond , Phys. Rev. APLRAAN1050-2947 71, 062503 (2005)10.1103/PhysRevA.71.062503] is the most economical way to achieve this, while still avoiding the computationally much heavier three-index conditions. A further extension to spin-adapted lifting conditions leads to increased accuracy in the intermediate repulsion regime. At the same time, we establish the feasibility of such studies to the more complicated phase diagram in two-dimensional Hubbard models.

Random pure states: Quantifying bipartite entanglement beyond the linear statistics.

PubMed

Vivo, Pierpaolo; Pato, Mauricio P; Oshanin, Gleb

2016-05-01

We analyze the properties of entangled random pure states of a quantum system partitioned into two smaller subsystems of dimensions N and M. Framing the problem in terms of random matrices with a fixed-trace constraint, we establish, for arbitrary N≤M, a general relation between the n-point densities and the cross moments of the eigenvalues of the reduced density matrix, i.e., the so-called Schmidt eigenvalues, and the analogous functionals of the eigenvalues of the Wishart-Laguerre ensemble of the random matrix theory. This allows us to derive explicit expressions for two-level densities, and also an exact expression for the variance of von Neumann entropy at finite N,M. Then, we focus on the moments E{K^{a}} of the Schmidt number K, the reciprocal of the purity. This is a random variable supported on [1,N], which quantifies the number of degrees of freedom effectively contributing to the entanglement. We derive a wealth of analytical results for E{K^{a}} for N=2 and 3 and arbitrary M, and also for square N=M systems by spotting for the latter a connection with the probability P(x_{min}^{GUE}≥sqrt[2N]ξ) that the smallest eigenvalue x_{min}^{GUE} of an N×N matrix belonging to the Gaussian unitary ensemble is larger than sqrt[2N]ξ. As a by-product, we present an exact asymptotic expansion for P(x_{min}^{GUE}≥sqrt[2N]ξ) for finite N as ξ→∞. Our results are corroborated by numerical simulations whenever possible, with excellent agreement.

Neural network based feed-forward high density associative memory

NASA Technical Reports Server (NTRS)

Daud, T.; Moopenn, A.; Lamb, J. L.; Ramesham, R.; Thakoor, A. P.

1987-01-01

A novel thin film approach to neural-network-based high-density associative memory is described. The information is stored locally in a memory matrix of passive, nonvolatile, binary connection elements with a potential to achieve a storage density of 10 to the 9th bits/sq cm. Microswitches based on memory switching in thin film hydrogenated amorphous silicon, and alternatively in manganese oxide, have been used as programmable read-only memory elements. Low-energy switching has been ascertained in both these materials. Fabrication and testing of memory matrix is described. High-speed associative recall approaching 10 to the 7th bits/sec and high storage capacity in such a connection matrix memory system is also described.

The Ameloblastin extracellular matrix molecule enhances bone fracture resistance and promotes rapid bone fracture healing

PubMed Central

Lu, Xuanyu; Li, Wenjin; Fukumoto, Satoshi; Yamada, Yoshihiko; Evans, Carla; Diekwisch, Thomas G.H.; Luan, Xianghong

2016-01-01

The extracellular matrix (ECM) provides structural support, cell migration anchorage, cell differentiation cues, and fine-tuned cell proliferation signals during all stages of bone fracture healing, including cartilaginous callus formation, callus remodeling, and bony bridging of the fracture gap. In the present study we have defined the role of the extracellular matrix protein ameloblastin (AMBN) in fracture resistance and fracture healing of mouse long bones. To this end, long bones from WT and AMBNΔ5-6 truncation model mice were subjected to biomechanical analysis, fracture healing assays, and stem cell colony formation comparisons. The effect of exogenous AMBN addition to fracture sites was also determined. Our data indicate that lack of a functional AMBN in the bone matrix resulted in 31% decreased femur bone mass and 40% reduced energy to failure. On a cellular level, AMBN function inhibition diminished the proliferative capacity of fracture repair callus cells, as evidenced by a 58% reduction in PCNA and a 40% reduction in Cyclin D1 gene expression, as well as PCNA immunohistochemistry. In terms of fracture healing, AMBN truncation was associated with an enhanced and prolonged chondrogenic phase, resulting in delayed mineralized tissue gene expression and delayed ossification of the fracture repair callus. Underscoring a role of AMBN in fracture healing, there was a 6.9-fold increase in AMBN expression at the fracture site one week after fracture, and distinct AMBN immunolabeling in the fracture gap. Finally, application of exogenous AMBN protein to bone fracture sites accelerated callus formation and bone fracture healing (33% increase in bone volume and 19% increase in bone mineral density), validating the findings of our AMBN loss of function studies. Together, these data demonstrate the functional importance of the AMBN extracellular matrix protein in bone fracture prevention and rapid fracture healing. PMID:26899203

Multiresolution quantum chemistry in multiwavelet bases: excited states from time-dependent Hartree–Fock and density functional theory via linear response

DOE PAGES

Yanai, Takeshi; Fann, George I.; Beylkin, Gregory; ...

2015-02-25

Using the fully numerical method for time-dependent Hartree–Fock and density functional theory (TD-HF/DFT) with the Tamm–Dancoff (TD) approximation we use a multiresolution analysis (MRA) approach to present our findings. From a reformulation with effective use of the density matrix operator, we obtain a general form of the HF/DFT linear response equation in the first quantization formalism. It can be readily rewritten as an integral equation with the bound-state Helmholtz (BSH) kernel for the Green's function. The MRA implementation of the resultant equation permits excited state calculations without virtual orbitals. Moreover, the integral equation is efficiently and adaptively solved using amore » numerical multiresolution solver with multiwavelet bases. Our implementation of the TD-HF/DFT methods is applied for calculating the excitation energies of H 2, Be, N 2, H 2O, and C 2H 4 molecules. The numerical errors of the calculated excitation energies converge in proportion to the residuals of the equation in the molecular orbitals and response functions. The energies of the excited states at a variety of length scales ranging from short-range valence excitations to long-range Rydberg-type ones are consistently accurate. It is shown that the multiresolution calculations yield the correct exponential asymptotic tails for the response functions, whereas those computed with Gaussian basis functions are too diffuse or decay too rapidly. Finally, we introduce a simple asymptotic correction to the local spin-density approximation (LSDA) so that in the TDDFT calculations, the excited states are correctly bound.« less

A second-order unconstrained optimization method for canonical-ensemble density-functional methods

NASA Astrophysics Data System (ADS)

Nygaard, Cecilie R.; Olsen, Jeppe

2013-03-01

A second order converging method of ensemble optimization (SOEO) in the framework of Kohn-Sham Density-Functional Theory is presented, where the energy is minimized with respect to an ensemble density matrix. It is general in the sense that the number of fractionally occupied orbitals is not predefined, but rather it is optimized by the algorithm. SOEO is a second order Newton-Raphson method of optimization, where both the form of the orbitals and the occupation numbers are optimized simultaneously. To keep the occupation numbers between zero and two, a set of occupation angles is defined, from which the occupation numbers are expressed as trigonometric functions. The total number of electrons is controlled by a built-in second order restriction of the Newton-Raphson equations, which can be deactivated in the case of a grand-canonical ensemble (where the total number of electrons is allowed to change). To test the optimization method, dissociation curves for diatomic carbon are produced using different functionals for the exchange-correlation energy. These curves show that SOEO favors symmetry broken pure-state solutions when using functionals with exact exchange such as Hartree-Fock and Becke three-parameter Lee-Yang-Parr. This is explained by an unphysical contribution to the exact exchange energy from interactions between fractional occupations. For functionals without exact exchange, such as local density approximation or Becke Lee-Yang-Parr, ensemble solutions are favored at interatomic distances larger than the equilibrium distance. Calculations on the chromium dimer are also discussed. They show that SOEO is able to converge to ensemble solutions for systems that are more complicated than diatomic carbon.

Engine materials characterization and damage monitoring by using x ray technologies

NASA Technical Reports Server (NTRS)

Baaklini, George Y.

1993-01-01

X ray attenuation measurement systems that are capable of characterizing density variations in monolithic ceramics and damage due to processing and/or mechanical testing in ceramic and intermetallic matrix composites are developed and applied. Noninvasive monitoring of damage accumulation and failure sequences in ceramic matrix composites is used during room-temperature tensile testing. This work resulted in the development of a point-scan digital radiography system and an in situ x ray material testing system. The former is used to characterize silicon carbide and silicon nitride specimens, and the latter is used to image the failure behavior of silicon-carbide-fiber-reinforced, reaction-bonded silicon nitride matrix composites. State-of-the-art x ray computed tomography is investigated to determine its capabilities and limitations in characterizing density variations of subscale engine components (e.g., a silicon carbide rotor, a silicon nitride blade, and a silicon-carbide-fiber-reinforced beta titanium matrix rod, rotor, and ring). Microfocus radiography, conventional radiography, scanning acoustic microscopy, and metallography are used to substantiate the x ray computed tomography findings. Point-scan digital radiography is a viable technique for characterizing density variations in monolithic ceramic specimens. But it is very limited and time consuming in characterizing ceramic matrix composites. Precise x ray attenuation measurements, reflecting minute density variations, are achieved by photon counting and by using microcollimators at the source and the detector. X ray computed tomography is found to be a unique x ray attenuation measurement technique capable of providing cross-sectional spatial density information in monolithic ceramics and metal matrix composites. X ray computed tomography is proven to accelerate generic composite component development. Radiographic evaluation before, during, and after loading shows the effect of preexisting volume flaws on the fracture behavior of composites. Results from one-, three-, five-, and eight-ply ceramic composite specimens show that x ray film radiography can monitor damage accumulation during tensile loading. Matrix cracking, fiber-matrix debonding, fiber bridging, and fiber pullout are imaged throughout the tensile loading of the specimens. In situ film radiography is found to be a practical technique for estimating interfacial shear strength between the silicon carbide fibers and the reaction-bonded silicon nitride matrix. It is concluded that pretest, in situ, and post-test x ray imaging can provide greater understanding of ceramic matrix composite mechanical behavior.

A photoemission moments model using density functional and transfer matrix methods applied to coating layers on surfaces: Theory

NASA Astrophysics Data System (ADS)

Jensen, Kevin L.; Finkenstadt, Daniel; Shabaev, Andrew; Lambrakos, Samuel G.; Moody, Nathan A.; Petillo, John J.; Yamaguchi, Hisato; Liu, Fangze

2018-01-01

Recent experimental measurements of a bulk material covered with a small number of graphene layers reported by Yamaguchi et al. [NPJ 2D Mater. Appl. 1, 12 (2017)] (on bialkali) and Liu et al. [Appl. Phys. Lett. 110, 041607 (2017)] (on copper) and the needs of emission models in beam optics codes have lead to substantial changes in a Moments model of photoemission. The changes account for (i) a barrier profile and density of states factor based on density functional theory (DFT) evaluations, (ii) a Drude-Lorentz model of the optical constants and laser penetration depth, and (iii) a transmission probability evaluated by an Airy Transfer Matrix Approach. Importantly, the DFT results lead to a surface barrier profile of a shape similar to both resonant barriers and reflectionless wells: the associated quantum mechanical transmission probabilities are shown to be comparable to those recently required to enable the Moments (and Three Step) model to match experimental data but for reasons very different than the assumption by conventional wisdom that a barrier is responsible. The substantial modifications of the Moments model components, motivated by computational materials methods, are developed. The results prepare the Moments model for use in treating heterostructures and discrete energy level systems (e.g., quantum dots) proposed for decoupling the opposing metrics of performance that undermine the performance of advanced light sources like the x-ray Free Electron Laser. The consequences of the modified components on quantum yield, emittance, and emission models needed by beam optics codes are discussed.

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.

Independent control of matrix adhesiveness and stiffness within a 3D self-assembling peptide hydrogel.

PubMed

Hogrebe, Nathaniel J; Reinhardt, James W; Tram, Nguyen K; Debski, Anna C; Agarwal, Gunjan; Reilly, Matthew A; Gooch, Keith J

2018-04-01

A cell's insoluble microenvironment has increasingly been shown to exert influence on its function. In particular, matrix stiffness and adhesiveness strongly impact behaviors such as cell spreading and differentiation, but materials that allow for independent control of these parameters within a fibrous, stromal-like microenvironment are very limited. In the current work, we devise a self-assembling peptide (SAP) system that facilitates user-friendly control of matrix stiffness and RGD (Arg-Gly-Asp) concentration within a hydrogel possessing a microarchitecture similar to stromal extracellular matrix. In this system, the RGD-modified SAP sequence KFE-RGD and the scrambled sequence KFE-RDG can be directly swapped for one another to change RGD concentration at a given matrix stiffness and total peptide concentration. Stiffness is controlled by altering total peptide concentration, and the unmodified base peptide KFE-8 can be included to further increase this stiffness range due to its higher modulus. With this tunable system, we demonstrate that human mesenchymal stem cell morphology and differentiation are influenced by both gel stiffness and the presence of functional cell binding sites in 3D culture. Specifically, cells 24 hours after encapsulation were only able to spread out in stiffer matrices containing KFE-RGD. Upon addition of soluble adipogenic factors, soft gels facilitated the greatest adipogenesis as determined by the presence of lipid vacuoles and PPARγ-2 expression, while increasing KFE-RGD concentration at a given stiffness had a negative effect on adipogenesis. This three-component hydrogel system thus allows for systematic investigation of matrix stiffness and RGD concentration on cell behavior within a fibrous, three-dimensional matrix. Physical cues from a cell's surrounding environment-such as the density of cell binding sites and the stiffness of the surrounding material-are increasingly being recognized as key regulators of cell function. Currently, most synthetic biomaterials used to independently tune these parameters lack the fibrous structure characteristic of stromal extracellular matrix, which can be important to cells naturally residing within stromal tissues. In this manuscript, we describe a 3D hydrogel encapsulation system that provides user-friendly control over matrix stiffness and binding site concentration within the context of a stromal-like microarchitecture. Binding site concentration and gel stiffness both influenced cell spreading and differentiation, highlighting the utility of this system to study the independent effects of these material properties on cell function. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Highly ordered molecular rotor matrix on a nanopatterned template: titanyl phthalocyanine molecules on FeO/Pt(111).

PubMed

Lu, Shuangzan; Huang, Min; Qin, Zhihui; Yu, Yinghui; Guo, Qinmin; Cao, Gengyu

2018-08-03

Molecular rotors, motors and gears play important roles in artificial molecular machines, in which rotor and motor matrices are highly desirable for large-scale bottom-up fabrication of molecular machines. Here we demonstrate the fabrication of a highly ordered molecular rotor matrix by depositing nonplanar dipolar titanyl phthalocyanine (TiOPc, C 32 H 16 N 8 OTi) molecules on a Moiré patterned dipolar FeO/Pt(111) substrate. TiOPc molecules with O atoms pointing outwards from the substrate (upward) or towards the substrate (downward) are alternatively adsorbed on the fcc sites by strong lateral confinement. The adsorbed molecules, i.e. two kinds of molecular rotors, show different scanning tunneling microscopy images, thermal stabilities and rotational characteristics. Density functional theory calculations clarify that TiOPc molecules anchoring upwards with high adsorption energies correspond to low-rotational-rate rotors, while those anchoring downwards with low adsorption energies correspond to high-rotational-rate rotors. A robust rotor matrix fully occupied by low-rate rotors is fabricated by depositing molecules on the substrate at elevated temperature. Such a paradigm opens up a promising route to fabricate functional molecular rotor matrices, driven motor matrices and even gear groups on solid substrates.

Landscape attributes as drivers of the geographical variation in density of Sapajus nigritus Kerr, 1792, a primate endemic to the Atlantic Forest

NASA Astrophysics Data System (ADS)

Hendges, Carla D.; Melo, Geruza L.; Gonçalves, Alberto S.; Cerezer, Felipe O.; Cáceres, Nilton C.

2017-10-01

Neotropical primates are among the most well studied forest mammals concerning their population densities. However, few studies have evaluated the factors that influence the spatial variation in the population density of primates, which limits the possibility of inferences towards this animal group, especially at the landscape-level. Here, we compiled density data of Sapajus nigritus from 21 forest patches of the Brazilian Atlantic Forest. We tested the effects of climatic variables (temperature, precipitation), landscape attributes (number of patches, mean inter-patch isolation distance, matrix modification index) and patch size on the population density using linear models and the Akaike information criterion. Our findings showed that the density of S. nigritus is influenced by landscape attributes, particularly by fragmentation and matrix modification. Overall, moderately fragmented landscapes and those surrounded by matrices with intermediate indexes of temporal modification (i.e., crop plantations, forestry) are related to high densities of this species. These results support the assumptions that ecologically flexible species respond positively to forest fragmentation. However, the non-linear relationship between S. nigritus density and number of patches suggests that even the species that are most tolerant to forest cover changes seem to respond positively only at an intermediate level of habitat fragmentation, being dependent of both a moderate degree of forest cover and a high quality matrix. The results we found here can be a common response to fragmentation for those forest dweller species that are able to use the matrix as complementary foraging sites.

Matrix density effects on the mechanical properties of SiC fiber-reinforced silicon nitride matrix properties

NASA Technical Reports Server (NTRS)

Bhatt, Ramakrishna T.; Kiser, Lames D.

1990-01-01

The room temperature mechanical properties were measured for SiC fiber reinforced reaction-bonded silicon nitride composites (SiC/RBSN) of different densities. The composites consisted of approx. 30 vol percent uniaxially aligned 142 micron diameter SiC fibers (Textron SCS-6) in a reaction-bonded Si3N4 matrix. The composite density was varied by changing the consolidation pressure during RBSN processing and by hot isostatically pressing the SiC/RBSN composites. Results indicate that as the consolidation pressure was increased from 27 to 138 MPa, the average pore size of the nitrided composites decreased from 0.04 to 0.02 microns and the composite density increased from 2.07 to 2.45 gm/cc. Nonetheless, these improvements resulted in only small increases in the first matrix cracking stress, primary elastic modulus, and ultimate tensile strength values of the composites. In contrast, HIP consolidation of SiC/RBSN resulted in a fully dense material whose first matrix cracking stress and elastic modulus were approx. 15 and 50 percent higher, respectively, and ultimate tensile strength values were approx. 40 percent lower than those for unHIPed SiC/RBSN composites. The modulus behavior for all specimens can be explained by simple rule-of-mixture theory. Also, the loss in ultimate strength for the HIPed composites appears to be related to a degradation in fiber strength at the HIP temperature. However, the density effect on matrix fracture strength was much less than would be expected based on typical monolithic Si3N4 behavior, suggesting that composite theory is indeed operating. Possible practical implications of these observations are discussed.

Superfluidity, Bose-Einstein condensation, and structure in one-dimensional Luttinger liquids

NASA Astrophysics Data System (ADS)

Vranješ Markić, L.; Vrcan, H.; Zuhrianda, Z.; Glyde, H. R.

2018-01-01

We report diffusion Monte Carlo (DMC) and path integral Monte Carlo (PIMC) calculations of the properties of a one-dimensional (1D) Bose quantum fluid. The equation of state, the superfluid fraction ρS/ρ0 , the one-body density matrix n (x ) , the pair distribution function g (x ) , and the static structure factor S (q ) are evaluated. The aim is to test Luttinger liquid (LL) predictions for 1D fluids over a wide range of fluid density and LL parameter K . The 1D Bose fluid examined is a single chain of 4He atoms confined to a line in the center of a narrow nanopore. The atoms cannot exchange positions in the nanopore, the criterion for 1D. The fluid density is varied from the spinodal density where the 1D liquid is unstable to droplet formation to the density of bulk liquid 4He. In this range, K varies from K >2 at low density, where a robust superfluid is predicted, to K <0.5 , where fragile 1D superflow and solidlike peaks in S (q ) are predicted. For uniform pore walls, the ρS/ρ0 scales as predicted by LL theory. The n (x ) and g (x ) show long range oscillations and decay with x as predicted by LL theory. The amplitude of the oscillations is large at high density (small K ) and small at low density (large K ). The K values obtained from different properties agree well verifying the internal structure of LL theory. In the presence of disorder, the ρS/ρ0 does not scale as predicted by LL theory. A single vJ parameter in the LL theory that recovers LL scaling was not found. The one body density matrix (OBDM) in disorder is well predicted by LL theory. The "dynamical" superfluid fraction, ρSD/ρ0 , is determined. The physics of the deviation from LL theory in disorder and the "dynamical" ρSD/ρ0 are discussed.

The tissue-type plasminogen activator–plasminogen activator inhibitor 1 complex promotes neurovascular injury in brain trauma: evidence from mice and humans

PubMed Central

Sashindranath, Maithili; Sales, Eunice; Daglas, Maria; Freeman, Roxann; Samson, Andre L.; Cops, Elisa J.; Beckham, Simone; Galle, Adam; McLean, Catriona; Morganti-Kossmann, Cristina; Rosenfeld, Jeffrey V.; Madani, Rime; Vassalli, Jean-Dominique; Su, Enming J.; Lawrence, Daniel A.

2012-01-01

The neurovascular unit provides a dynamic interface between the circulation and central nervous system. Disruption of neurovascular integrity occurs in numerous brain pathologies including neurotrauma and ischaemic stroke. Tissue plasminogen activator is a serine protease that converts plasminogen to plasmin, a protease that dissolves blood clots. Besides its role in fibrinolysis, tissue plasminogen activator is abundantly expressed in the brain where it mediates extracellular proteolysis. However, proteolytically active tissue plasminogen activator also promotes neurovascular disruption after ischaemic stroke; the molecular mechanisms of this process are still unclear. Tissue plasminogen activator is naturally inhibited by serine protease inhibitors (serpins): plasminogen activator inhibitor-1, neuroserpin or protease nexin-1 that results in the formation of serpin:protease complexes. Proteases and serpin:protease complexes are cleared through high-affinity binding to low-density lipoprotein receptors, but their binding to these receptors can also transmit extracellular signals across the plasma membrane. The matrix metalloproteinases are the second major proteolytic system in the mammalian brain, and like tissue plasminogen activators are pivotal to neurological function but can also degrade structures of the neurovascular unit after injury. Herein, we show that tissue plasminogen activator potentiates neurovascular damage in a dose-dependent manner in a mouse model of neurotrauma. Surprisingly, inhibition of activity following administration of plasminogen activator inhibitor-1 significantly increased cerebrovascular permeability. This led to our finding that formation of complexes between tissue plasminogen activator and plasminogen activator inhibitor-1 in the brain parenchyma facilitates post-traumatic cerebrovascular damage. We demonstrate that following trauma, the complex binds to low-density lipoprotein receptors, triggering the induction of matrix metalloproteinase-3. Accordingly, pharmacological inhibition of matrix metalloproteinase-3 attenuates neurovascular permeability and improves neurological function in injured mice. Our results are clinically relevant, because concentrations of tissue plasminogen activator: plasminogen activator inhibitor-1 complex and matrix metalloproteinase-3 are significantly elevated in cerebrospinal fluid of trauma patients and correlate with neurological outcome. In a separate study, we found that matrix metalloproteinase-3 and albumin, a marker of cerebrovascular damage, were significantly increased in brain tissue of patients with neurotrauma. Perturbation of neurovascular homeostasis causing oedema, inflammation and cell death is an important cause of acute and long-term neurological dysfunction after trauma. A role for the tissue plasminogen activator–matrix metalloproteinase axis in promoting neurovascular disruption after neurotrauma has not been described thus far. Targeting tissue plasminogen activator: plasminogen activator inhibitor-1 complex signalling or downstream matrix metalloproteinase-3 induction may provide viable therapeutic strategies to reduce cerebrovascular permeability after neurotrauma. PMID:22822039

A Scalable O(N) Algorithm for Large-Scale Parallel First-Principles Molecular Dynamics Simulations

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

Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

2014-01-01

Traditional algorithms for first-principles molecular dynamics (FPMD) simulations only gain a modest capability increase from current petascale computers, due to their O(N 3) complexity and their heavy use of global communications. To address this issue, we are developing a truly scalable O(N) complexity FPMD algorithm, based on density functional theory (DFT), which avoids global communications. The computational model uses a general nonorthogonal orbital formulation for the DFT energy functional, which requires knowledge of selected elements of the inverse of the associated overlap matrix. We present a scalable algorithm for approximately computing selected entries of the inverse of the overlap matrix,more » based on an approximate inverse technique, by inverting local blocks corresponding to principal submatrices of the global overlap matrix. The new FPMD algorithm exploits sparsity and uses nearest neighbor communication to provide a computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic orbitals are confined, and a cutoff beyond which the entries of the overlap matrix can be omitted when computing selected entries of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to O(100K) atoms on O(100K) processors, with a wall-clock time of O(1) minute per molecular dynamics time step.« less

Functional hepatocyte clusters on bioactive blend silk matrices towards generating bioartificial liver constructs.

PubMed

Janani, G; Nandi, Samit K; Mandal, Biman B

2018-02-01

The creation of in vitro functional hepatic tissue simulating micro-environmental niche of native liver is a keen area of research due to its demand in bioartificial liver (BAL) and cell-based tissue engineering. Here, we investigated the potential of novel blend (BA) silk scaffold fabricated by blending mulberry (Bombyx mori, BM) silk fibroin with cell adhesion motif (RGD) rich non-mulberry (Antheraea assamensis, AA) silk fibroin, in generating a functional liver construct. Three-dimensional (3D) porous silk scaffolds (BM, AA and BA) were physico-chemically characterized and functionally evaluated using human hepatocarcinoma cells (HepG2) and primary neonatal rat hepatocytes. The growth and distribution of hepatocytes within the scaffolds were tracked by FESEM, alamar blue proliferation assay and live/dead staining. Hemocompatible BA scaffolds supported the formation of high density hepatocyte clusters, facilitating cell-matrix and cell-cell interactions. Blend scaffolds evinced enhanced liver-specific functions of cultured hepatocytes in terms of albumin synthesis, urea synthesis and cytochrome P450 enzyme activity over 21 days. Subcutaneous implantation of scaffolds demonstrated minimal macrophage infiltration in blend scaffolds. These findings substantiate that the integral property of blend (BA) scaffold offers a befitting environment by influencing spheroidal growth of hepatocytes with enhanced biological activity. Collectively, the present study provides a new 3D bio-matrix niche for growing functional liver cells that would have future prospects in BAL as well as regenerative medicine. An end stage liver disease called cirrhosis perturbs the self-healing ability and physiological functions of liver. Due to the scarcity of healthy donors, a functional in vitro hepatic construct retaining the liver-specific functions is in great demand for its prospects in bioartificial liver (BAL) and cell-based tissue engineering. Physicochemical attributes of a matrix influence the behavior of cultured hepatocytes in terms of attachment, morphology and functionality. Mulberry and non-mulberry silk fibroin presents unique amino acid sequence with difference in hydrophobicity and crystallinity. Considering this, the present study focuses on the development of a suitable three-dimensional (3D) bioactive matrix incorporating both mulberry silk fibroin and cell adhesion motif (RGD) rich non-mulberry silk fibroin. Porous silk blend scaffolds facilitated the formation of hepatocyte clusters with enhanced liver-specific functions emphasizing both cell-cell and cell-matrix interactions. Hemocompatibility and integral property of blend scaffolds offers a biological niche for seeding functional liver cells that would have future prospects in biohybrid devices. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Ammonium nitrate-polymer glasses: a new concept for phase and thermal stabilization of ammonium nitrate.

PubMed

Lang, Anthony J; Vyazovkin, Sergey

2008-09-11

Dissolving of ammonium nitrate in highly polar polymers such as poly(vinylpyrrolidone) and/or poly(acrylamide) can result in the formation of single-phase glassy solid materials, in which NH 4 (+) and NO 3 (-) are separated through an ion-dipole interaction with the polymer matrix. Below the glass transition temperature of the polymer matrix the resulting materials remain phase and thermally stable as demonstrated through the absence of decomposition as well as the solid-solid transitions and melting of ammonium nitrate. The structure of the materials is explored by Fourier transform infrared spectroscopy and density functional calculations. Differential scanning calorimetry, thermogravimetry, and isoconversional kinetic analysis are applied to characterize the thermal behavior of the materials.

Reaction of iminopropadienones with amines: mechanistic explanations of zwitterionic intermediate, ketene and ketenimine formation.

PubMed

Koch, Rainer; Finnerty, Justin J; Bruhn, Torsten; Borget, Fabien; Wentrup, Curt

2008-09-25

The complex reaction of thermally generated iminopropadienones with amines in the gas phase and upon matrix deposition and its varying product composition is investigated using density functional theory. In the high energy gas phase addition a single amine molecule reacts readily with iminopropadienone with the decisive step being a 1,3-hydrogen shift and activation barriers of at least 100 kJ/mol. In accordance with the experiment, the formation of ketenes is favored. In the condensed phase of an amine matrix, the utilization of amine dimers both as reagents and as explicit solvents lowers the activation energy required to a feasible 20-30 kJ/mol and predicts ketenimines as the main products, as observed experimentally.

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

PubMed

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

2017-10-10

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

Performance of low-rank QR approximation of the finite element Biot-Savart law

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

White, D; Fasenfest, B

2006-10-16

In this paper we present a low-rank QR method for evaluating the discrete Biot-Savart law. Our goal is to develop an algorithm that is easily implemented on parallel computers. It is assumed that the known current density and the unknown magnetic field are both expressed in a finite element expansion, and we wish to compute the degrees-of-freedom (DOF) in the basis function expansion of the magnetic field. The matrix that maps the current DOF to the field DOF is full, but if the spatial domain is properly partitioned the matrix can be written as a block matrix, with blocks representingmore » distant interactions being low rank and having a compressed QR representation. While an octree partitioning of the matrix may be ideal, for ease of parallel implementation we employ a partitioning based on number of processors. The rank of each block (i.e. the compression) is determined by the specific geometry and is computed dynamically. In this paper we provide the algorithmic details and present computational results for large-scale computations.« less

The nanostructure of porous cobalt coatings deposited by magnetron sputtering in helium atmosphere.

PubMed

Lacroix, B; Godinho, V; Fernández, A

2018-05-01

In this work, (scanning) transmission electron microscopy has been used to study the nanostructure of porous cobalt coatings obtained by magnetron sputtering using helium as process gas. This nanostructure consists of closed pores of different nanometric size (about 4-20 nm) that are distributed all over a nanocrystalline Co matrix and filled with the deposition gas. Spatially resolved electron energy-loss spectroscopy analysis was applied to measure and map, with high lateral resolution, the relevant physical properties (density, pressure and He-K edge shift) of helium trapped inside these individual nanopores, in order to provide new insights about the growth mechanism involved in such systems. In particular, a coefficient of proportionality, C = 0.039 eV nm 3 , between the blue shift of the He K-edge and the He density has been found. In addition, very high He densities (10-100 at./nm 3 ) and pressures in the gigapascal range (0.05-5.0 GPa) have been measured. The linear dependence of these parameters as a function of the inverse radii obeying to the Laplace-Young law for most of the pores suggests that their formation during the coating's growth takes place in regime of elastic deformation of the Co matrix. Copyright © 2018 Elsevier Ltd. All rights reserved.

Mechanism for odd-electron anion generation of dihydroxybenzoic acid isomers in matrix-assisted laser desorption/ionization mass spectrometry with density functional theory calculations.

PubMed

Yamagaki, Tohru; Takeuchi, Michika; Watanabe, Takehiro; Sugahara, Kohtaro; Takeuchi, Takae

2016-12-30

Proton and radical are transferred between matrices and matrix and analyte in matrix-assisted laser desorption/ionization (MALDI) and these transfers drive ionization of analytes. The odd-electron anion [M-2H] •- was generated in dihydroxybenzoic acids (DHBs) and the ion abundance of the 2,5-DHB was the highest among six DHB isomers. We were interested in the mechanism of the ion generation of the odd-electron anion. The observed [M-2H] •- and [M-3H] - ions, which were generated with the hydrogen radical removed from the phenolic hydroxyl groups (OH) in DHB isomers, were analyzed using negative-ion MALDI-MS. The enthalpy for ion generation and their stable structures were calculated using the density functional theory (DFT) calculation program Gaussian 09 with the B3LYP functional and the 6-31+G(d) basis set. The number of observed [M-2H] •- and [M-3H] - ions of the DHB isomers was dependent on the positions of the phenolic OH groups in the DHB isomers because the carboxy group interacts with the ortho OH group due to neighboring group participation, as confirmed from the stable structures of the [M-2H] •- anions calculated with the Gaussian 09 program. The DHB isomers were placed into three categories according to the number of the ions. Odd-electron anions ([M-2H] •- ) and [M-2H • -H] - ([M-3H] - ) ions were generated from DHB isomers due to removal of the hydrogen radical from the phenolic groups. The enthalpy for ion generation revealed that ion formation proceeds via a two-step pathway through the [M-M] - ion as an intermediate. © 2016 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd. © 2016 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd.

Image-based 3D modeling study of the influence of vessel density and blood hemoglobin concentration on tumor oxygenation and response to irradiation.

PubMed

Lagerlöf, Jakob H; Kindblom, Jon; Cortez, Eliane; Pietras, Kristian; Bernhardt, Peter

2013-02-01

Hypoxia is one of the most important factors influencing clinical outcome after radiotherapy. Improved knowledge of factors affecting the levels and distribution of oxygen within a tumor is needed. The authors constructed a theoretical 3D model based on histological images to analyze the influence of vessel density and hemoglobin (Hb) concentration on the response to irradiation. The pancreases of a Rip-Tag2 mouse, a model of malignant insulinoma, were excised, cryosectioned, immunostained, and photographed. Vessels were identified by image thresholding and a 3D vessel matrix assembled. The matrix was reduced to functional vessel segments and enlarged by replication. The steady-state oxygen tension field of the tumor was calculated by iteratively employing Green's function method for diffusion and the Michaelis-Menten model for consumption. The impact of vessel density on the radiation response was studied by removing a number of randomly selected vessels. The impact of Hb concentration was studied by independently changing vessel oxygen partial pressure (pO(2)). For each oxygen distribution, the oxygen enhancement ratio (OER) was calculated and the mean absorbed dose at which the tumor control probability (TCP) was 0.99 (D(99)) was determined using the linear-quadratic cell survival model (LQ model). Decreased pO(2) shifted the oxygen distribution to lower values, whereas decreased vessel density caused the distribution to widen and shift to lower values. Combined scenarios caused lower-shifted distributions, emphasising log-normal characteristics. Vessel reduction combined with increased blood pO(2) caused the distribution to widen due to a lack of vessels. The most pronounced radiation effect of increased pO(2) occurred with tumor tissue with 50% of the maximum vessel density used in the simulations. A 51% decrease in D(99), from 123 to 60 Gy, was found between the lowest and highest pO(2) concentrations. Our results indicate that an intermediate vascular density region exists where enhanced blood oxygen concentration may be beneficial for radiation response. The results also suggest that it is possible to distinguish between diffusion-limited and anemic hypoxia from the characteristics of the pO(2) distribution.

Charge and Spin Dynamics of the Hubbard Chains

NASA Technical Reports Server (NTRS)

Park, Youngho; Liang, Shoudan

1999-01-01

We calculate the local correlation functions of charge and spin for the one-chain and two-chain Hubbard model using density matrix renormalization group method and the recursion technique. Keeping only finite number of states we get good accuracy for the low energy excitations. We study the charge and spin gaps, bandwidths and weights of the spectra for various values of the on-site Coulomb interaction U and the electron filling. In the low energy part, the local correlation functions are different for the charge and spin. The bandwidths are proportional to t for the charge and J for the spin respectively.

Lithium-coated polymeric matrix as a minimum volume-change and dendrite-free lithium metal anode

PubMed Central

Liu, Yayuan; Lin, Dingchang; Liang, Zheng; Zhao, Jie; Yan, Kai; Cui, Yi

2016-01-01

Lithium metal is the ideal anode for the next generation of high-energy-density batteries. Nevertheless, dendrite growth, side reactions and infinite relative volume change have prevented it from practical applications. Here, we demonstrate a promising metallic lithium anode design by infusing molten lithium into a polymeric matrix. The electrospun polyimide employed is stable against highly reactive molten lithium and, via a conformal layer of zinc oxide coating to render the surface lithiophilic, molten lithium can be drawn into the matrix, affording a nano-porous lithium electrode. Importantly, the polymeric backbone enables uniform lithium stripping/plating, which successfully confines lithium within the matrix, realizing minimum volume change and effective dendrite suppression. The porous electrode reduces the effective current density; thus, flat voltage profiles and stable cycling of more than 100 cycles is achieved even at a high current density of 5 mA cm−2 in both carbonate and ether electrolyte. The advantages of the porous, polymeric matrix provide important insights into the design principles of lithium metal anodes. PMID:26987481

Lithium-coated polymeric matrix as a minimum volume-change and dendrite-free lithium metal anode

DOE PAGES

Liu, Yayuan; Lin, Dingchang; Liang, Zheng; ...

2016-03-18

Lithium metal is the ideal anode for the next generation of high-energy-density batteries. Nevertheless, dendrite growth, side reactions and infinite relative volume change have prevented it from practical applications. Here, we demonstrate a promising metallic lithium anode design by infusing molten lithium into a polymeric matrix. The electrospun polyimide employed is stable against highly reactive molten lithium and, via a conformal layer of zinc oxide coating to render the surface lithiophilic, molten lithium can be drawn into the matrix, affording a nano-porous lithium electrode. Importantly, the polymeric backbone enables uniform lithium stripping/plating, which successfully confines lithium within the matrix, realizingmore » minimum volume change and effective dendrite suppression. The porous electrode reduces the effective current density; thus, flat voltage profiles and stable cycling of more than 100 cycles is achieved even at a high current density of 5 mA cm -2 in both carbonate and ether electrolyte. Furthermore, the advantages of the porous, polymeric matrix provide important insights into the design principles of lithium metal anodes.« less

Lithium-coated polymeric matrix as a minimum volume-change and dendrite-free lithium metal anode

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

Liu, Yayuan; Lin, Dingchang; Liang, Zheng

Lithium metal is the ideal anode for the next generation of high-energy-density batteries. Nevertheless, dendrite growth, side reactions and infinite relative volume change have prevented it from practical applications. Here, we demonstrate a promising metallic lithium anode design by infusing molten lithium into a polymeric matrix. The electrospun polyimide employed is stable against highly reactive molten lithium and, via a conformal layer of zinc oxide coating to render the surface lithiophilic, molten lithium can be drawn into the matrix, affording a nano-porous lithium electrode. Importantly, the polymeric backbone enables uniform lithium stripping/plating, which successfully confines lithium within the matrix, realizingmore » minimum volume change and effective dendrite suppression. The porous electrode reduces the effective current density; thus, flat voltage profiles and stable cycling of more than 100 cycles is achieved even at a high current density of 5 mA cm -2 in both carbonate and ether electrolyte. Furthermore, the advantages of the porous, polymeric matrix provide important insights into the design principles of lithium metal anodes.« less

Ab initio calculation of resonant Raman intensities of transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Miranda, Henrique; Reichardt, Sven; Molina-Sanchez, Alejandro; Wirtz, Ludger

Raman spectroscopy is used to characterize optical and vibrational properties of materials. Its computational simulation is important for the interpretation of experimental results. Two approaches are the bond polarizability model and density functional perturbation theory. However, both are known to not capture resonance effects. These resonances and quantum interference effects are important to correctly reproduce the intensities as a function of laser energy as, e.g., reported for the case of multi-layer MoTe21.We present two fully ab initio approaches that overcome this limitation. In the first, we calculate finite difference derivatives of the dielectric susceptibility with the phonon displacements2. In the second we calculate electron-light and electron-phonon matrix elements from density functional theory and use them to evaluate expressions for the Raman intensity derived from time-dependent perturbation theory. These expressions are implemented in a computer code that performs the calculations as a post-processing step. We compare both methods and study the case of triple-layer MoTe2. Luxembourg National Research Fund (FNR).

CD163 as a marker of M2 macrophage, contribute to predicte aggressiveness and prognosis of Kazakh esophageal squamous cell carcinoma.

PubMed

Hu, Jian Ming; Liu, Kai; Liu, Ji Hong; Jiang, Xian Li; Wang, Xue Li; Chen, Yun Zhao; Li, Shu Gang; Zou, Hong; Pang, Li Juan; Liu, Chun Xia; Cui, Xiao Bin; Yang, Lan; Zhao, Jin; Shen, Xi Hua; Jiang, Jin Fang; Liang, Wei Hua; Yuan, Xiang Lin; Li, Feng

2017-03-28

M2 macrophages was domesticated by tumor microenvironment to produce some angiogenic molecules and protease, facilitating angiogenesis and matrix breakdown, promoting tumor invasive and metastasis. However, The function of M2 macrophages to progression of eophageal carcinoma, especially Kazakh esophageal carcinoma is still dimness. This study aims to investigate M2 macrophages correlated with matrix metalloproteinase-9 (MMP9) and microvessel density, and the role in the progression of Kazakh esophageal squamous cell carcinoma. CD163 and CD34 as the marker of M2 macrophages and endothelial cells, were used to identify the M2 macrophages density and microvessel density, respectively. Immunohistochemistry staining was evaluated the expression of MMP9. The number of infiltrated CD163-positive M2 macrophages in tumor islets and stroma was significantly higher than in cancer adjacent normal tissues. The increased of M2 macrophages and microvessel density were significantly correlated with more malignant phenotypes including lymph node metastasis and clinical stage progression. Meanwhile, the expression of MMP9 showed much higher level in esophageal squamous cell carcinoma than that in cancer adjacent normal tissues, and high expression of MMP9 in Kazakh esophageal squamous cell carcinoma was significantly associated with age, depth of tumor invasion, lymph node metastasis, and tumor clinical stage. The quantity of M2 macrophages in tumor stroma was positively associated with microvessel density and the expression of MMP9, and as an independent poorly prognostic factor for overall survival time of Kazakh esophageal squamous cell carcinoma. These findings suggest the increased number of M2 macrophages correlated with high expression of MMP9 and high microvessel density may contribute to the tumor aggressiveness and angiogenesis, promoting the progression of Kazakh esophageal squamous cell carcinoma.

Theoretical and numerical aspects of fluid-saturated elasto-plastic soils

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

Ehlers, W.

1995-12-31

The theoretical and numerical treatment of fluid-saturated porous solid materials generally falls into the category of porous media models, which are described within the framework of the classical theory of mixtures extended by the concept of volume fractions (porous media theories). In particular, this concept allows for the description of saturated, unsaturated and empty porous matrix materials, thus offering a well-founded theoretical background for a lot of engineering problems occurring, for instance, in the fields of geomechanics (soil and rock mechanics as well as glacier and rock ice mechanics), oil producing industries, sintering technologies, biomechanics, etc. In the present contribution,more » theoretical and numerical studies are outlined to describe a two-phase material composed of an incompressible elasto-plastic soil matrix saturated by an incompressible viscous pore fluid. In this context, the phenomenon of phase incompressibility is well known as a microscopic effect not implying bulk incompressibility in the macro regime. This is seen from the fact that even if the material density functions of the individual constituents are constant during deformation, the corresponding bulk densities can still change through changes in the volume fractions. Within the framework of a pure mechanical theory, constitutive equations are given for both the solid and the fluid partial stress tensors and for the interaction force acting between the two materials. Concerning the porous soil matrix, the elastic properties are described by an elasticity law of Hookean type, while the plastic range is governed by a {open_quote}single surface{close_quote} yield function exhibiting a smooth and closed shape in the principal stress space together with a non-associated flow rule. The viscosity effects of the pore fluid are included in the fluid stress tensor and in the drag force.« less

EPS production by Propionibacterium freudenreichii facilitates its immobilization for propionic acid production.

PubMed

Belgrano, F D S; Verçoza, B R F; Rodrigues, J C F; Hatti-Kaul, R; Pereira, N

2018-04-28

Immobilization of microbial cells is a useful strategy for developing high cell density bioreactors with improved stability and productivity for production of different chemicals. Functionalization of the immobilization matrix or biofilm forming property of some strains has been utilized for achieving cell attachment. The aim of the present study was to investigate the production of exopolysaccharide (EPS) by Propionibacterium freudenreichii C.I.P 59.32 and utilize this feature for immobilization of the cells on porous glass beads for production of propionic acid. Propionibacterium freudenreichii was shown to produce both capsular and excreted EPS during batch cultivations using glucose as carbon source. Different electron microscopy techniques confirmed the secretion of EPS and formation of cellular aggregates. The excreted EPS was mainly composed of mannose and glucose in a 5·3 : 1 g g -1 ratio. Immobilization of the cells on untreated and polyethyleneimine (PEI)-treated Poraver beads in a bioreactor was evaluated. Higher productivity and yield of propionic acid (0·566 g l -1  h -1 and 0·314 g g -1 , respectively) was achieved using cells immobilized to untreated beads and EPS production reached 617·5 mg l -1 after 48 h. These results suggest an important role of EPS-producing strains for improving cell immobilization and propionic acid production. This study demonstrates the EPS-producing microbe to be easily immobilized on a solid matrix and to be used in a bioprocess. Such a system could be optimized for achieving high cell density in fermentations without the need for functionalization of the matrix. © 2018 The Society for Applied Microbiology.

Strain Rate Dependency of Bronze Metal Matrix Composite Mechanical Properties as a Function of Casting Technique

NASA Astrophysics Data System (ADS)

Brown, Lloyd; Joyce, Peter; Radice, Joshua; Gregorian, Dro; Gobble, Michael

2012-07-01

Strain rate dependency of mechanical properties of tungsten carbide (WC)-filled bronze castings fabricated by centrifugal and sedimentation-casting techniques are examined, in this study. Both casting techniques are an attempt to produce a functionally graded material with high wear resistance at a chosen surface. Potential applications of such materials include shaft bushings, electrical contact surfaces, and brake rotors. Knowledge of strain rate-dependent mechanical properties is recommended for predicting component response due to dynamic loading or impact events. A brief overview of the casting techniques for the materials considered in this study is followed by an explanation of the test matrix and testing techniques. Hardness testing, density measurement, and determination of the volume fraction of WC particles are performed throughout the castings using both image analysis and optical microscopy. The effects of particle filling on mechanical properties are first evaluated through a microhardness survey of the castings. The volume fraction of WC particles is validated using a thorough density survey and a rule-of-mixtures model. Split Hopkinson Pressure Bar (SHPB) testing of various volume fraction specimens is conducted to determine strain dependence of mechanical properties and to compare the process-property relationships between the two casting techniques. The baseline performances of C95400 bronze are provided for comparison. The results show that the addition of WC particles improves microhardness significantly for the centrifugally cast specimens, and, to a lesser extent, in the sedimentation-cast specimens, largely because the WC particles are more concentrated as a result of the centrifugal-casting process. Both metal matrix composites (MMCs) demonstrate strain rate dependency, with sedimentation casting having a greater, but variable, effects on material response. This difference is attributed to legacy effects from the casting process, namely, porosity and localized WC particle grouping.

Metrics of Cellular and Vascular Infiltration of Human Acellular Dermal Matrix in Ventral Hernia Repairs

PubMed Central

Campbell, Kristin Turza; Burns, Nadja K.; Ensor, Joe; Butler, Charles E.

2012-01-01

Background Human acellular dermal matrix (HADM) is used for ventral hernia repair, as it resists infection and remodels via surrounding tissue. However, the tissue source and impact of basement membrane (BM) on cell and vessel infiltration have not been determined. We hypothesized that musculofascia would be the primary tissue source of cells and vessels infiltrating into HADM and the BM would inhibit infiltration. Methods Fifty-six guinea pigs underwent inlay HADM ventral hernia repair with the BM oriented toward or away from the peritoneum. At postoperative weeks 1, 2, or 4, repair sites were completely excised. Histologic and immunohistochemical analyses were performed to quantify cell and vessel density within repair-site zones, including interface (lateral, beneath musculofascia) and center (beneath subcutaneous fat) zones. Cell and vessel quantities were compared as functions of zone, BM orientation, and time. Results Cellular and vascular infiltration increased over time universally. The interface demonstrated greater mean cell density than the center (weeks 1 and 2, p=0.01, p<0.0001). Cell density was greater with the BM oriented toward the peritoneum at week 4 (p=0.02). The interface zone had greater mean vessel density than the center zone at week 4 (p<0.0001). Orienting the BM toward the peritoneum increased vessel density at week 4 (p=0.0004). Conclusion Cellular and vascular infiltration into HADM for ventral hernia repairs was greater from musculofascia than subcutaneous and the BM inhibited cellular and vascular. HADM should be placed adjacent to the best vascularizing tissue to improve fibrovascular incorporation. PMID:22456361

Stockholder projector analysis: A Hilbert-space partitioning of the molecular one-electron density matrix with orthogonal projectors

NASA Astrophysics Data System (ADS)

Vanfleteren, Diederik; Van Neck, Dimitri; Bultinck, Patrick; Ayers, Paul W.; Waroquier, Michel

2012-01-01

A previously introduced partitioning of the molecular one-electron density matrix over atoms and bonds [D. Vanfleteren et al., J. Chem. Phys. 133, 231103 (2010)] is investigated in detail. Orthogonal projection operators are used to define atomic subspaces, as in Natural Population Analysis. The orthogonal projection operators are constructed with a recursive scheme. These operators are chemically relevant and obey a stockholder principle, familiar from the Hirshfeld-I partitioning of the electron density. The stockholder principle is extended to density matrices, where the orthogonal projectors are considered to be atomic fractions of the summed contributions. All calculations are performed as matrix manipulations in one-electron Hilbert space. Mathematical proofs and numerical evidence concerning this recursive scheme are provided in the present paper. The advantages associated with the use of these stockholder projection operators are examined with respect to covalent bond orders, bond polarization, and transferability.

Computational study of the electronic spectra of the rare gas fluorohydrides HRgF (Rg = Ar, Kr, Xe, Rn)

NASA Astrophysics Data System (ADS)

van Hoeve, Miriam D.; Klobukowski, Mariusz

2018-03-01

Simulation of the electronic spectra of HRgF (Rg = Ar, Kr, Xe, Rn) was carried out using the time-dependent density functional method, with the CAMB3LYP functional and several basis sets augmented with even-tempered diffuse functions. A full spectral assignment for the HRgF systems was done. The effect of the rare gas matrix on the HRgF (Rg = Ar and Kr) spectra was investigated and it was found that the matrix blue-shifted the spectra. Scalar relativistic effects on the spectra were also studied and it was found that while the excitation energies of HArF and HKrF were insignificantly affected by relativistic effects, most of the excitation energies of HXeF and HRnF were red-shifted. Spin-orbit coupling was found to significantly affect excitation energies in HRnF. Analysis of performance of the model core potential basis set relative to all-electron (AE) basis sets showed that the former basis set increased computational efficiency and gave results similar to those obtained with the AE basis set.

Creating Perfused Functional Vascular Channels Using 3D Bio-Printing Technology

PubMed Central

Lee, Vivian K.; Kim, Diana Y.; Ngo, Haygan; Lee, Young; Seo, Lan; Yoo, Seung-Schik; Vincent, Peter A.; Dai, Guohao

2014-01-01

We developed a methodology using 3D bio-printing technology to create a functional in vitro vascular channel with perfused open lumen using only cells and biological matrices. The fabricated vasculature has a tight, confluent endothelium lining, presenting barrier function for both plasma protein and high-molecular weight dextran molecule. The fluidic vascular channel is capable of supporting the viability of tissue up to 5mm in distance at 5 million cells/mL density under the physiological flow condition. In static-cultured vascular channels, active angiogenic sprouting from the vessel surface was observed whereas physiological flow strongly suppressed this process. Gene expression analysis were reported in this study to show the potential of this vessel model in vascular biology research. The methods have great potential in vascularized tissue fabrication using 3D bio-printing technology as the vascular channel is simultaneously created while cells and matrix are printed around the channel in desired 3D patterns. It can also serve as a unique experimental tool for investigating fundamental mechanisms of vascular remodeling with extracellular matrix and maturation process under 3D flow condition. PMID:24965886

Propagation of Circularly Polarized Light Through a Two-Dimensional Random Medium

NASA Astrophysics Data System (ADS)

Gorodnichev, E. E.

2017-12-01

The problem of small-angle multiple-scattering of circularly polarized light in a two-dimensional medium with large fiberlike inhomogeneities is studied. The attenuation lengths for elements the density matrix are calculated. It is found that with increasing the sample thickness the intensity of waves polarized along the fibers decays faster than the other density matrix elements. With further increase in the thickness, the off-diagonal element which is responsible for correlation between the cross-polarized waves dissapears. In the case of very thick samples the scattered field proves to be polarized perpendicular to the fibers. It is shown that the difference in the attenuation lengths of the density matrix elements results in a non-monotonic depth dependence of the degree of polarization.

Polyaniline-CuO hybrid nanocomposite with enhanced electrical conductivity

NASA Astrophysics Data System (ADS)

de Souza, Vânia S.; da Frota, Hidembergue O.; Sanches, Edgar A.

2018-02-01

A hybrid nanocomposite based on a polymer matrix constituted of Polyaniline Emeraldine-salt form (PANI-ES) reinforced by copper oxide II (CuO) particles was obtained by in situ polymerization. Structural, morphological and electrical properties of the pure materials and nanocomposite form were investigated. The presence of CuO particles in the nanocomposite material affected the natural alignment of the polymer chains. XRD technique allowed the visualization of the polymer amorphization in the nanocomposite form, suggesting an interaction between both phases. The FTIR spectra confirmed this molecular interaction due to the blue shift of the characteristic absorption peaks of PANI-ES in the nanocomposite form. SEM images revealed that the polymer nanofiber morphology was no longer observed in the nanocomposite. The CuO spherical particles are randomly dispersed in the polymer matrix. The density functional theory plus the Coulomb interaction method revealed a charge transfer from PANI to CuO slab. Moreover, the density of states (DOS) has revealed that the nanocomposite behaves as a metal. In agreement, the electrical conductivity showed an increase of 60% in the nanocomposite material.

The initiation and growth of delaminations induced by matrix microcracks in laminated composites

NASA Technical Reports Server (NTRS)

Nairn, J. A.; Hu, S.

1992-01-01

A recent variational mechanics analysis of microcracking damage in cross-ply laminates of the form /(S)/90n/s, where (S) is any orthotropic sublaminate much stiffer than /90n/, has been extended to account for the presence of delaminations emanating from the tips of microcracks in the /90 2n/T sublaminate. The new two-dimensional stress analysis is used to calculate the total strain energy, effective modulus, and longitudinal thermal expansion coefficient for a laminate having microcracks and delaminations. These results are used to calculate the energy release rate for the initiation and growth of a delamination induced by a matrix microcrack. At low crack densities, /(S)/90n/s laminates are expected to fail by microcracking and to show little or no delamination. At some critical crack density, which is a function of laminate structure and material properties, the energy release rate for delamination exceeds that for microcracking and delamination is predicted to dominate over microcracking. A quasi-three-dimensional model is used to predict the propagation of arbitrarily shaped delamination fronts. All predictions agree with experimental observations.

Transfer-matrix study of a hard-square lattice gas with two kinds of particles and density anomaly

NASA Astrophysics Data System (ADS)

Oliveira, Tiago J.; Stilck, Jürgen F.

2015-09-01

Using transfer matrix and finite-size scaling methods, we study the thermodynamic behavior of a lattice gas with two kinds of particles on the square lattice. Only excluded volume interactions are considered, so that the model is athermal. Large particles exclude the site they occupy and its four first neighbors, while small particles exclude only their site. Two thermodynamic phases are found: a disordered phase where large particles occupy both sublattices with the same probability and an ordered phase where one of the two sublattices is preferentially occupied by them. The transition between these phases is continuous at small concentrations of the small particles and discontinuous at larger concentrations, both transitions are separated by a tricritical point. Estimates of the central charge suggest that the critical line is in the Ising universality class, while the tricritical point has tricritical Ising (Blume-Emery-Griffiths) exponents. The isobaric curves of the total density as functions of the fugacity of small or large particles display a minimum in the disordered phase.

Wavelets in electronic structure calculations

NASA Astrophysics Data System (ADS)

Modisette, Jason Perry

1997-09-01

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

Effect of wood flour content on the optical color, surface chemistry, mechanical and morphological properties of wood flour/recycled high density polyethylene (rHDPE) composite

NASA Astrophysics Data System (ADS)

Sheng, Chan Kok; Amin, Khairul Anuar Mat; Kee, Kwa Bee; Hassan, Mohd Faiz; Ali, E. Ghapur E.

2018-05-01

In this study, effect of wood flour content on the color, surface chemistry, mechanical properties and surface morphology of wood-plastic composite (WPC) on different mixture ratios of recycled high density polyethylene (rHDPE) and wood flour were investigated in detail. The presence of wood flour in the composite indicates a significant total color change and a decrease of lightness. Functional groups of wood flour in WPC can be seen clearer from the Fourier transform infrared (FTIR) spectra as the wood flour content increases. The mechanical tensile testing shows that the tensile strength of Young's modulus is improved, whereas the strain and elongation at break were reduced by the addition of wood flour. The gap between the wood flour microvoid fibre and rHDPE matrix becomes closer when the wood flour content is increased as observed by scanning electron microscope (SEM) image. This finding implies a significant improvement on the interaction of interfacial adhesion between the rHDPE matrix and wood flour filler in the present WPC.

Crossover between superconductivity and magnetism in SrRuO3 mesocrystal embedded YBa2Cu3O7-x heterostructures.

PubMed

Suresh, Vandrangi; Lin, Jheng-Cyuan; Liu, Heng-Jui; Zhang, Zaoli; Chiang, Ping-Chih; Hsun, Yu-Ching; Chen, Yi-Chun; Lin, Jiunn-Yuan; Chu, Ying-Hao

2016-11-03

The competition between superconductivity and ferromagnetism poses great challenges and has attracted renewed interest for applications in novel spintronic devices. In order to emphasize their interactions, we fabricated a heterostructure composed of superconducting YBa 2 Cu 3 O 7-δ (YBCO) film embedded with itinerant ferromagnetic SrRuO 3 (SRO) mesocrystals. Starting from a doping concentration of 10 vol% of SRO mesocrystal in a YBCO matrix, corresponding to the density of SRO nanocrystals ∼5 × 10 9 cm -2 , which exhibits the typical characteristic of a metal-superconductor transition, and then increasing the magnetic interactions as a function of SRO embedment, the electronic correlation and the interplay between superconductivity and magnetism throughout the temperature regime were investigated. A metal-insulator transition in the normal state of YBCO and a crossover between superconductivity and magnetism at low temperatures were found upon increasing the density of nano-size SRO crystallites in the YBCO matrix as a consequence of competing interactions between these two ordered phases.

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

Magnetic phase diagrams of amorphous (Ni100-xFex)-metalloid alloys: The key role of the electronic density of states at the Fermi level for the onset of magnetic order

NASA Astrophysics Data System (ADS)

Kiss, L. F.; Bakonyi, I.

2017-11-01

There have been extended studies on the appearance of ferromagnetism in transition-metal-metalloid (MD) glasses. In particular, the paramagnetic (PM) to ferromagnetic (FM) transition has been investigated on numerous (Ni100-xFex)-MD alloys upon the introduction of Fe where MD can represent a combination of various metalloid elements, while keeping the metal/metalloid ratio constant. It has been reported that adding a sufficient amount of Fe to a Pauli PM Ni-MD alloy matrix first induces a spin-glass (SG) state at low temperatures which goes over to a PM state at higher temperatures. Beyond a certain Fe content, xc, the SG state transforms to a FM state upon increasing the temperature. By plotting the characteristic transition temperatures as a function of the Fe content, a magnetic phase diagram can be constructed for each Ni-Fe-MD system which has a multicritical point (MCP) at xc. By using the reported magnetic phase diagrams of various Ni-Fe-MD alloy systems, it is shown that the critical Fe content, xc scales inversely with the density of states at the Fermi level, N(EF), of the parent Ni-MD matrix. This means that the higher the N(EF), the lower the critical Fe content to induce ferromagnetism in the Ni-MD matrix. This is then discussed in terms of the Stoner enhancement factor, S, which characterizes the tendency of the matrix to become ferromagnetic.

Muscle-tendon units localization and activation level analysis based on high-density surface EMG array and NMF algorithm

NASA Astrophysics Data System (ADS)

Huang, Chengjun; Chen, Xiang; Cao, Shuai; Zhang, Xu

2016-12-01

Objective. Some skeletal muscles can be subdivided into smaller segments called muscle-tendon units (MTUs). The purpose of this paper is to propose a framework to locate the active region of the corresponding MTUs within a single skeletal muscle and to analyze the activation level varieties of different MTUs during a dynamic motion task. Approach. Biceps brachii and gastrocnemius were selected as targeted muscles and three dynamic motion tasks were designed and studied. Eight healthy male subjects participated in the data collection experiments, and 128-channel surface electromyographic (sEMG) signals were collected with a high-density sEMG electrode grid (a grid consists of 8 rows and 16 columns). Then the sEMG envelopes matrix was factorized into a matrix of weighting vectors and a matrix of time-varying coefficients by nonnegative matrix factorization algorithm. Main results. The experimental results demonstrated that the weightings vectors, which represent invariant pattern of muscle activity across all channels, could be used to estimate the location of MTUs and the time-varying coefficients could be used to depict the variation of MTUs activation level during dynamic motion task. Significance. The proposed method provides one way to analyze in-depth the functional state of MTUs during dynamic tasks and thus can be employed on multiple noteworthy sEMG-based applications such as muscle force estimation, muscle fatigue research and the control of myoelectric prostheses. This work was supported by the National Nature Science Foundation of China under Grant 61431017 and 61271138.

Single-Sided Noinvasive Inspection of Multielement Sample Using Fan-Beam Multiplexed Compton Scatter Tomography

DTIC Science & Technology

2000-05-01

a vector , ρ "# represents the set of voxel densities sorted into a vector , and ( )A ρ $# "# represents a 8 mapping of the voxel densities to...density vector in equation (4) suggests that solving for ρ "# by direct inversion is not possible, calling for an iterative technique beginning with...the vector of measured spectra, and D is the diagonal matrix of the inverse of the variances. The diagonal matrix provides weighting terms, which

Enhancing Post-Expansion Chondrogenic Potential of Costochondral Cells in Self-Assembled Neocartilage

PubMed Central

Murphy, Meghan K.; Huey, Daniel J.; Reimer, Andrew J.; Hu, Jerry C.; Athanasiou, Kyriacos A.

2013-01-01

The insufficient healing capacity of articular cartilage necessitates mechanically functional biologic tissue replacements. Using cells to form biomimetic cartilage implants is met with the challenges of cell scarcity and donor site morbidity, requiring expanded cells that possess the ability to generate robust neocartilage. To address this, this study assesses the effects of expansion medium supplementation (bFGF, TFP, FBS) and self-assembled construct seeding density (2, 3, 4 million cells/5 mm dia. construct) on the ability of costochondral cells to generate biochemically and biomechanically robust neocartilage. Results show TFP (1 ng/mL TGF-β1, 5 ng/mL bFGF, 10 ng/mL PDGF) supplementation of serum-free chondrogenic expansion medium enhances the post-expansion chondrogenic potential of costochondral cells, evidenced by increased glycosaminoglycan content, decreased type I/II collagen ratio, and enhanced compressive properties. Low density (2 million cells/construct) enhances matrix synthesis and tensile and compressive mechanical properties. Combined, TFP and Low density interact to further enhance construct properties. That is, with TFP, Low density increases type II collagen content by over 100%, tensile stiffness by over 300%, and compressive moduli by over 140%, compared with High density. In conclusion, the interaction of TFP and Low density seeding enhances construct material properties, allowing for a mechanically functional, biomimetic cartilage to be formed using clinically relevant costochondral cells. PMID:23437288

C library for topological study of the electronic charge density.

PubMed

Vega, David; Aray, Yosslen; Rodríguez, Jesús

2012-12-05

The topological study of the electronic charge density is useful to obtain information about the kinds of bonds (ionic or covalent) and the atom charges on a molecule or crystal. For this study, it is necessary to calculate, at every space point, the electronic density and its electronic density derivatives values up to second order. In this work, a grid-based method for these calculations is described. The library, implemented for three dimensions, is based on a multidimensional Lagrange interpolation in a regular grid; by differentiating the resulting polynomial, the gradient vector, the Hessian matrix and the Laplacian formulas were obtained for every space point. More complex functions such as the Newton-Raphson method (to find the critical points, where the gradient is null) and the Cash-Karp Runge-Kutta method (used to make the gradient paths) were programmed. As in some crystals, the unit cell has angles different from 90°, the described library includes linear transformations to correct the gradient and Hessian when the grid is distorted (inclined). Functions were also developed to handle grid containing files (grd from DMol® program, CUBE from Gaussian® program and CHGCAR from VASP® program). Each one of these files contains the data for a molecular or crystal electronic property (such as charge density, spin density, electrostatic potential, and others) in a three-dimensional (3D) grid. The library can be adapted to make the topological study in any regular 3D grid by modifying the code of these functions. Copyright © 2012 Wiley Periodicals, Inc.

Identification of metal s states in Sn-doped anatase by polarisation dependent hard X-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Regoutz, A.; Oropeza, F. E.; Poll, C. G.; Payne, D. J.; Palgrave, R. G.; Panaccione, G.; Borgatti, F.; Agrestini, S.; Utsumi, Y.; Tsuei, K. D.; Liao, Y. F.; Watson, G. W.; Egdell, R. G.

2016-03-01

The contributions of Sn 5s and Ti 4s states to the valence band electronic structure of Sn-doped anatase have been identified by hard X-ray photoelectron spectroscopy. The metal s state intensity is strongly enhanced relative to that of O 2p states at high photon energies due to matrix element effects when electrons are detected parallel to the direction of the polarisation vector of the synchrotron beam, but becomes negligible in the perpendicular direction. The experimental spectra in both polarisations are in good agreement with cross section and asymmetry parameter weighted partial densities of states derived from density functional theory calculations.

Hydrogen Permeability of Polymer Matrix Composites at Cryogenic Temperatures

NASA Technical Reports Server (NTRS)

Grenoble, Ray W.; Gates, Thomas S

2005-01-01

This paper presents experimental methods and results of an ongoing study of the correlation between damage state and hydrogen gas permeability of laminated composite materials under mechanical strains and thermal loads. A specimen made from IM-7/977-2 composite material has been mechanically cycled at room temperature to induce microcrack damage. Crack density and tensile modulus were observed as functions of number of cycles. Damage development was found to occur most quickly in the off-axis plies near the outside of the laminate. Permeability measurements were made after 170,000 cycles and 430,000 cycles. Leak rate was found to depend on applied mechanical strain, crack density, and test temperature.

Theoretical Model for Volume Fraction of UC, 235U Enrichment, and Effective Density of Final U 10Mo Alloy

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

Devaraj, Arun; Prabhakaran, Ramprashad; Joshi, Vineet V.

2016-04-12

The purpose of this document is to provide a theoretical framework for (1) estimating uranium carbide (UC) volume fraction in a final alloy of uranium with 10 weight percent molybdenum (U-10Mo) as a function of final alloy carbon concentration, and (2) estimating effective 235U enrichment in the U-10Mo matrix after accounting for loss of 235U in forming UC. This report will also serve as a theoretical baseline for effective density of as-cast low-enriched U-10Mo alloy. Therefore, this report will serve as the baseline for quality control of final alloy carbon content

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

Miller, William H., E-mail: millerwh@berkeley.edu; Cotton, Stephen J., E-mail: StephenJCotton47@gmail.com

It is pointed out that the classical phase space distribution in action-angle (a-a) variables obtained from a Wigner function depends on how the calculation is carried out: if one computes the standard Wigner function in Cartesian variables (p, x), and then replaces p and x by their expressions in terms of a-a variables, one obtains a different result than if the Wigner function is computed directly in terms of the a-a variables. Furthermore, the latter procedure gives a result more consistent with classical and semiclassical theory—e.g., by incorporating the Bohr-Sommerfeld quantization condition (quantum states defined by integer values of themore » action variable) as well as the Heisenberg correspondence principle for matrix elements of an operator between such states—and has also been shown to be more accurate when applied to electronically non-adiabatic applications as implemented within the recently developed symmetrical quasi-classical (SQC) Meyer-Miller (MM) approach. Moreover, use of the Wigner function (obtained directly) in a-a variables shows how our standard SQC/MM approach can be used to obtain off-diagonal elements of the electronic density matrix by processing in a different way the same set of trajectories already used (in the SQC/MM methodology) to obtain the diagonal elements.« less

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

Miller, William H.; Cotton, Stephen J.

It is pointed out that the classical phase space distribution in action-angle (a-a) variables obtained from a Wigner function depends on how the calculation is carried out: if one computes the standard Wigner function in Cartesian variables (p, x), and then replaces p and x by their expressions in terms of a-a variables, one obtains a different result than if the Wigner function is computed directly in terms of the a-a variables. Furthermore, the latter procedure gives a result more consistent with classical and semiclassical theory - e.g., by incorporating the Bohr-Sommerfeld quantization condition (quantum states defined by integer valuesmore » of the action variable) as well as the Heisenberg correspondence principle for matrix elements of an operator between such states - and has also been shown to be more accurate when applied to electronically non-adiabatic applications as implemented within the recently developed symmetrical quasi-classical (SQC) Meyer-Miller (MM) approach. Moreover, use of the Wigner function (obtained directly) in a-a variables shows how our standard SQC/MM approach can be used to obtain off-diagonal elements of the electronic density matrix by processing in a different way the same set of trajectories already used (in the SQC/MM methodology) to obtain the diagonal elements.« less

Generalized Wishart Mixtures for Unsupervised Classification of PolSAR Data

NASA Astrophysics Data System (ADS)

Li, Lan; Chen, Erxue; Li, Zengyuan

2013-01-01

This paper presents an unsupervised clustering algorithm based upon the expectation maximization (EM) algorithm for finite mixture modelling, using the complex wishart probability density function (PDF) for the probabilities. The mixture model enables to consider heterogeneous thematic classes which could not be better fitted by the unimodal wishart distribution. In order to make it fast and robust to calculate, we use the recently proposed generalized gamma distribution (GΓD) for the single polarization intensity data to make the initial partition. Then we use the wishart probability density function for the corresponding sample covariance matrix to calculate the posterior class probabilities for each pixel. The posterior class probabilities are used for the prior probability estimates of each class and weights for all class parameter updates. The proposed method is evaluated and compared with the wishart H-Alpha-A classification. Preliminary results show that the proposed method has better performance.

Local Descriptors of Dynamic and Nondynamic Correlation.

PubMed

Ramos-Cordoba, Eloy; Matito, Eduard

2017-06-13

Quantitatively accurate electronic structure calculations rely on the proper description of electron correlation. A judicious choice of the approximate quantum chemistry method depends upon the importance of dynamic and nondynamic correlation, which is usually assesed by scalar measures. Existing measures of electron correlation do not consider separately the regions of the Cartesian space where dynamic or nondynamic correlation are most important. We introduce real-space descriptors of dynamic and nondynamic electron correlation that admit orbital decomposition. Integration of the local descriptors yields global numbers that can be used to quantify dynamic and nondynamic correlation. Illustrative examples over different chemical systems with varying electron correlation regimes are used to demonstrate the capabilities of the local descriptors. Since the expressions only require orbitals and occupation numbers, they can be readily applied in the context of local correlation methods, hybrid methods, density matrix functional theory, and fractional-occupancy density functional theory.

Comparative analysis of quantum cascade laser modeling based on density matrices and non-equilibrium Green's functions

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

Lindskog, M., E-mail: martin.lindskog@teorfys.lu.se; Wacker, A.; Wolf, J. M.

2014-09-08

We study the operation of an 8.5 μm quantum cascade laser based on GaInAs/AlInAs lattice matched to InP using three different simulation models based on density matrix (DM) and non-equilibrium Green's function (NEGF) formulations. The latter advanced scheme serves as a validation for the simpler DM schemes and, at the same time, provides additional insight, such as the temperatures of the sub-band carrier distributions. We find that for the particular quantum cascade laser studied here, the behavior is well described by simple quantum mechanical estimates based on Fermi's golden rule. As a consequence, the DM model, which includes second order currents,more » agrees well with the NEGF results. Both these simulations are in accordance with previously reported data and a second regrown device.« less

Competing phases, phase separation, and coexistence in the extended one-dimensional bosonic Hubbard model

DOE PAGES

Batrouni, G. G.; Rousseau, V. G.; Scalettar, R. T.; ...

2014-11-17

Here, we study the phase diagram of the one-dimensional bosonic Hubbard model with contact (U) and near neighbor (V ) interactions focusing on the gapped Haldane insulating (HI) phase which is characterized by an exotic nonlocal order parameter. The parameter regime (U, V and μ) where this phase exists and how it competes with other phases such as the supersolid (SS) phase, is incompletely understood. We use the Stochastic Green Function quantum Monte Carlo algorithm as well as the density matrix renormalization group to map out the phase diagram. The HI exists only at = 1, the SS phase existsmore » for a very wide range of parameters (including commensurate fillings) and displays power law decay in the one body Green function were our main conclusions. Additionally, we show that at fixed integer density, the system exhibits phase separation in the (U, V ) plane.« less

Infrared spectroscopy and density functional calculations on titanium-dinitrogen complexes

NASA Astrophysics Data System (ADS)

Yoo, Hae-Wook; Choi, Changhyeok; Cho, Soo Gyeong; Jung, Yousung; Choi, Myong Yong

2018-04-01

Titanium-nitrogen complexes were generated by laser ablated titanium (Ti) atoms and N2 gas molecules in this study. These complexes were isolated on the pre-deposited solid Ar matrix on the pre-cooled KBr window (T ∼ 5.4 K), allowing infrared spectra to be measured. Laser ablation experiments with 15N2 isotope provided distinct isotopic shifts in the infrared spectra that strongly implicated the formation of titanium-nitrogen complexes, Ti(NN)x. Density functional theory (DFT) calculations were employed to investigate the molecular structures, electronic ground state, relative energies, and IR frequencies of the anticipated Ti(NN)x complexes. Based on laser ablation experiments and DFT calculations, we were able to assign multiple Ti(NN)x (x = 1-6) species. Particularly, Ti(NN)5 and Ti(NN)6, which have high nitrogen content, may serve as good precursors in preparing polynitrogens.

Self-amplified CMOS image sensor using a current-mode readout circuit

NASA Astrophysics Data System (ADS)

Santos, Patrick M.; de Lima Monteiro, Davies W.; Pittet, Patrick

2014-05-01

The feature size of the CMOS processes decreased during the past few years and problems such as reduced dynamic range have become more significant in voltage-mode pixels, even though the integration of more functionality inside the pixel has become easier. This work makes a contribution on both sides: the possibility of a high signal excursion range using current-mode circuits together with functionality addition by making signal amplification inside the pixel. The classic 3T pixel architecture was rebuild with small modifications to integrate a transconductance amplifier providing a current as an output. The matrix with these new pixels will operate as a whole large transistor outsourcing an amplified current that will be used for signal processing. This current is controlled by the intensity of the light received by the matrix, modulated pixel by pixel. The output current can be controlled by the biasing circuits to achieve a very large range of output signal levels. It can also be controlled with the matrix size and this permits a very high degree of freedom on the signal level, observing the current densities inside the integrated circuit. In addition, the matrix can operate at very small integration times. Its applications would be those in which fast imaging processing, high signal amplification are required and low resolution is not a major problem, such as UV image sensors. Simulation results will be presented to support: operation, control, design, signal excursion levels and linearity for a matrix of pixels that was conceived using this new concept of sensor.

Construction of CASCI-type wave functions for very large active spaces.

PubMed

Boguslawski, Katharina; Marti, Konrad H; Reiher, Markus

2011-06-14

We present a procedure to construct a configuration-interaction expansion containing arbitrary excitations from an underlying full-configuration-interaction-type wave function defined for a very large active space. Our procedure is based on the density-matrix renormalization group (DMRG) algorithm that provides the necessary information in terms of the eigenstates of the reduced density matrices to calculate the coefficient of any basis state in the many-particle Hilbert space. Since the dimension of the Hilbert space scales binomially with the size of the active space, a sophisticated Monte Carlo sampling routine is employed. This sampling algorithm can also construct such configuration-interaction-type wave functions from any other type of tensor network states. The configuration-interaction information obtained serves several purposes. It yields a qualitatively correct description of the molecule's electronic structure, it allows us to analyze DMRG wave functions converged for the same molecular system but with different parameter sets (e.g., different numbers of active-system (block) states), and it can be considered a balanced reference for the application of a subsequent standard multi-reference configuration-interaction method.

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

PubMed

Abbey, Colette A; Bayless, Kayla J

2014-09-01

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

Spin-adapted matrix product states and operators

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

Keller, Sebastian, E-mail: sebastian.keller@phys.chem.ethz.ch; Reiher, Markus, E-mail: markus.reiher@phys.chem.ethz.ch

Matrix product states (MPSs) and matrix product operators (MPOs) allow an alternative formulation of the density matrix renormalization group algorithm introduced by White. Here, we describe how non-abelian spin symmetry can be exploited in MPSs and MPOs by virtue of the Wigner–Eckart theorem at the example of the spin-adapted quantum chemical Hamiltonian operator.

Gaussian windows: A tool for exploring multivariate data

NASA Technical Reports Server (NTRS)

Jaeckel, Louis A.

1990-01-01

Presented here is a method for interactively exploring a large set of quantitative multivariate data, in order to estimate the shape of the underlying density function. It is assumed that the density function is more or less smooth, but no other specific assumptions are made concerning its structure. The local structure of the data in a given region may be examined by viewing the data through a Gaussian window, whose location and shape are chosen by the user. A Gaussian window is defined by giving each data point a weight based on a multivariate Gaussian function. The weighted sample mean and sample covariance matrix are then computed, using the weights attached to the data points. These quantities are used to compute an estimate of the shape of the density function in the window region. The local structure of the data is described by a method similar to the method of principal components. By taking many such local views of the data, we can form an idea of the structure of the data set. The method is applicable in any number of dimensions. The method can be used to find and describe simple structural features such as peaks, valleys, and saddle points in the density function, and also extended structures in higher dimensions. With some practice, we can apply our geometrical intuition to these structural features in any number of dimensions, so that we can think about and describe the structure of the data. Since the computations involved are relatively simple, the method can easily be implemented on a small computer.

Band gap engineering in finite elongated graphene nanoribbon heterojunctions: Tight-binding model

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

Tayo, Benjamin O.

2015-08-15

A simple model based on the divide and conquer rule and tight-binding (TB) approximation is employed for studying the role of finite size effect on the electronic properties of elongated graphene nanoribbon (GNR) heterojunctions. In our model, the GNR heterojunction is divided into three parts: a left (L) part, middle (M) part, and right (R) part. The left part is a GNR of width W{sub L}, the middle part is a GNR of width W{sub M}, and the right part is a GNR of width W{sub R}. We assume that the left and right parts of the GNR heterojunction interactmore » with the middle part only. Under this approximation, the Hamiltonian of the system can be expressed as a block tridiagonal matrix. The matrix elements of the tridiagonal matrix are computed using real space nearest neighbor orthogonal TB approximation. The electronic structure of the GNR heterojunction is analyzed by computing the density of states. We demonstrate that for heterojunctions for which W{sub L} = W{sub R}, the band gap of the system can be tuned continuously by varying the length of the middle part, thus providing a new approach to band gap engineering in GNRs. Our TB results were compared with calculations employing divide and conquer rule in combination with density functional theory (DFT) and were found to agree nicely.« less

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.

Quantum confinement effects on electronic photomobilities at nanostructured semiconductor surfaces: Si(111) without and with adsorbed Ag clusters

NASA Astrophysics Data System (ADS)

Hembree, Robert H.; Vazhappilly, Tijo; Micha, David A.

2017-12-01

The conductivity of holes and electrons photoexcited in Si slabs is affected by the slab thickness and by adsorbates. The mobilities of those charged carriers depend on how many layers compose the slab, and this has important scientific and technical consequences for the understanding of photovoltaic materials. A previously developed general computational procedure combining density matrix and electronic band structure treatments has been applied to extensive calculations of mobilities of photoexcited electrons and holes at Si(111) nanostructured surfaces with varying slab thickness and for varying photon energies, to investigate the expected change in mobility magnitudes as the slab thickness is increased. Results have been obtained with and without adsorbed silver clusters for comparison of their optical and photovoltaic properties. Band states were generated using a modified ab initio density functional treatment with the PBE exchange and correlation density functionals and with periodic boundary conditions for large atomic supercells. An energy gap correction was applied to the unoccupied orbital energies of each band structure by running more accurate HSE hybrid functional calculations for a Si(111) slab. Photoexcited state populations for slabs with 6, 8, 10, and 12 layers were generated using a steady state reduced density matrix including dissipative effects due to energy exchange with excitons and phonons in the medium. Mobilities have been calculated from the derivatives of voltage-driven electronic energies with respect to electronic momentum, for each energy band and for the average over bands. Results show two clear trends: (a) adding Ag increases the hole photomobilities and (b) decreasing the slab thickness increases hole photomobilities. The increased hole populations in 6- and 8-layer systems and the large increase in hole mobility for these thinner slabs can be interpreted as a quantum confinement effect of hole orbitals. As the slab thickness increases to ten and twelve layers, the effect of silver adsorbates decreases leading to smaller relative enhancements to the conduction electron and hole mobilities, but the addition of the silver nanoclusters still increases the absorbance of light and the mobility of holes compared to their mobilities in the pure Si slabs.

Floating matrix tablets based on low density foam powder: effects of formulation and processing parameters on drug release.

PubMed

Streubel, A; Siepmann, J; Bodmeier, R

2003-01-01

The aim of this study was to develop and physicochemically characterize single unit, floating controlled drug delivery systems consisting of (i). polypropylene foam powder, (ii). matrix-forming polymer(s), (iii). drug, and (iv). filler (optional). The highly porous foam powder provided low density and, thus, excellent in vitro floating behavior of the tablets. All foam powder-containing tablets remained floating for at least 8 h in 0.1 N HCl at 37 degrees C. Different types of matrix-forming polymers were studied: hydroxypropyl methylcellulose (HPMC), polyacrylates, sodium alginate, corn starch, carrageenan, gum guar and gum arabic. The tablets eroded upon contact with the release medium, and the relative importance of drug diffusion, polymer swelling and tablet erosion for the resulting release patterns varied significantly with the type of matrix former. The release rate could effectively be modified by varying the "matrix-forming polymer/foam powder" ratio, the initial drug loading, the tablet geometry (radius and height), the type of matrix-forming polymer, the use of polymer blends and the addition of water-soluble or water-insoluble fillers (such as lactose or microcrystalline cellulose). The floating behavior of the low density drug delivery systems could successfully be combined with accurate control of the drug release patterns.

Nonlinear optical microscopy reveals invading endothelial cells anisotropically alter three-dimensional collagen matrices

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

Lee, P.-F.; Yeh, Alvin T.; Bayless, Kayla J.

The interactions between endothelial cells (ECs) and the extracellular matrix (ECM) are fundamental in mediating various steps of angiogenesis, including cell adhesion, migration and sprout formation. Here, we used a noninvasive and non-destructive nonlinear optical microscopy (NLOM) technique to optically image endothelial sprouting morphogenesis in three-dimensional (3D) collagen matrices. We simultaneously captured signals from collagen fibers and endothelial cells using second harmonic generation (SHG) and two-photon excited fluorescence (TPF), respectively. Dynamic 3D imaging revealed EC interactions with collagen fibers along with quantifiable alterations in collagen matrix density elicited by EC movement through and morphogenesis within the matrix. Specifically, we observedmore » increased collagen density in the area between bifurcation points of sprouting structures and anisotropic increases in collagen density around the perimeter of lumenal structures, but not advancing sprout tips. Proteinase inhibition studies revealed membrane-associated matrix metalloproteinase were utilized for sprout advancement and lumen expansion. Rho-associated kinase (p160ROCK) inhibition demonstrated that the generation of cell tension increased collagen matrix alterations. This study followed sprouting ECs within a 3D matrix and revealed that the advancing structures recognize and significantly alter their extracellular environment at the periphery of lumens as they progress.« less

QCDNUM: Fast QCD evolution and convolution

NASA Astrophysics Data System (ADS)

Botje, M.

2011-02-01

The QCDNUM program numerically solves the evolution equations for parton densities and fragmentation functions in perturbative QCD. Un-polarised parton densities can be evolved up to next-to-next-to-leading order in powers of the strong coupling constant, while polarised densities or fragmentation functions can be evolved up to next-to-leading order. Other types of evolution can be accessed by feeding alternative sets of evolution kernels into the program. A versatile convolution engine provides tools to compute parton luminosities, cross-sections in hadron-hadron scattering, and deep inelastic structure functions in the zero-mass scheme or in generalised mass schemes. Input to these calculations are either the QCDNUM evolved densities, or those read in from an external parton density repository. Included in the software distribution are packages to calculate zero-mass structure functions in un-polarised deep inelastic scattering, and heavy flavour contributions to these structure functions in the fixed flavour number scheme. Program summaryProgram title: QCDNUM version: 17.00 Catalogue identifier: AEHV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Public Licence No. of lines in distributed program, including test data, etc.: 45 736 No. of bytes in distributed program, including test data, etc.: 911 569 Distribution format: tar.gz Programming language: Fortran-77 Computer: All Operating system: All RAM: Typically 3 Mbytes Classification: 11.5 Nature of problem: Evolution of the strong coupling constant and parton densities, up to next-to-next-to-leading order in perturbative QCD. Computation of observable quantities by Mellin convolution of the evolved densities with partonic cross-sections. Solution method: Parametrisation of the parton densities as linear or quadratic splines on a discrete grid, and evolution of the spline coefficients by solving (coupled) triangular matrix equations with a forward substitution algorithm. Fast computation of convolution integrals as weighted sums of spline coefficients, with weights derived from user-given convolution kernels. Restrictions: Accuracy and speed are determined by the density of the evolution grid. Running time: Less than 10 ms on a 2 GHz Intel Core 2 Duo processor to evolve the gluon density and 12 quark densities at next-to-next-to-leading order over a large kinematic range.

Improved Dielectric Properties and Energy Storage Density of Poly(vinylidene fluoride-co-hexafluoropropylene) Nanocomposite with Hydantoin Epoxy Resin Coated BaTiO3.

PubMed

Luo, Hang; Zhang, Dou; Jiang, Chao; Yuan, Xi; Chen, Chao; Zhou, Kechao

2015-04-22

Energy storage materials are urgently demanded in modern electric power supply and renewable energy systems. The introduction of inorganic fillers to polymer matrix represents a promising avenue for the development of high energy density storage materials, which combines the high dielectric constant of inorganic fillers with supernal dielectric strength of polymer matrix. However, agglomeration and phase separation of inorganic fillers in the polymer matrix remain the key barriers to promoting the practical applications of the composites for energy storage. Here, we developed a low-cost and environmentally friendly route to modifying BaTiO3 (BT) nanoparticles by a kind of water-soluble hydantoin epoxy resin. The modified BT nanoparticles exhibited homogeneous dispersion in the ferroelectric polymer poly(vinylidene fluoride-co-hexafluoropropylene) (P(VDF-HFP)) matrix and strong interfacial adhesion with the polymer matrix. The dielectric constants of the nanocomposites increased significantly with the increase of the coated BT loading, while the dielectric loss of the nanocomposites was still as low as that of the pure P(VDF-HFP). The energy storage density of the nanocomposites was largely enhanced with the coated BT loading at the same electric field. The nanocomposite with 20 vol % BT exhibited an estimated maximum energy density of 8.13 J cm(-3), which was much higher than that of pure P(VDF-HFP) and other dielectric polymers. The findings of this research could provide a feasible approach to produce high energy density materials for practical application in energy storage.

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

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

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue

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

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

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

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue

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

Mussel-inspired Fluoro-Polydopamine Functionalization of Titanium Dioxide Nanowires for Polymer Nanocomposites with Significantly Enhanced Energy Storage Capability.

PubMed

Wang, Guanyao; Huang, Xingyi; Jiang, Pingkai

2017-02-22

High-dielectric-constant polymer nanocomposites are demonstrated to show great promise as energy storage materials. However, the large electrical mismatch and incompatibility between nanofillers and polymer matrix usually give rise to significantly reduced breakdown strength and weak energy storage capability. Therefore, rational selection and elaborate functionalization of nanofillers to optimize the performance of polymer nanocomposites are vital. Herein, inspired by adhesive proteins in mussels, a facile modification by fluoro-polydopamine is employed to reinforce the compatibility of TiO 2 nanowires in the fluoropolymer matrix. The loading of 2.5 vol % f-DOPA@TiO 2 NWs leads to an ultrahigh discharged energy density of 11.48 J cm -3 at 530 MV m -1 , more than three times of commercial biaxial-oriented polypropylene (BOPP, 3.56 J cm -3 at 600 MV m -1 ). A gratifying high energy density of 9.12 J cm -3 has also been obtained with nanofiller loading as high as 15 vol % at 360 MV m -1 , which is nearly double to that of pure P(VDF-HFP) (4.76 J cm -3 at 360 MV m -1 ). This splendid energy storage capability seems to rival or exceed most of previously reported nano-TiO 2 based nanocomposites. The methods presented here provide deep insights into the design of polymer nanocomposites for energy storage applications.

Mussel-inspired Fluoro-Polydopamine Functionalization of Titanium Dioxide Nanowires for Polymer Nanocomposites with Significantly Enhanced Energy Storage Capability

NASA Astrophysics Data System (ADS)

Wang, Guanyao; Huang, Xingyi; Jiang, Pingkai

2017-02-01

High-dielectric-constant polymer nanocomposites are demonstrated to show great promise as energy storage materials. However, the large electrical mismatch and incompatibility between nanofillers and polymer matrix usually give rise to significantly reduced breakdown strength and weak energy storage capability. Therefore, rational selection and elaborate functionalization of nanofillers to optimize the performance of polymer nanocomposites are vital. Herein, inspired by adhesive proteins in mussels, a facile modification by fluoro-polydopamine is employed to reinforce the compatibility of TiO2 nanowires in the fluoropolymer matrix. The loading of 2.5 vol % f-DOPA@TiO2 NWs leads to an ultrahigh discharged energy density of 11.48 J cm-3 at 530 MV m-1, more than three times of commercial biaxial-oriented polypropylene (BOPP, 3.56 J cm-3 at 600 MV m-1). A gratifying high energy density of 9.12 J cm-3 has also been obtained with nanofiller loading as high as 15 vol % at 360 MV m-1, which is nearly double to that of pure P(VDF-HFP) (4.76 J cm-3 at 360 MV m-1). This splendid energy storage capability seems to rival or exceed most of previously reported nano-TiO2 based nanocomposites. The methods presented here provide deep insights into the design of polymer nanocomposites for energy storage applications.

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

DOE PAGES

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue; ...

2017-12-01

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

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

DOE PAGES

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue; ...

2017-08-24

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

Composites of low-density trialuminides: Particulate and long fiber reinforcements

NASA Technical Reports Server (NTRS)

Kumar, K. S.; Dipietro, M. S.; Brown, S. A.; Whittenberger, J. D.

1992-01-01

An examination of the ternary L1(sub 2) trialuminides, Al66Ti25Mn9, Al67Ti25Cr8, and Al22Ti8Fe3 in compression, bending, and tension revealed that none of these compounds exhibited a desirable balance of strength, ductility, and oxidation resistance. Subsequently, specific quaternary and quinary compositions were cast, homogenized, and isothermally forged. Both, the monolithic material and its particulate reinforced counterparts were examined in compression, three point bend, and tension as a function of temperature, and at high temperatures as a function of strain rate. An alternate approach that was examined in this program to enhance the low temperature damage tolerance of these materials was to incorporate long refractory metal wires in the matrix. In summary, it appears that of the various matrix compositions examined, ternary Al66Ti25Mn9 exhibits the best balance in strength, ductility, and oxidation resistance. Although the idea of refractory metal wire reinforcement is an attractive one, a successful combination remains to be identified.

Double and Triple Si-H-M Bridge Bonds: Matrix Infrared Spectra and Theoretical Calculations for Reaction Products of Silane with Ti, Zr, and Hf Atoms.

PubMed

Xu, Bing; Shi, Peipei; Huang, Tengfei; Wang, Xuefeng; Andrews, Lester

2017-05-25

Infrared spectra of matrix isolated dibridged Si(μ-H) 2 MH 2 and tribridged Si(μ-H) 3 MH molecules (M = Zr and Hf) were observed following the laser-ablated metal atom reactions with SiH 4 during condensation in excess argon and neon, but only the latter species was observed with titanium. Assignments of the major vibrational modes, which included terminal MH, MH 2 and hydrogen bridge Si-H-M stretching modes, were confirmed by the appropriate SiD 4 isotopic shifts and density functional vibrational frequency calculations (B3LYP and BPW91). The Si-H-M hydrogen bridge bond is calculated as weak covalent interaction and compared with the C-H···M agostic interaction in terms of electron localization function (ELF) analysis and noncovalent interaction index (NCI) calculations. Furthermore, the different products of Ti, Zr, and Hf reactions with SiH 4 are discussed in detail.

Phase-field study of ripening and rearrangement of precipitates under chemomechanical coupling

NASA Astrophysics Data System (ADS)

Schwarze, C.; Gupta, A.; Hickel, T.; Darvishi Kamachali, R.

2017-05-01

We investigate the evolution of large number of δ' coherent precipitates from a supersaturated Al-8 at.% Li alloy using large-scale phase-field simulations. A chemomechanical cross-coupling between mechanical relaxation and diffusion is taken into account by considering the dependence of elastic constants of the matrix phase onto the local concentration of solute atoms. The elastic constants as a function of solute concentration have been obtained using density functional theory calculations. As a result of the coupling, inverse ripening has been observed where the smaller precipitates grow at the expense of the larger ones. This is due to size-dependent concentration gradients existing around the precipitates. At the same time, precipitates rearrange themselves as a consequence of minimization of the total elastic energy of the system. It is found that the anisotropy of the chemomechanical coupling leads to the formation of new patterns of elasticity in the matrix thereby resulting in new alignments of the precipitates.

Energy spectrum and electrical conductivity of graphene with a nitrogen impurity

NASA Astrophysics Data System (ADS)

Repetskii, S. P.; Vyshivanaya, I. G.; Skotnikov, V. A.; Yatsenyuk, A. A.

2015-04-01

The electronic structure of graphene with a nitrogen impurity has been studied based on the model of tight binding using exchange-correlation potentials in the density-functional theory. Wave functions of 2 s and 2 p states of neutral noninteracting carbon atoms have been chosen as the basis. When studying the matrix elements of the Hamiltonian, the first three coordination shells have been taken into account. It has been established that the hybridization of electron-energy bands leads to the splitting of the electron energy spectrum near the Fermi level. Due to the overlap of the energy bands, the arising gap behaves as a quasi-gap, in which the density of the electron levels is much lower than in the rest of the spectrum. It has been established that the conductivity of graphene decreases with increasing nitrogen concentration. Since the increase in the nitrogen concentration leads to an increase in the density of states at the Fermi level, the decrease in the conductivity is due to a sharper decrease in the time of relaxation of the electron sates.

Universality and Thouless energy in the supersymmetric Sachdev-Ye-Kitaev model

NASA Astrophysics Data System (ADS)

García-García, Antonio M.; Jia, Yiyang; Verbaarschot, Jacobus J. M.

2018-05-01

We investigate the supersymmetric Sachdev-Ye-Kitaev (SYK) model, N Majorana fermions with infinite range interactions in 0 +1 dimensions. We have found that, close to the ground state E ≈0 , discrete symmetries alter qualitatively the spectral properties with respect to the non-supersymmetric SYK model. The average spectral density at finite N , which we compute analytically and numerically, grows exponentially with N for E ≈0 . However the chiral condensate, which is normalized with respect the total number of eigenvalues, vanishes in the thermodynamic limit. Slightly above E ≈0 , the spectral density grows exponentially with the energy. Deep in the quantum regime, corresponding to the first O (N ) eigenvalues, the average spectral density is universal and well described by random matrix ensembles with chiral and superconducting discrete symmetries. The dynamics for E ≈0 is investigated by level fluctuations. Also in this case we find excellent agreement with the prediction of chiral and superconducting random matrix ensembles for eigenvalue separations smaller than the Thouless energy, which seems to scale linearly with N . Deviations beyond the Thouless energy, which describes how ergodicity is approached, are universally characterized by a quadratic growth of the number variance. In the time domain, we have found analytically that the spectral form factor g (t ), obtained from the connected two-level correlation function of the unfolded spectrum, decays as 1 /t2 for times shorter but comparable to the Thouless time with g (0 ) related to the coefficient of the quadratic growth of the number variance. Our results provide further support that quantum black holes are ergodic and therefore can be classified by random matrix theory.

Tuning three-dimensional collagen matrix stiffness independently of collagen concentration modulates endothelial cell behavior.

PubMed

Mason, Brooke N; Starchenko, Alina; Williams, Rebecca M; Bonassar, Lawrence J; Reinhart-King, Cynthia A

2013-01-01

Numerous studies have described the effects of matrix stiffening on cell behavior using two-dimensional synthetic surfaces; however, less is known about the effects of matrix stiffening on cells embedded in three-dimensional in vivo-like matrices. A primary limitation in investigating the effects of matrix stiffness in three dimensions is the lack of materials that can be tuned to control stiffness independently of matrix density. Here, we use collagen-based scaffolds where the mechanical properties are tuned using non-enzymatic glycation of the collagen in solution, prior to polymerization. Collagen solutions glycated prior to polymerization result in collagen gels with a threefold increase in compressive modulus without significant changes to the collagen architecture. Using these scaffolds, we show that endothelial cell spreading increases with matrix stiffness, as does the number and length of angiogenic sprouts and the overall spheroid outgrowth. Differences in sprout length are maintained even when the receptor for advanced glycation end products is inhibited. Our results demonstrate the ability to de-couple matrix stiffness from matrix density and structure in collagen gels, and that increased matrix stiffness results in increased sprouting and outgrowth. Copyright © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Investigations on the properties of NH4HCO3 filled natural rubber based magnetorheological elastomers (MREs)

NASA Astrophysics Data System (ADS)

Fan, Lili; Wang, Guoping; Wang, Wenju; Shi, Guanxin; Yang, Fufeng; Rui, Xiaoting

2018-04-01

Various anisotropic magnetorheological elastomers (MREs) were synthesized using the rubber mixing technique. Magnetic and temperature distributions of the experimental equipment and test instruments were analyzed by the ANSYS. NH4HCO3 was filled in the natural rubber matrix to modify properties of MREs. Microstructures and compositions of samples were studied by the scanning electron microscope (SEM), the energy dispersive x-ray spectroscopy (EDAX) analysis and x-ray powder diffraction (XRD). Via vibrating sample magnetometer (VSM) and density functional theory (DFT) method, the magnetic property of carbonyl iron (CI) was illuminated. The shear storage modulus and MR effect of MREs were investigated by the dynamic mechanical analyzer (DMA). It indicated that distributions of magnetic and temperature in the experimental and testing devices were uniform. Before vulcanization, CI particles were uniformly distributed in the matrix, while a CI chain structure was formed and embedded in the matrix after the vulcanization process. Moderate addition of NH4HCO3 accelerated the rubber vulcanization and enhanced the MR effect.

Large-Area High-Performance Flexible Pressure Sensor with Carbon Nanotube Active Matrix for Electronic Skin.

PubMed

Nela, Luca; Tang, Jianshi; Cao, Qing; Tulevski, George; Han, Shu-Jen

2018-03-14

Artificial "electronic skin" is of great interest for mimicking the functionality of human skin, such as tactile pressure sensing. Several important performance metrics include mechanical flexibility, operation voltage, sensitivity, and accuracy, as well as response speed. In this Letter, we demonstrate a large-area high-performance flexible pressure sensor built on an active matrix of 16 × 16 carbon nanotube thin-film transistors (CNT TFTs). Made from highly purified solution tubes, the active matrix exhibits superior flexible TFT performance with high mobility and large current density, along with a high device yield of nearly 99% over 4 inch sample area. The fully integrated flexible pressure sensor operates within a small voltage range of 3 V and shows superb performance featuring high spatial resolution of 4 mm, faster response than human skin (<30 ms), and excellent accuracy in sensing complex objects on both flat and curved surfaces. This work may pave the road for future integration of high-performance electronic skin in smart robotics and prosthetic solutions.

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.

Confinement of anomalous liquids in nanoporous matrices.

PubMed

Strekalova, Elena G; Luo, Jiayuan; Stanley, H Eugene; Franzese, Giancarlo; Buldyrev, Sergey V

2012-09-07

Using molecular dynamics simulations, we investigate the effects of different nanoconfinements on complex liquids-e.g., colloids or protein solutions-with density anomalies and a liquid-liquid phase transition (LLPT). In all the confinements, we find a strong depletion effect with a large increase in liquid density near the confining surface. If the nanoconfinement is modeled by an ordered matrix of nanoparticles, we find that the anomalies are preserved. On the contrary, if the confinement is modeled by a disordered matrix of nanoparticles, we find a drastically different phase diagram: the LLPT shifts to lower pressures and temperatures, and the anomalies become weaker, as the disorder increases. We find that the density heterogeneities induced by the disordered matrix are responsible for the weakening of the LLPT and the disappearance of the anomalies.

Quantum Effects at a Proton Relaxation at Low Temperatures

NASA Astrophysics Data System (ADS)

Kalytka, V. A.; Korovkin, M. V.

2016-11-01

Quantum effects during migratory polarization in multi-well crystals (including multi-well silicates and crystalline hydrates) are investigated in a variable electric field at low temperatures by direct quantum-mechanical calculations. Based on analytical solution of the quantum Liouville kinetic equation in the linear approximation for the polarizing field, the non-stationary density matrix is calculated for an ensemble of non-interacting protons moving in the field of one-dimensional multi-well crystal potential relief of rectangular shape. An expression for the complex dielectric constant convenient for a comparison with experiment and calculation of relaxer parameters is derived using the nonequilibrium polarization density matrix. The density matrix apparatus can be used for analytical investigation of the quantum mechanism of spontaneous polarization of a ferroelectric material (KDP and DKDP).

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.

Caracterisation dielectrique de nanocomposites LLDPE/nano-glaises: Fidelite des techniques et proprietes electriques

NASA Astrophysics Data System (ADS)

Daran-Daneau, Cyril

In order to answer the energetic needs of the future, insulation, which is the central piece of high voltage equipment, has to be reinvented. Nanodielectrics seem to be the promise of a mayor technological breakthrough. Based on nanocomposites with a linear low density polyethylene matrix reinforced by nano-clays and manufactured from a commercial master batch, the present thesis aims to characterise the accuracy of measurement techniques applied on nanodielectrics and also the dielectric properties of these materials. Thus, dielectric spectroscopy accuracy both in frequency and time domain is analysed with a specific emphasis on the impact of gold sputtering of the samples and on the measurements transposition from time domain to frequency domain. Also, when measuring dielectric strength, the significant role of surrounding medium and sample thickness on the variation of the alpha scale factor is shown and analysed in relation with the presence of surface partial discharges. Taking into account these limits and for different nanoparticles composition, complex permittivity as a function of frequency, linearity and conductivity as a function of applied electric field is studied with respect to the role that seems to play nanometrics interfaces. Similarly, dielectric strength variation as a function of nano-clays content is investigated with respect to the partial discharge resistance improvement that seems be induced by nanoparticle addition. Finally, an opening towards nanostructuration of underground cables' insulation is proposed considering on one hand the dielectric characterisation of polyethylene matrix reinforced by nano-clays or nano-silica nanodielectrics and on the other hand a succinct cost analysis. Keywords: nanodielectric, linear low density polyethylene, nanoclays, dielectric spectroscopy, dielectric breakdown

A photoemission moments model using density functional and transfer matrix methods applied to coating layers on surfaces: Theory

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

Jensen, Kevin L.; Finkenstadt, Daniel; Shabaev, Andrew

Recent experimental measurements of a bulk material covered with a small number of graphene layers reported by Yamaguchi et al. [NPJ 2D Mater. Appl. 1, 12 (2017)] (on bialkali) and Liu et al.[Appl. Phys. Lett. 110, 041607 (2017)] (on copper) and the needs of emission models in beam optics codes have lead to substantial changes in a Moments model of photoemission. The changes account for (i) a barrier profile and density of states factor based on density functional theory (DFT) evaluations, (ii) a Drude-Lorentz model of the optical constants and laser penetration depth, and (iii) a transmission probability evaluated bymore » an Airy Transfer Matrix Approach. Importantly, the DFT results lead to a surface barrier profile of a shape similar to both resonant barriers and reflectionless wells: the associated quantum mechanical transmission probabilities are shown to be comparable to those recently required to enable the Moments (and Three Step) model to match experimental data but for reasons very different than the assumption by conventional wisdom that a barrier is responsible. The substantial modifications of the Moments model components, motivated by computational materials methods, are developed. The results prepare the Moments model for use in treating heterostructures and discrete energy level systems (e.g., quantum dots) proposed for decoupling the opposing metrics of performance that undermine the performance of advanced light sources like the x-ray Free Electron Laser. The consequences of the modified components on quan-tum yield, emittance, and emission models needed by beam optics codes are discussed. Published by AIP Publishing. https://doi.org/10.1063/1.5008600« less

A photoemission moments model using density functional and transfer matrix methods applied to coating layers on surfaces: Theory

DOE PAGES

Jensen, Kevin L.; Finkenstadt, Daniel; Shabaev, Andrew; ...

2018-01-28

Recent experimental measurements of a bulk material covered with a small number of graphene layers reported by Yamaguchi et al. [NPJ 2D Mater. Appl. 1, 12 (2017)] (on bialkali) and Liu et al.[Appl. Phys. Lett. 110, 041607 (2017)] (on copper) and the needs of emission models in beam optics codes have lead to substantial changes in a Moments model of photoemission. The changes account for (i) a barrier profile and density of states factor based on density functional theory (DFT) evaluations, (ii) a Drude-Lorentz model of the optical constants and laser penetration depth, and (iii) a transmission probability evaluated bymore » an Airy Transfer Matrix Approach. Importantly, the DFT results lead to a surface barrier profile of a shape similar to both resonant barriers and reflectionless wells: the associated quantum mechanical transmission probabilities are shown to be comparable to those recently required to enable the Moments (and Three Step) model to match experimental data but for reasons very different than the assumption by conventional wisdom that a barrier is responsible. The substantial modifications of the Moments model components, motivated by computational materials methods, are developed. The results prepare the Moments model for use in treating heterostructures and discrete energy level systems (e.g., quantum dots) proposed for decoupling the opposing metrics of performance that undermine the performance of advanced light sources like the x-ray Free Electron Laser. The consequences of the modified components on quan-tum yield, emittance, and emission models needed by beam optics codes are discussed. Published by AIP Publishing. https://doi.org/10.1063/1.5008600« less

Squared eigenvalue condition numbers and eigenvector correlations from the single ring theorem

NASA Astrophysics Data System (ADS)

Belinschi, Serban; Nowak, Maciej A.; Speicher, Roland; Tarnowski, Wojciech

2017-03-01

We extend the so-called ‘single ring theorem’ (Feinberg and Zee 1997 Nucl. Phys. B 504 579), also known as the Haagerup-Larsen theorem (Haagerup and Larsen 2000 J. Funct. Anal. 176 331). We do this by showing that in the limit when the size of the matrix goes to infinity a particular correlator between left and right eigenvectors of the relevant non-hermitian matrix X, being the spectral density weighted by the squared eigenvalue condition number, is given by a simple formula involving only the radial spectral cumulative distribution function of X. We show that this object allows the calculation of the conditional expectation of the squared eigenvalue condition number. We give examples and provide a cross-check of the analytic prediction by the large scale numerics.

Photoionization of Benzene and Small Polycyclic Aromatic Hydrocarbons in Ultraviolet-Processed Astrophysical Ices: A Computational Study

NASA Technical Reports Server (NTRS)

Woon, D. E.; Park, J.-Y.

2004-01-01

We employed density functional theory (DFT) calculations to model the photoionization behavior of benzene and small polycyclic aromatic hydrocarbons when they are embedded in a matrix of water ice in order to investigate issues raised by recent experimental work by Gudipati and Allamandola. The ionization energies of benzene, naphthalene, anthracene, and pyrene were found to be lowered by 1.5-2.1 eV in water ice. Low-lying vertical electronic excitation energies were computed with time-dependent DFT for both neutral and ionized species and are found in both cases to be remarkably unaffected by the ice matrix. Chemical behavior in ultraviolet-photoprocessed ices is also discussed, with a focus on electron recombination and pathways leading to phenol and analogous products.

Rupture in cemented granular media: application to wheat endosperm

NASA Astrophysics Data System (ADS)

Topin, V.; Delenne, J.-Y.; Radjai, F.

2009-06-01

The mechanical origin of the wheat hardness used to classify wheat flours is an open issue. Wheat endosperm can be considered as a cemented granular material, consisting of densely packed solid particles (the starch granules) and a pore-filling solid matrix (the protein) sticking to the particles. We use the lattice element method to investigate cemented granular materials with a texture close to that of wheat endosperm and with variable matrix volume fraction and particle-matrix adherence. From the shape of the probability density of vertical stresses we distinguish weak, intermediate and strong stresses. The large stresses occur mostly at the contact zones as in noncohesive granular media with a decreasing exponential distribution. The weak forces reflect the arching effect. The intermediate stresses belong mostly to the bulk of the particles and their distribution is well fit to a Gaussian distribution. We also observe that the stress chains are essentially guided by the cementing matrix in tension and by the particulate backbone in compression. Crack formation is analyzed in terms of particle damage as a function of matrix volume fraction and particle-matrix adherence. Our data provide evidence for three regimes of crack propagation depending on the crack path through the material. We find that particle damage scales well with the relative toughness of the particle-matrix interface. The interface toughness appears therefore to be strongly correlated with particle damage and determines transition from soft to hard behavior in wheat endosperm.

Recursive Factorization of the Inverse Overlap Matrix in Linear-Scaling Quantum Molecular Dynamics Simulations.

PubMed

Negre, Christian F A; Mniszewski, Susan M; Cawkwell, Marc J; Bock, Nicolas; Wall, Michael E; Niklasson, Anders M N

2016-07-12

We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive, iterative refinement of an initial guess of Z (inverse square root of the overlap matrix S). The initial guess of Z is obtained beforehand by using either an approximate divide-and-conquer technique or dynamical methods, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under the incomplete, approximate, iterative refinement of Z. Linear-scaling performance is obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables efficient shared-memory parallelization. As we show in this article using self-consistent density-functional-based tight-binding MD, our approach is faster than conventional methods based on the diagonalization of overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4158-atom water-solvated polyalanine system, we find an average speedup factor of 122 for the computation of Z in each MD step.

Recursive Factorization of the Inverse Overlap Matrix in Linear Scaling Quantum Molecular Dynamics Simulations

DOE PAGES

Negre, Christian F. A; Mniszewski, Susan M.; Cawkwell, Marc Jon; ...

2016-06-06

We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive iterative re nement of an initial guess Z of the inverse overlap matrix S. The initial guess of Z is obtained beforehand either by using an approximate divide and conquer technique or dynamically, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under incomplete approximate iterative re nement of Z. Linear scaling performance ismore » obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables e cient shared memory parallelization. As we show in this article using selfconsistent density functional based tight-binding MD, our approach is faster than conventional methods based on the direct diagonalization of the overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4,158 atom water-solvated polyalanine system we nd an average speedup factor of 122 for the computation of Z in each MD step.« less

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.

Simple derivation of the Lindblad equation

NASA Astrophysics Data System (ADS)

Pearle, Philip

2012-07-01

The Lindblad equation is an evolution equation for the density matrix in quantum theory. It is the general linear, Markovian, form which ensures that the density matrix is Hermitian, trace 1, positive and completely positive. Some elementary examples of the Lindblad equation are given. The derivation of the Lindblad equation presented here is ‘simple’ in that all it uses is the expression of a Hermitian matrix in terms of its orthonormal eigenvectors and real eigenvalues. Thus, it is appropriate for students who have learned the algebra of quantum theory. Where helpful, arguments are first given in a two-dimensional Hilbert space.

Detection of density dependence requires density manipulations and calculation of lambda.

PubMed

Fowler, N L; Overath, R Deborah; Pease, Craig M

2006-03-01

To investigate density-dependent population regulation in the perennial bunchgrass Bouteloua rigidiseta, we experimentally manipulated density by removing adults or adding seeds to replicate quadrats in a natural population for three annual intervals. We monitored the adjacent control quadrats for 14 annual intervals. We constructed a population projection matrix for each quadrat in each interval, calculated lambda, and did a life table response experiment (LTRE) analysis. We tested the effects of density upon lambda by comparing experimental and control quadrats, and by an analysis of the 15-year observational data set. As measured by effects on lambda and on N(t+1/Nt in the experimental treatments, negative density dependence was strong: the population was being effectively regulated. The relative contributions of different matrix elements to treatment effect on lambda differed among years and treatments; overall the pattern was one of small contributions by many different life cycle stages. In contrast, density dependence could not be detected using only the observational (control quadrats) data, even though this data set covered a much longer time span. Nor did experimental effects on separate matrix elements reach statistical significance. These results suggest that ecologists may fail to detect density dependence when it is present if they have only descriptive, not experimental, data, do not have data for the entire life cycle, or analyze life cycle components separately.

Ab initio molecular dynamics in a finite homogeneous electric field.

PubMed

Umari, P; Pasquarello, Alfredo

2002-10-07

We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

Single-particle spectral functions in the normal phase of a strongly attractive Bose-Fermi mixture

NASA Astrophysics Data System (ADS)

Fratini, E.; Pieri, P.

2013-07-01

We calculate the single-particle spectral functions and quasiparticle dispersions for a Bose-Fermi mixture when the boson-fermion attraction is sufficiently strong to suppress completely the condensation of bosons at zero temperature. Within a T-matrix diagrammatic approach, we vary the boson-fermion attraction from the critical value where the boson condensate first disappears to the strongly attractive (molecular) regime and study the effect of both mass and density imbalance on the spectral weights and dispersions. An interesting spectrum of particle-hole excitations mixing two different Fermi surfaces is found. These unconventional excitations could be produced and explored experimentally with radio-frequency spectroscopy.

Nonharmonicity in vibrated granular solids

NASA Astrophysics Data System (ADS)

Schreck, Carl

2012-02-01

We have shown that granular packings composed of frictionless particles with repulsive contact interactions are strongly nonharmonic. When infinitesimally perturbed along linear response eigenmodes of the static packing, energy leaks from the original mode of vibration to a continuum of frequencies due solely to contact breaking even when the system is under significant compression. Further, vibrated packings possess well-defined equilibrium positions that are different than those of the unperturbed packing. The vibrational density of states obtained using the displacement matrix and velocity autocorrelation function methods exhibit an increase in the number of low-frequency modes over that obtained from linear response of the static packing. The form of the density of states in vibrated granular packings is reminiscent of the low-frequency behavior of the vibrational density of states in fluid systems. We also investigate the effects of inter-particle friction, dissipation, particle shape, and degree of positional order on the density of states and thermal transport properties in driven granular packings.

Matrix-Product-State Algorithm for Finite Fractional Quantum Hall Systems

NASA Astrophysics Data System (ADS)

Liu, Zhao; Bhatt, R. N.

2015-09-01

Exact diagonalization is a powerful tool to study fractional quantum Hall (FQH) systems. However, its capability is limited by the exponentially increasing computational cost. In order to overcome this difficulty, density-matrix-renormalization-group (DMRG) algorithms were developed for much larger system sizes. Very recently, it was realized that some model FQH states have exact matrix-product-state (MPS) representation. Motivated by this, here we report a MPS code, which is closely related to, but different from traditional DMRG language, for finite FQH systems on the cylinder geometry. By representing the many-body Hamiltonian as a matrix-product-operator (MPO) and using single-site update and density matrix correction, we show that our code can efficiently search the ground state of various FQH systems. We also compare the performance of our code with traditional DMRG. The possible generalization of our code to infinite FQH systems and other physical systems is also discussed.

Thermodynamic properties of water in confined environments: a Monte Carlo study

NASA Astrophysics Data System (ADS)

Gladovic, Martin; Bren, Urban; Urbic, Tomaž

2018-05-01

Monte Carlo simulations of Mercedes-Benz water in a crowded environment were performed. The simulated systems are representative of both composite, porous or sintered materials and living cells with typical matrix packings. We studied the influence of overall temperature as well as the density and size of matrix particles on water density, particle distributions, hydrogen bond formation and thermodynamic quantities. Interestingly, temperature and space occupancy of matrix exhibit a similar effect on water properties following the competition between the kinetic and the potential energy of the system, whereby temperature increases the kinetic and matrix packing decreases the potential contribution. A novel thermodynamic decomposition approach was applied to gain insight into individual contributions of different types of inter-particle interactions. This decomposition proved to be useful and in good agreement with the total thermodynamic quantities especially at higher temperatures and matrix packings, where higher-order potential-energy mixing terms lose their importance.

Fetal brain extracellular matrix boosts neuronal network formation in 3D bioengineered model of cortical brain tissue.

PubMed

Sood, Disha; Chwalek, Karolina; Stuntz, Emily; Pouli, Dimitra; Du, Chuang; Tang-Schomer, Min; Georgakoudi, Irene; Black, Lauren D; Kaplan, David L

2016-01-01

The extracellular matrix (ECM) constituting up to 20% of the organ volume is a significant component of the brain due to its instructive role in the compartmentalization of functional microdomains in every brain structure. The composition, quantity and structure of ECM changes dramatically during the development of an organism greatly contributing to the remarkably sophisticated architecture and function of the brain. Since fetal brain is highly plastic, we hypothesize that the fetal brain ECM may contain cues promoting neural growth and differentiation, highly desired in regenerative medicine. Thus, we studied the effect of brain-derived fetal and adult ECM complemented with matricellular proteins on cortical neurons using in vitro 3D bioengineered model of cortical brain tissue. The tested parameters included neuronal network density, cell viability, calcium signaling and electrophysiology. Both, adult and fetal brain ECM as well as matricellular proteins significantly improved neural network formation as compared to single component, collagen I matrix. Additionally, the brain ECM improved cell viability and lowered glutamate release. The fetal brain ECM induced superior neural network formation, calcium signaling and spontaneous spiking activity over adult brain ECM. This study highlights the difference in the neuroinductive properties of fetal and adult brain ECM and suggests that delineating the basis for this divergence may have implications for regenerative medicine.

Fibroblast contractility and growth in plastic compressed collagen gel scaffolds with microstructures correlated with hydraulic permeability.

PubMed

Serpooshan, Vahid; Muja, Naser; Marelli, Benedetto; Nazhat, Showan N

2011-03-15

Scaffold microstructure is hypothesized to influence physical and mechanical properties of collagen gels, as well as cell function within the matrix. Plastic compression under increasing load was conducted to produce scaffolds with increasing collagen fibrillar densities ranging from 0.3 to above 4.1 wt % with corresponding hydraulic permeability (k) values that ranged from 1.05 to 0.03 μm², as determined using the Happel model. Scanning electron microscopy revealed that increasing the level of collagen gel compression yielded a concomitant reduction in pore size distribution and a slight increase in average fibril bundle diameter. Decreasing k delayed the onset of contraction and significantly reduced both the total extent and the maximum rate of contraction induced by NIH3T3 fibroblasts seeded at a density of either 6.0 x 10⁴ or 1.5 x 10⁵ cells mL⁻¹. At the higher cell density, however, the effect of k reduction on collagen gel contraction was overcome by an accelerated onset of contraction which led to an increase in both the total extent and the maximum rate of contraction. AlamarBlue™ measurements indicated that the metabolic activity of fibroblasts within collagen gels increased as k decreased. Moreover, increasing seeded cell density from 2.0 x 10⁴ to 1.5 x 10⁵ cells mL⁻¹ significantly increased NIH3T3 proliferation. In conclusion, fibroblast-matrix interactions can be optimized by defining the microstructural properties of collagen scaffolds through k adjustment which in turn, is dependent on the cell seeding density. Copyright © 2011 Wiley Periodicals, Inc.

Matrix density effects on the mechanical properties of SiC/RBSN composites

NASA Technical Reports Server (NTRS)

Bhatt, Ramakrishna T.; Kiser, James D.

1990-01-01

The room temperature mechanical properties were measured for SiC fiber reinforced reaction-bonded silicon nitride composites (SiC/RBSN) of different densities. The composites consisted of approx. 30 vol percent uniaxially aligned 142 micron diameter SiC fibers (Textron SCS-6) in a reaction-bonded Si3N4 matrix. The composite density was varied by changing the consolidation pressure during RBSN processing and by hot isostatically pressing the SiC/RBSN composites. Results indicate that as the consolidation pressure was increased from 27 to 138 MPa, the average pore size of the nitrided composites decreased from 0.04 to 0.02 microns and the composite density increased from 2.07 to 2.45 gm/cc. Nonetheless, these improvements resulted in only small increases in the first matrix cracking stress, primary elastic modulus, and ultimate tensile strength values of the composites. In contrast, HIP consolidation of SiC/RBSN resulted in a fully dense material whose first matrix cracking stress and elastic modulus were approx. 15 and 50 percent higher, respectively, and ultimate tensile strength values were approx. 40 percent lower than those for unHIPed SiC/RBSN composites. The modulus behavior for all specimens can be explained by simple rule-of-mixture theory. Also, the loss in ultimate strength for the HIPed composites appears to be related to a degradation in fiber strength at the HIP temperature. However, the density effect on matrix fracture strength was much less than would be expected based on typical monolithic Si3N4 behavior, suggesting that composite theory is indeed operating. Possible practical implications of these observations are discussed.

Entanglement transitions induced by large deviations

NASA Astrophysics Data System (ADS)

Bhosale, Udaysinh T.

2017-12-01

The probability of large deviations of the smallest Schmidt eigenvalue for random pure states of bipartite systems, denoted as A and B , is computed analytically using a Coulomb gas method. It is shown that this probability, for large N , goes as exp[-β N2Φ (ζ ) ] , where the parameter β is the Dyson index of the ensemble, ζ is the large deviation parameter, while the rate function Φ (ζ ) is calculated exactly. Corresponding equilibrium Coulomb charge density is derived for its large deviations. Effects of the large deviations of the extreme (largest and smallest) Schmidt eigenvalues on the bipartite entanglement are studied using the von Neumann entropy. Effect of these deviations is also studied on the entanglement between subsystems 1 and 2, obtained by further partitioning the subsystem A , using the properties of the density matrix's partial transpose ρ12Γ. The density of states of ρ12Γ is found to be close to the Wigner's semicircle law with these large deviations. The entanglement properties are captured very well by a simple random matrix model for the partial transpose. The model predicts the entanglement transition across a critical large deviation parameter ζ . Log negativity is used to quantify the entanglement between subsystems 1 and 2. Analytical formulas for it are derived using the simple model. Numerical simulations are in excellent agreement with the analytical results.

Entanglement transitions induced by large deviations.

PubMed

Bhosale, Udaysinh T

2017-12-01

The probability of large deviations of the smallest Schmidt eigenvalue for random pure states of bipartite systems, denoted as A and B, is computed analytically using a Coulomb gas method. It is shown that this probability, for large N, goes as exp[-βN^{2}Φ(ζ)], where the parameter β is the Dyson index of the ensemble, ζ is the large deviation parameter, while the rate function Φ(ζ) is calculated exactly. Corresponding equilibrium Coulomb charge density is derived for its large deviations. Effects of the large deviations of the extreme (largest and smallest) Schmidt eigenvalues on the bipartite entanglement are studied using the von Neumann entropy. Effect of these deviations is also studied on the entanglement between subsystems 1 and 2, obtained by further partitioning the subsystem A, using the properties of the density matrix's partial transpose ρ_{12}^{Γ}. The density of states of ρ_{12}^{Γ} is found to be close to the Wigner's semicircle law with these large deviations. The entanglement properties are captured very well by a simple random matrix model for the partial transpose. The model predicts the entanglement transition across a critical large deviation parameter ζ. Log negativity is used to quantify the entanglement between subsystems 1 and 2. Analytical formulas for it are derived using the simple model. Numerical simulations are in excellent agreement with the analytical results.

Structural and stereological analysis of elastic fibers in the glans penis of young men.

PubMed

Andrade, F; Cardoso, G P; Bastos, Ana Luiza; Costa, W; Chagas, M; Babinski, M

2012-01-01

The extracellular matrix is an important element in penile function and pathology, although little is known about its components in human glans. This study evaluates the morphological organization and volumetric density of elastic fibers in the glans penis of young men without any evidence of urogenital disease at autopsy or medical history. Penile glans were obtained from five young men who died of causes not related to the urogenital tract, ranging in age from 18 to 30 years (mean 24 years). Samples were fixed in formalin, embedded in paraffin, and histologically processed. Tissue was analyzed by light microscopy using Weigert's resorcin-fuchsin, after previous oxidation with oxone. The point-counting method was used for morphometrical evaluation. Quantities were expressed as volumetric densities (Vv) and were determined on 25 random fields for each individual. Elastic system fibers were easily identified. These fibers had tortuous profile and surrounded sinusoids in the glans penis. An irregular elastic fibers network was identified in the mucosa, while in the corpus spongiosum the elastic fibers were longitudinally distributed. Volumetric density of elastic fibers in the glans penis is 29.4% ± 3.1. These data could provide valuable information in order to draw parallels regarding patients with erectile dysfunction. Further studies regarding extracellular matrix of the penis are necessary to better elucidate the relation between elastic fibers and erectile dysfunction.

A far-wing line shape theory which satisfies the detailed balance principle

NASA Technical Reports Server (NTRS)

Ma, Q.; Tipping, R. H.; Hartmann, J.-M.; Boulet, C.

1995-01-01

A far-wing theory in which the validity of the detailed balance principle is maintained in each step of the derivation is presented. The role of the total density matrix including the initial correlations is analyzed rigorously. By factoring out the rapidly varying terms in the complex-time development operator in the interaction representation, better approximate expressions can be obtained. As a result, the spectral density can be expressed in terms of the line-coupling functions in which two coupled lines are arranged symmetrically and whose frequency detunings are omega - 1/2(omega(sub ji) + omega (sub j'i'). Using the approximate values omega - omega(sub ji) results in expressions that do not satisfy the detailed balance principle. However, this principle remains satisfied for the symmetrized spectral density in which not only the coupled lines are arranged symmetrically, but also the initial and final states belonging to the same lines are arranged symmetrically as well.

Quantum crystallography: A perspective.

PubMed

Massa, Lou; Matta, Chérif F

2018-06-30

Extraction of the complete quantum mechanics from X-ray scattering data is the ultimate goal of quantum crystallography. This article delivers a perspective for that possibility. It is desirable to have a method for the conversion of X-ray diffraction data into an electron density that reflects the antisymmetry of an N-electron wave function. A formalism for this was developed early on for the determination of a constrained idempotent one-body density matrix. The formalism ensures pure-state N-representability in the single determinant sense. Applications to crystals show that quantum mechanical density matrices of large molecules can be extracted from X-ray scattering data by implementing a fragmentation method termed the kernel energy method (KEM). It is shown how KEM can be used within the context of quantum crystallography to derive quantum mechanical properties of biological molecules (with low data-to-parameters ratio). © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

A minimal model for the structural energetics of VO2

NASA Astrophysics Data System (ADS)

Kim, Chanul; Marianetti, Chris; The Marianetti Group Team

Resolving the structural, magnetic, and electronic structure of VO2 from the first-principles of quantum mechanics is still a forefront problem despite decades of attention. Hybrid functionals have been shown to qualitatively ruin the structural energetics. While density functional theory (DFT) combined with cluster extensions of dynamical mean-field theory (DMFT) have demonstrated promising results in terms of the electronic properties, structural phase stability has not yet been addressed. In order to capture the basic physics of the structural transition, we propose a minimal model of VO2 based on the one dimensional Peierls-Hubbard model and parameterize this based on DFT calculations of VO2. The total energy versus dimerization in the minimal mode is then solved numerically exactly using density matrix renormalization group (DMRG) and compared to the Hartree-Fock solution. We demonstrate that the Hartree-Fock solution exhibits the same pathologies as DFT+U, and spin density functional theory for that matter, while the DMRG solution is consistent with experimental observation. Our results demonstrate the critical role of non-locality in the total energy, and this will need to be accounted for to obtain a complete description of VO2 from first-principles. The authors acknowledge support from FAME, one of six centers of STARnet, a Semiconductor Research Corporation program sponsored by MARCO and DARPA.

Density-matrix description of heteronuclear decoupling in A mX n systems

NASA Astrophysics Data System (ADS)

McClung, R. E. D.; John, Boban K.

A detailed investigation of the effects of ordinary noise decoupling and spherical randomization decoupling on the elements of the density matrix for A mX n spin systems is presented. The elements are shown to reach steady-state values in the rotating frame of the decoupled nuclei when the decoupling field is strong and is applied for a sufficient time interval. The steady-state values are found to be linear combinations of the density-matrix elements at the beginning of the decoupling period, and often involve mixing of populations with multiple-quantum coherences, and mixing of the perpendicular components of the magnetization with higher coherences. This description of decoupling is shown to account for the "illusions" of spin decoupling in 2D gated-decoupler 13C J-resolved spectra reported by Levitt et al.

Optimization of metabolite detection by quantum mechanics simulations in magnetic resonance spectroscopy.

PubMed

Gambarota, Giulio

2017-07-15

Magnetic resonance spectroscopy (MRS) is a well established modality for investigating tissue metabolism in vivo. In recent years, many efforts by the scientific community have been directed towards the improvement of metabolite detection and quantitation. Quantum mechanics simulations allow for investigations of the MR signal behaviour of metabolites; thus, they provide an essential tool in the optimization of metabolite detection. In this review, we will examine quantum mechanics simulations based on the density matrix formalism. The density matrix was introduced by von Neumann in 1927 to take into account statistical effects within the theory of quantum mechanics. We will discuss the main steps of the density matrix simulation of an arbitrary spin system and show some examples for the strongly coupled two spin system. Copyright © 2016 Elsevier Inc. All rights reserved.

Functionalized Buckyballs for Visualizing Microbial Species in Different States and Environments

DOE PAGES

Cheng, Qingsu; Aravind, Ashwin; Buckley, Matthew; ...

2015-09-08

To date, in situ visualization of microbial density has remained an open problem. Here, functionalized buckyballs (e.g., C60-pyrrolidine tris acid) are shown to be a versatile platform that allows internalization within a microorganism without either adhering to the cell wall and cell membrane or binding to a matrix substrate such as soil. These molecular probes are validated via multi-scale imaging, to show association with microorganisms via fluorescence microscopy, positive cellular uptake via electron microscopy, and non-specific binding to the substrates through a combination of fluorescence and autoradiography imaging. In conclusion, we also demonstrate that cysteine-functionalized C60- pyrrolidine tris acid canmore » differentiate live and dead microorganisms.« less

Inequalities in tobacco outlet density by race, ethnicity and socioeconomic status, 2012, USA: results from the ASPiRE Study.

PubMed

Lee, Joseph G L; Sun, Dennis L; Schleicher, Nina M; Ribisl, Kurt M; Luke, Douglas A; Henriksen, Lisa

2017-05-01

Evidence of racial/ethnic inequalities in tobacco outlet density is limited by: (1) reliance on studies from single counties or states, (2) limited attention to spatial dependence, and (3) an unclear theory-based relationship between neighbourhood composition and tobacco outlet density. In 97 counties from the contiguous USA, we calculated the 2012 density of likely tobacco outlets (N=90 407), defined as tobacco outlets per 1000 population in census tracts (n=17 667). We used 2 spatial regression techniques, (1) a spatial errors approach in GeoDa software and (2) fitting a covariance function to the errors using a distance matrix of all tract centroids. We examined density as a function of race, ethnicity, income and 2 indicators identified from city planning literature to indicate neighbourhood stability (vacant housing, renter-occupied housing). The average density was 1.3 tobacco outlets per 1000 persons. Both spatial regression approaches yielded similar results. In unadjusted models, tobacco outlet density was positively associated with the proportion of black residents and negatively associated with the proportion of Asian residents, white residents and median household income. There was no association with the proportion of Hispanic residents. Indicators of neighbourhood stability explained the disproportionate density associated with black residential composition, but inequalities by income persisted in multivariable models. Data from a large sample of US counties and results from 2 techniques to address spatial dependence strengthen evidence of inequalities in tobacco outlet density by race and income. Further research is needed to understand the underlying mechanisms in order to strengthen interventions. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Laplace approximation for Bessel functions of matrix argument

NASA Astrophysics Data System (ADS)

Butler, Ronald W.; Wood, Andrew T. A.

2003-06-01

We derive Laplace approximations to three functions of matrix argument which arise in statistics and elsewhere: matrix Bessel A[nu]; matrix Bessel B[nu]; and the type II confluent hypergeometric function of matrix argument, [Psi]. We examine the theoretical and numerical properties of the approximations. On the theoretical side, it is shown that the Laplace approximations to A[nu], B[nu] and [Psi] given here, together with the Laplace approximations to the matrix argument functions 1F1 and 2F1 presented in Butler and Wood (Laplace approximations to hyper-geometric functions with matrix argument, Ann. Statist. (2002)), satisfy all the important confluence relations and symmetry relations enjoyed by the original functions.

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

Yanai, Takeshi; Fann, George I.; Beylkin, Gregory

Using the fully numerical method for time-dependent Hartree–Fock and density functional theory (TD-HF/DFT) with the Tamm–Dancoff (TD) approximation we use a multiresolution analysis (MRA) approach to present our findings. From a reformulation with effective use of the density matrix operator, we obtain a general form of the HF/DFT linear response equation in the first quantization formalism. It can be readily rewritten as an integral equation with the bound-state Helmholtz (BSH) kernel for the Green's function. The MRA implementation of the resultant equation permits excited state calculations without virtual orbitals. Moreover, the integral equation is efficiently and adaptively solved using amore » numerical multiresolution solver with multiwavelet bases. Our implementation of the TD-HF/DFT methods is applied for calculating the excitation energies of H 2, Be, N 2, H 2O, and C 2H 4 molecules. The numerical errors of the calculated excitation energies converge in proportion to the residuals of the equation in the molecular orbitals and response functions. The energies of the excited states at a variety of length scales ranging from short-range valence excitations to long-range Rydberg-type ones are consistently accurate. It is shown that the multiresolution calculations yield the correct exponential asymptotic tails for the response functions, whereas those computed with Gaussian basis functions are too diffuse or decay too rapidly. Finally, we introduce a simple asymptotic correction to the local spin-density approximation (LSDA) so that in the TDDFT calculations, the excited states are correctly bound.« less

Majorization as a Tool for Optimizing a Class of Matrix Functions.

ERIC Educational Resources Information Center

Kiers, Henk A.

1990-01-01

General algorithms are presented that can be used for optimizing matrix trace functions subject to certain constraints on the parameters. The parameter set that minimizes the majorizing function also decreases the matrix trace function, providing a monotonically convergent algorithm for minimizing the matrix trace function iteratively. (SLD)

Fast Nonlinear Generalized Inversion of Gravity Data with Application to the Three-Dimensional Crustal Density Structure of Sichuan Basin, Southwest China

NASA Astrophysics Data System (ADS)

Wang, Jun; Meng, Xiaohong; Li, Fang

2017-11-01

Generalized inversion is one of the important steps in the quantitative interpretation of gravity data. With appropriate algorithm and parameters, it gives a view of the subsurface which characterizes different geological bodies. However, generalized inversion of gravity data is time consuming due to the large amount of data points and model cells adopted. Incorporating of various prior information as constraints deteriorates the above situation. In the work discussed in this paper, a method for fast nonlinear generalized inversion of gravity data is proposed. The fast multipole method is employed for forward modelling. The inversion objective function is established with weighted data misfit function along with model objective function. The total objective function is solved by a dataspace algorithm. Moreover, depth weighing factor is used to improve depth resolution of the result, and bound constraint is incorporated by a transfer function to limit the model parameters in a reliable range. The matrix inversion is accomplished by a preconditioned conjugate gradient method. With the above algorithm, equivalent density vectors can be obtained, and interpolation is performed to get the finally density model on the fine mesh in the model domain. Testing on synthetic gravity data demonstrated that the proposed method is faster than conventional generalized inversion algorithm to produce an acceptable solution for gravity inversion problem. The new developed inversion method was also applied for inversion of the gravity data collected over Sichuan basin, southwest China. The established density structure in this study helps understanding the crustal structure of Sichuan basin and provides reference for further oil and gas exploration in this area.

Function of Matrix IGF-1 in Coupling Bone Resorption and Formation

PubMed Central

Crane, Janet L.; Cao, Xu

2013-01-01

Balancing bone resorption and formation is the quintessential component for the prevention of osteoporosis. Signals that determine the recruitment, replication, differentiation, function, and apoptosis of osteoblasts and osteoclasts direct bone remodeling and determine whether bone tissue is gained, lost, or balanced. Therefore understanding the signaling pathways involved in the coupling process will help develop further targets for osteoporosis therapy, by blocking bone resorption or enhancing bone formation in a space and time dependent manner. Insulin-like growth factor type 1 (IGF-1) has long been known to play a role in bone strength. It is one of the most abundant substances in the bone matrix, circulates systemically and is secreted locally, and has a direct relationship with bone mineral density. Recent data has helped further our understanding of the direct role of IGF-1 signaling in coupling bone remodeling which will be discussed in this review. The bone marrow microenvironment plays a critical role in the fate of MSCs and HSCs and thus how IGF-1 interacts with other factors in the microenvironment are equally important. While previous clinical trials with IGF-1 administration have been unsuccessful at enhancing bone formation, advances in basic science studies have provided insight into further mechanisms that should be considered for future trials. Additional basic science studies dissecting the regulation and the function of matrix IGF-1 in modeling and remodeling will continue to provide further insight for future directions for anabolic therapies for osteoporosis. PMID:24068256

Function of matrix IGF-1 in coupling bone resorption and formation.

PubMed

Crane, Janet L; Cao, Xu

2014-02-01

Balancing bone resorption and formation is the quintessential component for the prevention of osteoporosis. Signals that determine the recruitment, replication, differentiation, function, and apoptosis of osteoblasts and osteoclasts direct bone remodeling and determine whether bone tissue is gained, lost, or balanced. Therefore, understanding the signaling pathways involved in the coupling process will help develop further targets for osteoporosis therapy, by blocking bone resorption or enhancing bone formation in a space- and time-dependent manner. Insulin-like growth factor type 1 (IGF-1) has long been known to play a role in bone strength. It is one of the most abundant substances in the bone matrix, circulates systemically and is secreted locally, and has a direct relationship with bone mineral density. Recent data has helped further our understanding of the direct role of IGF-1 signaling in coupling bone remodeling which will be discussed in this review. The bone marrow microenvironment plays a critical role in the fate of mesenchymal stem cells and hematopoietic stem cells and thus how IGF-1 interacts with other factors in the microenvironment are equally important. While previous clinical trials with IGF-1 administration have been unsuccessful at enhancing bone formation, advances in basic science studies have provided insight into further mechanisms that should be considered for future trials. Additional basic science studies dissecting the regulation and the function of matrix IGF-1 in modeling and remodeling will continue to provide further insight for future directions for anabolic therapies for osteoporosis.

Functional Response and Matrix Population Model of Podisus nigrispinus (Dallas, 1851) (Hemiptera: Pentatomidae) fed on Chrysomya putoria (Wiedemann, 1818) (Diptera: Calliphoridae) as Alternative Prey.

PubMed

Botteon, V W; Neves, J A; Godoy, W A C

2017-04-01

Among the predators with high potential for use in biological control, the species of the genus Podisus (Hemiptera: Pentatomidae) have received special attention for laboratory rearing, since they feed on different agricultural and forestry pest insects. However, the type of diet offered to insects in the laboratory may affect the viability of populations, expressed essentially by demographic parameters such as survival and fecundity. This study assessed demographic and development aspects in experimental populations of Podisus nigrispinus (Dallas, 1851) fed on larvae of Chrysomya putoria (Wiedemann, 1818) (Diptera: Calliphoridae) as an alternative prey. The demographic parameters fecundity and survival were investigated in life stages of P. nigrispinus with ecological modeling, by applying the Leslie matrix population model, producing histograms of life stages in successive time steps. The functional response of P. nigrispinus was also investigated on seven densities of C. putoria third-instar larvae at 24 and 48 h. The survival of predators that reached adulthood was 65% and the development time from egg to adult was 23.15 days. The predator showed a type III functional response for consumption of C. putoria at 24 and 48 h. The Leslie-matrix simulation of the age structure provided perpetuation of the predator population over time steps and the prey proved to be feasible for use in rearing and maintenance of P. nigrispinus in the laboratory.

Comparison of collagen matrix treatment impregnated with platelet rich plasma vs bone marrow.

PubMed

Minamimura, Ai; Ichioka, Shigeru; Sano, Hitomi; Sekiya, Naomi

2014-02-01

This study has reported the efficacy of an autologous bone marrow-impregnated collagen matrix experimentally and clinically. Then, it reflected that platelet rich plasma (PRP) was as good a source of growth factors as bone marrow and available in a less invasive procedure. This study aimed to compare the efficacy of a PRP-impregnated collagen matrix with that of a bone marrow-impregnated collagen matrix by quantifying wound size and capillary density using genetically diabetic db/db mice. Bone marrow cells were obtained from femurs of ddy mice. Then, a small amount of collagen matrix was immersed in bone marrow suspension. This is called a bone marrow-impregnated collagen matrix. PRP was obtained from healthy human blood and a small amount of collagen matrix was immersed in PRP. This is called a PRP-impregnated collagen matrix. A bone marrow-impregnated collagen matrix and PRP-impregnated collagen matrix were applied to excisional skin wounds on a genetically healing-impaired mouse (n = 6) and wounds were evaluated 6 days after the procedure. Wounds were divided into two groups: PRP (n = 6), in which a PRP-impregnated collagen matrix was applied; and bone marrow (n = 6), in which collagen immersed in a bone marrow suspension was applied. There was no significant difference between the PRP and bone-marrow groups in the rate of vascular density increase or wound size decrease. The present study suggested that the PRP-impregnated collagen matrix promotes repair processes at least as strongly as the bone marrow-impregnated collagen matrix. Given lower invasiveness, the PRP-impregnated collagen matrix would have advantages in clinical use.

Efficient evaluation of nonlocal operators in density functional theory

NASA Astrophysics Data System (ADS)

Chen, Ying-Chih; Chen, Jing-Zhe; Michaud-Rioux, Vincent; Shi, Qing; Guo, Hong

2018-02-01

We present a method which combines plane waves (PW) and numerical atomic orbitals (NAO) to efficiently evaluate nonlocal operators in density functional theory with periodic boundary conditions. Nonlocal operators are first expanded using PW and then transformed to NAO so that the problem of distance-truncation is avoided. The general formalism is implemented using the hybrid functional HSE06 where the nonlocal operator is the exact exchange. Comparison of electronic structures of a wide range of semiconductors to a pure PW scheme validates the accuracy of our method. Due to the locality of NAO, thus sparsity of matrix representations of the operators, the computational complexity of the method is asymptotically quadratic in the number of electrons. Finally, we apply the technique to investigate the electronic structure of the interface between a single-layer black phosphorous and the high-κ dielectric material c -HfO2 . We predict that the band offset between the two materials is 1.29 eV and 2.18 eV for valence and conduction band edges, respectively, and such offsets are suitable for 2D field-effect transistor applications.

Generalized non-equilibrium vertex correction method in coherent medium theory for quantum transport simulation of disordered nanoelectronics

NASA Astrophysics Data System (ADS)

Yan, Jiawei; Ke, Youqi

In realistic nanoelectronics, disordered impurities/defects are inevitable and play important roles in electron transport. However, due to the lack of effective quantum transport method, the important effects of disorders remain poorly understood. Here, we report a generalized non-equilibrium vertex correction (NVC) method with coherent potential approximation to treat the disorder effects in quantum transport simulation. With this generalized NVC method, any averaged product of two single-particle Green's functions can be obtained by solving a set of simple linear equations. As a result, the averaged non-equilibrium density matrix and various important transport properties, including averaged current, disordered induced current fluctuation and the averaged shot noise, can all be efficiently computed in a unified scheme. Moreover, a generalized form of conditionally averaged non-equilibrium Green's function is derived to incorporate with density functional theory to enable first-principles simulation. We prove the non-equilibrium coherent potential equals the non-equilibrium vertex correction. Our approach provides a unified, efficient and self-consistent method for simulating non-equilibrium quantum transport through disorder nanoelectronics. Shanghaitech start-up fund.

Effect of process parameters on the density and porosity of laser melted AlSi10Mg/SiC metal matrix composite

NASA Astrophysics Data System (ADS)

Famodimu, Omotoyosi H.; Stanford, Mark; Oduoza, Chike F.; Zhang, Lijuan

2018-06-01

Laser melting of aluminium alloy—AlSi10Mg has increasingly been used to create specialised products in various industrial applications, however, research on utilising laser melting of aluminium matrix composites in replacing specialised parts have been slow on the uptake. This has been attributed to the complexity of the laser melting process, metal/ceramic feedstock for the process and the reaction of the feedstock material to the laser. Thus, an understanding of the process, material microstructure and mechanical properties is important for its adoption as a manufacturing route of aluminium metal matrix composites. The effects of several parameters of the laser melting process on the mechanical blended composite were thus investigated in this research. This included single track formations of the matrix alloy and the composite alloyed with 5% and 10% respectively for their reaction to laser melting and the fabrication of density blocks to investigate the relative density and porosity over different scan speeds. The results from these experiments were utilised in determining a process window in fabricating near-fully dense parts.

Collective neutrino oscillations and neutrino wave packets

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

Akhmedov, Evgeny; Lindner, Manfred; Kopp, Joachim, E-mail: akhmedov@mpi-hd.mpg.de, E-mail: jkopp@uni-mainz.de, E-mail: lindner@mpi-hd.mpg.de

Effects of decoherence by wave packet separation on collective neutrino oscillations in dense neutrino gases are considered. We estimate the length of the wave packets of neutrinos produced in core collapse supernovae and the expected neutrino coherence length, and then proceed to consider the decoherence effects within the density matrix formalism of neutrino flavour transitions. First, we demonstrate that for neutrino oscillations in vacuum the decoherence effects are described by a damping term in the equation of motion of the density matrix of a neutrino as a whole (as contrasted to that of the fixed-momentum components of the neutrino densitymore » matrix). Next, we consider neutrino oscillations in ordinary matter and dense neutrino backgrounds, both in the adiabatic and non-adiabatic regimes. In the latter case we study two specific models of adiabaticity violation—one with short-term and another with extended non-adiabaticity. It is demonstrated that, while in the adiabatic case a damping term is present in the equation of motion of the neutrino density matrix (just like in the vacuum oscillation case), no such term in general appears in the non-adiabatic regime.« less