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 matrix approach to the hot-electron stimulated photodesorption

NASA Astrophysics Data System (ADS)

Kühn, Oliver; May, Volkhard

1996-07-01

The dissipative dynamics of the laser-induced nonthermal desorption of small molecules from a metal surface is investigated here. Based on the density matrix formalism a multi-state model is introduced which explicitly takes into account the continuum of electronic states in the metal. Various relaxation mechanisms for the electronic degrees of freedom are shown to govern the desorption dynamics and hence the desorption probability. Particular attention is paid to the modeling of the time dependence of the electron energy distribution in the metal which reflects different excitation conditions.

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.

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.

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

Full Quantum Dynamics Simulation of a Realistic Molecular System Using the Adaptive Time-Dependent Density Matrix Renormalization Group Method.

PubMed

Yao, Yao; Sun, Ke-Wei; Luo, Zhen; Ma, Haibo

2018-01-18

The accurate theoretical interpretation of ultrafast time-resolved spectroscopy experiments relies on full quantum dynamics simulations for the investigated system, which is nevertheless computationally prohibitive for realistic molecular systems with a large number of electronic and/or vibrational degrees of freedom. In this work, we propose a unitary transformation approach for realistic vibronic Hamiltonians, which can be coped with using the adaptive time-dependent density matrix renormalization group (t-DMRG) method to efficiently evolve the nonadiabatic dynamics of a large molecular system. We demonstrate the accuracy and efficiency of this approach with an example of simulating the exciton dissociation process within an oligothiophene/fullerene heterojunction, indicating that t-DMRG can be a promising method for full quantum dynamics simulation in large chemical systems. Moreover, it is also shown that the proper vibronic features in the ultrafast electronic process can be obtained by simulating the two-dimensional (2D) electronic spectrum by virtue of the high computational efficiency of the t-DMRG method.

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

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.

A density matrix-based method for the linear-scaling calculation of dynamic second- and third-order properties at the Hartree-Fock and Kohn-Sham density functional theory levels.

PubMed

Kussmann, Jörg; Ochsenfeld, Christian

2007-11-28

A density matrix-based time-dependent self-consistent field (D-TDSCF) method for the calculation of dynamic polarizabilities and first hyperpolarizabilities using the Hartree-Fock and Kohn-Sham density functional theory approaches is presented. The D-TDSCF method allows us to reduce the asymptotic scaling behavior of the computational effort from cubic to linear for systems with a nonvanishing band gap. The linear scaling is achieved by combining a density matrix-based reformulation of the TDSCF equations with linear-scaling schemes for the formation of Fock- or Kohn-Sham-type matrices. In our reformulation only potentially linear-scaling matrices enter the formulation and efficient sparse algebra routines can be employed. Furthermore, the corresponding formulas for the first hyperpolarizabilities are given in terms of zeroth- and first-order one-particle reduced density matrices according to Wigner's (2n+1) rule. The scaling behavior of our method is illustrated for first exemplary calculations with systems of up to 1011 atoms and 8899 basis functions.

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.

Micromechanics effects in creep of metal-matrix composites

NASA Astrophysics Data System (ADS)

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

1995-12-01

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

The density matrix method in photonic bandgap and antiferromagnetic materials

NASA Astrophysics Data System (ADS)

Barrie, Scott B.

In this thesis, a theory for dispersive polaritonic bandgap (DPBG) and photonic bandgap (PBG) materials is developed. An ensemble of multi-level nanoparticles, such as non-interacting two-, three- and four-level atoms doped in DPBG and PBG materials is considered. The optical properties of these materials such as spontaneous emission, line broadening, fluorescence and narrowing of the natural linewidth have been studied using the density matrix method. Numerical simulations for these properties have been performed for the DPBG materials SiC and InAs, and for a PBG material with a 20 percent gap-to-midgap ratio. When a three-level nanoparticle is doped into a DPBG material, it is predicted that one or two bound states exist when one or both resonance energies, respectively, lie in the bandgap. It is shown when a resonance energy lies below the bandgap, its spectral density peak weakens and broadens as the resonance energy increases to the lower band edge. For the first time it is predicted that when a nanoparticle's resonance energy lies above the bandgap, its spectral density peak weakens and broadens as the resonance energy increases. A relation is also found between spectral structure and gap-to-midgap ratios. The dressed states of a two-level atom doped into a DPBG material under the influence of an intense monochromatic laser field are examined. The splitting of the dressed state energies is calculated, and it is predicted that the splitting depends on the polariton density of states and the Rabi frequency of laser field. The fluoresence is also examined, and for the first time two distinct control processes are found for the transition from one peak to three peaks. It was previously known that the Rabi frequency controlled the Stark effect, but this thesis predicts that the local of the peak with respect to the optical bandgap can cause a transition from one to three peaks even with a weak Rabi frequency. The transient linewidth narrowing of PBG crystal emission peaks doped with four-level atoms is studied. It is found that linewidth narrowing is only dependent upon time delay when the resonance energy is not near a band edge. This is a new discovery. The density matrix method is employed to find the critical magnetic field at which spin flopping occurs in antiferromagnetic high temperature superconductors. It is found that this magnetic field depends upon the temperature, the anisotropy parameter and the doping concentration. Results are calculated for 1-2-3 HTSCs. Keywords. Quantum Optics, Density Matrix, Photonic Bandgap Materials, Dispersive Polaritonic Bandgap Materials, Antiferromagnets.

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.

Measures for the Dynamics in a Few-Body Quantum System with Harmonic Interactions

NASA Astrophysics Data System (ADS)

Nagy, I.; Pipek, J.; Glasser, M. L.

2018-01-01

We determine the exact time-dependent non-idempotent one-particle reduced density matrix and its spectral decomposition for a harmonically confined two-particle correlated one-dimensional system when the interaction terms in the Schrödinger Hamiltonian are changed abruptly. Based on this matrix in coordinate space we derive a precise condition for the equivalence of the purity and the overlap-square of the correlated and non-correlated wave functions as the model system with harmonic interactions evolves in time. This equivalence holds only if the interparticle interactions are affected, while the confinement terms are unaffected within the stability range of the system. Under this condition we analyze various time-dependent measures of entanglement and demonstrate that, depending on the magnitude of the changes made in the Hamiltonian, periodic, logarithmically increasing or constant value behavior of the von Neumann entropy can occur.

Density matrix-based time-dependent configuration interaction approach to ultrafast spin-flip dynamics

NASA Astrophysics Data System (ADS)

Wang, Huihui; Bokarev, Sergey I.; Aziz, Saadullah G.; Kühn, Oliver

2017-08-01

Recent developments in attosecond spectroscopy yield access to the correlated motion of electrons on their intrinsic timescales. Spin-flip dynamics is usually considered in the context of valence electronic states, where spin-orbit coupling is weak and processes related to the electron spin are usually driven by nuclear motion. However, for core-excited states, where the core-hole has a nonzero angular momentum, spin-orbit coupling is strong enough to drive spin-flips on a much shorter timescale. Using density matrix-based time-dependent restricted active space configuration interaction including spin-orbit coupling, we address an unprecedentedly short spin-crossover for the example of L-edge (2p→3d) excited states of a prototypical Fe(II) complex. This process occurs on a timescale, which is faster than that of Auger decay (∼4 fs) treated here explicitly. Modest variations of carrier frequency and pulse duration can lead to substantial changes in the spin-state yield, suggesting its control by soft X-ray light.

A real-time extension of density matrix embedding theory for non-equilibrium electron dynamics

NASA Astrophysics Data System (ADS)

Kretchmer, Joshua S.; Chan, Garnet Kin-Lic

2018-02-01

We introduce real-time density matrix embedding theory (DMET), a dynamical quantum embedding theory for computing non-equilibrium electron dynamics in strongly correlated systems. As in the previously developed static DMET, real-time DMET partitions the system into an impurity corresponding to the region of interest coupled to the surrounding environment, which is efficiently represented by a quantum bath of the same size as the impurity. In this work, we focus on a simplified single-impurity time-dependent formulation as a first step toward a multi-impurity theory. The equations of motion of the coupled impurity and bath embedding problem are derived using the time-dependent variational principle. The accuracy of real-time DMET is compared to that of time-dependent complete active space self-consistent field (TD-CASSCF) theory and time-dependent Hartree-Fock (TDHF) theory for a variety of quantum quenches in the single impurity Anderson model (SIAM), in which the Hamiltonian is suddenly changed (quenched) to induce a non-equilibrium state. Real-time DMET shows a marked improvement over the mean-field TDHF, converging to the exact answer even in the non-trivial Kondo regime of the SIAM. However, as expected from analogous behavior in static DMET, the constrained structure of the real-time DMET wavefunction leads to a slower convergence with respect to active space size, in the single-impurity formulation, relative to TD-CASSCF. Our initial results suggest that real-time DMET provides a promising framework to simulate non-equilibrium electron dynamics in which strong electron correlation plays an important role, and lays the groundwork for future multi-impurity formulations.

A real-time extension of density matrix embedding theory for non-equilibrium electron dynamics.

PubMed

Kretchmer, Joshua S; Chan, Garnet Kin-Lic

2018-02-07

We introduce real-time density matrix embedding theory (DMET), a dynamical quantum embedding theory for computing non-equilibrium electron dynamics in strongly correlated systems. As in the previously developed static DMET, real-time DMET partitions the system into an impurity corresponding to the region of interest coupled to the surrounding environment, which is efficiently represented by a quantum bath of the same size as the impurity. In this work, we focus on a simplified single-impurity time-dependent formulation as a first step toward a multi-impurity theory. The equations of motion of the coupled impurity and bath embedding problem are derived using the time-dependent variational principle. The accuracy of real-time DMET is compared to that of time-dependent complete active space self-consistent field (TD-CASSCF) theory and time-dependent Hartree-Fock (TDHF) theory for a variety of quantum quenches in the single impurity Anderson model (SIAM), in which the Hamiltonian is suddenly changed (quenched) to induce a non-equilibrium state. Real-time DMET shows a marked improvement over the mean-field TDHF, converging to the exact answer even in the non-trivial Kondo regime of the SIAM. However, as expected from analogous behavior in static DMET, the constrained structure of the real-time DMET wavefunction leads to a slower convergence with respect to active space size, in the single-impurity formulation, relative to TD-CASSCF. Our initial results suggest that real-time DMET provides a promising framework to simulate non-equilibrium electron dynamics in which strong electron correlation plays an important role, and lays the groundwork for future multi-impurity formulations.

Coherent π-electron dynamics of (P)-2,2'-biphenol induced by ultrashort linearly polarized UV pulses: Angular momentum and ring current

NASA Astrophysics Data System (ADS)

Mineo, H.; Lin, S. H.; Fujimura, Y.

2013-02-01

The results of a theoretical investigation of coherent π-electron dynamics for nonplanar (P)-2,2'-biphenol induced by ultrashort linearly polarized UV pulses are presented. Expressions for the time-dependent coherent angular momentum and ring current are derived by using the density matrix method. The time dependence of these coherences is determined by the off-diagonal density matrix element, which can be obtained by solving the coupled equations of motion of the electronic-state density matrix. Dephasing effects on coherent angular momentum and ring current are taken into account within the Markov approximation. The magnitudes of the electronic angular momentum and current are expressed as the sum of expectation values of the corresponding operators in the two phenol rings (L and R rings). Here, L (R) denotes the phenol ring in the left (right)-hand side of (P)-2,2'-biphenol. We define the bond current between the nearest neighbor carbon atoms Ci and Cj as an electric current through a half plane perpendicular to the Ci-Cj bond. The bond current can be expressed in terms of the inter-atomic bond current. The inter-atomic bond current (bond current) depends on the position of the half plane on the bond and has the maximum value at the center. The coherent ring current in each ring is defined by averaging over the bond currents. Since (P)-2,2'-biphenol is nonplanar, the resultant angular momentum is not one-dimensional. Simulations of the time-dependent coherent angular momentum and ring current of (P)-2,2'-biphenol excited by ultrashort linearly polarized UV pulses are carried out using the molecular parameters obtained by the time-dependent density functional theory (TD-DFT) method. Oscillatory behaviors in the time-dependent angular momentum (ring current), which can be called angular momentum (ring current) quantum beats, are classified by the symmetry of the coherent state, symmetric or antisymmetric. The bond current of the bridge bond linking the L and R rings is zero for the symmetric coherent state, while it is nonzero for the antisymmetric coherent state. The magnitudes of ring current and ring current-induced magnetic field are also evaluated, and their possibility as a control parameter in ultrafast switching devices is discussed. The present results give a detailed description of the theoretical treatment reported in our previous paper [H. Mineo, M. Yamaki, Y. Teranish, M. Hayashi, S. H. Lin, and Y. Fujimura, J. Am. Chem. Soc. 134, 14279 (2012), 10.1021/ja3047848].

Coherent π-electron dynamics of (P)-2,2'-biphenol induced by ultrashort linearly polarized UV pulses: angular momentum and ring current.

PubMed

Mineo, H; Lin, S H; Fujimura, Y

2013-02-21

The results of a theoretical investigation of coherent π-electron dynamics for nonplanar (P)-2,2'-biphenol induced by ultrashort linearly polarized UV pulses are presented. Expressions for the time-dependent coherent angular momentum and ring current are derived by using the density matrix method. The time dependence of these coherences is determined by the off-diagonal density matrix element, which can be obtained by solving the coupled equations of motion of the electronic-state density matrix. Dephasing effects on coherent angular momentum and ring current are taken into account within the Markov approximation. The magnitudes of the electronic angular momentum and current are expressed as the sum of expectation values of the corresponding operators in the two phenol rings (L and R rings). Here, L (R) denotes the phenol ring in the left (right)-hand side of (P)-2,2'-biphenol. We define the bond current between the nearest neighbor carbon atoms Ci and Cj as an electric current through a half plane perpendicular to the Ci-Cj bond. The bond current can be expressed in terms of the inter-atomic bond current. The inter-atomic bond current (bond current) depends on the position of the half plane on the bond and has the maximum value at the center. The coherent ring current in each ring is defined by averaging over the bond currents. Since (P)-2,2'-biphenol is nonplanar, the resultant angular momentum is not one-dimensional. Simulations of the time-dependent coherent angular momentum and ring current of (P)-2,2'-biphenol excited by ultrashort linearly polarized UV pulses are carried out using the molecular parameters obtained by the time-dependent density functional theory (TD-DFT) method. Oscillatory behaviors in the time-dependent angular momentum (ring current), which can be called angular momentum (ring current) quantum beats, are classified by the symmetry of the coherent state, symmetric or antisymmetric. The bond current of the bridge bond linking the L and R rings is zero for the symmetric coherent state, while it is nonzero for the antisymmetric coherent state. The magnitudes of ring current and ring current-induced magnetic field are also evaluated, and their possibility as a control parameter in ultrafast switching devices is discussed. The present results give a detailed description of the theoretical treatment reported in our previous paper [H. Mineo, M. Yamaki, Y. Teranish, M. Hayashi, S. H. Lin, and Y. Fujimura, J. Am. Chem. Soc. 134, 14279 (2012)].

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.

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.

Matrix Population Model for Estimating Effects from Time-Varying Aquatic Exposures: Technical Documentation

EPA Science Inventory

The Office of Pesticide Programs models daily aquatic pesticide exposure values for 30 years in its risk assessments. However, only a fraction of that information is typically used in these assessments. The population model employed herein is a deterministic, density-dependent pe...

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.

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.

Weak Measurement and Quantum Smoothing of a Superconducting Qubit

NASA Astrophysics Data System (ADS)

Tan, Dian

In quantum mechanics, the measurement outcome of an observable in a quantum system is intrinsically random, yielding a probability distribution. The state of the quantum system can be described by a density matrix rho(t), which depends on the information accumulated until time t, and represents our knowledge about the system. The density matrix rho(t) gives probabilities for the outcomes of measurements at time t. Further probing of the quantum system allows us to refine our prediction in hindsight. In this thesis, we experimentally examine a quantum smoothing theory in a superconducting qubit by introducing an auxiliary matrix E(t) which is conditioned on information obtained from time t to a final time T. With the complete information before and after time t, the pair of matrices [rho(t), E(t)] can be used to make smoothed predictions for the measurement outcome at time t. We apply the quantum smoothing theory in the case of continuous weak measurement unveiling the retrodicted quantum trajectories and weak values. In the case of strong projective measurement, while the density matrix rho(t) with only diagonal elements in a given basis |n〉 may be treated as a classical mixture, we demonstrate a failure of this classical mixture description in determining the smoothed probabilities for the measurement outcome at time t with both diagonal rho(t) and diagonal E(t). We study the correlations between quantum states and weak measurement signals and examine aspects of the time symmetry of continuous quantum measurement. We also extend our study of quantum smoothing theory to the case of resonance fluorescence of a superconducting qubit with homodyne measurement and observe some interesting effects such as the modification of the excited state probabilities, weak values, and evolution of the predicted and retrodicted trajectories.

Comment on ``Time-Dependent Density-Matrix Renormalization Group: A Systematic Method for the Study of Quantum Many-Body Out-of-Equilibrium Systems''

NASA Astrophysics Data System (ADS)

Luo, H. G.; Xiang, T.; Wang, X. Q.

2003-07-01

A Comment on the Letter by

Cosmological space-times with resolved Big Bang in Yang-Mills matrix models

NASA Astrophysics Data System (ADS)

Steinacker, Harold C.

2018-02-01

We present simple solutions of IKKT-type matrix models that can be viewed as quantized homogeneous and isotropic cosmological space-times, with finite density of microstates and a regular Big Bang (BB). The BB arises from a signature change of the effective metric on a fuzzy brane embedded in Lorentzian target space, in the presence of a quantized 4-volume form. The Hubble parameter is singular at the BB, and becomes small at late times. There is no singularity from the target space point of view, and the brane is Euclidean "before" the BB. Both recollapsing and expanding universe solutions are obtained, depending on the mass parameters.

Spectral function from Reduced Density Matrix Functional Theory

NASA Astrophysics Data System (ADS)

Romaniello, Pina; di Sabatino, Stefano; Berger, Jan A.; Reining, Lucia

2015-03-01

In this work we focus on the calculation of the spectral function, which determines, for example, photoemission spectra, from reduced density matrix functional theory. Starting from its definition in terms of the one-body Green's function we derive an expression for the spectral function that depends on the natural occupation numbers and on an effective energy which accounts for all the charged excitations. This effective energy depends on the two-body as well as higher-order density matrices. Various approximations to this expression are explored by using the exactly solvable Hubbard chains.

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

PubMed

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

2016-10-01

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

A single-electron picture based on the multiconfiguration time-dependent Hartree-Fock method: application to the anisotropic ionization and subsequent high-harmonic generation of the CO molecule

NASA Astrophysics Data System (ADS)

Ohmura, S.; Kato, T.; Oyamada, T.; Koseki, S.; Ohmura, H.; Kono, H.

2018-02-01

The mechanisms of anisotropic near-IR tunnel ionization and high-order harmonic generation (HHG) in a CO molecule are theoretically investigated by using the multiconfiguration time-dependent Hartree-Fock (MCTDHF) method developed for the simulation of multielectron dynamics of molecules. The multielectron dynamics obtained by numerically solving the equations of motion (EOMs) in the MCTDHF method is converted to a single orbital picture in the natural orbital representation where the first-order reduced density matrix is diagonalized. The ionization through each natural orbital is examined and the process of HHG is classified into different optical paths designated by a combinations of initial, intermediate and final natural orbitals. The EOMs for natural spin-orbitals are also derived within the framework of the MCTDHF, which maintains the first-order reduced density matrix to be a diagonal one throughout the time propagation of a many-electron wave function. The orbital dependent, time-dependent effective potentials that govern the dynamics of respective time-dependent natural orbitals are deduced from the derived EOMs, of which the temporal variation can be used to interpret the motion of the electron density associated with each natural spin-orbital. The roles of the orbital shape, multiorbital ionization, linear Stark effect and multielectron interaction in the ionization and HHG of a CO molecule are revealed by the effective potentials obtained. When the laser electric field points to the nucleus O from C, tunnel ionization from the C atom side is enhanced; a hump structure originating from multielectron interaction is then formed on the top of the field-induced distorted barrier of the HOMO effective potential. This hump formation, responsible for the directional anisotropy of tunnel ionization, restrains the influence of the linear Stark effect on the energy shifts of bound states.

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

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

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

2015-02-15

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

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.

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.

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

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.

Dynamical mean-field theory, density-matrix embedding theory, and rotationally invariant slave bosons: A unified perspective

NASA Astrophysics Data System (ADS)

Ayral, Thomas; Lee, Tsung-Han; Kotliar, Gabriel

2017-12-01

We present a unified perspective on dynamical mean-field theory (DMFT), density-matrix embedding theory (DMET), and rotationally invariant slave bosons (RISB). We show that DMET can be regarded as a simplification of the RISB method where the quasiparticle weight is set to unity. This relation makes it easy to transpose extensions of a given method to another: For instance, a temperature-dependent version of RISB can be used to derive a temperature-dependent free-energy formula for DMET.

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."

Diffusion of Conserved Charges in Relativistic Heavy Ion Collisions

NASA Astrophysics Data System (ADS)

Greif, Moritz; Fotakis, Jan. A.; Denicol, Gabriel S.; Greiner, Carsten

2018-06-01

We demonstrate that the diffusion currents do not depend only on gradients of their corresponding charge density, but that the different diffusion charge currents are coupled. This happens in such a way that it is possible for density gradients of a given charge to generate dissipative currents of another charge. Within this scheme, the charge diffusion coefficient is best viewed as a matrix, in which the diagonal terms correspond to the usual charge diffusion coefficients, while the off-diagonal terms describe the coupling between the different currents. In this Letter, we calculate for the first time the complete diffusion matrix for hot and dense nuclear matter, including baryon, electric, and strangeness charges. We find that the baryon diffusion current is strongly affected by baryon charge gradients but also by its coupling to gradients in strangeness. The electric charge diffusion current is found to be strongly affected by electric and strangeness gradients, whereas strangeness currents depend mostly on strange and baryon gradients.

Effect of chiral symmetry on chaotic scattering from Majorana zero modes.

PubMed

Schomerus, H; Marciani, M; Beenakker, C W J

2015-04-24

In many of the experimental systems that may host Majorana zero modes, a so-called chiral symmetry exists that protects overlapping zero modes from splitting up. This symmetry is operative in a superconducting nanowire that is narrower than the spin-orbit scattering length, and at the Dirac point of a superconductor-topological insulator heterostructure. Here we show that chiral symmetry strongly modifies the dynamical and spectral properties of a chaotic scatterer, even if it binds only a single zero mode. These properties are quantified by the Wigner-Smith time-delay matrix Q=-iℏS^{†}dS/dE, the Hermitian energy derivative of the scattering matrix, related to the density of states by ρ=(2πℏ)^{-1}TrQ. We compute the probability distribution of Q and ρ, dependent on the number ν of Majorana zero modes, in the chiral ensembles of random-matrix theory. Chiral symmetry is essential for a significant ν dependence.

Strongly correlated fermions after a quantum quench.

PubMed

Manmana, S R; Wessel, S; Noack, R M; Muramatsu, A

2007-05-25

Using the adaptive time-dependent density-matrix renormalization group method, we study the time evolution of strongly correlated spinless fermions on a one-dimensional lattice after a sudden change of the interaction strength. For certain parameter values, two different initial states (e.g., metallic and insulating) lead to observables which become indistinguishable after relaxation. We find that the resulting quasistationary state is nonthermal. This result holds for both integrable and nonintegrable variants of the system.

Comment on "Nonuniqueness of algebraic first-order density-matrix functionals"

NASA Astrophysics Data System (ADS)

Gritsenko, O. V.

2018-02-01

Wang and Knowles (WK) [Phys. Rev. A 92, 012520 (2015), 10.1103/PhysRevA.92.012520] have given a counterexample to the conventional in reduced density-matrix functional theory representation of the second-order reduced density matrix (2RDM) Γi j ,k l in the basis of the natural orbitals as a function Γi j ,k l(n ) of the orbital occupation numbers (ONs) ni. The observed nonuniqueness of Γi j ,k l for prototype systems of different symmetry has been interpreted as the inherent inability of ON functions to reproduce the 2RDM, due to the insufficient information contained in the 1RDM spectrum. In this Comment, it is argued that, rather than totally invalidating Γi j ,k l(n ) , the WK example exposes its symmetry dependence which, as well as the previously established analogous dependence in density functional theory, is demonstrated with a general formulation based on the Levy constrained search.

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.

On the mixing time in the Wang-Landau algorithm

NASA Astrophysics Data System (ADS)

Fadeeva, Marina; Shchur, Lev

2018-01-01

We present preliminary results of the investigation of the properties of the Markov random walk in the energy space generated by the Wang-Landau probability. We build transition matrix in the energy space (TMES) using the exact density of states for one-dimensional and two-dimensional Ising models. The spectral gap of TMES is inversely proportional to the mixing time of the Markov chain. We estimate numerically the dependence of the mixing time on the lattice size, and extract the mixing exponent.

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.

Dynamical mean-field theory, density-matrix embedding theory, and rotationally invariant slave bosons: A unified perspective

DOE PAGES

Ayral, Thomas; Lee, Tsung-Han; Kotliar, Gabriel

2017-12-26

In this paper, we present a unified perspective on dynamical mean-field theory (DMFT), density-matrix embedding theory (DMET), and rotationally invariant slave bosons (RISB). We show that DMET can be regarded as a simplification of the RISB method where the quasiparticle weight is set to unity. Finally, this relation makes it easy to transpose extensions of a given method to another: For instance, a temperature-dependent version of RISB can be used to derive a temperature-dependent free-energy formula for DMET.

Dynamical mean-field theory, density-matrix embedding theory, and rotationally invariant slave bosons: A unified perspective

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

Ayral, Thomas; Lee, Tsung-Han; Kotliar, Gabriel

In this paper, we present a unified perspective on dynamical mean-field theory (DMFT), density-matrix embedding theory (DMET), and rotationally invariant slave bosons (RISB). We show that DMET can be regarded as a simplification of the RISB method where the quasiparticle weight is set to unity. Finally, this relation makes it easy to transpose extensions of a given method to another: For instance, a temperature-dependent version of RISB can be used to derive a temperature-dependent free-energy formula for DMET.

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).

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.

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.

Characterization of viscoelastic response and damping of composite materials used in flywheel rotors

NASA Astrophysics Data System (ADS)

Chen, Jianmin

The long-term goal for spacecraft flywheel systems with higher energy density at the system level requires new and innovative composite material concepts. Multi-Direction Composite (MDC) offers significant advantages over traditional filament-wound and multi-ring press-fit filament-wound wheels in providing higher energy density (i.e., less mass), better crack resistance, and enhanced safety. However there is a lack of systematic characterization for dynamic properties of MDC composite materials. In order to improve the flywheel materials reliability, durability and life time, it is very important to evaluate the time dependent aging effects and damping properties of MDC material, which are significant dynamic parameter for vibration and sound control, fatigue endurance, and impact resistance. The physical aging effects are quantified based on a set of creep curves measured at different aging time or different aging temperature. One parameter (tau) curve fit was proposed to represent the relationship of aging time and aging temperature between different master curves. The long term mechanical behavior was predicted by obtained master curves. The time and temperature shift factors of matrix were obtained from creep curves and the aging time shift rate were calculated. The aging effects on composite are obtained from experiments and compared with prediction. The mechanical quasi-behavior of MDC composite was analyzed. The correspondence principle was used to relate quasi-static elastic properties of composite materials to time-dependent properties of its constituent materials (i.e., fiber and matrix). The Prony series combined with the multi-data fitting method was applied to inverse Laplace transform and to calculate the time dependent stiffness matrix effectively. Accelerated time-dependent deformation of two flywheel rim designs were studied for a period equivalent to 31 years and are compared with hoop reinforcement only composite. Damping of pure resin and T700/epoxy composite lamina and laminate in longitudinal and transverse directions were investigated experimentally and analytically. The effect of aging on damping was also studied by placing samples at 60°C in an oven for extended periods. Damping master curves versus frequency were constructed from individual curves at different temperatures based on the Arrhenius equation. The damping response of the composite lamina was used to predict the response of laminate composites. Analytical results give close numerical values to experimental results from damping of cantilever beam laminated composite samples.

Interaction of electromagnetic fields with chondrocytes in gel culture

NASA Astrophysics Data System (ADS)

Grodzinsky, Alan J.; Buschmann, Michael D.; Gluzband, Yehezkiel A.

1992-01-01

The specific objectives of this research period were: (1) to quantify the effect of applied electric fields on chondrocyte metabolism, using a range of stimulation frequencies and amplitudes; (2) to compare the chondrocyte biosynthetic response to applied fields at early times in agarose gel culture before an extracellular matrix has accumulated and at later times after significant deposition of matrix around and between the cells; and (3) to begin to interpret the biosynthetic response to applied fields in terms of models of physical mechanisms. The results of these studies suggest that electric fields applied to chondrocytes in agarose can modulate the synthesis of proteoglycans and protein constituents. Biosynthesis may be inhibited or stimulated depending on the amplitude of the applied current density. In addition, the presence of extracellular matrix may enhance the ability of normal chondrocytes and cells in intact cartilage to respond to electric fields, although the presence of matrix was not required for the stimulatory response to be observed with Swarm rat chondrosarcoma cells.

Revealing electronic open quantum systems with subsystem TDDFT

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

Krishtal, Alisa, E-mail: alisa.krishtal@rutgers.edu; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu

2016-03-28

Open quantum systems (OQSs) are perhaps the most realistic systems one can approach through simulations. In recent years, describing OQSs with Density Functional Theory (DFT) has been a prominent avenue of research with most approaches based on a density matrix partitioning in conjunction with an ad-hoc description of system-bath interactions. We propose a different theoretical approach to OQSs based on partitioning of the electron density. Employing the machinery of subsystem DFT (and its time-dependent extension), we provide a novel way of isolating and analyzing the various terms contributing to the coupling between the system and the surrounding bath. To illustratemore » the theory, we provide numerical simulations on a toy system (a molecular dimer) and on a condensed phase system (solvated excimer). The simulations show that non-Markovian dynamics in the electronic system-bath interactions are important in chemical applications. For instance, we show that the superexchange mechanism of transport in donor-bridge-acceptor systems is a non-Markovian interaction between the donor-acceptor (OQS) with the bridge (bath) which is fully characterized by real-time subsystem time-dependent DFT.« less

Revealing electronic open quantum systems with subsystem TDDFT.

PubMed

Krishtal, Alisa; Pavanello, Michele

2016-03-28

Open quantum systems (OQSs) are perhaps the most realistic systems one can approach through simulations. In recent years, describing OQSs with Density Functional Theory (DFT) has been a prominent avenue of research with most approaches based on a density matrix partitioning in conjunction with an ad-hoc description of system-bath interactions. We propose a different theoretical approach to OQSs based on partitioning of the electron density. Employing the machinery of subsystem DFT (and its time-dependent extension), we provide a novel way of isolating and analyzing the various terms contributing to the coupling between the system and the surrounding bath. To illustrate the theory, we provide numerical simulations on a toy system (a molecular dimer) and on a condensed phase system (solvated excimer). The simulations show that non-Markovian dynamics in the electronic system-bath interactions are important in chemical applications. For instance, we show that the superexchange mechanism of transport in donor-bridge-acceptor systems is a non-Markovian interaction between the donor-acceptor (OQS) with the bridge (bath) which is fully characterized by real-time subsystem time-dependent DFT.

Revealing electronic open quantum systems with subsystem TDDFT

NASA Astrophysics Data System (ADS)

Krishtal, Alisa; Pavanello, Michele

2016-03-01

Open quantum systems (OQSs) are perhaps the most realistic systems one can approach through simulations. In recent years, describing OQSs with Density Functional Theory (DFT) has been a prominent avenue of research with most approaches based on a density matrix partitioning in conjunction with an ad-hoc description of system-bath interactions. We propose a different theoretical approach to OQSs based on partitioning of the electron density. Employing the machinery of subsystem DFT (and its time-dependent extension), we provide a novel way of isolating and analyzing the various terms contributing to the coupling between the system and the surrounding bath. To illustrate the theory, we provide numerical simulations on a toy system (a molecular dimer) and on a condensed phase system (solvated excimer). The simulations show that non-Markovian dynamics in the electronic system-bath interactions are important in chemical applications. For instance, we show that the superexchange mechanism of transport in donor-bridge-acceptor systems is a non-Markovian interaction between the donor-acceptor (OQS) with the bridge (bath) which is fully characterized by real-time subsystem time-dependent DFT.

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.

Density-dependence interacts with extrinsic mortality in shaping life histories

PubMed Central

Burger, Oskar; Kozłowski, Jan

2017-01-01

The role of extrinsic mortality in shaping life histories is poorly understood. However, substantial evidence suggests that extrinsic mortality interacts with density-dependence in crucial ways. We develop a model combining Evolutionarily Stable Strategies with a projection matrix that allows resource allocation to growth, tissue repairs, and reproduction. Our model examines three cases, with density-dependence acting on: (i) mortality, (ii) fecundity, and (iii) production rate. We demonstrate that density-independent extrinsic mortality influences the rate of aging, age at maturity, growth rate, and adult size provided that density-dependence acts on fertility or juvenile mortality. However, density-independent extrinsic mortality has no effect on these life history traits when density-dependence acts on survival. We show that extrinsic mortality interacts with density-dependence via a compensation mechanism: the higher the extrinsic mortality the lower the strength of density-dependence. However, this compensation fully offsets the effect of extrinsic mortality only if density-dependence acts on survival independently of age. Both the age-pattern and the type of density-dependence are crucial for shaping life history traits. PMID:29049399

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.

Direct evaluation of boson dynamics via finite-temperature time-dependent variation with multiple Davydov states.

PubMed

Fujihashi, Yuta; Wang, Lu; Zhao, Yang

2017-12-21

Recent advances in quantum optics allow for exploration of boson dynamics in dissipative many-body systems. However, the traditional descriptions of quantum dissipation using reduced density matrices are unable to capture explicit information of bath dynamics. In this work, efficient evaluation of boson dynamics is demonstrated by combining the multiple Davydov Ansatz with finite-temperature time-dependent variation, going beyond what state-of-the-art density matrix approaches are capable to offer for coupled electron-boson systems. To this end, applications are made to excitation energy transfer in photosynthetic systems, singlet fission in organic thin films, and circuit quantum electrodynamics in superconducting devices. Thanks to the multiple Davydov Ansatz, our analysis of boson dynamics leads to clear revelation of boson modes strongly coupled to electronic states, as well as in-depth description of polaron creation and destruction in the presence of thermal fluctuations.

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 .

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

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.

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

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

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.

A matrix-based approach to solving the inverse Frobenius-Perron problem using sequences of density functions of stochastically perturbed dynamical systems

NASA Astrophysics Data System (ADS)

Nie, Xiaokai; Coca, Daniel

2018-01-01

The paper introduces a matrix-based approach to estimate the unique one-dimensional discrete-time dynamical system that generated a given sequence of probability density functions whilst subjected to an additive stochastic perturbation with known density.

A matrix-based approach to solving the inverse Frobenius-Perron problem using sequences of density functions of stochastically perturbed dynamical systems.

PubMed

Nie, Xiaokai; Coca, Daniel

2018-01-01

The paper introduces a matrix-based approach to estimate the unique one-dimensional discrete-time dynamical system that generated a given sequence of probability density functions whilst subjected to an additive stochastic perturbation with known density.

Exchange-correlation approximations for reduced-density-matrix-functional theory at finite temperature: Capturing magnetic phase transitions in the homogeneous electron gas

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

Baldsiefen, Tim; Cangi, Attila; Eich, F. G.

Here, we derive an intrinsically temperature-dependent approximation to the correlation grand potential for many-electron systems in thermodynamical equilibrium in the context of finite-temperature reduced-density-matrix-functional theory (FT-RDMFT). We demonstrate its accuracy by calculating the magnetic phase diagram of the homogeneous electron gas. We compare it to known limits from highly accurate quantum Monte Carlo calculations as well as to phase diagrams obtained within existing exchange-correlation approximations from density functional theory and zero-temperature RDMFT.

Exchange-correlation approximations for reduced-density-matrix-functional theory at finite temperature: Capturing magnetic phase transitions in the homogeneous electron gas

DOE PAGES

Baldsiefen, Tim; Cangi, Attila; Eich, F. G.; ...

2017-12-18

Here, we derive an intrinsically temperature-dependent approximation to the correlation grand potential for many-electron systems in thermodynamical equilibrium in the context of finite-temperature reduced-density-matrix-functional theory (FT-RDMFT). We demonstrate its accuracy by calculating the magnetic phase diagram of the homogeneous electron gas. We compare it to known limits from highly accurate quantum Monte Carlo calculations as well as to phase diagrams obtained within existing exchange-correlation approximations from density functional theory and zero-temperature RDMFT.

Crowding of Interacting Fluid Particles in Porous Media through Molecular Dynamics: Breakdown of Universality for Soft Interactions.

PubMed

Schnyder, Simon K; Horbach, Jürgen

2018-02-16

Molecular dynamics simulations of interacting soft disks confined in a heterogeneous quenched matrix of soft obstacles show dynamics which is fundamentally different from that of hard disks. The interactions between the disks can enhance transport when their density is increased, as disks cooperatively help each other over the finite energy barriers in the matrix. The system exhibits a transition from a diffusive to a localized state, but the transition is strongly rounded. Effective exponents in the mean-squared displacement can be observed over three decades in time but depend on the density of the disks and do not correspond to asymptotic behavior in the vicinity of a critical point, thus, showing that it is incorrect to relate them to the critical exponents in the Lorentz model scenario. The soft interactions are, therefore, responsible for a breakdown of the universality of the dynamics.

Crowding of Interacting Fluid Particles in Porous Media through Molecular Dynamics: Breakdown of Universality for Soft Interactions

NASA Astrophysics Data System (ADS)

Schnyder, Simon K.; Horbach, Jürgen

2018-02-01

Molecular dynamics simulations of interacting soft disks confined in a heterogeneous quenched matrix of soft obstacles show dynamics which is fundamentally different from that of hard disks. The interactions between the disks can enhance transport when their density is increased, as disks cooperatively help each other over the finite energy barriers in the matrix. The system exhibits a transition from a diffusive to a localized state, but the transition is strongly rounded. Effective exponents in the mean-squared displacement can be observed over three decades in time but depend on the density of the disks and do not correspond to asymptotic behavior in the vicinity of a critical point, thus, showing that it is incorrect to relate them to the critical exponents in the Lorentz model scenario. The soft interactions are, therefore, responsible for a breakdown of the universality of the dynamics.

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.

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.

Role of geomechanically grown fractures on dispersive transport in heterogeneous geological formations.

PubMed

Nick, H M; Paluszny, A; Blunt, M J; Matthai, S K

2011-11-01

A second order in space accurate implicit scheme for time-dependent advection-dispersion equations and a discrete fracture propagation model are employed to model solute transport in porous media. We study the impact of the fractures on mass transport and dispersion. To model flow and transport, pressure and transport equations are integrated using a finite-element, node-centered finite-volume approach. Fracture geometries are incrementally developed from a random distributions of material flaws using an adoptive geomechanical finite-element model that also produces fracture aperture distributions. This quasistatic propagation assumes a linear elastic rock matrix, and crack propagation is governed by a subcritical crack growth failure criterion. Fracture propagation, intersection, and closure are handled geometrically. The flow and transport simulations are separately conducted for a range of fracture densities that are generated by the geomechanical finite-element model. These computations show that the most influential parameters for solute transport in fractured porous media are as follows: fracture density and fracture-matrix flux ratio that is influenced by matrix permeability. Using an equivalent fracture aperture size, computed on the basis of equivalent permeability of the system, we also obtain an acceptable prediction of the macrodispersion of poorly interconnected fracture networks. The results hold for fractures at relatively low density.

A cross-diffusion system derived from a Fokker-Planck equation with partial averaging

NASA Astrophysics Data System (ADS)

Jüngel, Ansgar; Zamponi, Nicola

2017-02-01

A cross-diffusion system for two components with a Laplacian structure is analyzed on the multi-dimensional torus. This system, which was recently suggested by P.-L. Lions, is formally derived from a Fokker-Planck equation for the probability density associated with a multi-dimensional Itō process, assuming that the diffusion coefficients depend on partial averages of the probability density with exponential weights. A main feature is that the diffusion matrix of the limiting cross-diffusion system is generally neither symmetric nor positive definite, but its structure allows for the use of entropy methods. The global-in-time existence of positive weak solutions is proved and, under a simplifying assumption, the large-time asymptotics is investigated.

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

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

Changes in seasonal climate outpace compensatory density-dependence in eastern brook trout

USGS Publications Warehouse

Bassar, Ronald D.; Letcher, Benjamin H.; Nislow, Keith H.; Whiteley, Andrew R.

2016-01-01

Understanding how multiple extrinsic (density-independent) factors and intrinsic (density-dependent) mechanisms influence population dynamics has become increasingly urgent in the face of rapidly changing climates. It is particularly unclear how multiple extrinsic factors with contrasting effects among seasons are related to declines in population numbers and changes in mean body size and whether there is a strong role for density-dependence. The primary goal of this study was to identify the roles of seasonal variation in climate driven environmental direct effects (mean stream flow and temperature) versus density-dependence on population size and mean body size in eastern brook trout (Salvelinus fontinalis). We use data from a 10-year capture-mark-recapture study of eastern brook trout in four streams in Western Massachusetts, USA to parameterize a discrete-time population projection model. The model integrates matrix modeling techniques used to characterize discrete population structures (age, habitat type and season) with integral projection models (IPMs) that characterize demographic rates as continuous functions of organismal traits (in this case body size). Using both stochastic and deterministic analyses we show that decreases in population size are due to changes in stream flow and temperature and that these changes are larger than what can be compensated for through density-dependent responses. We also show that the declines are due mostly to increasing mean stream temperatures decreasing the survival of the youngest age class. In contrast, increases in mean body size over the same period are the result of indirect changes in density with a lesser direct role of climate-driven environmental change.

Analytical results for the time-dependent current density distribution of expanding ultracold gases after a sudden change of the confining potential

NASA Astrophysics Data System (ADS)

Boumaza, R.; Bencheikh, K.

2017-12-01

Using the so-called operator product expansion to lowest order, we extend the work in Campbell et al (2015 Phys. Rev. Lett 114 125302) by deriving a simple analytical expression for the long-time asymptotic one-body reduced density matrix during free expansion for a one-dimensional system of bosons with large atom number interacting through a repulsive delta potential initially confined by a potential well. This density matrix allows direct access to the momentum distribution and also to the mass current density. For initially confining power-law potentials we give explicit expressions, in the limits of very weak and very strong interaction, for the current density distributions during the free expansion. In the second part of the work we consider the expansion of ultracold gas from a confining harmonic trap to another harmonic trap with a different frequency. For the case of a quantum impenetrable gas of bosons (a Tonks-Girardeau gas) with a given atom number, we present an exact analytical expression for the mass current distribution (mass transport) after release from one harmonic trap to another harmonic trap. It is shown that, for a harmonically quenched Tonks-Girardeau gas, the current distribution is a suitable collective observable and under the weak quench regime, it exhibits oscillations at the same frequencies as those recently predicted for the peak momentum distribution in the breathing mode. The analysis is extended to other possible quenched systems.

Extended Lagrangian Excited State Molecular Dynamics

DOE PAGES

Bjorgaard, Josiah August; Sheppard, Daniel Glen; Tretiak, Sergei; ...

2018-01-09

In this work, an extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born–Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both formore » the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. In conclusion, the XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree–Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).« less

Extended Lagrangian Excited State Molecular Dynamics

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

Bjorgaard, Josiah August; Sheppard, Daniel Glen; Tretiak, Sergei

In this work, an extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born–Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both formore » the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. In conclusion, the XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree–Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).« less

Extended Lagrangian Excited State Molecular Dynamics.

PubMed

Bjorgaard, J A; Sheppard, D; Tretiak, S; Niklasson, A M N

2018-02-13

An extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born-Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. The XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree-Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).

Measuring order in disordered systems and disorder in ordered systems: Random matrix theory for isotropic and nematic liquid crystals and its perspective on pseudo-nematic domains

NASA Astrophysics Data System (ADS)

Zhao, Yan; Stratt, Richard M.

2018-05-01

Surprisingly long-ranged intermolecular correlations begin to appear in isotropic (orientationally disordered) phases of liquid crystal forming molecules when the temperature or density starts to close in on the boundary with the nematic (ordered) phase. Indeed, the presence of slowly relaxing, strongly orientationally correlated, sets of molecules under putatively disordered conditions ("pseudo-nematic domains") has been apparent for some time from light-scattering and optical-Kerr experiments. Still, a fully microscopic characterization of these domains has been lacking. We illustrate in this paper how pseudo-nematic domains can be studied in even relatively small computer simulations by looking for order-parameter tensor fluctuations much larger than one would expect from random matrix theory. To develop this idea, we show that random matrix theory offers an exact description of how the probability distribution for liquid-crystal order parameter tensors converges to its macroscopic-system limit. We then illustrate how domain properties can be inferred from finite-size-induced deviations from these random matrix predictions. A straightforward generalization of time-independent random matrix theory also allows us to prove that the analogous random matrix predictions for the time dependence of the order-parameter tensor are similarly exact in the macroscopic limit, and that relaxation behavior of the domains can be seen in the breakdown of the finite-size scaling required by that random-matrix theory.

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.

Halogen atom effect on the photophysical properties of substituted aza-BODIPY derivatives.

PubMed

De Simone, B C; Mazzone, G; Pirillo, J; Russo, N; Sicilia, E

2017-01-18

The influence of halogen atom substitution (Br and I), in different amounts and positions in an aza-BODIPY skeleton, on the photophysical properties of some aza-BODIPY derivatives has been investigated by using density functional theory and its time-dependent extension. The heavy atom effect on excitation energies, singlet-triplet energy gaps and spin-orbit matrix elements has been considered. The maximum absorption within the therapeutic window has been confirmed for all the aza-BODIPY derivatives. The feasible intersystem spin crossing pathways for the population of the lowest triplet state, that will depend on the values of the spin-orbit matrix elements, the energy gap as well as the orbital composition of the involved states have been found to most likely involve the S 1 and T 1 or T 2 states. The outcomes of computations support the potential therapeutic use of these compounds as photosensitizers in photodynamic therapy.

A diffusion model-free framework with echo time dependence for free-water elimination and brain tissue microstructure characterization.

PubMed

Molina-Romero, Miguel; Gómez, Pedro A; Sperl, Jonathan I; Czisch, Michael; Sämann, Philipp G; Jones, Derek K; Menzel, Marion I; Menze, Bjoern H

2018-03-23

The compartmental nature of brain tissue microstructure is typically studied by diffusion MRI, MR relaxometry or their correlation. Diffusion MRI relies on signal representations or biophysical models, while MR relaxometry and correlation studies are based on regularized inverse Laplace transforms (ILTs). Here we introduce a general framework for characterizing microstructure that does not depend on diffusion modeling and replaces ill-posed ILTs with blind source separation (BSS). This framework yields proton density, relaxation times, volume fractions, and signal disentanglement, allowing for separation of the free-water component. Diffusion experiments repeated for several different echo times, contain entangled diffusion and relaxation compartmental information. These can be disentangled by BSS using a physically constrained nonnegative matrix factorization. Computer simulations, phantom studies, together with repeatability and reproducibility experiments demonstrated that BSS is capable of estimating proton density, compartmental volume fractions and transversal relaxations. In vivo results proved its potential to correct for free-water contamination and to estimate tissue parameters. Formulation of the diffusion-relaxation dependence as a BSS problem introduces a new framework for studying microstructure compartmentalization, and a novel tool for free-water elimination. © 2018 International Society for Magnetic Resonance in Medicine.

Anodization Mechanism on SiC Nanoparticle Reinforced Al Matrix Composites Produced by Power Metallurgy.

PubMed

Ferreira, Sonia C; Conde, Ana; Arenas, María A; Rocha, Luis A; Velhinho, Alexandre

2014-12-19

Specimens of aluminum-based composites reinforced by silicon carbide nanoparticles (Al/SiC np ) produced by powder metallurgy (PM) were anodized under voltage control in tartaric-sulfuric acid (TSA). In this work, the influence of the amount of SiC np on the film growth during anodizing was investigated. The current density versus time response and the morphology of the porous alumina film formed at the composite surface are compared to those concerning a commercial aluminum alloy (AA1050) anodized under the same conditions. The processing method of the aluminum alloys influences the efficiency of the anodizing process, leading to a lower thicknesses for the unreinforced Al-PM alloy regarding the AA1050. The current density versus time response is strongly dependent on the amount of SiC np . The current peaks and the steady-state current density recorded at each voltage step increases with the SiC np volume fraction due to the oxidation of the SiC np . The formation mechanism of the anodic film on Al/SiC np composites is different from that occurring in AA1050, partly due the heterogeneous distribution of the reinforcement particles in the metallic matrix, but also to the entrapment of SiC np in the anodic film.

Anodization Mechanism on SiC Nanoparticle Reinforced Al Matrix Composites Produced by Power Metallurgy

PubMed Central

Ferreira, Sonia C.; Conde, Ana; Arenas, María A.; Rocha, Luis A.; Velhinho, Alexandre

2014-01-01

Specimens of aluminum-based composites reinforced by silicon carbide nanoparticles (Al/SiCnp) produced by powder metallurgy (PM) were anodized under voltage control in tartaric-sulfuric acid (TSA). In this work, the influence of the amount of SiCnp on the film growth during anodizing was investigated. The current density versus time response and the morphology of the porous alumina film formed at the composite surface are compared to those concerning a commercial aluminum alloy (AA1050) anodized under the same conditions. The processing method of the aluminum alloys influences the efficiency of the anodizing process, leading to a lower thicknesses for the unreinforced Al-PM alloy regarding the AA1050. The current density versus time response is strongly dependent on the amount of SiCnp. The current peaks and the steady-state current density recorded at each voltage step increases with the SiCnp volume fraction due to the oxidation of the SiCnp. The formation mechanism of the anodic film on Al/SiCnp composites is different from that occurring in AA1050, partly due the heterogeneous distribution of the reinforcement particles in the metallic matrix, but also to the entrapment of SiCnp in the anodic film. PMID:28788295

Microfluidic engineered high cell density three-dimensional neural cultures

NASA Astrophysics Data System (ADS)

Cullen, D. Kacy; Vukasinovic, Jelena; Glezer, Ari; La Placa, Michelle C.

2007-06-01

Three-dimensional (3D) neural cultures with cells distributed throughout a thick, bioactive protein scaffold may better represent neurobiological phenomena than planar correlates lacking matrix support. Neural cells in vivo interact within a complex, multicellular environment with tightly coupled 3D cell-cell/cell-matrix interactions; however, thick 3D neural cultures at cell densities approaching that of brain rapidly decay, presumably due to diffusion limited interstitial mass transport. To address this issue, we have developed a novel perfusion platform that utilizes forced intercellular convection to enhance mass transport. First, we demonstrated that in thick (>500 µm) 3D neural cultures supported by passive diffusion, cell densities <=5.0 × 103 cells mm-3 were required for survival. In 3D neuronal and neuronal-astrocytic co-cultures with increased cell density (>=104 cells mm-3), continuous medium perfusion at 2.0-11.0 µL min-1 improved viability compared to non-perfused cultures (p < 0.01), which exhibited widespread cell death and matrix degradation. In perfused cultures, survival was dependent on proximity to the perfusion source at 2.00-6.25 µL min-1 (p < 0.05); however, at perfusion rates of 10.0-11.0 µL min-1 survival did not depend on the distance from the perfusion source, and resulted in a preservation of cell density with >90% viability in both neuronal cultures and neuronal-astrocytic co-cultures. This work demonstrates the utility of forced interstitial convection in improving the survival of high cell density 3D engineered neural constructs and may aid in the development of novel tissue-engineered systems reconstituting 3D cell-cell/cell-matrix interactions.

The feasibility and stability of large complex biological networks: a random matrix approach.

PubMed

Stone, Lewi

2018-05-29

In the 70's, Robert May demonstrated that complexity creates instability in generic models of ecological networks having random interaction matrices A. Similar random matrix models have since been applied in many disciplines. Central to assessing stability is the "circular law" since it describes the eigenvalue distribution for an important class of random matrices A. However, despite widespread adoption, the "circular law" does not apply for ecological systems in which density-dependence operates (i.e., where a species growth is determined by its density). Instead one needs to study the far more complicated eigenvalue distribution of the community matrix S = DA, where D is a diagonal matrix of population equilibrium values. Here we obtain this eigenvalue distribution. We show that if the random matrix A is locally stable, the community matrix S = DA will also be locally stable, providing the system is feasible (i.e., all species have positive equilibria D > 0). This helps explain why, unusually, nearly all feasible systems studied here are locally stable. Large complex systems may thus be even more fragile than May predicted, given the difficulty of assembling a feasible system. It was also found that the degree of stability, or resilience of a system, depended on the minimum equilibrium population.

3-D time-domain induced polarization tomography: a new approach based on a source current density formulation

NASA Astrophysics Data System (ADS)

Soueid Ahmed, A.; Revil, A.

2018-04-01

Induced polarization (IP) of porous rocks can be associated with a secondary source current density, which is proportional to both the intrinsic chargeability and the primary (applied) current density. This gives the possibility of reformulating the time domain induced polarization (TDIP) problem as a time-dependent self-potential-type problem. This new approach implies a change of strategy regarding data acquisition and inversion, allowing major time savings for both. For inverting TDIP data, we first retrieve the electrical resistivity distribution. Then, we use this electrical resistivity distribution to reconstruct the primary current density during the injection/retrieval of the (primary) current between the current electrodes A and B. The time-lapse secondary source current density distribution is determined given the primary source current density and a distribution of chargeability (forward modelling step). The inverse problem is linear between the secondary voltages (measured at all the electrodes) and the computed secondary source current density. A kernel matrix relating the secondary observed voltages data to the source current density model is computed once (using the electrical conductivity distribution), and then used throughout the inversion process. This recovered source current density model is in turn used to estimate the time-dependent chargeability (normalized voltages) in each cell of the domain of interest. Assuming a Cole-Cole model for simplicity, we can reconstruct the 3-D distributions of the relaxation time τ and the Cole-Cole exponent c by fitting the intrinsic chargeability decay curve to a Cole-Cole relaxation model for each cell. Two simple cases are studied in details to explain this new approach. In the first case, we estimate the Cole-Cole parameters as well as the source current density field from a synthetic TDIP data set. Our approach is successfully able to reveal the presence of the anomaly and to invert its Cole-Cole parameters. In the second case, we perform a laboratory sandbox experiment in which we mix a volume of burning coal and sand. The algorithm is able to localize the burning coal both in terms of electrical conductivity and chargeability.

Breast density characterization using texton distributions.

PubMed

Petroudi, Styliani; Brady, Michael

2011-01-01

Breast density has been shown to be one of the most significant risks for developing breast cancer, with women with dense breasts at four to six times higher risk. The Breast Imaging Reporting and Data System (BI-RADS) has a four class classification scheme that describes the different breast densities. However, there is great inter and intra observer variability among clinicians in reporting a mammogram's density class. This work presents a novel texture classification method and its application for the development of a completely automated breast density classification system. The new method represents the mammogram using textons, which can be thought of as the building blocks of texture under the operational definition of Leung and Malik as clustered filter responses. The new proposed method characterizes the mammographic appearance of the different density patterns by evaluating the texton spatial dependence matrix (TDSM) in the breast region's corresponding texton map. The TSDM is a texture model that captures both statistical and structural texture characteristics. The normalized TSDM matrices are evaluated for mammograms from the different density classes and corresponding texture models are established. Classification is achieved using a chi-square distance measure. The fully automated TSDM breast density classification method is quantitatively evaluated on mammograms from all density classes from the Oxford Mammogram Database. The incorporation of texton spatial dependencies allows for classification accuracy reaching over 82%. The breast density classification accuracy is better using texton TSDM compared to simple texton histograms.

Ultrafast energy transfer with competing channels: Non-equilibrium Förster and Modified Redfield theories

NASA Astrophysics Data System (ADS)

Seibt, Joachim; Mančal, Tomáš

2017-05-01

We derive equations of motion for the reduced density matrix of a molecular system which undergoes energy transfer dynamics competing with fast internal conversion channels. Environmental degrees of freedom of such a system have no time to relax to quasi-equilibrium in the electronic excited state of the donor molecule, and thus the conditions of validity of Förster and Modified Redfield theories in their standard formulations do not apply. We derive non-equilibrium versions of the two well-known rate theories and apply them to the case of carotenoid-chlorophyll energy transfer. Although our reduced density matrix approach does not account for the formation of vibronic excitons, it still confirms the important role of the donor ground-state vibrational states in establishing the resonance energy transfer conditions. We show that it is essential to work with a theory valid in a strong system-bath interaction regime to obtain correct dependence of the rates on donor-acceptor energy gap.

Chopped random-basis quantum optimization

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

Caneva, Tommaso; Calarco, Tommaso; Montangero, Simone

2011-08-15

In this work, we describe in detail the chopped random basis (CRAB) optimal control technique recently introduced to optimize time-dependent density matrix renormalization group simulations [P. Doria, T. Calarco, and S. Montangero, Phys. Rev. Lett. 106, 190501 (2011)]. Here, we study the efficiency of this control technique in optimizing different quantum processes and we show that in the considered cases we obtain results equivalent to those obtained via different optimal control methods while using less resources. We propose the CRAB optimization as a general and versatile optimal control technique.

Complex absorbing potential based Lorentzian fitting scheme and time dependent quantum transport.

PubMed

Xie, Hang; Kwok, Yanho; Jiang, Feng; Zheng, Xiao; Chen, GuanHua

2014-10-28

Based on the complex absorbing potential (CAP) method, a Lorentzian expansion scheme is developed to express the self-energy. The CAP-based Lorentzian expansion of self-energy is employed to solve efficiently the Liouville-von Neumann equation of one-electron density matrix. The resulting method is applicable for both tight-binding and first-principles models and is used to simulate the transient currents through graphene nanoribbons and a benzene molecule sandwiched between two carbon-atom chains.

Role of small-norm components in extended random-phase approximation

NASA Astrophysics Data System (ADS)

Tohyama, Mitsuru

2017-09-01

The role of the small-norm amplitudes in extended random-phase approximation (RPA) theories such as the particle-particle and hole-hole components of one-body amplitudes and the two-body amplitudes other than two-particle/two-hole components are investigated for the one-dimensional Hubbard model using an extended RPA derived from the time-dependent density matrix theory. It is found that these amplitudes cannot be neglected in strongly interacting regions where the effects of ground-state correlations are significant.

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

Imaging diffusive media using time-independent and time-harmonic sources: dependence of image quality on imaging algorithms, target volume, weight matrix, and view angles

NASA Astrophysics Data System (ADS)

Chang, Jenghwa; Aronson, Raphael; Graber, Harry L.; Barbour, Randall L.

1995-05-01

We present results examining the dependence of image quality for imaging in dense scattering media as influenced by the choice of parameters pertaining to the physical measurement and factors influencing the efficiency of the computation. The former includes the density of the weight matrix as affected by the target volume, view angle, and source condition. The latter includes the density of the weight matrix and type of algorithm used. These were examined by solving a one-step linear perturbation equation derived from the transport equation using three different algorithms: POCS, CGD, and SART algorithms with contraints. THe above were explored by evaluating four different 3D cylindrical phantom media: a homogeneous medium, an media containing a single black rod on the axis, a single black rod parallel to the axis, and thirteen black rods arrayed in the shape of an 'X'. Solutions to the forward problem were computed using Monte Carlo methods for an impulse source, from which was calculated time- independent and time harmonic detector responses. The influence of target volume on image quality and computational efficiency was studied by computing solution to three types of reconstructions: 1) 3D reconstruction, which considered each voxel individually, 2) 2D reconstruction, which assumed that symmetry along the cylinder axis was know a proiri, 3) 2D limited reconstruction, which assumed that only those voxels in the plane of the detectors contribute information to the detecot readings. The effect of view angle was explored by comparing computed images obtained from a single source, whose position was varied, as well as for the type of tomographic measurement scheme used (i.e., radial scan versus transaxial scan). The former condition was also examined for the dependence of the above on choice of source condition [ i.e., cw (2D reconstructions) versus time-harmonic (2D limited reconstructions) source]. The efficiency of the computational effort was explored, principally, by conducting a weight matrix 'threshold titration' study. This involved computing the ratio of each matrix element to the maximum element of its row and setting this to zero if the ratio was less than a preselected threshold. Results obtained showed that all three types of reconstructions provided good image quality. The 3D reconstruction outperformed the other two reconstructions. The time required for 2D and 2D limited reconstruction is much less (< 10%) than that for the 3D reconstruction. The 'threshold titration' study shows that artifacts were present when the threshold was 5% or higher, and no significant differences of image quality were observed when the thresholds were less tha 1%, in which case 38% (21,849 of 57,600) of the total weight elements were set to zero. Restricting the view angle produced degradation in image quality, but, in all cases, clearly recognizable images were obtained.

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.

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.

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.

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.

Development and application of a density dependent matrix ...

EPA Pesticide Factsheets

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

N-representability-driven reconstruction of the two-electron reduced-density matrix for a real-time time-dependent electronic structure method

NASA Astrophysics Data System (ADS)

Jeffcoat, David B.; DePrince, A. Eugene

2014-12-01

Propagating the equations of motion (EOM) for the one-electron reduced-density matrix (1-RDM) requires knowledge of the corresponding two-electron RDM (2-RDM). We show that the indeterminacy of this expression can be removed through a constrained optimization that resembles the variational optimization of the ground-state 2-RDM subject to a set of known N-representability conditions. Electronic excitation energies can then be obtained by propagating the EOM for the 1-RDM and following the dipole moment after the system interacts with an oscillating external electric field. For simple systems with well-separated excited states whose symmetry differs from that of the ground state, excitation energies obtained from this method are comparable to those obtained from full configuration interaction computations. Although the optimized 2-RDM satisfies necessary N-representability conditions, the procedure cannot guarantee a unique mapping from the 1-RDM to the 2-RDM. This deficiency is evident in the mean-field-quality description of transitions to states of the same symmetry as the ground state, as well as in the inability of the method to describe Rabi oscillations.

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.

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

Molecular properties of excited electronic state: Formalism, implementation, and applications of analytical second energy derivatives within the framework of the time-dependent density functional theory/molecular mechanics

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

Zeng, Qiao; Liang, WanZhen, E-mail: liangwz@xmu.edu.cn; Liu, Jie

2014-05-14

This work extends our previous works [J. Liu and W. Z. Liang, J. Chem. Phys. 135, 014113 (2011); J. Liu and W. Z. Liang, J. Chem. Phys. 135, 184111 (2011)] on analytical excited-state energy Hessian within the framework of time-dependent density functional theory (TDDFT) to couple with molecular mechanics (MM). The formalism, implementation, and applications of analytical first and second energy derivatives of TDDFT/MM excited state with respect to the nuclear and electric perturbations are presented. Their performances are demonstrated by the calculations of adiabatic excitation energies, and excited-state geometries, harmonic vibrational frequencies, and infrared intensities for a number ofmore » benchmark systems. The consistent results with the full quantum mechanical method and other hybrid theoretical methods indicate the reliability of the current numerical implementation of developed algorithms. The computational accuracy and efficiency of the current analytical approach are also checked and the computational efficient strategies are suggested to speed up the calculations of complex systems with many MM degrees of freedom. Finally, we apply the current analytical approach in TDDFT/MM to a realistic system, a red fluorescent protein chromophore together with part of its nearby protein matrix. The calculated results indicate that the rearrangement of the hydrogen bond interactions between the chromophore and the protein matrix is responsible for the large Stokes shift.« less

Development of an adaptive harvest management program for Taiga bean geese

USGS Publications Warehouse

Johnson, Fred A.; Alhainen, Mikko; Fox, Anthony D.; Madsen, Jesper

2016-01-01

This report describes recent progress in specifying the elements of an adaptive harvest program for taiga bean goose. It describes harvest levels appropriate for first rebuilding the population of the Central Management Unit and then maintaining it near the goal specified in the AEWA International Single Species Action Plan (ISSAP). This report also provides estimates of the length of time it would take under ideal conditions (no density dependence and no harvest) to rebuild depleted populations in the Western and Eastern Management Units. We emphasize that our estimates are a first approximation because detailed demographic information is lacking for taiga bean geese. Using allometric relationships, we estimated parameters of a thetalogistic matrix population model. The mean intrinsic rate of growth was estimated as r = 0.150 (90% credible interval: 0.120 – 0.182). We estimated the mean form of density dependence as   2.361 (90% credible interval: 0.473 – 11.778), suggesting the strongest density dependence occurs when the population is near its carrying capacity. Based on expert opinion, carrying capacity (i.e., population size expected in the absence of hunting) for the Central Management Unit was estimated as K  87,900 (90% credible interval: 82,000 – 94,100). The ISSAP specifies a population goal for the Central Management Unit of 60,000 – 80,000 individuals in winter; thus, we specified a preliminary objective function as one which would minimize the difference between this goal and population size. Using the concept of stochastic dominance to explicitly account for uncertainty in demography, we determined that optimal harvest rates for 5, 10, 15, and 20-year time horizons were h = 0.00, 0.02, 0.05, and 0.06, respectively. These optima represent a tradeoff between the harvest rate and the time required to achieve and maintain a population size within desired bounds. We recognize, however, that regulation of absolute harvest rather than harvest rate is more practical, but our matrix model does not permit one to calculate an exact harvest associated with a specific harvest rate. Approximate harvests for current population size in the Central Management Unit are 0, 1,200, 2,300, and 3,500 for the 5, 10, 15, and 20-year time horizons, respectively. Populations of taiga bean geese in the Western and Eastern Units would require at least 10 and 13 years, respectively, to reach their minimum goals under the most optimistic of scenarios. The presence of harvest, density dependence, or environmental variation could extend these time frames considerably. Finally, we stress that development and implementation of internationally coordinated monitoring programs will be essential to further development and implementation of an adaptive harvest management program.

From Geometry Optimization to Time Dependent Molecular Structure Modeling: Method Developments, ab initio Theories and Applications

NASA Astrophysics Data System (ADS)

Liang, Wenkel

This dissertation consists of two general parts: (I) developments of optimization algorithms (both nuclear and electronic degrees of freedom) for time-independent molecules and (II) novel methods, first-principle theories and applications in time dependent molecular structure modeling. In the first part, we discuss in specific two new algorithms for static geometry optimization, the eigenspace update (ESU) method in nonredundant internal coordinate that exhibits an enhanced performace with up to a factor of 3 savings in computational cost for large-sized molecular systems; the Car-Parrinello density matrix search (CP-DMS) method that enables direct minimization of the SCF energy as an effective alternative to conventional diagonalization approach. For the second part, we consider the time dependence and first presents two nonadiabatic dynamic studies that model laser controlled molecular photo-dissociation for qualitative understandings of intense laser-molecule interaction, using ab initio direct Ehrenfest dynamics scheme implemented with real-time time-dependent density functional theory (RT-TDDFT) approach developed in our group. Furthermore, we place our special interest on the nonadiabatic electronic dynamics in the ultrafast time scale, and presents (1) a novel technique that can not only obtain energies but also the electron densities of doubly excited states within a single determinant framework, by combining methods of CP-DMS with RT-TDDFT; (2) a solvated first-principles electronic dynamics method by incorporating the polarizable continuum solvation model (PCM) to RT-TDDFT, which is found to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. (3) applications of the PCM-RT-TDDFT method to study the intramolecular charge-transfer (CT) dynamics in a C60 derivative. Such work provides insights into the characteristics of ultrafast dynamics in photoexcited fullerene derivatives, and aids in the rational design for pre-dissociative exciton in the intramolecular CT process in organic solar cells.

Growth and yield of all-aged Douglas-fir -- western hemlock forest stands: a matrix model with stand diversity effects.

Treesearch

Jingjing Liang; Joseph Buonglorno; Robert A. Monserud

2005-01-01

A density-dependent matrix model was developed for Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) -- western hemlock (Tsuga heterophylla (Raf.) Sarg.) forest stands in the Pacific Northwest of the United States. The model predicted the number and volume of trees for 4 species groups and 19 diameter classes. The parameters...

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.

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.

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

PubMed

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

2018-03-28

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

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.

Modeling the densification of metal matrix composite monotape

NASA Technical Reports Server (NTRS)

Elzey, D. M.; Wadley, H. N. G.

1993-01-01

We present a first model that enables prediction of the density (and its time evolution) of a monotape lay-up subjected to a hot isostatic or vacuum hot pressing consolidation cycle. Our approach is to break down the complicated (and probabilistic) consolidation problem into simple, analyzable parts and to combine them in a way that correctly represents the statistical aspects of the problem, the change in the problem's interior geometry, and the evolving contributions of the different deformation mechanisms. The model gives two types of output. One is in the form of maps showing the relative density dependence upon pressure, temperature, and time for step function temperature and pressure cycles. They are useful for quickly determining the best place to begin developing an optimized process. The second gives the evolution of density over time for any (arbitrary) applied temperature and pressure cycle. This has promise for refining process cycles and possibly for process control. Examples of the models application are given for Ti3Al + Nb, gamma TiAl, Ti6Al4V, and pure aluminum.

Generation of Stationary Non-Gaussian Time Histories with a Specified Cross-spectral Density

DOE PAGES

Smallwood, David O.

1997-01-01

The paper reviews several methods for the generation of stationary realizations of sampled time histories with non-Gaussian distributions and introduces a new method which can be used to control the cross-spectral density matrix and the probability density functions (pdfs) of the multiple input problem. Discussed first are two methods for the specialized case of matching the auto (power) spectrum, the skewness, and kurtosis using generalized shot noise and using polynomial functions. It is then shown that the skewness and kurtosis can also be controlled by the phase of a complex frequency domain description of the random process. The general casemore » of matching a target probability density function using a zero memory nonlinear (ZMNL) function is then covered. Next methods for generating vectors of random variables with a specified covariance matrix for a class of spherically invariant random vectors (SIRV) are discussed. Finally the general case of matching the cross-spectral density matrix of a vector of inputs with non-Gaussian marginal distributions is presented.« 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

We present two efficient iterative algorithms for solving the linear response eigen- value 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 a product eigenvalue problem that is self-adjoint with respect to a K-inner product. 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-innermore » product. The solution of the product eigenvalue problem yields one component of the eigenvector associated with the original eigenvalue problem. However, the other component of the eigenvector can be easily recovered in a postprocessing procedure. Therefore, the algorithms we present here are more efficient than existing algorithms that try to approximate both components of the eigenvectors simultaneously. The efficiency of the new algorithms is demonstrated by numerical examples.« less

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.

Dynamic current susceptibility as a probe of Majorana bound states in nanowire-based Josephson junctions

NASA Astrophysics Data System (ADS)

Trif, Mircea; Dmytruk, Olesia; Bouchiat, Hélène; Aguado, Ramón; Simon, Pascal

2018-02-01

We theoretically study a Josephson junction based on a semiconducting nanowire subject to a time-dependent flux bias. We establish a general density-matrix approach for the dynamical response of the Majorana junction and calculate the resulting flux-dependent susceptibility using both microscopic and effective low-energy descriptions for the nanowire. We find that the diagonal component of the susceptibility, associated with the dynamics of the Majorana state populations, dominates over the standard Kubo contribution for a wide range of experimentally relevant parameters. The diagonal term, explored, in this Rapid Communication, in the context of Majorana physics, allows probing accurately the presence of Majorana bound states in the junction.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

A Gaussian Wave Packet Propagation Approach to Vibrationally Resolved Optical Spectra at Non-Zero Temperatures.

PubMed

Reddy, Ch Sridhar; Prasad, M Durga

2016-04-28

An effective time dependent approach based on a method that is similar to the Gaussian wave packet propagation (GWP) technique of Heller is developed for the computation of vibrationally resolved electronic spectra at finite temperatures in the harmonic, Franck-Condon/Hertzberg-Teller approximations. Since the vibrational thermal density matrix of the ground electronic surface and the time evolution operator on that surface commute, it is possible to write the spectrum generating correlation function as a trace of the time evolved doorway state. In the stated approximations, the doorway state is a superposition of the harmonic oscillator zero and one quantum eigenfunctions and thus can be propagated by the GWP. The algorithm has an O(N(3)) dependence on the number of vibrational modes. An application to pyrene absorption spectrum at two temperatures is presented as a proof of the concept.

Simulation of Particle Size Effect on Dynamic Properties and Fracture of PTFE-W-Al Composites

NASA Astrophysics Data System (ADS)

Herbold, E. B.; Cai, J.; Benson, D. J.; Nesterenko, V. F.

2007-12-01

Recent investigations of the dynamic compressive strength of cold isostatically pressed composites of polytetrafluoroethylene (PTFE), tungsten (W) and aluminum (Al) powders show significant differences depending on the size of metallic particles. The addition of W increases the density and changes the overall strength of the sample depending on the size of W particles. To investigate relatively large deformations, multi-material Eulerian and arbitrary Lagrangian-Eulerian methods, which have the ability to efficiently handle the formation of free surfaces, were used. The calculations indicate that the increased sample strength with fine metallic particles is due to the dynamic formation of force chains. This phenomenon occurs for samples with a higher porosity of the PTFE matrix compared to samples with larger particle size of W and a higher density PTFE matrix.

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 density functional approach to ferrogels

NASA Astrophysics Data System (ADS)

Cremer, P.; Heinen, M.; Menzel, A. M.; Löwen, H.

2017-07-01

Ferrogels consist of magnetic colloidal particles embedded in an elastic polymer matrix. As a consequence, their structural and rheological properties are governed by a competition between magnetic particle-particle interactions and mechanical matrix elasticity. Typically, the particles are permanently fixed within the matrix, which makes them distinguishable by their positions. Over time, particle neighbors do not change due to the fixation by the matrix. Here we present a classical density functional approach for such ferrogels. We map the elastic matrix-induced interactions between neighboring colloidal particles distinguishable by their positions onto effective pairwise interactions between indistinguishable particles similar to a ‘pairwise pseudopotential’. Using Monte-Carlo computer simulations, we demonstrate for one-dimensional dipole-spring models of ferrogels that this mapping is justified. We then use the pseudopotential as an input into classical density functional theory of inhomogeneous fluids and predict the bulk elastic modulus of the ferrogel under various conditions. In addition, we propose the use of an ‘external pseudopotential’ when one switches from the viewpoint of a one-dimensional dipole-spring object to a one-dimensional chain embedded in an infinitely extended bulk matrix. Our mapping approach paves the way to describe various inhomogeneous situations of ferrogels using classical density functional concepts of inhomogeneous fluids.

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.

Featureless classification of light curves

NASA Astrophysics Data System (ADS)

Kügler, S. D.; Gianniotis, N.; Polsterer, K. L.

2015-08-01

In the era of rapidly increasing amounts of time series data, classification of variable objects has become the main objective of time-domain astronomy. Classification of irregularly sampled time series is particularly difficult because the data cannot be represented naturally as a vector which can be directly fed into a classifier. In the literature, various statistical features serve as vector representations. In this work, we represent time series by a density model. The density model captures all the information available, including measurement errors. Hence, we view this model as a generalization to the static features which directly can be derived, e.g. as moments from the density. Similarity between each pair of time series is quantified by the distance between their respective models. Classification is performed on the obtained distance matrix. In the numerical experiments, we use data from the OGLE (Optical Gravitational Lensing Experiment) and ASAS (All Sky Automated Survey) surveys and demonstrate that the proposed representation performs up to par with the best currently used feature-based approaches. The density representation preserves all static information present in the observational data, in contrast to a less-complete description by features. The density representation is an upper boundary in terms of information made available to the classifier. Consequently, the predictive power of the proposed classification depends on the choice of similarity measure and classifier, only. Due to its principled nature, we advocate that this new approach of representing time series has potential in tasks beyond classification, e.g. unsupervised learning.

Multi-layer multi-configuration time-dependent Hartree (ML-MCTDH) approach to the correlated exciton-vibrational dynamics in the FMO complex

NASA Astrophysics Data System (ADS)

Schulze, Jan; Shibl, Mohamed F.; Al-Marri, Mohammed J.; Kühn, Oliver

2016-05-01

The coupled quantum dynamics of excitonic and vibrational degrees of freedom is investigated for high-dimensional models of the Fenna-Matthews-Olson complex. This includes a seven- and an eight-site model with 518 and 592 harmonic vibrational modes, respectively. The coupling between local electronic transitions and vibrations is described within the Huang-Rhys model using parameters that are obtained by discretization of an experimental spectral density. Different pathways of excitation energy flow are analyzed in terms of the reduced one-exciton density matrix, focussing on the role of vibrational and vibronic excitations. Distinct features due to both competing time scales of vibrational and exciton motion and vibronically assisted transfer are observed. The question of the effect of initial state preparation is addressed by comparing the case of an instantaneous Franck-Condon excitation at a single site with that of a laser field excitation.

Electrochemical disinfection using boron-doped diamond electrode--the synergetic effects of in situ ozone and free chlorine generation.

PubMed

Rajab, Mohamad; Heim, Carolin; Letzel, Thomas; Drewes, Jörg E; Helmreich, Brigitte

2015-02-01

This work investigated the capability of using a boron-doped diamond (BDD) electrode for bacterial disinfection in different water matrices containing varying amounts of chloride. The feed water containing Pseudomonas aeruginosa was electrochemically treated while applying different electrode conditions. Depending on the applied current density and the exposure time, inactivation between 4- and 8-log of the targeted microorganisms could be achieved. The disinfection efficiency was driven by the generation of free chlorine as a function of chloride concentration in the water. A synergetic effect of generating both free chlorine and ozone in situ during the disinfection process resulted in an effective bactericidal impact. The formation of the undesired by-products chlorate and perchlorate depended on the water matrix, the applied current density and the desired target disinfection level. In case of synthetic water with a low chloride concentration (20 mg L(-1)) and an applied current density of 167 mA cm(-2), a 6-log inactivation of Pseudomonas aeruginosa could be achieved after 5 min of exposure. The overall energy consumption ranged between 0.3 and 0.6 kW h m(-3) depending on the applied current density and water chemistry. Electrochemical water disinfection represents a suitable and efficient process for producing pathogen-free water without the use of any chemicals. Copyright © 2014 Elsevier Ltd. All rights reserved.

Influence of mechanical rock properties and fracture healing rate on crustal fluid flow dynamics

NASA Astrophysics Data System (ADS)

Sachau, Till; Bons, Paul; Gomez-Rivas, Enrique; Koehn, Daniel; de Riese, Tamara

2016-04-01

Fluid flow in the Earth's crust is very slow over extended periods of time, during which it occurs within the connected pore space of rocks. If the fluid production rate exceeds a certain threshold, matrix permeability alone is insufficient to drain the fluid volume and fluid pressure builds up, thereby reducing the effective stress supported by the rock matrix. Hydraulic fractures form once the effective pressure exceeds the tensile strength of the rock matrix and act subsequently as highly effective fluid conduits. Once local fluid pressure is sufficiently low again, flow ceases and fractures begin to heal. Since fluid flow is controlled by the alternation of fracture permeability and matrix permeability, the flow rate in the system is strongly discontinuous and occurs in intermittent pulses. Resulting hydraulic fracture networks are largely self-organized: opening and subsequent healing of hydraulic fractures depends on the local fluid pressure and on the time-span between fluid pulses. We simulate this process with a computer model and describe the resulting dynamics statistically. Special interest is given to a) the spatially and temporally discontinuous formation and closure of fractures and fracture networks and b) the total flow rate over time. The computer model consists of a crustal-scale dual-porosity setup. Control parameters are the pressure- and time-dependent fracture healing rate, and the strength and the permeability of the intact rock. Statistical analysis involves determination of the multifractal properties and of the power spectral density of the temporal development of the total drainage rate and hydraulic fractures. References Bons, P. D. (2001). The formation of large quartz veins by rapid ascent of fluids in mobile hydrofractures. Tectonophysics, 336, 1-17. Miller, S. a., & Nur, A. (2000). Permeability as a toggle switch in fluid-controlled crustal processes. Earth and Planetary Science Letters, 183(1-2), 133-146. Sachau, T., Bons, P. D., & Gomez-Rivas, E. (2015). Transport efficiency and dynamics of hydraulic fracture networks. Frontiers in Physics, 3.

ac-driven vortices and the Hall effect in a superconductor with a tilted washboard pinning potential

NASA Astrophysics Data System (ADS)

Shklovskij, Valerij A.; Dobrovolskiy, Oleksandr V.

2008-09-01

The Langevin equation for a two-dimensional (2D) nonlinear guided vortex motion in a tilted cosine pinning potential in the presence of an ac is exactly solved in terms of a matrix continued fraction at arbitrary value of the Hall effect. The influence of an ac of arbitrary amplitude and frequency on the dc and ac magnetoresistivity tensors is analyzed. The ac density and frequency dependence of the overall shape and the number and position of the Shapiro steps on the anisotropic current-voltage characteristics are considered. The influence of a subcritical or overcritical dc on the time-dependent stationary ac longitudinal and transverse resistive vortex responses (on the frequency of an ac drive Ω ) in terms of the nonlinear impedance tensor Ẑ and the nonlinear ac response at Ω harmonics are studied. Analytical formulas for 2D temperature-dependent linear impedance tensor ẐL in the presence of a dc which depend on the angle α between the current-density vector and the guiding direction of the washboard planar pinning potential are derived and analyzed. Influence of α anisotropy and the Hall effect on the nonlinear power absorption by vortices is discussed.

On the stability of the electronic system in transition metal dichalcogenides.

PubMed

Faraggi, M N; Zubizarreta, X; Arnau, A; Silkin, V M

2016-05-11

Based on first-principles calculations, we prove that the origin of charge-density wave formation in metallic layered transition metal dichalcogenides (TMDC) is not due to an electronic effect, like the Fermi surface (FS) nesting, as it had been proposed. In particular, we consider NbSe2, NbS2, TaSe2, and TaS2 as representative examples of 2H-TMDC polytypes. Our main result consists that explicit inclusion of the matrix elements in first-principles calculations of the electron susceptibility [Formula: see text] removes, due to strong momentum dependence of the matrix elements, almost all the information about the FS topologies in the resulting [Formula: see text]. This finding strongly supports an interpretation in which the momentum dependence of the electron-phonon interaction is the only reason why the phenomenon of charge-density waves appears in this class of materials.

Calculating Path-Dependent Travel Time Prediction Variance and Covariance fro a Global Tomographic P-Velocity Model

NASA Astrophysics Data System (ADS)

Ballard, S.; Hipp, J. R.; Encarnacao, A.; Young, C. J.; Begnaud, M. L.; Phillips, W. S.

2012-12-01

Seismic event locations can be made more accurate and precise by computing predictions of seismic travel time through high fidelity 3D models of the wave speed in the Earth's interior. Given the variable data quality and uneven data sampling associated with this type of model, it is essential that there be a means to calculate high-quality estimates of the path-dependent variance and covariance associated with the predicted travel times of ray paths through the model. In this paper, we describe a methodology for accomplishing this by exploiting the full model covariance matrix and show examples of path-dependent travel time prediction uncertainty computed from SALSA3D, our global, seamless 3D tomographic P-velocity model. Typical global 3D models have on the order of 1/2 million nodes, so the challenge in calculating the covariance matrix is formidable: 0.9 TB storage for 1/2 of a symmetric matrix, necessitating an Out-Of-Core (OOC) blocked matrix solution technique. With our approach the tomography matrix (G which includes Tikhonov regularization terms) is multiplied by its transpose (GTG) and written in a blocked sub-matrix fashion. We employ a distributed parallel solution paradigm that solves for (GTG)-1 by assigning blocks to individual processing nodes for matrix decomposition update and scaling operations. We first find the Cholesky decomposition of GTG which is subsequently inverted. Next, we employ OOC matrix multiplication methods to calculate the model covariance matrix from (GTG)-1 and an assumed data covariance matrix. Given the model covariance matrix, we solve for the travel-time covariance associated with arbitrary ray-paths by summing the model covariance along both ray paths. Setting the paths equal and taking the square root yields the travel prediction uncertainty for the single path.

Two Coils Resonant Ramsey's Method for the Measurement of Time Reversal Invariance Violation in Neutron Transmission.

PubMed

Loukachevitch, V V; Aldushchenkov, A V

2005-01-01

It is proposed within the framework of Ramsey's method to register two-dimensional spectra, depending on the neutron phase and neutron energy, for measuring parity (P) and time (T) violating amplitudes of the interaction of polarized neutrons with polarized (139)La nuclei in region of the p-wave resonance. The form of the phase spectrum and corresponding expressions for the asymmetries are obtained on the basis of a formalism of a spin density matrix. It is shown that the ratio of the P,T,-violating to P-violating imaginary amplitudes can be obtained from the measurements of the neutron phase spectrum with polarized and unpolarized (139)La target.

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.

Entropy production in a photovoltaic cell

NASA Astrophysics Data System (ADS)

Ansari, Mohammad H.

2017-05-01

We evaluate entropy production in a photovoltaic cell that is modeled by four electronic levels resonantly coupled to thermally populated field modes at different temperatures. We use a formalism recently proposed, the so-called multiple parallel worlds, to consistently address the nonlinearity of entropy in terms of density matrix. Our result shows that entropy production is the difference between two flows: a semiclassical flow that linearly depends on occupational probabilities, and another flow that depends nonlinearly on quantum coherence and has no semiclassical analog. We show that entropy production in the cells depends on environmentally induced decoherence time and energy detuning. We characterize regimes where reversal flow of information takes place from a cold to hot bath. Interestingly, we identify a lower bound on entropy production, which sets limitations on the statistics of dissipated heat in the cells.

Cardiac differentiation of cardiosphere-derived cells in scaffolds mimicking morphology of the cardiac extracellular matrix.

PubMed

Xu, Yanyi; Patnaik, Sourav; Guo, Xiaolei; Li, Zhenqing; Lo, Wilson; Butler, Ryan; Claude, Andrew; Liu, Zhenguo; Zhang, Ge; Liao, Jun; Anderson, Peter M; Guan, Jianjun

2014-08-01

Stem cell therapy has the potential to regenerate heart tissue after myocardial infarction (MI). The regeneration is dependent upon cardiac differentiation of the delivered stem cells. We hypothesized that timing of the stem cell delivery determines the extent of cardiac differentiation as cell differentiation is dependent on matrix properties such as biomechanics, structure and morphology, and these properties in cardiac extracellular matrix (ECM) continuously vary with time after MI. In order to elucidate the relationship between ECM properties and cardiac differentiation, we created an in vitro model based on ECM-mimicking fibers and a type of cardiac progenitor cell, cardiosphere-derived cells (CDCs). A simultaneous fiber electrospinning and cell electrospraying technique was utilized to fabricate constructs. By blending a highly soft hydrogel with a relatively stiff polyurethane and modulating fabrication parameters, tissue constructs with similar cell adhesion property but different global modulus, single fiber modulus, fiber density and fiber alignment were achieved. The CDCs remained alive within the constructs during a 1week culture period. CDC cardiac differentiation was dependent on the scaffold modulus, fiber volume fraction and fiber alignment. Two constructs with relatively low scaffold modulus, ∼50-60kPa, most significantly directed the CDC differentiation into mature cardiomyocytes as evidenced by gene expressions of cardiac troponin T (cTnT), calcium channel (CACNA1c) and cardiac myosin heavy chain (MYH6), and protein expressions of cardiac troponin I (cTnI) and connexin 43 (CX43). Of these two low-modulus constructs, the extent of differentiation was greater for lower fiber alignment and higher fiber volume fraction. These results suggest that cardiac ECM properties may have an effect on cardiac differentiation of delivered stem cells. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

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.

On corrected formula for irradiated graphene quantum conductivity

NASA Astrophysics Data System (ADS)

Firsova, N. E.

2017-09-01

Graphene membrane irradiated by weak activating periodic electric field in terahertz range is considered. The corrected formula for the graphene quantum conductivity is found. The obtained formula gives complex conjugate results when radiation polarization direction is clockwise or it is opposite clockwise. The found formula allows us to see that the graphene membrane is an oscillating contour. Its eigen frequency coincides with a singularity point of the conductivity and depends on the electrons concentration. So the graphene membrane could be used as an antenna or a transistor and its eigen frequency could be tuned by doping in a large terahertz-infrared frequency range. The obtained formula allows us also to calculate the graphene membrane quantum inductivity and capacitance. The found dependence on electrons concentration is consistent with experiments. The method of the proof is based on study of the time-dependent density matrix. The exact solution of von Neumann equation for density matrix is found for our case in linear approximation on the external field. On this basis the induced current is studied and then the formula for quantum conductivity as a function of external field frequency and temperature is obtained. The method of the proof suggested in this paper could be used to study other problems. The found formula for quantum conductivity can be used to correct the SPPs Dispersion Relation and for the description of radiation process. It would be useful to take the obtained results into account when constructing devices containing graphene membrane nanoantenna. Such project could make it possible to create wireless communications among nanosystems. This would be promising research area of energy harvesting applications.

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

Herbrych, Jacek W.; Feiguin, Adrian E.; Dagotto, Elbio R.

Here, we present a time-dependent density-matrix renormalization group investigation of the quantum distillation process within the Fermi-Hubbard model on a quasi-one-dimensional ladder geometry. The term distillation refers to the dynamical, spatial separation of singlons and doublons in the sudden expansion of interacting particles in an optical lattice, i.e., the release of a cloud of atoms from a trapping potential. Remarkably, quantum distillation can lead to a contraction of the doublon cloud, resulting in an increased density of the doublons in the core region compared to the initial state. As a main result, we show that this phenomenon is not limitedmore » to chains that were previously studied. Interestingly, there are additional dynamical processes on the two-leg ladder such as density oscillations and self-trapping of defects that lead to a less efficient distillation process. An investigation of the time evolution starting from product states provides an explanation for this behavior. Initial product states are also considered since in optical lattice experiments, such states are often used as the initial setup. We propose configurations that lead to a fast and efficient quantum distillation.« less

Stochastic population dynamics of a montane ground-dwelling squirrel.

PubMed

Hostetler, Jeffrey A; Kneip, Eva; Van Vuren, Dirk H; Oli, Madan K

2012-01-01

Understanding the causes and consequences of population fluctuations is a central goal of ecology. We used demographic data from a long-term (1990-2008) study and matrix population models to investigate factors and processes influencing the dynamics and persistence of a golden-mantled ground squirrel (Callospermophilus lateralis) population, inhabiting a dynamic subalpine habitat in Colorado, USA. The overall deterministic population growth rate λ was 0.94±SE 0.05 but it varied widely over time, ranging from 0.45±0.09 in 2006 to 1.50±0.12 in 2003, and was below replacement (λ<1) for 9 out of 18 years. The stochastic population growth rate λ(s) was 0.92, suggesting a declining population; however, the 95% CI on λ(s) included 1.0 (0.52-1.60). Stochastic elasticity analysis showed that survival of adult females, followed by survival of juvenile females and litter size, were potentially the most influential vital rates; analysis of life table response experiments revealed that the same three life history variables made the largest contributions to year-to year changes in λ. Population viability analysis revealed that, when the influences of density dependence and immigration were not considered, the population had a high (close to 1.0 in 50 years) probability of extinction. However, probability of extinction declined to as low as zero when density dependence and immigration were considered. Destabilizing effects of stochastic forces were counteracted by regulating effects of density dependence and rescue effects of immigration, which allowed our study population to bounce back from low densities and prevented extinction. These results suggest that dynamics and persistence of our study population are determined synergistically by density-dependence, stochastic forces, and immigration.

Stochastic Population Dynamics of a Montane Ground-Dwelling Squirrel

PubMed Central

Hostetler, Jeffrey A.; Kneip, Eva; Van Vuren, Dirk H.; Oli, Madan K.

2012-01-01

Understanding the causes and consequences of population fluctuations is a central goal of ecology. We used demographic data from a long-term (1990–2008) study and matrix population models to investigate factors and processes influencing the dynamics and persistence of a golden-mantled ground squirrel (Callospermophilus lateralis) population, inhabiting a dynamic subalpine habitat in Colorado, USA. The overall deterministic population growth rate λ was 0.94±SE 0.05 but it varied widely over time, ranging from 0.45±0.09 in 2006 to 1.50±0.12 in 2003, and was below replacement (λ<1) for 9 out of 18 years. The stochastic population growth rate λs was 0.92, suggesting a declining population; however, the 95% CI on λs included 1.0 (0.52–1.60). Stochastic elasticity analysis showed that survival of adult females, followed by survival of juvenile females and litter size, were potentially the most influential vital rates; analysis of life table response experiments revealed that the same three life history variables made the largest contributions to year-to year changes in λ. Population viability analysis revealed that, when the influences of density dependence and immigration were not considered, the population had a high (close to 1.0 in 50 years) probability of extinction. However, probability of extinction declined to as low as zero when density dependence and immigration were considered. Destabilizing effects of stochastic forces were counteracted by regulating effects of density dependence and rescue effects of immigration, which allowed our study population to bounce back from low densities and prevented extinction. These results suggest that dynamics and persistence of our study population are determined synergistically by density-dependence, stochastic forces, and immigration. PMID:22479616

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).

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

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

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.

Pulsed field gradients in simulations of one- and two-dimensional NMR spectra.

PubMed

Meresi, G H; Cuperlovic, M; Palke, W E; Gerig, J T

1999-03-01

A method for the inclusion of the effects of z-axis pulsed field gradients in computer simulations of an arbitrary pulsed NMR experiment with spin (1/2) nuclei is described. Recognizing that the phase acquired by a coherence following the application of a z-axis pulsed field gradient bears a fixed relation to its order and the spatial position of the spins in the sample tube, the sample is regarded as a collection of volume elements, each phase-encoded by a characteristic, spatially dependent precession frequency. The evolution of the sample's density matrix is thus obtained by computing the evolution of the density matrix for each volume element. Following the last gradient pulse, these density matrices are combined to form a composite density matrix which evolves through the rest of the experiment to yield the observable signal. This approach is implemented in a program which includes capabilities for rigorous inclusion of spin relaxation by dipole-dipole, chemical shift anisotropy, and random field mechanisms, plus the effects of arbitrary RF fields. Mathematical procedures for accelerating these calculations are described. The approach is illustrated by simulations of representative one- and two-dimensional NMR experiments. Copyright 1999 Academic Press.

Interaction-induced conducting-non-conducting transition of ultra-cold atoms in one-dimensional optical lattices

NASA Astrophysics Data System (ADS)

Chien, Chih-Chun; Gruss, Daniel; Di Ventra, Massimiliano; Zwolak, Michael

2013-06-01

The study of time-dependent, many-body transport phenomena is increasingly within reach of ultra-cold atom experiments. We show that the introduction of spatially inhomogeneous interactions, e.g., generated by optically controlled collisions, induce negative differential conductance in the transport of atoms in one-dimensional optical lattices. Specifically, we simulate the dynamics of interacting fermionic atoms via a micro-canonical transport formalism within both a mean-field and a higher-order approximation, as well as with a time-dependent density-matrix renormalization group (DMRG). For weakly repulsive interactions, a quasi-steady-state atomic current develops that is similar to the situation occurring for electronic systems subject to an external voltage bias. At the mean-field level, we find that this atomic current is robust against the details of how the interaction is switched on. Further, a conducting-non-conducting transition exists when the interaction imbalance exceeds some threshold from both our approximate and time-dependent DMRG simulations. This transition is preceded by the atomic equivalent of negative differential conductivity observed in transport across solid-state structures.

Quantum transport under ac drive from the leads: A Redfield quantum master equation approach

NASA Astrophysics Data System (ADS)

Purkayastha, Archak; Dubi, Yonatan

2017-08-01

Evaluating the time-dependent dynamics of driven open quantum systems is relevant for a theoretical description of many systems, including molecular junctions, quantum dots, cavity-QED experiments, cold atoms experiments, and more. Here, we formulate a rigorous microscopic theory of an out-of-equilibrium open quantum system of noninteracting particles on a lattice weakly coupled bilinearly to multiple baths and driven by periodically varying thermodynamic parameters like temperature and chemical potential of the bath. The particles can be either bosonic or fermionic and the lattice can be of any dimension and geometry. Based on the Redfield quantum master equation under Born-Markov approximation, we derive a linear differential equation for an equal time two point correlation matrix, sometimes also called a single-particle density matrix, from which various physical observables, for example, current, can be calculated. Various interesting physical effects, such as resonance, can be directly read off from the equations. Thus, our theory is quite general and gives quite transparent and easy-to-calculate results. We validate our theory by comparing with exact numerical simulations. We apply our method to a generic open quantum system, namely, a double quantum dot coupled to leads with modulating chemical potentials. The two most important experimentally relevant insights from this are as follows: (i) Time-dependent measurements of current for symmetric oscillating voltages (with zero instantaneous voltage bias) can point to the degree of asymmetry in the system-bath coupling and (ii) under certain conditions time-dependent currents can exceed time-averaged currents by several orders of magnitude, and can therefore be detected even when the average current is below the measurement threshold.

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

NASA Astrophysics Data System (ADS)

Nakatani, Naoki; Chan, Garnet Kin-Lic

2013-04-01

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

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.

Modelling interactions of toxicants and density dependence in wildlife populations

USGS Publications Warehouse

Schipper, Aafke M.; Hendriks, Harrie W.M.; Kauffman, Matthew J.; Hendriks, A. Jan; Huijbregts, Mark A.J.

2013-01-01

1. A major challenge in the conservation of threatened and endangered species is to predict population decline and design appropriate recovery measures. However, anthropogenic impacts on wildlife populations are notoriously difficult to predict due to potentially nonlinear responses and interactions with natural ecological processes like density dependence. 2. Here, we incorporated both density dependence and anthropogenic stressors in a stage-based matrix population model and parameterized it for a density-dependent population of peregrine falcons Falco peregrinus exposed to two anthropogenic toxicants [dichlorodiphenyldichloroethylene (DDE) and polybrominated diphenyl ethers (PBDEs)]. Log-logistic exposure–response relationships were used to translate toxicant concentrations in peregrine falcon eggs to effects on fecundity. Density dependence was modelled as the probability of a nonbreeding bird acquiring a breeding territory as a function of the current number of breeders. 3. The equilibrium size of the population, as represented by the number of breeders, responded nonlinearly to increasing toxicant concentrations, showing a gradual decrease followed by a relatively steep decline. Initially, toxicant-induced reductions in population size were mitigated by an alleviation of the density limitation, that is, an increasing probability of territory acquisition. Once population density was no longer limiting, the toxicant impacts were no longer buffered by an increasing proportion of nonbreeders shifting to the breeding stage, resulting in a strong decrease in the equilibrium number of breeders. 4. Median critical exposure concentrations, that is, median toxicant concentrations in eggs corresponding with an equilibrium population size of zero, were 33 and 46 μg g−1 fresh weight for DDE and PBDEs, respectively. 5. Synthesis and applications. Our modelling results showed that particular life stages of a density-limited population may be relatively insensitive to toxicant impacts until a critical threshold is crossed. In our study population, toxicant-induced changes were observed in the equilibrium number of nonbreeding rather than breeding birds, suggesting that monitoring efforts including both life stages are needed to timely detect population declines. Further, by combining quantitative exposure–response relationships with a wildlife demographic model, we provided a method to quantify critical toxicant thresholds for wildlife population persistence.

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

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.

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

NASA Technical Reports Server (NTRS)

Bowman, Randy; Noebe, Ronald

1989-01-01

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

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.

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

UV absorption spectrum of allene radical cations in solid argon

NASA Astrophysics Data System (ADS)

Chin, Chih-Hao; Lin, Meng-Yeh; Huang, Tzu-Ping; Wu, Yu-Jong

2018-05-01

Electron bombardment during deposition of an Ar matrix containing a small proportion of allene generated allene cations. Further irradiation of the matrix sample at 385 nm destroyed the allene cations and formed propyne cations in solid Ar. Both cations were identified according to previously reported IR absorption bands. Using a similar technique, we recorded the ultraviolet absorption spectrum of allene cations in solid Ar. The vibrationally resolved progression recorded in the range of 266-237 nm with intervals of about 800 cm-1 was assigned to the A2E ← X2E transition of allene cations, and the broad continuum absorption recorded in the region of 229-214 nm was assigned to their B2A1 ← X2E transition. These assignments were made based on the observed photolytic behavior of the progressions and the vertical excitation energies and oscillator strengths calculated using time-dependent density functional theory.

Intermittent hydrostatic pressure inhibits matrix metalloproteinase and pro-inflammatory mediator release from human osteoarthritic chondrocytes in vitro.

PubMed

Trindade, Michael C D; Shida, Jun-ichi; Ikenoue, Takashi; Lee, Mel S; Lin, Eric Y; Yaszay, Burt; Yerby, Scott; Goodman, Stuart B; Schurman, David J; Smith, R Lane

2004-09-01

This study tested the hypothesis that intermittent hydrostatic pressure applied to human osteoarthritic chondrocytes modulates matrix metalloproteinase and pro-inflammatory mediator release in vitro. Human osteoarthritic articular chondrocytes were isolated and cultured as primary high-density monolayers. For testing, chondrocyte cultures were transferred to serum-free medium and maintained without loading or with exposure to intermittent hydrostatic pressure (IHP) at 10 MPa at a frequency of 1 Hz for periods of 6, 12 and 24 h. Levels of matrix metalloproteinase-2, -9 (MMP-2, -9), tissue inhibitor of metalloproteinase-1 (TIMP-1), and the pro-inflammatory mediators, interleukin-6 (IL-6) and monocyte chemoattractant protein-1 (MCP-1), released into the culture medium were assessed by ELISA. Matrix metalloproteinase activity was confirmed by zymographic analysis. In the absence of IHP, levels of MMP-2, TIMP-1, IL-6, and MCP-1 in the chondrocyte culture medium increased in a time-dependent manner. Application of IHP decreased MMP-2 levels at all time periods tested, relative to unloaded control cultures maintained for the same time periods. Although 84/82 kDa bands were faintly detectable by zymography, MMP-9 levels were not quantifiable in medium from loaded or unloaded cultures by ELISA. TIMP-1 levels were not altered in response to IHP at any time period tested. IL-6 and MCP-1 levels decreased in cultures exposed to IHP at 12 and 24 h, relative to unloaded control cultures maintained for the same time periods. IHP decreased release of MMP-2, IL-6 and MCP-1 by osteoarthritic chondrocytes in vitro suggesting that pressure influences cartilage stability by modulating chondrocyte expression of these degradative and pro-inflammatory proteins in vivo.

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.

On regularizing the MCTDH equations of motion

NASA Astrophysics Data System (ADS)

Meyer, Hans-Dieter; Wang, Haobin

2018-03-01

The Multiconfiguration Time-Dependent Hartree (MCTDH) approach leads to equations of motion (EOM) which become singular when there are unoccupied so-called single-particle functions (SPFs). Starting from a Hartree product, all SPFs, except the first one, are unoccupied initially. To solve the MCTDH-EOMs numerically, one therefore has to remove the singularity by a regularization procedure. Usually the inverse of a density matrix is regularized. Here we argue and show that regularizing the coefficient tensor, which in turn regularizes the density matrix as well, leads to an improved performance of the EOMs. The initially unoccupied SPFs are rotated faster into their "correct direction" in Hilbert space and the final results are less sensitive to the choice of the value of the regularization parameter. For a particular example (a spin-boson system studied with a transformed Hamiltonian), we could even show that only with the new regularization scheme could one obtain correct results. Finally, in Appendix A, a new integration scheme for the MCTDH-EOMs developed by Lubich and co-workers is discussed. It is argued that this scheme does not solve the problem of the unoccupied natural orbitals because this scheme ignores the latter and does not propagate them at all.

The density matrix renormalization group algorithm on kilo-processor architectures: Implementation and trade-offs

NASA Astrophysics Data System (ADS)

Nemes, Csaba; Barcza, Gergely; Nagy, Zoltán; Legeza, Örs; Szolgay, Péter

2014-06-01

In the numerical analysis of strongly correlated quantum lattice models one of the leading algorithms developed to balance the size of the effective Hilbert space and the accuracy of the simulation is the density matrix renormalization group (DMRG) algorithm, in which the run-time is dominated by the iterative diagonalization of the Hamilton operator. As the most time-dominant step of the diagonalization can be expressed as a list of dense matrix operations, the DMRG is an appealing candidate to fully utilize the computing power residing in novel kilo-processor architectures. In the paper a smart hybrid CPU-GPU implementation is presented, which exploits the power of both CPU and GPU and tolerates problems exceeding the GPU memory size. Furthermore, a new CUDA kernel has been designed for asymmetric matrix-vector multiplication to accelerate the rest of the diagonalization. Besides the evaluation of the GPU implementation, the practical limits of an FPGA implementation are also discussed.

Multilayer-MCTDH approach to the energy transfer dynamics in the LH2 antenna complex

NASA Astrophysics Data System (ADS)

Shibl, Mohamed F.; Schulze, Jan; Al-Marri, Mohammed J.; Kühn, Oliver

2017-09-01

The multilayer multiconfiguration time-dependent Hartree method is used to study the coupled exciton-vibrational dynamics in a high-dimensional nonameric model of the LH2 antenna complex of purple bacteria. The exciton-vibrational coupling is parametrized within the Huang-Rhys model according to phonon and intramolecular vibrational modes derived from an experimental bacteriochlorophyll spectral density. In contrast to reduced density matrix approaches, the Schrödinger equation is solved explicitly, giving access to the full wave function. This facilitates an unbiased analysis in terms of the coupled dynamics of excitonic and vibrational degrees of freedom. For the present system, we identify spectator modes for the B800 to B800 transfer and we find a non-additive effect of phonon and intramolecular vibrational modes on the B800 to B850 exciton transfer.

Dynamics anomaly in high-density amorphous ice between 0.7 and 1.1 GPa

NASA Astrophysics Data System (ADS)

Handle, Philip H.; Loerting, Thomas

2016-02-01

We studied high-density amorphous ices between 0.004 and 1.6 GPa by isobaric in situ volumetry and by subsequent ex situ x-ray diffraction and differential scanning calorimetry at 1 bar. Our observations indicate two processes, namely, relaxation in the amorphous matrix and crystallization, taking place at well-separated time scales. For this reason, we are able to report rate constants of crystallization kX and glass-transition temperatures Tg in an unprecedented pressure range. Tg's agree within ±3 K with earlier work in the small pressure range where there is overlap. Both Tg and kX show a pressure anomaly between 0.7 and 1.1 GPa, namely, a kX minimum and a Tg maximum. This anomalous pressure dependence suggests a continuous phase transition from high- (HDA) to very-high-density amorphous ice (VHDA) and faster hydrogen bond dynamics in VHDA. We speculate this phenomenology can be rationalized by invoking the crossing of a Widom line between 0.7 and 1.1 GPa emanating from a low-lying HDA-VHDA critical point. Furthermore, we interpret the volumetric relaxation of the amorphous matrix to be accompanied by viscosity change to explain the findings such that the liquid state can be accessed prior to the crystallization temperature TX at <0.4 GPa and >0.8 GPa.

Path-Dependent Travel Time Prediction Variance and Covariance for a Global Tomographic P- and S-Velocity Model

NASA Astrophysics Data System (ADS)

Hipp, J. R.; Ballard, S.; Begnaud, M. L.; Encarnacao, A. V.; Young, C. J.; Phillips, W. S.

2015-12-01

Recently our combined SNL-LANL research team has succeeded in developing a global, seamless 3D tomographic P- and S-velocity model (SALSA3D) that provides superior first P and first S travel time predictions at both regional and teleseismic distances. However, given the variable data quality and uneven data sampling associated with this type of model, it is essential that there be a means to calculate high-quality estimates of the path-dependent variance and covariance associated with the predicted travel times of ray paths through the model. In this paper, we describe a methodology for accomplishing this by exploiting the full model covariance matrix and show examples of path-dependent travel time prediction uncertainty computed from our latest tomographic model. Typical global 3D SALSA3D models have on the order of 1/2 million nodes, so the challenge in calculating the covariance matrix is formidable: 0.9 TB storage for 1/2 of a symmetric matrix, necessitating an Out-Of-Core (OOC) blocked matrix solution technique. With our approach the tomography matrix (G which includes a prior model covariance constraint) is multiplied by its transpose (GTG) and written in a blocked sub-matrix fashion. We employ a distributed parallel solution paradigm that solves for (GTG)-1 by assigning blocks to individual processing nodes for matrix decomposition update and scaling operations. We first find the Cholesky decomposition of GTG which is subsequently inverted. Next, we employ OOC matrix multiplication methods to calculate the model covariance matrix from (GTG)-1 and an assumed data covariance matrix. Given the model covariance matrix, we solve for the travel-time covariance associated with arbitrary ray-paths by summing the model covariance along both ray paths. Setting the paths equal and taking the square root yields the travel prediction uncertainty for the single path.

Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework.

PubMed

Morzan, Uriel N; Ramírez, Francisco F; Oviedo, M Belén; Sánchez, Cristián G; Scherlis, Damián A; Lebrero, Mariano C González

2014-04-28

This article presents a time dependent density functional theory (TDDFT) implementation to propagate the Kohn-Sham equations in real time, including the effects of a molecular environment through a Quantum-Mechanics Molecular-Mechanics (QM-MM) hamiltonian. The code delivers an all-electron description employing Gaussian basis functions, and incorporates the Amber force-field in the QM-MM treatment. The most expensive parts of the computation, comprising the commutators between the hamiltonian and the density matrix-required to propagate the electron dynamics-, and the evaluation of the exchange-correlation energy, were migrated to the CUDA platform to run on graphics processing units, which remarkably accelerates the performance of the code. The method was validated by reproducing linear-response TDDFT results for the absorption spectra of several molecular species. Two different schemes were tested to propagate the quantum dynamics: (i) a leap-frog Verlet algorithm, and (ii) the Magnus expansion to first-order. These two approaches were confronted, to find that the Magnus scheme is more efficient by a factor of six in small molecules. Interestingly, the presence of iron was found to seriously limitate the length of the integration time step, due to the high frequencies associated with the core-electrons. This highlights the importance of pseudopotentials to alleviate the cost of the propagation of the inner states when heavy nuclei are present. Finally, the methodology was applied to investigate the shifts induced by the chemical environment on the most intense UV absorption bands of two model systems of general relevance: the formamide molecule in water solution, and the carboxy-heme group in Flavohemoglobin. In both cases, shifts of several nanometers are observed, consistently with the available experimental data.

Multi-layer multi-configuration time-dependent Hartree (ML-MCTDH) approach to the correlated exciton-vibrational dynamics in the FMO complex

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

Schulze, Jan; Kühn, Oliver, E-mail: oliver.kuehn@uni-rostock.de; Shibl, Mohamed F., E-mail: mfshibl@qu.edu.qa

2016-05-14

The coupled quantum dynamics of excitonic and vibrational degrees of freedom is investigated for high-dimensional models of the Fenna-Matthews-Olson complex. This includes a seven- and an eight-site model with 518 and 592 harmonic vibrational modes, respectively. The coupling between local electronic transitions and vibrations is described within the Huang-Rhys model using parameters that are obtained by discretization of an experimental spectral density. Different pathways of excitation energy flow are analyzed in terms of the reduced one-exciton density matrix, focussing on the role of vibrational and vibronic excitations. Distinct features due to both competing time scales of vibrational and exciton motionmore » and vibronically assisted transfer are observed. The question of the effect of initial state preparation is addressed by comparing the case of an instantaneous Franck-Condon excitation at a single site with that of a laser field excitation.« less

Variational path integral molecular dynamics and hybrid Monte Carlo algorithms using a fourth order propagator with applications to molecular systems

NASA Astrophysics Data System (ADS)

Kamibayashi, Yuki; Miura, Shinichi

2016-08-01

In the present study, variational path integral molecular dynamics and associated hybrid Monte Carlo (HMC) methods have been developed on the basis of a fourth order approximation of a density operator. To reveal various parameter dependence of physical quantities, we analytically solve one dimensional harmonic oscillators by the variational path integral; as a byproduct, we obtain the analytical expression of the discretized density matrix using the fourth order approximation for the oscillators. Then, we apply our methods to realistic systems like a water molecule and a para-hydrogen cluster. In the HMC, we adopt two level description to avoid the time consuming Hessian evaluation. For the systems examined in this paper, the HMC method is found to be about three times more efficient than the molecular dynamics method if appropriate HMC parameters are adopted; the advantage of the HMC method is suggested to be more evident for systems described by many body interaction.

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

PubMed Central

Milovanovic, Petar; Djuric, Marija; Rakocevic, Zlatko

2012-01-01

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

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

PubMed

Milovanovic, Petar; Djuric, Marija; Rakocevic, Zlatko

2012-11-01

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

Light-Cone and Diffusive Propagation of Correlations in a Many-Body Dissipative System.

PubMed

Bernier, Jean-Sébastien; Tan, Ryan; Bonnes, Lars; Guo, Chu; Poletti, Dario; Kollath, Corinna

2018-01-12

We analyze the propagation of correlations after a sudden interaction change in a strongly interacting quantum system in contact with an environment. In particular, we consider an interaction quench in the Bose-Hubbard model, deep within the Mott-insulating phase, under the effect of dephasing. We observe that dissipation effectively speeds up the propagation of single-particle correlations while reducing their coherence. In contrast, for two-point density correlations, the initial ballistic propagation regime gives way to diffusion at intermediate times. Numerical simulations, based on a time-dependent matrix product state algorithm, are supplemented by a quantitatively accurate fermionic quasiparticle approach providing an intuitive description of the initial dynamics in terms of holon and doublon excitations.

Novel silica surface charge density mediated control of the optical properties of embedded optically active materials and its application for fiber optic pH sensing at elevated temperatures.

PubMed

Wang, Congjun; Ohodnicki, Paul R; Su, Xin; Keller, Murphy; Brown, Thomas D; Baltrus, John P

2015-02-14

Silica and silica incorporated nanocomposite materials have been extensively studied for a wide range of applications. Here we demonstrate an intriguing optical effect of silica that, depending on the solution pH, amplifies or attenuates the optical absorption of a variety of embedded optically active materials with very distinct properties, such as plasmonic Au nanoparticles, non-plasmonic Pt nanoparticles, and the organic dye rhodamine B (not a pH indicator), coated on an optical fiber. Interestingly, the observed optical response to varying pH appears to follow the surface charge density of the silica matrix for all the three different optically active materials. To the best of our knowledge, this optical effect has not been previously reported and it appears universal in that it is likely that any optically active material can be incorporated into the silica matrix to respond to solution pH or surface charge density variations. A direct application of this effect is for optical pH sensing which has very attractive features that can enable minimally invasive, remote, real time and continuous distributed pH monitoring. Particularly, as demonstrated here, using highly stable metal nanoparticles embedded in an inorganic silica matrix can significantly improve the capability of pH sensing in extremely harsh environments which is of increasing importance for applications in unconventional oil and gas resource recovery, carbon sequestration, water quality monitoring, etc. Our approach opens a pathway towards possible future development of robust optical pH sensors for the most demanding environmental conditions. The newly discovered optical effect of silica also offers the potential for control of the optical properties of optically active materials for a range of other potential applications such as electrochromic devices.

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.

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.

The effect of the molecular orientation on the release of antimicrobial substances from uniaxially drawn polymer matrixes.

PubMed

Iconomopoulou, S M; Voyiatzis, G A

2005-03-21

A new method of controlled release of low molecular weight biocides incorporated in polymer matrixes is described. The molecular orientation of uniaxially drawn biocide doped polymer films is suggested as a significant parameter for controlled release monitoring. Triclosan, a well-established widespread antibacterial agent, has been incorporated into high density polyethylene (HDPE) films that have been subsequently uniaxially drawn at different draw ratios. The molecular orientation developed was estimated utilizing polarized mu-Raman spectra. Biocide incorporated polymer films, drawn at different draw ratios, have been immersed in ethanol-water solutions (EtOH) and in physiological saline. The release of Triclosan out of the polymer matrix was probed with UV-Vis absorption spectroscopy for a period of time up to 15 months. In all cases, although the film surface of the drawn samples exposed to the liquid solution was higher than the undrawn one, the relevant release rate from the drawn specimens was lower than the non-stretched samples depending on the molecular orientation developed during the drawing process. A note is made of the fact that no significant molecular orientation relaxation of the polyethylene films has been observed even after such a long time of immersion of the drawn films in the liquid solutions.

Photoluminescence investigation of type-II GaSb/GaAs quantum dots grown by liquid phase epitaxy

NASA Astrophysics Data System (ADS)

Wang, Yang; Hu, Shuhong; Xie, Hao; Lin, Hongyu; lu, Hongbo; Wang, Chao; Sun, Yan; Dai, Ning

2018-06-01

GaSb quantum dots (QDs) with an areal density of ∼1 × 1010 cm-2 are successfully grown by the modified (rapid slider) liquid phase epitaxy technique. The morphology of the QDs has been investigated by scanning electron microscope (SEM) and atom force microscope (AFM). The power-dependence and temperature-dependence photoluminescence (PL) spectra have been studied. The bright room-temperature PL suggests a good luminescence quality of GaSb QDs/GaAs matrix system. The type-II alignment of the GaSb QDs/GaAs matrix system is verified by the blue-shift of the QDs peak with the increase of excitation power. From the temperature-dependence PL spectra, the activation energy of QDs is determined to be 111 meV.

DENSITY FRACTIONATION OF FOREST SOILS: METHODOLOGICAL QUESTIONS AND INTERPRETATION OF INCUBATION RESULTS AND TURNOVER TIME IN AN ECOSYSTEM CONTEXT

EPA Science Inventory

Soil organic matter (SOM) is often separated by physical means to simplify a complex matrix into discrete fractions. A frequent approach to isolating two or more fractions is based on differing particle densities and uses a high density liquid such as sodium polytungstate (SPT). ...

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).

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

Density-matrix approach for the electroluminescence of molecules in a scanning tunneling microscope.

PubMed

Tian, Guangjun; Liu, Ji-Cai; Luo, Yi

2011-04-29

The electroluminescence (EL) of molecules confined inside a nanocavity in the scanning tunneling microscope possesses many intriguing but unexplained features. We present here a general theoretical approach based on the density-matrix formalism to describe the EL from molecules near a metal surface induced by both electron tunneling and localized surface plasmon excitations simultaneously. It reveals the underlying physical mechanism for the external bias dependent EL. The important role played by the localized surface plasmon on the EL is highlighted. Calculations for porphyrin derivatives have reproduced corresponding experimental spectra and nicely explained the observed unusual large variation of emission spectral profiles. This general theoretical approach can find many applications in the design of molecular electronic and photonic devices.

Elevated-Temperature Life Limiting Behavior of Hi-Nicalon SiC/SiC Ceramic Matrix Composite in Interlaminar Shear

DTIC Science & Technology

2007-03-02

ceramic matrix composites (CMCs), particularly in aeroengine applications, are dependent on better understanding of their life limiting properties such as... vibration technique, ASTM C 1259 [10]), and 2.36±0.02 g/cm 3 bulk density, all estimated at ambient temperature [5,10]. A typical micrograph of the cross...It is necessary to use appropriate aeroengine environments to better describe life limiting behavior of the material in interlaminar shear. This may

Does the performance of wet granulation and tablet hardness affect the drug dissolution profile of carvedilol in matrix tablets?

PubMed

Košir, Darjan; Ojsteršek, Tadej; Vrečer, Franc

2018-06-14

Wet granulation is mostly used process for manufacturing matrix tablets. Compared to the direct compression method, it allows for a better flow and compressibility properties of compression mixtures. Granulation, including process parameters and tableting, can influence critical quality attributes (CQAs) of hydrophilic matrix tablets. One of the most important CQAs is the drug release profile. We studied the influence of granulation process parameters (type of nozzle and water quantity used as granulation liquid) and tablet hardness on the drug release profile. Matrix tablets contained HPMC K4M hydrophilic matrix former and carvedilol as a model drug. The influence of selected HPMC characteristics on the drug release profile was also evaluated using two additional HPMC batches. For statistical evaluation, partial least square (PLS) models were generated for each time point of the drug release profile using the same number of latent factors. In this way, it was possible to evaluate how the importance of factors influencing drug dissolution changes in dependence on time throughout the drug release profile. The results of statistical evaluation show that the granulation process parameters (granulation liquid quantity and type of nozzle) and tablet hardness significantly influence the release profile. On the other hand, the influence of HPMC characteristics is negligible in comparison to the other factors studied. Using a higher granulation liquid quantity and the standard nozzle type results in larger granules with a higher density and lower porosity, which leads to a slower drug release profile. Lower tablet hardness also slows down the release profile.

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.

Floquet Engineering in Quantum Chains

NASA Astrophysics Data System (ADS)

Kennes, D. M.; de la Torre, A.; Ron, A.; Hsieh, D.; Millis, A. J.

2018-03-01

We consider a one-dimensional interacting spinless fermion model, which displays the well-known Luttinger liquid (LL) to charge density wave (CDW) transition as a function of the ratio between the strength of the interaction U and the hopping J . We subject this system to a spatially uniform drive which is ramped up over a finite time interval and becomes time periodic in the long-time limit. We show that by using a density matrix renormalization group approach formulated for infinite system sizes, we can access the large-time limit even when the drive induces finite heating. When both the initial and long-time states are in the gapless (LL) phase, the final state has power-law correlations for all ramp speeds. However, when the initial and final state are gapped (CDW phase), we find a pseudothermal state with an effective temperature that depends on the ramp rate, both for the Magnus regime in which the drive frequency is very large compared to other scales in the system and in the opposite limit where the drive frequency is less than the gap. Remarkably, quantum defects (instantons) appear when the drive tunes the system through the quantum critical point, in a realization of the Kibble-Zurek mechanism.

Lindblad and Bloch equations for conversion of a neutron into an antineutron

NASA Astrophysics Data System (ADS)

Kerbikov, B. O.

2018-07-01

We propose a new approach based on the Lindblad and Bloch equations for the density matrix to the problem of a neutron into an antineutron conversion. We consider three strategies to search for conversion: experiments with trapped neutrons, oscillations in nuclei, and quasi-free propagation. We draw a distinction between n n bar oscillations in which the probability that a neutron transforms into an antineutron depends on time according to the sine-square law and the non-oscillatory overdamped n n bar conversion. We show that in all three cases decoherence due to the interaction with the environment leads to non-oscillatory evolution.

Application of Glass Fiber Waste Polypropylene Aggregate in Lightweight Concrete – thermal properties

NASA Astrophysics Data System (ADS)

Citek, D.; Rehacek, S.; Pavlik, Z.; Kolisko, J.; Dobias, D.; Pavlikova, M.

2018-03-01

Actual paper focus on thermal properties of a sustainable lightweight concrete incorporating high volume of waste polypropylene aggregate as partial substitution of natural aggregate. In presented experiments a glass fiber reinforced polypropylene (GFPP) which is a by-product of PP tubes production, partially substituted fine natural silica aggregate in 10, 20, 30, 40 and 50 mass %. Results were compared with a reference concrete mix without plastic waste in order to quantify the effect of GFPP use on concrete properties. Main material physical parameters were studied (bulk density, matrix density without air content, and particle size distribution). Especially a thermal transport and storage properties of GFPP were examined in dependence on compaction time. For the developed lightweight concrete, thermal properties were accessed using transient impulse technique, where the measurement was done in dependence on moisture content (from the fully water saturated state to dry state). It was found that the tested lightweight concrete should be prospective construction material possessing improved thermal insulation function and the reuse of waste plastics in concrete composition was beneficial both from the environmental and financial point of view.

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

Analysis of transition-metal acetylacetonate complexes by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Wyatt, Mark F; Havard, Stephen; Stein, Bridget K; Brenton, A Gareth

2008-01-01

Transition-metal acetylacetonate complexes of the form Metal(acac)(2), where Metal = Fe(II), Co(II), Ni(II), Cu(II), and Zn(II), and Metal(acac)(3), where Metal = V(III), Cr(III), Mn(III), Fe(III), and Co(III), were investigated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). The data was acquired using the aprotic, electron transfer matrix, 2-[(2E)-3-(4-tert-butylphenyl)-2-methylprop-2-enylidene]malononitrile (DCTB), and the observation of positive radical ions is shown clearly to depend on the metal element and the oxidation state it occupies. The ionization energy of DCTB was calculated to be 8.08 eV by density functional theory methods, which is notably lower than the experimental value, but within the range of other computational values. This value is very close to those of the analytes, so the existing electron transfer mechanism which is based on the ionization energies of the matrix and analyte, cannot be used predictively. Similarly, the data neither proves nor disproves the validity of the existing electron transfer ionization mechanism, with respect to metal coordination complexes without strong chromophores. In this case, periodic trends may be more useful in explaining the observed species and the prediction of species from sets of similar complexes. The addition of a sodium salt benefits the MALDI-TOFMS characterization of certain compounds studied, but the benefit of the addition of ammonium or silver salts is negligible.

Time-resolved electronic and optical properties of a thiolate-protected Au38 nanocluster

NASA Astrophysics Data System (ADS)

Meng, Qingguo; May, Stanley P.; Berry, Mary T.; Kilin, Dmitri S.

2015-02-01

Density functional theory and density matrix theory are employed to investigate the time-dependent optical and electronic properties of an Au14 nanocluster protected by six cyclic thiolate ligands, Au4(SCH3)4. The Au14[Au4(SCH3)4]6 nanocluster, i.e. Au38(SCH3)24, is equivalent to a truncated-octahedral face-centred cubic Au38 core coated by a monolayer of 24 methylthiol molecules. The electronic and optical properties, such as density of states, linear absorption spectra, nonradiative nonadiabatic dissipative electronic dynamics and radiative emission spectra were calculated and compared for the core Au14 and thiolate-protected Au38(SCH3)24 nanocluster. The main observation from computed photoluminescence for both models is a mechanism of radiative emission. Specifically, a strong contribution to light emission intensity originates from intraband transitions inside the conduction band (CB) in addition to interband LUMO → HOMO transition (HOMO: highest occupied molecular orbital and LUMO: lowest unoccupied molecular orbital). Such comparison clarifies the contributions from Au core and methylthiol ligands to the electronic and optical properties of the Au38(SCH3)24 nanocluster.

Reduced-Density-Matrix Description of Decoherence and Relaxation Processes for Electron-Spin Systems

NASA Astrophysics Data System (ADS)

Jacobs, Verne

2017-04-01

Electron-spin systems are investigated using a reduced-density-matrix description. Applications of interest include trapped atomic systems in optical lattices, semiconductor quantum dots, and vacancy defect centers in solids. Complimentary time-domain (equation-of-motion) and frequency-domain (resolvent-operator) formulations are self-consistently developed. The general non-perturbative and non-Markovian formulations provide a fundamental framework for systematic evaluations of corrections to the standard Born (lowest-order-perturbation) and Markov (short-memory-time) approximations. Particular attention is given to decoherence and relaxation processes, as well as spectral-line broadening phenomena, that are induced by interactions with photons, phonons, nuclear spins, and external electric and magnetic fields. These processes are treated either as coherent interactions or as environmental interactions. The environmental interactions are incorporated by means of the general expressions derived for the time-domain and frequency-domain Liouville-space self-energy operators, for which the tetradic-matrix elements are explicitly evaluated in the diagonal-resolvent, lowest-order, and Markov (short-memory time) approximations. Work supported by the Office of Naval Research through the Basic Research Program at The Naval Research Laboratory.

Accelerating molecular property calculations with nonorthonormal Krylov space methods

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

Furche, Filipp; Krull, Brandon T.; Nguyen, Brian D.

Here, we formulate Krylov space methods for large eigenvalue problems and linear equation systems that take advantage of decreasing residual norms to reduce the cost of matrix-vector multiplication. The residuals are used as subspace basis without prior orthonormalization, which leads to generalized eigenvalue problems or linear equation systems on the Krylov space. These nonorthonormal Krylov space (nKs) algorithms are favorable for large matrices with irregular sparsity patterns whose elements are computed on the fly, because fewer operations are necessary as the residual norm decreases as compared to the conventional method, while errors in the desired eigenpairs and solution vectors remainmore » small. We consider real symmetric and symplectic eigenvalue problems as well as linear equation systems and Sylvester equations as they appear in configuration interaction and response theory. The nKs method can be implemented in existing electronic structure codes with minor modifications and yields speed-ups of 1.2-1.8 in typical time-dependent Hartree-Fock and density functional applications without accuracy loss. The algorithm can compute entire linear subspaces simultaneously which benefits electronic spectra and force constant calculations requiring many eigenpairs or solution vectors. The nKs approach is related to difference density methods in electronic ground state calculations, and particularly efficient for integral direct computations of exchange-type contractions. By combination with resolution-of-the-identity methods for Coulomb contractions, three- to fivefold speed-ups of hybrid time-dependent density functional excited state and response calculations are achieved.« less

Accelerating molecular property calculations with nonorthonormal Krylov space methods

DOE PAGES

Furche, Filipp; Krull, Brandon T.; Nguyen, Brian D.; ...

2016-05-03

Here, we formulate Krylov space methods for large eigenvalue problems and linear equation systems that take advantage of decreasing residual norms to reduce the cost of matrix-vector multiplication. The residuals are used as subspace basis without prior orthonormalization, which leads to generalized eigenvalue problems or linear equation systems on the Krylov space. These nonorthonormal Krylov space (nKs) algorithms are favorable for large matrices with irregular sparsity patterns whose elements are computed on the fly, because fewer operations are necessary as the residual norm decreases as compared to the conventional method, while errors in the desired eigenpairs and solution vectors remainmore » small. We consider real symmetric and symplectic eigenvalue problems as well as linear equation systems and Sylvester equations as they appear in configuration interaction and response theory. The nKs method can be implemented in existing electronic structure codes with minor modifications and yields speed-ups of 1.2-1.8 in typical time-dependent Hartree-Fock and density functional applications without accuracy loss. The algorithm can compute entire linear subspaces simultaneously which benefits electronic spectra and force constant calculations requiring many eigenpairs or solution vectors. The nKs approach is related to difference density methods in electronic ground state calculations, and particularly efficient for integral direct computations of exchange-type contractions. By combination with resolution-of-the-identity methods for Coulomb contractions, three- to fivefold speed-ups of hybrid time-dependent density functional excited state and response calculations are achieved.« less

Use of an Inverse Method for Time Series to Estimate the Dynamics of and Management Strategies for the Box Jellyfish Carybdea marsupialis.

PubMed

Bordehore, Cesar; Fuentes, Verónica L; Segarra, Jose G; Acevedo, Melisa; Canepa, Antonio; Raventós, Josep

2015-01-01

Frequently, population ecology of marine organisms uses a descriptive approach in which their sizes and densities are plotted over time. This approach has limited usefulness for design strategies in management or modelling different scenarios. Population projection matrix models are among the most widely used tools in ecology. Unfortunately, for the majority of pelagic marine organisms, it is difficult to mark individuals and follow them over time to determine their vital rates and built a population projection matrix model. Nevertheless, it is possible to get time-series data to calculate size structure and densities of each size, in order to determine the matrix parameters. This approach is known as a "demographic inverse problem" and it is based on quadratic programming methods, but it has rarely been used on aquatic organisms. We used unpublished field data of a population of cubomedusae Carybdea marsupialis to construct a population projection matrix model and compare two different management strategies to lower population to values before year 2008 when there was no significant interaction with bathers. Those strategies were by direct removal of medusae and by reducing prey. Our results showed that removal of jellyfish from all size classes was more effective than removing only juveniles or adults. When reducing prey, the highest efficiency to lower the C. marsupialis population occurred when prey depletion affected prey of all medusae sizes. Our model fit well with the field data and may serve to design an efficient management strategy or build hypothetical scenarios such as removal of individuals or reducing prey. TThis This sdfsdshis method is applicable to other marine or terrestrial species, for which density and population structure over time are available.

A cubic scaling algorithm for excited states calculations in particle-particle random phase approximation

NASA Astrophysics Data System (ADS)

Lu, Jianfeng; Yang, Haizhao

2017-07-01

The particle-particle random phase approximation (pp-RPA) has been shown to be capable of describing double, Rydberg, and charge transfer excitations, for which the conventional time-dependent density functional theory (TDDFT) might not be suitable. It is thus desirable to reduce the computational cost of pp-RPA so that it can be efficiently applied to larger molecules and even solids. This paper introduces an O (N3) algorithm, where N is the number of orbitals, based on an interpolative separable density fitting technique and the Jacobi-Davidson eigensolver to calculate a few low-lying excitations in the pp-RPA framework. The size of the pp-RPA matrix can also be reduced by keeping only a small portion of orbitals with orbital energy close to the Fermi energy. This reduced system leads to a smaller prefactor of the cubic scaling algorithm, while keeping the accuracy for the low-lying excitation energies.

A new approach for the calculation of response spectral density of a linear stationary random multidegree of freedom system

NASA Astrophysics Data System (ADS)

Sharan, A. M.; Sankar, S.; Sankar, T. S.

1982-08-01

A new approach for the calculation of response spectral density for a linear stationary random multidegree of freedom system is presented. The method is based on modifying the stochastic dynamic equations of the system by using a set of auxiliary variables. The response spectral density matrix obtained by using this new approach contains the spectral densities and the cross-spectral densities of the system generalized displacements and velocities. The new method requires significantly less computation time as compared to the conventional method for calculating response spectral densities. Two numerical examples are presented to compare quantitatively the computation time.

Development and application of a density dependent matrix population model for Atlantic killifish (Fundulus heteroclitus)

EPA Science Inventory

Ranging along the Atlantic coast from US Florida to the Maritime Provinces of Canada, the Atlantic killifish (Fundulus heteroclitus) is an important and well-studied model organism for understanding the effects of pollutants and other stressors in estuarine and marine ecosystems....

On the Role of Processing Parameters in Producing Recycled Aluminum AA6061 Based Metal Matrix Composite (MMC-AlR) Prepared Using Hot Press Forging (HPF) Process

PubMed Central

Ahmad, Azlan; Lajis, Mohd Amri

2017-01-01

Solid-state recycling, which involves the direct recycling of scrap metal into bulk material using severe plastic deformation, has emerged as a potential alternative to the conventional remelting and recycling techniques. Hot press forging has been identified as a sustainable direct recycling technique that has fewer steps and maintains excellent material performance. An experimental investigation was conducted to explore the hardness and density of a recycled aluminum-based metal matrix composite by varying operating temperature and holding time. A mixture of recycled aluminum, AA6061, and aluminum oxide were simultaneously heated to 430, 480, and 530 °C and forged for 60, 90, and 120 min. We found a positive increase in microhardness and density for all composites. The hardness increased approximately 33.85%, while density improved by about 15.25% whenever the temperature or the holding time were increased. Based on qualitative analysis, the composite endures substantial plastic deformation due to the presence of hardness properties due to the aluminum oxide embedded in the aluminum matrix. These increases were significantly affected by the operating temperature; the holding time also had a subordinate role in enhancing the metal matrix composite properties. Furthermore, in an effort to curb the shortage of primary resources, this study reviewed the promising performance of secondary resources produced by using recycled aluminum and aluminum oxide as the base matrix and reinforcement constituent, respectively. This study is an outline for machining practitioners and the manufacturing industry to help increase industry sustainability with the aim of preserving the Earth for our community in the future. PMID:28925963

On the Role of Processing Parameters in Producing Recycled Aluminum AA6061 Based Metal Matrix Composite (MMC-AlR) Prepared Using Hot Press Forging (HPF) Process.

PubMed

Ahmad, Azlan; Lajis, Mohd Amri; Yusuf, Nur Kamilah

2017-09-19

Solid-state recycling, which involves the direct recycling of scrap metal into bulk material using severe plastic deformation, has emerged as a potential alternative to the conventional remelting and recycling techniques. Hot press forging has been identified as a sustainable direct recycling technique that has fewer steps and maintains excellent material performance. An experimental investigation was conducted to explore the hardness and density of a recycled aluminum-based metal matrix composite by varying operating temperature and holding time. A mixture of recycled aluminum, AA6061, and aluminum oxide were simultaneously heated to 430, 480, and 530 °C and forged for 60, 90, and 120 min. We found a positive increase in microhardness and density for all composites. The hardness increased approximately 33.85%, while density improved by about 15.25% whenever the temperature or the holding time were increased. Based on qualitative analysis, the composite endures substantial plastic deformation due to the presence of hardness properties due to the aluminum oxide embedded in the aluminum matrix. These increases were significantly affected by the operating temperature; the holding time also had a subordinate role in enhancing the metal matrix composite properties. Furthermore, in an effort to curb the shortage of primary resources, this study reviewed the promising performance of secondary resources produced by using recycled aluminum and aluminum oxide as the base matrix and reinforcement constituent, respectively. This study is an outline for machining practitioners and the manufacturing industry to help increase industry sustainability with the aim of preserving the Earth for our community in the future.

The diffusivity and solubility of deuterium in a high chromium martensitic steel

NASA Astrophysics Data System (ADS)

Forcey, K. S.; Iordanova, I.; Yaneva, M.

1997-01-01

The permeability, diffusivity and solubility of deuterium in the martensitic stainless steel MANET II have been studied in the temperature range 194-465°C by applying a time dependent gas-phase permeation technique. It was found that the temperature dependence of diffusivity and solubility could not be described by a simple Arrhenius expression over the entire temperature range investigated. At lower temperatures (below about 330°C) the diffusivity was found to be greatly reduced by the effects of trapping. Oriani's model has been applied to obtain the trapping energy and number density of the traps as well as the relative amounts of deuterium dissolved at lattice and trap sites. It is suggested that the most likely sites for trapping are at interfaces between the martensitic laths and between second phase particles and the surrounding metal matrix.

Thermalization and light cones in a model with weak integrability breaking

DOE PAGES

Bertini, Bruno; Essler, Fabian H. L.; Groha, Stefan; ...

2016-12-09

Here, we employ equation-of-motion techniques to study the nonequilibrium dynamics in a lattice model of weakly interacting spinless fermions. Our model provides a simple setting for analyzing the effects of weak integrability-breaking perturbations on the time evolution after a quantum quench. We establish the accuracy of the method by comparing results at short and intermediate times to time-dependent density matrix renormalization group computations. For sufficiently weak integrability-breaking interactions we always observe prethermalization plateaus, where local observables relax to nonthermal values at intermediate time scales. At later times a crossover towards thermal behavior sets in. We determine the associated time scale,more » which depends on the initial state, the band structure of the noninteracting theory, and the strength of the integrability-breaking perturbation. Our method allows us to analyze in some detail the spreading of correlations and in particular the structure of the associated light cones in our model. We find that the interior and exterior of the light cone are separated by an intermediate region, the temporal width of which appears to scale with a universal power law t 1/3.« less

Theory of ion-matrix-sheath dynamics

NASA Astrophysics Data System (ADS)

Kos, L.; Tskhakaya, D. D.

2018-01-01

The time evolution of a one-dimensional, uni-polar ion sheath (an "ion matrix sheath") is investigated. The analytical solutions for the ion-fluid and Poisson's equations are found for an arbitrary time dependence of the wall-applied negative potential. In the case that the wall potential is large and remains constant after its ramp-up application, the explicit time dependencies of the sheath's parameters during the initial stage of the process are given. The characteristic rate of approaching the stationary state, satisfying the Child-Langmuir law, is determined.

Crystal growth in zinc borosilicate glasses

NASA Astrophysics Data System (ADS)

Kullberg, Ana T. G.; Lopes, Andreia A. S.; Veiga, João P. B.; Monteiro, Regina C. C.

2017-01-01

Glass samples with a molar composition (64+x)ZnO-(16-x)B2O3-20SiO2, where x=0 or 1, were successfully synthesized using a melt-quenching technique. Based on differential thermal analysis data, the produced glass samples were submitted to controlled heat-treatments at selected temperatures (610, 615 and 620 °C) during various times ranging from 8 to 30 h. The crystallization of willemite (Zn2SiO4) within the glass matrix was confirmed by means of X-ray diffraction (XRD) and scanning electron microscopy (SEM). Under specific heat-treatment conditions, transparent nanocomposite glass-ceramics were obtained, as confirmed by UV-vis spectroscopy. The influence of temperature, holding time and glass composition on crystal growth was investigated. The mean crystallite size was determined by image analysis on SEM micrographs. The results indicated an increase on the crystallite size and density with time and temperature. The change of crystallite size with time for the heat-treatments at 615 and 620 °C depended on the glass composition. Under fixed heat-treatment conditions, the crystallite density was comparatively higher for the glass composition with higher ZnO content.

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

Kong Lingmin; Feng Zhechuan; Wu Zhengyun

Four types of self-assembled InAs/GaAs quantum dots (QDs) were grown by molecular beam epitaxy and studied via temperature-dependent and time-resolved photoluminescence (PL) spectroscopy measurements. A thin InGaAs stain reducing layer (SRL) is adopted which extends the emission wavelength to 1.3 mum and the influence of strain on QDs is investigated. The SRL releases the strain between the wetting layer and QDs, and enlarges the size of QDs, as shown by atomic force microscopy measurements. As the thickness of InAs layer decreases to 1.7 ML, the QDs with the SRL are chained to strings and the density of QDs increases significantly,more » which leads to an abnormal redshift of 1.3 mum PL peak at room temperature. PL peaks of InAs QDs with the SRL show redshift compared with the QDs directly deposited on GaAs matrix. The dependences of PL lifetime on the QD size, density and temperature (T) are systematically studied. It is observed that the PL lifetime of QDs is insensitive to T below 50 K. Beyond 50 K, increases and then drops at higher temperature, with a peak at T{sub C}, which was determined by the SRL and the thickness of InAs. We have also observed an obvious PL spectral redshift of the QDs with 1.7 ML InAs coverage on SRL at low T as the measuring time delays. The PL lifetime of QDs with the SRL is smaller than that of QDs without the SRL. The QDs with different densities have different PL lifetime dependence on the QDs size. These observations can be explained by the competition between the carrier redistribution and thermal emission.« less

Experimental Examination of Intraspecific Density-Dependent Competition during the Breeding Period in Monarch Butterflies (Danaus plexippus)

PubMed Central

Flockhart, D. T. Tyler; Martin, Tara G.; Norris, D. Ryan

2012-01-01

A central goal of population ecology is to identify the factors that regulate population growth. Monarch butterflies (Danaus plexippus) in eastern North America re-colonize the breeding range over several generations that result in population densities that vary across space and time during the breeding season. We used laboratory experiments to measure the strength of density-dependent intraspecific competition on egg laying rate and larval survival and then applied our results to density estimates of wild monarch populations to model the strength of density dependence during the breeding season. Egg laying rates did not change with density but larvae at high densities were smaller, had lower survival, and weighed less as adults compared to lower densities. Using mean larval densities from field surveys resulted in conservative estimates of density-dependent population reduction that varied between breeding regions and different phases of the breeding season. Our results suggest the highest levels of population reduction due to density-dependent intraspecific competition occur early in the breeding season in the southern portion of the breeding range. However, we also found that the strength of density dependence could be almost five times higher depending on how many life-stages were used as part of field estimates. Our study is the first to link experimental results of a density-dependent reduction in vital rates to observed monarch densities in the wild and show that the effects of density dependent competition in monarchs varies across space and time, providing valuable information for developing robust, year-round population models in this migratory organism. PMID:22984614

Basic characteristics of high-frequency Stark-effect modulation of CO2 lasers.

NASA Technical Reports Server (NTRS)

Claspy, P. C.; Pao, Y. H.

1971-01-01

The molecular Stark effect and its application to the modulation of infrared laser radiation have been investigated both theoretically and experimentally. Using a density matrix approach, a quantum mechanical description of the effect of a time-varying electric field on the absorption coefficient and refractive index of a molecular gas near an absorption line has been formulated. For modulation applications a quantity known as the ?modulation depth' is of prime importance. Theoretical expressions for the frequency dependence of the modulation depth show that the response to the frequency of a time-varying Stark field is separated into a nondispersive and a dispersive region, depending on whether the modulating frequency is less than or greater than the homogeneous absorption linewidth. Experimental results showing nondispersive modulation at frequencies to 30 MHz are presented. In addition it is shown that the response of modulation depth to Stark field amplitude is separated into linear and nonlinear regions, the field at which nonlinearities begin being determined by the absorption spectrum of the molecule being used.

Symmetry-conserving purification of quantum states within the density matrix renormalization group

DOE PAGES

Nocera, Alberto; Alvarez, Gonzalo

2016-01-28

The density matrix renormalization group (DMRG) algorithm was originally designed to efficiently compute the zero-temperature or ground-state properties of one-dimensional strongly correlated quantum systems. The development of the algorithm at finite temperature has been a topic of much interest, because of the usefulness of thermodynamics quantities in understanding the physics of condensed matter systems, and because of the increased complexity associated with efficiently computing temperature-dependent properties. The ancilla method is a DMRG technique that enables the computation of these thermodynamic quantities. In this paper, we review the ancilla method, and improve its performance by working on reduced Hilbert spaces andmore » using canonical approaches. Furthermore we explore its applicability beyond spins systems to t-J and Hubbard models.« less

Density fractionation of forest soils: methodological questions and interpretation of incubation results and turnover time in an ecosystem context

Treesearch

Susan E. Crow; Christopher W. Swanston; Kate Lajtha; J. Renee Brooks; Heath Keirstead

2007-01-01

Soil organic matter (SOM) is often separated by physical means to simplify a complex matrix into discrete fractions. A frequent approach to isolating two or more fractions is based on differing particle densities and uses a high density liquid such as sodium polytungstate (SPT). Soil density fractions are often interpreted as organic matter pools with different carbon...

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.

Quantum Dynamics of Solitons in Strongly Interacting Systems on Optical Lattices

NASA Astrophysics Data System (ADS)

Rubbo, Chester; Balakrishnan, Radha; Reinhardt, William; Satija, Indubala; Rey, Ana; Manmana, Salvatore

2012-06-01

We present results of the quantum dynamics of solitons in XXZ spin-1/2 systems which in general can be derived from a system of spinless fermions or hard-core bosons (HCB) with nearest neighbor interaction on a lattice. A mean-field treatment using spin-coherent states revealed analytic solutions of both bright and dark solitons [1]. We take these solutions and apply a full quantum evolution using the adaptive time-dependent density matrix renormalization group method (adaptive t-DMRG), which takes into account the effect of strong correlations. We use local spin observables, correlations functions, and entanglement entropies as measures for the stability of these soliton solutions over the simulation times. [4pt] [1] R. Balakrishnan, I.I. Satija, and C.W. Clark, Phys. Rev. Lett. 103, 230403 (2009).

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

Tang, Zhoufei; Ouyang, Xiaolong; Gong, Zhihao

An extended hierarchy equation of motion (HEOM) is proposed and applied to study the dynamics of the spin-boson model. In this approach, a complete set of orthonormal functions are used to expand an arbitrary bath correlation function. As a result, a complete dynamic basis set is constructed by including the system reduced density matrix and auxiliary fields composed of these expansion functions, where the extended HEOM is derived for the time derivative of each element. The reliability of the extended HEOM is demonstrated by comparison with the stochastic Hamiltonian approach under room-temperature classical ohmic and sub-ohmic noises and the multilayermore » multiconfiguration time-dependent Hartree theory under zero-temperature quantum ohmic noise. Upon increasing the order in the hierarchical expansion, the result obtained from the extended HOEM systematically converges to the numerically exact answer.« less

Long-term culture of rat hippocampal neurons at low density in serum-free medium: combination of the sandwich culture technique with the three-dimensional nanofibrous hydrogel PuraMatrix.

PubMed

Kaneko, Ai; Sankai, Yoshiyuki

2014-01-01

The primary culture of neuronal cells plays an important role in neuroscience. There has long been a need for methods enabling the long-term culture of primary neurons at low density, in defined serum-free medium. However, the lower the cell density, the more difficult it is to maintain the cells in culture. Therefore, we aimed to develop a method for long-term culture of neurons at low density, in serum-free medium, without the need for a glial feeder layer. Here, we describe the work leading to our determination of a protocol for long-term (>2 months) primary culture of rat hippocampal neurons in serum-free medium at the low density of 3×10(4) cells/mL (8.9×10(3) cells/cm2) without a glial feeder layer. Neurons were cultured on a three-dimensional nanofibrous hydrogel, PuraMatrix, and sandwiched under a coverslip to reproduce the in vivo environment, including the three-dimensional extracellular matrix, low-oxygen conditions, and exposure to concentrated paracrine factors. We examined the effects of varying PuraMatrix concentrations, the timing and presence or absence of a coverslip, the timing of neuronal isolation from embryos, cell density at plating, medium components, and changing the medium or not on parameters such as developmental pattern, cell viability, neuronal ratio, and neurite length. Using our method of combining the sandwich culture technique with PuraMatrix in Neurobasal medium/B27/L-glutamine for primary neuron culture, we achieved longer neurites (≥3,000 µm), greater cell viability (≥30%) for 2 months, and uniform culture across the wells. We also achieved an average neuronal ratio of 97%, showing a nearly pure culture of neurons without astrocytes. Our method is considerably better than techniques for the primary culture of neurons, and eliminates the need for a glial feeder layer. It also exhibits continued support for axonal elongation and synaptic activity for long periods (>6 weeks).

Boundary versus bulk behavior of time-dependent correlation functions in one-dimensional quantum systems

NASA Astrophysics Data System (ADS)

Eliëns, I. S.; Ramos, F. B.; Xavier, J. C.; Pereira, R. G.

2016-05-01

We study the influence of reflective boundaries on time-dependent responses of one-dimensional quantum fluids at zero temperature beyond the low-energy approximation. Our analysis is based on an extension of effective mobile impurity models for nonlinear Luttinger liquids to the case of open boundary conditions. For integrable models, we show that boundary autocorrelations oscillate as a function of time with the same frequency as the corresponding bulk autocorrelations. This frequency can be identified as the band edge of elementary excitations. The amplitude of the oscillations decays as a power law with distinct exponents at the boundary and in the bulk, but boundary and bulk exponents are determined by the same coupling constant in the mobile impurity model. For nonintegrable models, we argue that the power-law decay of the oscillations is generic for autocorrelations in the bulk, but turns into an exponential decay at the boundary. Moreover, there is in general a nonuniversal shift of the boundary frequency in comparison with the band edge of bulk excitations. The predictions of our effective field theory are compared with numerical results obtained by time-dependent density matrix renormalization group (tDMRG) for both integrable and nonintegrable critical spin-S chains with S =1 /2 , 1, and 3 /2 .

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

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

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

2005-11-01

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

Density Dependence and Growth Rate: Evolutionary Effects on Resistance Development to Bt (Bacillus thuringiensis).

PubMed

Martinez, Jeannette C; Caprio, Michael A; Friedenberg, Nicholas A

2018-02-09

It has long been recognized that pest population dynamics can affect the durability of a pesticide, but dose remains the primary component of insect resistance management (IRM). For transgenic pesticidal traits such as Bt (Bacillus thuringiensis Berliner (Bacillales: Bacillaceae)), dose (measured as the mortality of susceptibles caused by a toxin) is a relatively fixed characteristic and often falls below the standard definition of high dose. Hence, it is important to understand how pest population dynamics modify durability and what targets they present for IRM. We used a deterministic model of a generic arthropod pest to examine how timing and strength of density dependence interacted with population growth rate and Bt mortality to affect time to resistance. As in previous studies, durability typically reached a minimum at intermediate doses. However, high population growth rates could eliminate benefits of high dose. The timing of density dependence had a more subtle effect. If density dependence operated simultaneously with Bt mortality, durability was insensitive to its strengths. However, if density dependence was driven by postselection densities, decreasing its strength could increase durability. The strength of density dependence could affect durability of both single traits and pyramids, but its influence depended on the timing of density dependence and size of the refuge. Our findings suggest the utility of a broader definition of high dose, one that incorporates population-dynamic context. That maximum growth rates and timing and strength of interactions causing density dependent mortality can all affect durability, also highlights the need for ecologically integrated approaches to IRM research. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Time-dependent deformation of titanium metal matrix composites

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

Synthesis and characterization of metal-dielectric composites with copper nanoparticles embedded in a glass matrix: A multitechnique approach

NASA Astrophysics Data System (ADS)

Lipinska-Kalita, Kristina E.; Krol, Denise M.; Hemley, Russell J.; Mariotto, Gino; Kalita, Patricia E.; Ohki, Yoshimichi

2005-09-01

The precipitation and growth of copper nanoparticles in an optically transparent aluminosilicate glass matrix was investigated. The size of particles in this heterophase glass-based composite was modified in a controlled manner by isothermal heat treatments. A multitechnique approach, consisting of Raman scattering spectroscopy, high-resolution transmission electron microscopy, x-ray diffraction technique, and optical absorption spectroscopy, has been used to study the nucleation and crystallization processes. Optical absorption spectroscopy revealed the presence of intense absorption bands attributed to oscillations of free electrons, known as the surface-plasmon resonance band of copper particles, and confirmed a gradual increase of the particles' mean size and density with annealing time. The Raman scattering on acoustical phonons from Cu quantum dots in the glass matrix measured for off-resonance conditions demonstrated the presence of intense, inhomogeneously broadened peaks that have been assigned to the confined acoustic eigenmodes of copper nanoparticles. The particle-size dependence of the acoustic peak energies and the relation between the size distribution and bandwidths of these peaks were derived. High-resolution transmission electron microscopy was used to monitor the nucleation of the nanoparticles and to estimate their mean size.

Efficient calculation of beyond RPA correlation energies in the dielectric matrix formalism

NASA Astrophysics Data System (ADS)

Beuerle, Matthias; Graf, Daniel; Schurkus, Henry F.; Ochsenfeld, Christian

2018-05-01

We present efficient methods to calculate beyond random phase approximation (RPA) correlation energies for molecular systems with up to 500 atoms. To reduce the computational cost, we employ the resolution-of-the-identity and a double-Laplace transform of the non-interacting polarization propagator in conjunction with an atomic orbital formalism. Further improvements are achieved using integral screening and the introduction of Cholesky decomposed densities. Our methods are applicable to the dielectric matrix formalism of RPA including second-order screened exchange (RPA-SOSEX), the RPA electron-hole time-dependent Hartree-Fock (RPA-eh-TDHF) approximation, and RPA renormalized perturbation theory using an approximate exchange kernel (RPA-AXK). We give an application of our methodology by presenting RPA-SOSEX benchmark results for the L7 test set of large, dispersion dominated molecules, yielding a mean absolute error below 1 kcal/mol. The present work enables calculating beyond RPA correlation energies for significantly larger molecules than possible to date, thereby extending the applicability of these methods to a wider range of chemical systems.

Ability of matrix models to explain the past and predict the future of plant populations.

USGS Publications Warehouse

McEachern, Kathryn; Crone, Elizabeth E.; Ellis, Martha M.; Morris, William F.; Stanley, Amanda; Bell, Timothy; Bierzychudek, Paulette; Ehrlen, Johan; Kaye, Thomas N.; Knight, Tiffany M.; Lesica, Peter; Oostermeijer, Gerard; Quintana-Ascencio, Pedro F.; Ticktin, Tamara; Valverde, Teresa; Williams, Jennifer I.; Doak, Daniel F.; Ganesan, Rengaian; Thorpe, Andrea S.; Menges, Eric S.

2013-01-01

Uncertainty associated with ecological forecasts has long been recognized, but forecast accuracy is rarely quantified. We evaluated how well data on 82 populations of 20 species of plants spanning 3 continents explained and predicted plant population dynamics. We parameterized stage-based matrix models with demographic data from individually marked plants and determined how well these models forecast population sizes observed at least 5 years into the future. Simple demographic models forecasted population dynamics poorly; only 40% of observed population sizes fell within our forecasts' 95% confidence limits. However, these models explained population dynamics during the years in which data were collected; observed changes in population size during the data-collection period were strongly positively correlated with population growth rate. Thus, these models are at least a sound way to quantify population status. Poor forecasts were not associated with the number of individual plants or years of data. We tested whether vital rates were density dependent and found both positive and negative density dependence. However, density dependence was not associated with forecast error. Forecast error was significantly associated with environmental differences between the data collection and forecast periods. To forecast population fates, more detailed models, such as those that project how environments are likely to change and how these changes will affect population dynamics, may be needed. Such detailed models are not always feasible. Thus, it may be wiser to make risk-averse decisions than to expect precise forecasts from models.

Ability of matrix models to explain the past and predict the future of plant populations.

PubMed

Crone, Elizabeth E; Ellis, Martha M; Morris, William F; Stanley, Amanda; Bell, Timothy; Bierzychudek, Paulette; Ehrlén, Johan; Kaye, Thomas N; Knight, Tiffany M; Lesica, Peter; Oostermeijer, Gerard; Quintana-Ascencio, Pedro F; Ticktin, Tamara; Valverde, Teresa; Williams, Jennifer L; Doak, Daniel F; Ganesan, Rengaian; McEachern, Kathyrn; Thorpe, Andrea S; Menges, Eric S

2013-10-01

Uncertainty associated with ecological forecasts has long been recognized, but forecast accuracy is rarely quantified. We evaluated how well data on 82 populations of 20 species of plants spanning 3 continents explained and predicted plant population dynamics. We parameterized stage-based matrix models with demographic data from individually marked plants and determined how well these models forecast population sizes observed at least 5 years into the future. Simple demographic models forecasted population dynamics poorly; only 40% of observed population sizes fell within our forecasts' 95% confidence limits. However, these models explained population dynamics during the years in which data were collected; observed changes in population size during the data-collection period were strongly positively correlated with population growth rate. Thus, these models are at least a sound way to quantify population status. Poor forecasts were not associated with the number of individual plants or years of data. We tested whether vital rates were density dependent and found both positive and negative density dependence. However, density dependence was not associated with forecast error. Forecast error was significantly associated with environmental differences between the data collection and forecast periods. To forecast population fates, more detailed models, such as those that project how environments are likely to change and how these changes will affect population dynamics, may be needed. Such detailed models are not always feasible. Thus, it may be wiser to make risk-averse decisions than to expect precise forecasts from models. © 2013 Society for Conservation Biology.

Bone Mineral 31P and Matrix-Bound Water Densities Measured by Solid-State 1H and 31P MRI

PubMed Central

Seifert, Alan C.; Li, Cheng; Rajapakse, Chamith S.; Bashoor- Zadeh, Mahdieh; Bhagat, Yusuf A.; Wright, Alexander C.; Zemel, Babette S.; Zavaliangos, Antonios; Wehrli, Felix W.

2014-01-01

Bone is a composite material consisting of mineral and hydrated collagen fractions. MRI of bone is challenging due to extremely short transverse relaxation times, but solid-state imaging sequences exist that can acquire the short-lived signal from bone tissue. Previous work to quantify bone density via MRI used powerful experimental scanners. This work seeks to establish the feasibility of MRI-based measurement on clinical scanners of bone mineral and collagen-bound water densities, the latter as a surrogate of matrix density, and to examine the associations of these parameters with porosity and donors’ age. Mineral and matrix-bound water images of reference phantoms and cortical bone from 16 human donors, ages 27-97 years, were acquired by zero-echo-time 31P and 1H MRI on whole body 7T and 3T scanners, respectively. Images were corrected for relaxation and RF inhomogeneity to obtain density maps. Cortical porosity was measured by micro-CT, and apparent mineral density by pQCT. MRI-derived densities were compared to x-ray-based measurements by least-squares regression. Mean bone mineral 31P density was 6.74±1.22 mol/L (corresponding to 1129±204 mg/cc mineral), and mean bound water 1H density was 31.3±4.2 mol/L (corresponding to 28.3±3.7 %v/v). Both 31P and bound water (BW) densities were correlated negatively with porosity (31P: R2 = 0.32, p < 0.005; BW: R2 = 0.63, p < 0.0005) and age (31P: R2 = 0.39, p < 0.05; BW: R2 = 0.70, p < 0.0001), and positively with pQCT density (31P: R2 = 0.46, p < 0.05; BW: R2 = 0.50, p < 0.005). In contrast, the bone mineralization ratio (expressed here as the ratio of 31P density to bound water density), which is proportional to true bone mineralization, was found to be uncorrelated with porosity, age, or pQCT density. This work establishes the feasibility of image-based quantification of bone mineral and bound water densities using clinical hardware. PMID:24846186

Substrate engagement of integrins α5β1 and αvβ3 is necessary, but not sufficient, for high directional persistence in migration on fibronectin

PubMed Central

Missirlis, Dimitris; Haraszti, Tamás; Scheele, Catharina v. C.; Wiegand, Tina; Diaz, Carolina; Neubauer, Stefanie; Rechenmacher, Florian; Kessler, Horst; Spatz, Joachim P.

2016-01-01

The interplay between specific integrin-mediated matrix adhesion and directional persistence in cell migration is not well understood. Here, we characterized fibroblast adhesion and migration on the extracellular matrix glycoproteins fibronectin and vitronectin, focusing on the role of α5β1 and αvβ3 integrins. Fibroblasts manifested high directional persistence in migration on fibronectin-, but not vitronectin-coated substrates, in a ligand density-dependent manner. Fibronectin stimulated α5β1-dependent organization of the actin cytoskeleton into oriented, ventral stress fibers, and assembly of dynamic, polarized protrusions, characterized as regions free of stress fibers and rich in nascent adhesions at their edge. Such protrusions correlated with persistent, local leading edge advancement, but were not sufficient, nor necessary for directional migration over longer times. Selective blocking of αvβ3 or α5β1 integrins using small molecule integrin antagonists reduced directional persistence on fibronectin, indicating integrin cooperativity in maintaining directionality. On the other hand, patterned substrates, designed to selectively engage either integrin, or their combination, were not sufficient to establish directional migration. Overall, our study demonstrates adhesive coating-dependent regulation of directional persistence in fibroblast migration and challenges the generality of the previously suggested role of β1 and β3 integrins in directional migration. PMID:26987342

Vector-valued Jack polynomials and wavefunctions on the torus

NASA Astrophysics Data System (ADS)

Dunkl, Charles F.

2017-06-01

The Hamiltonian of the quantum Calogero-Sutherland model of N identical particles on the circle with 1/r 2 interactions has eigenfunctions consisting of Jack polynomials times the base state. By use of the generalized Jack polynomials taking values in modules of the symmetric group and the matrix solution of a system of linear differential equations one constructs novel eigenfunctions of the Hamiltonian. Like the usual wavefunctions each eigenfunction determines a symmetric probability density on the N-torus. The construction applies to any irreducible representation of the symmetric group. The methods depend on the theory of generalized Jack polynomials due to Griffeth, and the Yang-Baxter graph approach of Luque and the author.

Lattice-Assisted Spectroscopy: A Generalized Scanning Tunneling Microscope for Ultracold Atoms.

PubMed

Kantian, A; Schollwöck, U; Giamarchi, T

2015-10-16

We propose a scheme to measure the frequency-resolved local particle and hole spectra of any optical lattice-confined system of correlated ultracold atoms that offers single-site addressing and imaging, which is now an experimental reality. Combining perturbation theory and time-dependent density matrix renormalization group simulations, we quantitatively test and validate this approach of lattice-assisted spectroscopy on several one-dimensional example systems, such as the superfluid and Mott insulator, with and without a parabolic trap, and finally on edge states of the bosonic Su-Schrieffer-Heeger model. We highlight extensions of our basic scheme to obtain an even wider variety of interesting and important frequency resolved spectra.

Ground-state properties of anyons in a one-dimensional lattice

NASA Astrophysics Data System (ADS)

Tang, Guixin; Eggert, Sebastian; Pelster, Axel

2015-12-01

Using the Anyon-Hubbard Hamiltonian, we analyze the ground-state properties of anyons in a one-dimensional lattice. To this end we map the hopping dynamics of correlated anyons to an occupation-dependent hopping Bose-Hubbard model using the fractional Jordan-Wigner transformation. In particular, we calculate the quasi-momentum distribution of anyons, which interpolates between Bose-Einstein and Fermi-Dirac statistics. Analytically, we apply a modified Gutzwiller mean-field approach, which goes beyond a classical one by including the influence of the fractional phase of anyons within the many-body wavefunction. Numerically, we use the density-matrix renormalization group by relying on the ansatz of matrix product states. As a result it turns out that the anyonic quasi-momentum distribution reveals both a peak-shift and an asymmetry which mainly originates from the nonlocal string property. In addition, we determine the corresponding quasi-momentum distribution of the Jordan-Wigner transformed bosons, where, in contrast to the hard-core case, we also observe an asymmetry for the soft-core case, which strongly depends on the particle number density.

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.

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.

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

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

I-V characterization of a quantum well infrared photodetector with stepped and graded barriers

NASA Astrophysics Data System (ADS)

Nutku, F.; Erol, A.; Gunes, M.; Buklu, L. B.; Ergun, Y.; Arikan, M. C.

2012-09-01

I-V characterization of an n-type quantum well infrared photodetector which consists of stepped and graded barriers has been done under dark at temperatures between 20-300 K. Different current transport mechanisms and transition between them have been observed at temperature around 47 K. Activation energies of the electrons at various bias voltages have been obtained from the temperature dependent I-V measurements. Activation energy at zero bias has been calculated by extrapolating the bias dependence of the activation energies. Ground state energies and barrier heights of the four different quantum wells have been calculated by using an iterative technique, which depends on experimentally obtained activation energy. Ground state energies also have been calculated with transfer matrix technique and compared with iteration results. Incorporating the effect of high electron density induced electron exchange interaction on ground state energies; more consistent results with theoretical transfer matrix calculations have been obtained.

Tempo-spatially resolved dynamics of elec- trons and holes in bilayer MoS2 -WS2

NASA Astrophysics Data System (ADS)

Galicia-Hernandez, J. M.; Turkowski, V.; Hernandez-Cocoletzi, G.; Rahman, T. S.

We have performed a Density-Matrix Time-Dependent Density-Functional Theory analysis of the response of bilayer MoS2-WS2 to external laser-pulse perturbations. Time-resolved study of the dynamics of electrons and holes, including formation and dissociation of strongly-bound intra- and inter-layer excitonic states, shows that the experimentally observed ultrafast inter-layer MoS2 to WS2 migration of holes may be attributed to unusually large delocalization of the hole state which extends far into the inter-layer region. We also argue that the velocity of the hole transfer may be further enhanced by its interaction with transfer phonon modes. We analyze other possible consequences of the hole delocalization in the system, including reduction of the effects of the electron-electron and hole-hole repulsion in the trions and biexcitons as compared to that in the monolayers Work supported in part by DOE Grant No. DOE-DE-FG02-07ER46354 and by CONACYT Scholarship No. 23210 (J.M.G.H.).

Time Dependent Channel Packet Calculation of Two Nucleon Scattering Matrix Elements

DTIC Science & Technology

2010-03-01

solutions, 46 ( ) ( )1 1 11 ( ) cos sinL L L L Lr Akr j kr krψ δ η δ= −   (3.70) Here, A is an arbitrary constant, Lδ is the phase shift...iv AFIT/DS/ENP/10-M03 Abstract A new approach to calculating nucleon-nucleon scattering matrix...elements using a proven atomic time-dependent wave packet technique is investigated. Using this technique, reactant and product wave packets containing

On the Feynman-Hellmann theorem in quantum field theory and the calculation of matrix elements

DOE PAGES

Bouchard, Chris; Chang, Chia Cheng; Kurth, Thorsten; ...

2017-07-12

In this paper, the Feynman-Hellmann theorem can be derived from the long Euclidean-time limit of correlation functions determined with functional derivatives of the partition function. Using this insight, we fully develop an improved method for computing matrix elements of external currents utilizing only two-point correlation functions. Our method applies to matrix elements of any external bilinear current, including nonzero momentum transfer, flavor-changing, and two or more current insertion matrix elements. The ability to identify and control all the systematic uncertainties in the analysis of the correlation functions stems from the unique time dependence of the ground-state matrix elements and the fact that all excited states and contact terms are Euclidean-time dependent. We demonstrate the utility of our method with a calculation of the nucleon axial charge using gradient-flowed domain-wall valence quarks on themore » $$N_f=2+1+1$$ MILC highly improved staggered quark ensemble with lattice spacing and pion mass of approximately 0.15 fm and 310 MeV respectively. We show full control over excited-state systematics with the new method and obtain a value of $$g_A = 1.213(26)$$ with a quark-mass-dependent renormalization coefficient.« less

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

Critical Seismic Vector Random Excitations for Multiply Supported Structures

NASA Astrophysics Data System (ADS)

Sarkar, A.; Manohar, C. S.

1998-05-01

A method for determining critical power spectral density matrix models for earthquake excitations which maximize steady response variance of linear multiply supported extended structures and which also satisfy constraints on input variance, zero crossing rates, frequency content and transmission time lag has been developed. The optimization problem is shown to be non-linear in nature and solutions are obtained by using an iterative technique which is based on linear programming method. A constraint on entropy rate as a measure of uncertainty which can be expected in realistic earthquake ground motions is proposed which makes the critical excitations more realistic. Two special cases are also considered. Firstly, when knowledge of autospectral densities is available, the critical response is shown to be produced by fully coherent excitations which are neither in-phase nor out-of-phase. The critical phase between the excitation components depends on structural parameters, but independent of the auto-spectral densities of the excitations. Secondly, when the knowledge of autospectral densities and phase spectrum of the excitations is available, the critical response is shown to be produced by a system dependent coherence function representing neither fully coherent nor fully incoherent ground motions. The applications of these special cases are discussed in the context of land-based extended structures and secondary systems such as nuclear piping assembly. Illustrative examples on critical inputs and response of sdof and a long-span suspended cable which demonstrated the various features of the approach developed are presented.

Simple and Accurate Method for Central Spin Problems

NASA Astrophysics Data System (ADS)

Lindoy, Lachlan P.; Manolopoulos, David E.

2018-06-01

We describe a simple quantum mechanical method that can be used to obtain accurate numerical results over long timescales for the spin correlation tensor of an electron spin that is hyperfine coupled to a large number of nuclear spins. This method does not suffer from the statistical errors that accompany a Monte Carlo sampling of the exact eigenstates of the central spin Hamiltonian obtained from the algebraic Bethe ansatz, or from the growth of the truncation error with time in the time-dependent density matrix renormalization group (TDMRG) approach. As a result, it can be applied to larger central spin problems than the algebraic Bethe ansatz, and for longer times than the TDMRG algorithm. It is therefore an ideal method to use to solve central spin problems, and we expect that it will also prove useful for a variety of related problems that arise in a number of different research fields.

Photoinduced Hund excitons in the breakdown of a two-orbital Mott insulator

NASA Astrophysics Data System (ADS)

Rincón, Julián; Dagotto, Elbio; Feiguin, Adrian E.

2018-06-01

We study the photoinduced breakdown of a two-orbital Mott insulator and resulting metallic state. Using time-dependent density matrix renormalization group, we scrutinize the real-time dynamics of the half-filled two-orbital Hubbard model interacting with a resonant radiation field pulse. The breakdown, caused by production of doublon-holon pairs, is enhanced by Hund's exchange, which dynamically activates large orbital fluctuations. The melting of the Mott insulator is accompanied by a high to low spin transition with a concomitant reduction of antiferromagnetic spin fluctuations. Most notably, the overall time response is driven by the photogeneration of excitons with orbital character that are stabilized by Hund's coupling. These unconventional "Hund excitons" correspond to bound spin-singlet orbital-triplet doublon-holon pairs. We study exciton properties such as bandwidth, binding potential, and size within a semiclassical approach. The photometallic state results from a coexistence of Hund excitons and doublon-holon plasma.

Quench of non-Markovian coherence in the deep sub-Ohmic spin–boson model: A unitary equilibration scheme

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

Yao, Yao, E-mail: yaoyao@fudan.edu.cn

The deep sub-Ohmic spin–boson model shows a longstanding non-Markovian coherence at low temperature. Motivating to quench this robust coherence, the thermal effect is unitarily incorporated into the time evolution of the model, which is calculated by the adaptive time-dependent density matrix renormalization group algorithm combined with the orthogonal polynomials theory. Via introducing a unitary heating operator to the bosonic bath, the bath is heated up so that a majority portion of the bosonic excited states is occupied. It is found in this situation the coherence of the spin is quickly quenched even in the coherent regime, in which the non-Markovianmore » feature dominates. With this finding we come up with a novel way to implement the unitary equilibration, the essential term of the eigenstate-thermalization hypothesis, through a short-time evolution of the model.« less

Relaxation of photoexcitations in polaron-induced magnetic microstructures

NASA Astrophysics Data System (ADS)

Köhler, Thomas; Rajpurohit, Sangeeta; Schumann, Ole; Paeckel, Sebastian; Biebl, Fabian R. A.; Sotoudeh, Mohsen; Kramer, Stephan C.; Blöchl, Peter E.; Kehrein, Stefan; Manmana, Salvatore R.

2018-06-01

We investigate the evolution of a photoexcitation in correlated materials over a wide range of time scales. The system studied is a one-dimensional model of a manganite with correlated electron, spin, orbital, and lattice degrees of freedom, which we relate to the three-dimensional material Pr1 -xCaxMnO3 . The ground-state phases for the entire composition range are determined and rationalized by a coarse-grained polaron model. At half doping a pattern of antiferromagnetically coupled Zener polarons is realized. Using time-dependent density-matrix renormalization group (tDMRG), we treat the electronic quantum dynamics following the excitation. The emergence of quasiparticles is addressed, and the relaxation of the nonequilibrium quasiparticle distribution is investigated via a linearized quantum-Boltzmann equation. Our approach shows that the magnetic microstructure caused by the Zener polarons leads to an increase of the relaxation times of the excitation.

Generic dynamical features of quenched interacting quantum systems: Survival probability, density imbalance, and out-of-time-ordered correlator

NASA Astrophysics Data System (ADS)

Torres-Herrera, E. J.; García-García, Antonio M.; Santos, Lea F.

2018-02-01

We study numerically and analytically the quench dynamics of isolated many-body quantum systems. Using full random matrices from the Gaussian orthogonal ensemble, we obtain analytical expressions for the evolution of the survival probability, density imbalance, and out-of-time-ordered correlator. They are compared with numerical results for a one-dimensional-disordered model with two-body interactions and shown to bound the decay rate of this realistic system. Power-law decays are seen at intermediate times, and dips below the infinite time averages (correlation holes) occur at long times for all three quantities when the system exhibits level repulsion. The fact that these features are shared by both the random matrix and the realistic disordered model indicates that they are generic to nonintegrable interacting quantum systems out of equilibrium. Assisted by the random matrix analytical results, we propose expressions that describe extremely well the dynamics of the realistic chaotic system at different time scales.

Cucheb: A GPU implementation of the filtered Lanczos procedure

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Entanglement spectrum of random-singlet quantum critical points

NASA Astrophysics Data System (ADS)

Fagotti, Maurizio; Calabrese, Pasquale; Moore, Joel E.

2011-01-01

The entanglement spectrum (i.e., the full distribution of Schmidt eigenvalues of the reduced density matrix) contains more information than the conventional entanglement entropy and has been studied recently in several many-particle systems. We compute the disorder-averaged entanglement spectrum in the form of the disorder-averaged moments TrρAα̲ of the reduced density matrix ρA for a contiguous block of many spins at the random-singlet quantum critical point in one dimension. The result compares well in the scaling limit with numerical studies on the random XX model and is also expected to describe the (interacting) random Heisenberg model. Our numerical studies on the XX case reveal that the dependence of the entanglement entropy and spectrum on the geometry of the Hilbert space partition is quite different than for conformally invariant critical points.

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.

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

Mechanochemical switching between growth and differentiation during fibroblast growth factor-stimulated angiogenesis in vitro: role of extracellular matrix

PubMed Central

1989-01-01

The angiogenic factor, basic fibroblast growth factor (FGF), either stimulates endothelial cell growth or promotes capillary differentiation depending upon the microenvironment in which it acts. Analysis of various in vitro models of spontaneous angiogenesis, in combination with time-lapse cinematography, demonstrated that capillary tube formation was greatly facilitated by promoting multicellular retraction and cell elevation above the surface of the rigid culture dish or by culturing endothelial cells on malleable extracellular matrix (ECM) substrata. These observations suggested to us that mechanical (i.e., tension-dependent) interactions between endothelial cells and ECM may serve to regulate capillary development. To test this hypothesis, FGF-stimulated endothelial cells were grown in chemically defined medium on bacteriological (nonadhesive) dishes that were precoated with different densities of fibronectin. Extensive cell spreading and growth were promoted by fibronectin coating densities that were highly adhesive (greater than 500 ng/cm2), whereas cell rounding, detachment, and loss of viability were observed on dishes coated with low fibronectin concentrations (less than 100 ng/cm2). Intermediate fibronectin coating densities (100-500 ng/cm2) promoted cell extension, but they could not completely resist cell tractional forces. Partial retraction of multicellular aggregates resulted in cell shortening, cessation of growth, and formation of branching tubular networks within 24-48 h. Multicellular retraction and subsequent tube formation also could be elicited on highly adhesive dishes by overcoming the mechanical resistance of the substratum using higher cell plating numbers. Dishes coated with varying concentrations of type IV collagen or gelatin produced similar results. These results suggest that ECM components may act locally to regulate the growth and pattern- regulating actions of soluble FGF based upon their ability to resist cell-generated mechanical loads. Thus, we propose that FGF-stimulated endothelial cells may be "switched" between growth, differentiation, and involution modes during angiogenesis by altering the adhesivity or mechanical integrity of their ECM. PMID:2473081

Time dependent density functional calculation of plasmon response in clusters

NASA Astrophysics Data System (ADS)

Wang, Feng; Zhang, Feng-Shou; Eric, Suraud

2003-02-01

We have introduced a theoretical scheme for the efficient description of the optical response of a cluster based on the time-dependent density functional theory. The practical implementation is done by means of the fully fledged time-dependent local density approximation scheme, which is solved directly in the time domain without any linearization. As an example we consider the simple Na2 cluster and compute its surface plasmon photoabsorption cross section, which is in good agreement with the experiments.

Density regulation in Northeast Atlantic fish populations: Density dependence is stronger in recruitment than in somatic growth.

PubMed

Zimmermann, Fabian; Ricard, Daniel; Heino, Mikko

2018-05-01

Population regulation is a central concept in ecology, yet in many cases its presence and the underlying mechanisms are difficult to demonstrate. The current paradigm maintains that marine fish populations are predominantly regulated by density-dependent recruitment. While it is known that density-dependent somatic growth can be present too, its general importance remains unknown and most practical applications neglect it. This study aimed to close this gap by for the first time quantifying and comparing density dependence in growth and recruitment over a large set of fish populations. We fitted density-dependent models to time-series data on population size, recruitment and age-specific weight from commercially exploited fish populations in the Northeast Atlantic Ocean and the Baltic Sea. Data were standardized to enable a direct comparison within and among populations, and estimated parameters were used to quantify the impact of density regulation on population biomass. Statistically significant density dependence in recruitment was detected in a large proportion of populations (70%), whereas for density dependence in somatic growth the prevalence of density dependence depended heavily on the method (26% and 69%). Despite age-dependent variability, the density dependence in recruitment was consistently stronger among age groups and between alternative approaches that use weight-at-age or weight increments to assess growth. Estimates of density-dependent reduction in biomass underlined these results: 97% of populations with statistically significant parameters for growth and recruitment showed a larger impact of density-dependent recruitment on population biomass. The results reaffirm the importance of density-dependent recruitment in marine fishes, yet they also show that density dependence in somatic growth is not uncommon. Furthermore, the results are important from an applied perspective because density dependence in somatic growth affects productivity and catch composition, and therefore the benefits of maintaining fish populations at specific densities. © 2018 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Thermal properties of light-weight concrete with waste polypropylene aggregate

NASA Astrophysics Data System (ADS)

Záleská, Martina; Pokorný, Jaroslav; Pavlíková, Milena; Pavlík, Zbyšek

2017-07-01

Thermal properties of a sustainable light-weight concrete incorporating high volume of waste polypropylene as partial substitution of natural aggregate were studied in the paper. Glass fiber reinforced polypropylene (GFPP), a by-product of PP tubes production, partially substituted fine natural silica aggregate in 10, 20, 30, 40, and 50 mass%. In order to quantify the effect of GFPP use on concrete properties, a reference concrete mix without plastic waste was studied as well. For the applied GFPP, bulk density, matrix density, and particle size distribution were measured. Specific attention was paid to thermal transport and storage properties of GFPP that were examined in dependence on compaction time. For the developed light-weight concrete, thermal properties were accessed using transient impulse technique, whereas the measurement was done in dependence on moisture content, from the dry state to fully water saturated state. Additionally, the investigated thermal properties were plotted as function of porosity. The tested light-weight concrete was found to be prospective construction material possessing improved thermal insulation function. Moreover, the reuse of waste plastics in concrete composition was beneficial both from the environmental and financial point of view considering plastics low biodegradability and safe disposal.

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.

Complications pertaining to the detection and characterization of individual and embedded single walled carbon nanotubes by scanning electron microscopy

NASA Astrophysics Data System (ADS)

Orbaek, Alvin W.; Barron, Andrew R.

2013-03-01

Comparison of AFM and SEM images of single walled carbon nanotubes (SWNTs) grown within a dielectric matrix reveal subterranean nanotubes that are present within the matrix, and as such can be charge screened by the dielectric. Under adequate imaging conditions for the SWNT/silica sample the intensity of isolated nanotubes is found to be inversely proportional to the instrument dwell time (i.e., shorter dwell times were found to make SWNT intensities brighter). The threshold dwell time required to enable isolated tubes to be visible was found to be 10 μs moreover, the degree change in intensity was found to be nanotube specific, i.e., different SWNTs respond in a different manner at different dwell times. The results indicate that care should be taken when attempting to quantify number density and length distributions of SWNTs on or within a dielectric matrix.Comparison of AFM and SEM images of single walled carbon nanotubes (SWNTs) grown within a dielectric matrix reveal subterranean nanotubes that are present within the matrix, and as such can be charge screened by the dielectric. Under adequate imaging conditions for the SWNT/silica sample the intensity of isolated nanotubes is found to be inversely proportional to the instrument dwell time (i.e., shorter dwell times were found to make SWNT intensities brighter). The threshold dwell time required to enable isolated tubes to be visible was found to be 10 μs moreover, the degree change in intensity was found to be nanotube specific, i.e., different SWNTs respond in a different manner at different dwell times. The results indicate that care should be taken when attempting to quantify number density and length distributions of SWNTs on or within a dielectric matrix. Electronic supplementary information (ESI) available: Plots of SEM for cross over points, raw SEM images used for Fig. 5, and Fig. 6, SEM image of scattering centre, and SEM images with various scan directions at 10 μs dwell time. See DOI: 10.1039/c3nr00142c

Spin Andreev-like Reflection in Metal-Mott Insulator Heterostructures

DOE PAGES

Al-Hassanieh, K. A.; Rincón, Julián; Alvarez, G.; ...

2015-02-09

Here we used the time-dependent density-matrix renormalization group (tDMRG) to study the time evolution of electron wave packets in one-dimensional (1D) metal-superconductor heterostructures. The results show Andreev reflection at the interface, as expected. By combining these results with the well-known single- spin-species electron-hole transformation in the Hubbard model, we predict an analogous spin Andreev reflection in metal-Mott insulator heterostructures. This effect is numerically confirmed using 1D tDMRG, but it is expected to also be present in higher dimensions, as well as in more general Hamiltonians. We present an intuitive picture of the spin reflection, analogous to that of Andreev reflectionmore » at metal- superconductor interfaces. This allows us to discuss a novel antiferromagnetic proximity effect. Possible experimental realizations are discussed.« less

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.

A reformulation of the coupled perturbed self-consistent field equations entirely within a local atomic orbital density matrix-based scheme

NASA Astrophysics Data System (ADS)

Ochsenfeld, Christian; Head-Gordon, Martin

1997-05-01

To exploit the exponential decay found in numerical studies for the density matrix and its derivative with respect to nuclear displacements, we reformulate the coupled perturbed self-consistent field (CPSCF) equations and a quadratically convergent SCF (QCSCF) method for Hartree-Fock and density functional theory within a local density matrix-based scheme. Our D-CPSCF (density matrix-based CPSCF) and D-QCSCF schemes open the way for exploiting sparsity and to achieve asymptotically linear scaling of computational complexity with molecular size ( M), in case of D-CPSCF for all O( M) derivative densities. Furthermore, these methods are even for small molecules strongly competitive to conventional algorithms.

A Ranking Analysis/An Interlinking Approach of New Triangular Fuzzy Cognitive Maps and Combined Effective Time Dependent Matrix

NASA Astrophysics Data System (ADS)

Adiga, Shreemathi; Saraswathi, A.; Praveen Prakash, A.

2018-04-01

This paper aims an interlinking approach of new Triangular Fuzzy Cognitive Maps (TrFCM) and Combined Effective Time Dependent (CETD) matrix to find the ranking of the problems of Transgenders. Section one begins with an introduction that briefly describes the scope of Triangular Fuzzy Cognitive Maps (TrFCM) and CETD Matrix. Section two provides the process of causes of problems faced by Transgenders using Fuzzy Triangular Fuzzy Cognitive Maps (TrFCM) method and performs the calculations using the collected data among the Transgender. In Section 3, the reasons for the main causes for the problems of the Transgenders. Section 4 describes the Charles Spearmans coefficients of rank correlation method by interlinking of Triangular Fuzzy Cognitive Maps (TrFCM) Method and CETD Matrix. Section 5 shows the results based on our study.

Nonlinear programming models to optimize uneven-aged loblolly pine management

Treesearch

Benedict J. Schulte; Joseph. Buongiorno; Kenneth Skog

1999-01-01

Nonlinear programming models of uneven-aged loblolly pine (Pinus taeda L.) management were developed to identify sustainable management regimes which optimize: 1) soil expectation value (SEV), 2) tree diversity, or 3) annual sawtimber yields. The models use the equations of SouthPro, a site- and density-dependent, multi-species matrix growth and yield model that...

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.

Spatially varying density dependence drives a shifting mosaic of survival in a recovering apex predator (Canis lupus).

PubMed

O'Neil, Shawn T; Bump, Joseph K; Beyer, Dean E

2017-11-01

Understanding landscape patterns in mortality risk is crucial for promoting recovery of threatened and endangered species. Humans affect mortality risk in large carnivores such as wolves ( Canis lupus ), but spatiotemporally varying density dependence can significantly influence the landscape of survival. This potentially occurs when density varies spatially and risk is unevenly distributed. We quantified spatiotemporal sources of variation in survival rates of gray wolves ( C. lupus ) during a 21-year period of population recovery in the Upper Peninsula of Michigan, USA. We focused on mapping risk across time using Cox Proportional Hazards (CPH) models with time-dependent covariates, thus exploring a shifting mosaic of survival. Extended CPH models and time-dependent covariates revealed influences of seasonality, density dependence and experience, as well as individual-level factors and landscape predictors of risk. We used results to predict the shifting landscape of risk at the beginning, middle, and end of the wolf recovery time series. Survival rates varied spatially and declined over time. Long-term change was density-dependent, with landscape predictors such as agricultural land cover and edge densities contributing negatively to survival. Survival also varied seasonally and depended on individual experience, sex, and resident versus transient status. The shifting landscape of survival suggested that increasing density contributed to greater potential for human conflict and wolf mortality risk. Long-term spatial variation in key population vital rates is largely unquantified in many threatened, endangered, and recovering species. Variation in risk may indicate potential for source-sink population dynamics, especially where individuals preemptively occupy suitable territories, which forces new individuals into riskier habitat types as density increases. We encourage managers to explore relationships between adult survival and localized changes in population density. Density-dependent risk maps can identify increasing conflict areas or potential habitat sinks which may persist due to high recruitment in adjacent habitats.

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

Bouchard, Chris; Chang, Chia Cheng; Kurth, Thorsten

In this paper, the Feynman-Hellmann theorem can be derived from the long Euclidean-time limit of correlation functions determined with functional derivatives of the partition function. Using this insight, we fully develop an improved method for computing matrix elements of external currents utilizing only two-point correlation functions. Our method applies to matrix elements of any external bilinear current, including nonzero momentum transfer, flavor-changing, and two or more current insertion matrix elements. The ability to identify and control all the systematic uncertainties in the analysis of the correlation functions stems from the unique time dependence of the ground-state matrix elements and the fact that all excited states and contact terms are Euclidean-time dependent. We demonstrate the utility of our method with a calculation of the nucleon axial charge using gradient-flowed domain-wall valence quarks on themore » $$N_f=2+1+1$$ MILC highly improved staggered quark ensemble with lattice spacing and pion mass of approximately 0.15 fm and 310 MeV respectively. We show full control over excited-state systematics with the new method and obtain a value of $$g_A = 1.213(26)$$ with a quark-mass-dependent renormalization coefficient.« less

The ability of individuals to assess population density influences the evolution of emigration propensity and dispersal distance.

PubMed

Poethke, Hans Joachim; Gros, Andreas; Hovestadt, Thomas

2011-08-07

We analyze the simultaneous evolution of emigration and settlement decisions for actively dispersing species differing in their ability to assess population density. Using an individual-based model we simulate dispersal as a multi-step (patch to patch) movement in a world consisting of habitat patches surrounded by a hostile matrix. Each such step is associated with the same mortality risk. Our simulations show that individuals following an informed strategy, where emigration (and settlement) probability depends on local population density, evolve a lower (natal) emigration propensity but disperse over significantly larger distances - i.e. postpone settlement longer - than individuals performing density-independent emigration. This holds especially when variation in environmental conditions is spatially correlated. Both effects can be traced to the informed individuals' ability to better exploit existing heterogeneity in reproductive chances. Yet, already moderate distance-dependent dispersal costs prevent the evolution of multi-step (long-distance) dispersal, irrespective of the dispersal strategy. Copyright © 2011 Elsevier Ltd. All rights reserved.

Numerical simulation of freshwater/seawater interaction in a dual-permeability karst system with conduits: the development of discrete-continuum VDFST-CFP model

NASA Astrophysics Data System (ADS)

Xu, Zexuan; Hu, Bill

2016-04-01

Dual-permeability karst aquifers of porous media and conduit networks with significant different hydrological characteristics are widely distributed in the world. Discrete-continuum numerical models, such as MODFLOW-CFP and CFPv2, have been verified as appropriate approaches to simulate groundwater flow and solute transport in numerical modeling of karst hydrogeology. On the other hand, seawater intrusion associated with fresh groundwater resources contamination has been observed and investigated in numbers of coastal aquifers, especially under conditions of sea level rise. Density-dependent numerical models including SEAWAT are able to quantitatively evaluate the seawater/freshwater interaction processes. A numerical model of variable-density flow and solute transport - conduit flow process (VDFST-CFP) is developed to provide a better description of seawater intrusion and submarine groundwater discharge in a coastal karst aquifer with conduits. The coupling discrete-continuum VDFST-CFP model applies Darcy-Weisbach equation to simulate non-laminar groundwater flow in the conduit system in which is conceptualized and discretized as pipes, while Darcy equation is still used in continuum porous media. Density-dependent groundwater flow and solute transport equations with appropriate density terms in both conduit and porous media systems are derived and numerically solved using standard finite difference method with an implicit iteration procedure. Synthetic horizontal and vertical benchmarks are created to validate the newly developed VDFST-CFP model by comparing with other numerical models such as variable density SEAWAT, couplings of constant density groundwater flow and solute transport MODFLOW/MT3DMS and discrete-continuum CFPv2/UMT3D models. VDFST-CFP model improves the simulation of density dependent seawater/freshwater mixing processes and exchanges between conduit and matrix. Continuum numerical models greatly overestimated the flow rate under turbulent flow condition but discrete-continuum models provide more accurate results. Parameters sensitivities analysis indicates that conduit diameter and friction factor, matrix hydraulic conductivity and porosity are important parameters that significantly affect variable-density flow and solute transport simulation. The pros and cons of model assumptions, conceptual simplifications and numerical techniques in VDFST-CFP are discussed. In general, the development of VDFST-CFP model is an innovation in numerical modeling methodology and could be applied to quantitatively evaluate the seawater/freshwater interaction in coastal karst aquifers. Keywords: Discrete-continuum numerical model; Variable density flow and transport; Coastal karst aquifer; Non-laminar flow

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.

Dopant selection for control of charge carrier density and mobility in amorphous indium oxide thin-film transistors: Comparison between Si- and W-dopants

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

Mitoma, Nobuhiko, E-mail: MITOMA.Nobuhiko@nims.go.jp, E-mail: TSUKAGOSHI.Kazuhito@nims.go.jp; Kizu, Takio; Lin, Meng-Fang

The dependence of oxygen vacancy suppression on dopant species in amorphous indium oxide (a-InO{sub x}) thin film transistors (TFTs) is reported. In a-InO{sub x} TFTs incorporating equivalent atom densities of Si- and W-dopants, absorption of oxygen in the host a-InO{sub x} matrix was found to depend on difference of Gibbs free energy of the dopants for oxidation. For fully oxidized films, the extracted channel conductivity was higher in the a-InO{sub x} TFTs containing dopants of small ionic radius. This can be explained by a reduction in the ionic scattering cross sectional area caused by charge screening effects.

Evolution dependence of vanadium nitride nanoprecipitates on directionality of ion irradiation

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

Tan, L.; Kim, B. K.; Was, G. S.

The influence of the directionality of Fe 2+ ion irradiation on the evolution of vanadium nitride platelet–shaped nanoprecipitates at 500 °C was investigated in this paper in a ferritic alloy using transmission electron microscopy. When the ion-irradiation direction was approximately aligned with the initial particle length, particles grew longer and sectioned into shorter lengths at higher doses, resulting in increased particle densities. As ion-irradiation direction deviated from particle-length direction, some particles sectioned lengthwise and then dissolved, resulting in decreased particle densities. Surviving particles were transformed into parallelograms with a different orientation relationship with the matrix. Finally, nanoprecipitate evolution dependence onmore » beam-nanoprecipitate orientation is a process that may be different from reactor irradiation.« less

Evolution dependence of vanadium nitride nanoprecipitates on directionality of ion irradiation

DOE PAGES

Tan, L.; Kim, B. K.; Was, G. S.

2017-09-06

The influence of the directionality of Fe 2+ ion irradiation on the evolution of vanadium nitride platelet–shaped nanoprecipitates at 500 °C was investigated in this paper in a ferritic alloy using transmission electron microscopy. When the ion-irradiation direction was approximately aligned with the initial particle length, particles grew longer and sectioned into shorter lengths at higher doses, resulting in increased particle densities. As ion-irradiation direction deviated from particle-length direction, some particles sectioned lengthwise and then dissolved, resulting in decreased particle densities. Surviving particles were transformed into parallelograms with a different orientation relationship with the matrix. Finally, nanoprecipitate evolution dependence onmore » beam-nanoprecipitate orientation is a process that may be different from reactor irradiation.« less

Microplastic flow in SIC/AL composites

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

Shi, N.; Arsenault, R.J.

Experimentally it has been determined that if a composite containing a reinforcement which has a different (in general lower) thermal coefficient of expansion as compared to the matrix, then upon cooling from the processing or annealing temperature, plastic relaxation of the misfit strain will occur. Also, experimentally it has been shown that as the size of the reinforcement is increased, i.e., from small spheres to large spheres, there is a decrease in the summation of the effective plastic strain in the matrix. In other words there is a decrease in the average dislocation density in the matrix. However, if themore » shape of the reinforcement is changed from spherical to short fiber to continuous filament, then the dislocation density increases. This experimental data is obtained at a constant volume fraction. A very simple model of plastic relaxation based on prismatic punching of dislocations from the interface can account for the decrease in the dislocation density with an increase reinforcement size, and the increase in dislocation density when changing the shape from a sphere to a continuous filament. A FEM analysis of the shape factor is also capable of predicting the correct trend. However, at present the continuum mechanics methods that have been investigated can not predict the size dependence. A simple model to explain the size effect in Al{sub 2}O{sub 3}/NiAl composites based on the deformation characteristics of NiAl will be discussed.« less

Dynamic compressive loading enhances cartilage matrix synthesis and distribution and suppresses hypertrophy in hMSC-laden hyaluronic acid hydrogels.

PubMed

Bian, Liming; Zhai, David Y; Zhang, Emily C; Mauck, Robert L; Burdick, Jason A

2012-04-01

Mesenchymal stem cells (MSCs) are being recognized as a viable cell source for cartilage repair, and there is growing evidence that mechanical signals play a critical role in the regulation of stem cell chondrogenesis and in cartilage development. In this study we investigated the effect of dynamic compressive loading on chondrogenesis, the production and distribution of cartilage specific matrix, and the hypertrophic differentiation of human MSCs encapsulated in hyaluronic acid (HA) hydrogels during long term culture. After 70 days of culture, dynamic compressive loading increased the mechanical properties, as well as the glycosaminoglycan (GAG) and collagen contents of HA hydrogel constructs in a seeding density dependent manner. The impact of loading on HA hydrogel construct properties was delayed when applied to lower density (20 million MSCs/ml) compared to higher seeding density (60 million MSCs/ml) constructs. Furthermore, loading promoted a more uniform spatial distribution of cartilage matrix in HA hydrogels with both seeding densities, leading to significantly improved mechanical properties as compared to free swelling constructs. Using a previously developed in vitro hypertrophy model, dynamic compressive loading was also shown to significantly reduce the expression of hypertrophic markers by human MSCs and to suppress the degree of calcification in MSC-seeded HA hydrogels. Findings from this study highlight the importance of mechanical loading in stem cell based therapy for cartilage repair in improving neocartilage properties and in potentially maintaining the cartilage phenotype.

Emission mechanisms in stabilized iron-passivated porous silicon: Temperature and laser power dependences

NASA Astrophysics Data System (ADS)

Rahmani, M.; Moadhen, A.; Mabrouk Kamkoum, A.; Zaïbi, M.-A.; Chtourou, R.; Haji, L.; Oueslati, M.

2012-02-01

Photoluminescence (PL) measurements of porous silicon (PS) and iron-porous silicon nanocomposites (PS/Fe) with stable optical properties versus temperature and laser power density have been investigated. The presence of iron in PS matrix is confirmed by Raman spectroscopy. The PL intensity of PS and PS/Fe increases at low temperature, the evolution of integrated PL intensity follows the modified Arrhenius model. The incorporation of iron in PS matrix reduces the activation energy traducing the existence of shallow levels related to iron atoms. Also, the temperature dependence of the porous silicon PL peak position follows a linear evolution at high temperature and a quadratic one at low temperature. Such evolution is due to the thermal carriers' redistribution and an energy transfer. Similarly, we have compared the laser power dependence of the PL in PS and PS/Fe layers. The results prove that the recombination process in PS is realised through the lower energy traps localised in the electronic gap. However, the observed emission in PS/Fe is essentially due to direct transitions. So, we can conclude that the presence of iron in PS matrix induces a strong modification of the PL mechanisms.

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.

Equilibrium finite-frequency noise of an interacting mesoscopic capacitor studied in time-dependent density functional theory

NASA Astrophysics Data System (ADS)

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-03-01

We calculate the frequency-dependent equilibrium noise of a mesoscopic capacitor in time-dependent density functional theory (TDDFT). The capacitor is modeled as a single-level quantum dot with on-site Coulomb interaction and tunnel coupling to a nearby reservoir. The noise spectra are derived from linear-response conductances via the fluctuation-dissipation theorem. Thereby, we analyze the performance of a recently derived exchange-correlation potential with time-nonlocal density dependence in the finite-frequency linear-response regime. We compare our TDDFT noise spectra with real-time perturbation theory and find excellent agreement for noise frequencies below the reservoir temperature.

Toughening mechanism in elastomer-modified epoxy resins, part 2

NASA Technical Reports Server (NTRS)

Yee, A. F.; Pearson, R. A.

1984-01-01

The role of matrix ductility on the toughenability and toughening mechanism of elastomer-modified DGEBRA epoxies was investigated. Matrix ductility was varied by using epoxide resins of varying epoxide monomer molecular weights. These epoxide resins were cured using 4,4' diaminodiphenyl sulfone (DDS) and, in some cases, modified with 10% HYCAR(r)CTBN 1300X8. Fracture roughness values for the neat epoxies were found to be almost independent on the monomer molecular weight of the epoxide resin used. However, it was found that the fracture toughness of the elastomer-modified epoxies was very dependent upon the epoxide monomer molecular weight. Tensile dilatometry indicated that the toughening mechanism, when present, is similar to the mechanisms found for the piperidine cured epoxies in Part 1. SEM and OM corroborate this finding. Dynamic mechanical studies were conducted to shed light on the toughenability of the epoxies. The time-dependent small strain behavior of these epoxies were separated into their bulk and shear components. The bulk component is related to brittle fracture, whereas the shear component is related to yielding. It can be shown that the rates of shear and bulk strain energy buildup for a given stress are uniquely determined by the values of Poisson's ratio, nu. It was found that nu increases as the monomer molecular weight of the epoxide resin used increases. This increase in nu can be associated with the low temperature beta relaxation. The effect of increasing cross-link density is to shift the beta relaxation to higher temperatures and to decrease the magnitude of the beta relaxation. Thus, increasing cross-link density decreases nu and increases the tendency towards brittle fracture.

Multiband superconductivity and nanoscale inhomogeneity at oxide interfaces

NASA Astrophysics Data System (ADS)

Caprara, S.; Biscaras, J.; Bergeal, N.; Bucheli, D.; Hurand, S.; Feuillet-Palma, C.; Rastogi, A.; Budhani, R. C.; Lesueur, J.; Grilli, M.

2013-07-01

The two-dimensional electron gas at the LaTiO3/SrTiO3 or LaAlO3/SrTiO3 oxide interfaces becomes superconducting when the carrier density is tuned by gating. The measured resistance and superfluid density reveal an inhomogeneous superconductivity resulting from percolation of filamentary structures of superconducting “puddles” with randomly distributed critical temperatures, embedded in a nonsuperconducting matrix. Following the evidence that superconductivity is related to the appearance of high-mobility carriers, we model intrapuddle superconductivity by a multiband system within a weak coupling BCS scheme. The microscopic parameters, extracted by fitting the transport data with a percolative model, yield a consistent description of the dependence of the average intrapuddle critical temperature and superfluid density on the carrier density.

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.

Time-delayed behaviors of transient four-wave mixing signal intensity in inverted semiconductor with carrier-injection pumping

NASA Astrophysics Data System (ADS)

Hu, Zhenhua; Gao, Shen; Xiang, Bowen

2016-01-01

An analytical expression of transient four-wave mixing (TFWM) in inverted semiconductor with carrier-injection pumping was derived from both the density matrix equation and the complex stochastic stationary statistical method of incoherent light. Numerical analysis showed that the TFWM decayed decay is towards the limit of extreme homogeneous and inhomogeneous broadenings in atoms and the decaying time is inversely proportional to half the power of the net carrier densities for a low carrier-density injection and other high carrier-density injection, while it obeys an usual exponential decay with other decaying time that is inversely proportional to half the power of the net carrier density or it obeys an unusual exponential decay with the decaying time that is inversely proportional to a third power of the net carrier density for a moderate carrier-density injection. The results can be applied to studying ultrafast carrier dephasing in the inverted semiconductors such as semiconductor laser amplifier and semiconductor optical amplifier.

Low complexity Reed-Solomon-based low-density parity-check design for software defined optical transmission system based on adaptive puncturing decoding algorithm

NASA Astrophysics Data System (ADS)

Pan, Xiaolong; Liu, Bo; Zheng, Jianglong; Tian, Qinghua

2016-08-01

We propose and demonstrate a low complexity Reed-Solomon-based low-density parity-check (RS-LDPC) code with adaptive puncturing decoding algorithm for elastic optical transmission system. Partial received codes and the relevant column in parity-check matrix can be punctured to reduce the calculation complexity by adaptive parity-check matrix during decoding process. The results show that the complexity of the proposed decoding algorithm is reduced by 30% compared with the regular RS-LDPC system. The optimized code rate of the RS-LDPC code can be obtained after five times iteration.

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

NASA Technical Reports Server (NTRS)

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

1998-01-01

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

Molecular Dynamics Simulations of Poly(ethylene oxide) Grafted onto Silica Immersed in Melt of Homopolymers.

PubMed

Benková, Zuzana; Cordeiro, M Natália D S

2015-09-22

Tuning of surface properties plays an important role in applications ranging from material engineering to biomedicine/chemistry. The interactions of chains grafted to a solid support and exposed to a matrix of chemically identical chains represent an intriguing issue. In this work, the behavior of poly(ethylene oxide) (PEO) chains grafted irreversibly onto an amorphous silica and immersed in the matrix of free PEO chains of different polymerization degree is studied using molecular dynamics simulations. The density distributions of grafted and free PEO chains, the height of the grafted layer, overlap parameters, and orientation order parameters depend not only on the grafting density but also on the length of free chains which confirm the entropic nature of the interactions between the grafted and free chains. In order to achieve a complete expulsion of the free chains from the grafted layer, a grafting density as high as 3.5 nm(-2) is necessary. Free PEO chains of 9 monomers leave the grafted layer at lower grafting densities than the longer PEO chains of 18 monomers in contrast with the theoretical predictions. The height of the grafted layer evolves with the grafting density in the presence of free chains in qualitative agreement with the theoretical phase diagram.

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

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

Microscopic Scale Simulation of the Ablation of Fibrous Materials

NASA Technical Reports Server (NTRS)

Lachaud, Jean Romain; Mansour, Nagi N.

2010-01-01

Ablation by oxidation of carbon-fiber preforms impregnated in carbonized phenolic matrix is modeled at microscopic scale. Direct numerical simulations show that the carbonized phenolic matrix ablates in volume leaving the carbon fibers exposed. This is due to the fact that the reactivity of carbonized phenolic is higher than the reactivity of carbon fibers. After the matrix is depleted, the fibers ablate showing progressive reduction of their diameter. The overall material recession occurs when the fibers are consumed. Two materials with the same carbon-fiber preform, density and chemical composition, but with different matrix distributions are studied. These studies show that at moderate temperatures (< 1000 K) the microstructure of the material influences its recession rate; a fact that is not captured by current models that are based on chemical composition only. Surprisingly, the response of these impregnated-fiber materials is weakly dependent on the microstructure at very high temperatures (e.g., Stardust peak heating conditions: 3360K).

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

Comparison of the iterated equation of motion approach and the density matrix formalism for the quantum Rabi model

NASA Astrophysics Data System (ADS)

Kalthoff, Mona; Keim, Frederik; Krull, Holger; Uhrig, Götz S.

2017-05-01

The density matrix formalism and the equation of motion approach are two semi-analytical methods that can be used to compute the non-equilibrium dynamics of correlated systems. While for a bilinear Hamiltonian both formalisms yield the exact result, for any non-bilinear Hamiltonian a truncation is necessary. Due to the fact that the commonly used truncation schemes differ for these two methods, the accuracy of the obtained results depends significantly on the chosen approach. In this paper, both formalisms are applied to the quantum Rabi model. This allows us to compare the approximate results and the exact dynamics of the system and enables us to discuss the accuracy of the approximations as well as the advantages and the disadvantages of both methods. It is shown to which extent the results fulfill physical requirements for the observables and which properties of the methods lead to unphysical results.

Novel ionically crosslinked casein nanoparticles for flutamide delivery: formulation, characterization, and in vivo pharmacokinetics

PubMed Central

Elzoghby, Ahmed O; Helmy, Maged W; Samy, Wael M; Elgindy, Nazik A

2013-01-01

A novel particulate delivery matrix based on ionically crosslinked casein (CAS) nanoparticles was developed for controlled release of the poorly soluble anticancer drug flutamide (FLT). Nanoparticles were fabricated via oil-in-water emulsification then stabilized by ionic crosslinking of the positively charged CAS molecules below their isoelectric point, with the polyanionic crosslinker sodium tripolyphosphate. With the optimal preparation conditions, the drug loading and incorporation efficiency achieved were 8.73% and 64.55%, respectively. The nanoparticles exhibited a spherical shape with a size below 100 nm and a positive zeta potential (+7.54 to +17.3 mV). FLT was molecularly dispersed inside the nanoparticle protein matrix, as revealed by thermal analysis. The biodegradability of CAS nanoparticles in trypsin solution could be easily modulated by varying the sodium tripolyphosphate crosslinking density. A sustained release of FLT from CAS nanoparticles for up to 4 days was observed, depending on the crosslinking density. After intravenous administration of FLT-CAS nanoparticles into rats, CAS nanoparticles exhibited a longer circulation time and a markedly delayed blood clearance of FLT, with the half-life of FLT extended from 0.88 hours to 14.64 hours, compared with drug cosolvent. The results offer a promising method for tailoring biodegradable, drug-loaded CAS nanoparticles as controlled, long-circulating drug delivery systems of hydrophobic anticancer drugs in aqueous vehicles. PMID:23658490

Sintering behavior of U 80 at.%Zr powder compacts in a vacuum environment

NASA Astrophysics Data System (ADS)

Kim, Tae-Kyu; Lee, Chong-Tak; Sohn, Dong-Seong

2008-01-01

Sintering behavior of U-80 at.%Zr powder compacts in a temperature range from 1100 to 1500 °C in a vacuum of 1 × 10 -4 Pa was evaluated. The sintered density depended more on the sintering temperature than on the sintering time. The sintered specimens consisted of the δ-UZr 2 matrix with acicular α-Zr precipitates, but it still had un-reacted zirconium when the sintering temperature was 1100 °C. The uranium depletion near the surface of the specimens sintered at temperatures above 1300 °C was detected. Massive Zr(O) grains in the sintered specimen were found, and their formation was restrained when the cooling rate from the sintering temperature was increased.

Inverting pump-probe spectroscopy for state tomography of excitonic systems.

PubMed

Hoyer, Stephan; Whaley, K Birgitta

2013-04-28

We propose a two-step protocol for inverting ultrafast spectroscopy experiments on a molecular aggregate to extract the time-evolution of the excited state density matrix. The first step is a deconvolution of the experimental signal to determine a pump-dependent response function. The second step inverts this response function to obtain the quantum state of the system, given a model for how the system evolves following the probe interaction. We demonstrate this inversion analytically and numerically for a dimer model system, and evaluate the feasibility of scaling it to larger molecular aggregates such as photosynthetic protein-pigment complexes. Our scheme provides a direct alternative to the approach of determining all Hamiltonian parameters and then simulating excited state dynamics.

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).

Nonequilibrium Kondo effect in a magnetic field: auxiliary master equation approach

NASA Astrophysics Data System (ADS)

Fugger, Delia M.; Dorda, Antonius; Schwarz, Frauke; von Delft, Jan; Arrigoni, Enrico

2018-01-01

We study the single-impurity Anderson model out of equilibrium under the influence of a bias voltage ϕ and a magnetic field B. We investigate the interplay between the shift ({ω }B) of the Kondo peak in the spin-resolved density of states (DOS) and the one ({φ }B) of the conductance anomaly. In agreement with experiments and previous theoretical calculations we find that, while the latter displays a rather linear behavior with an almost constant slope as a function of B down to the Kondo scale, the DOS shift first features a slower increase reaching the same behavior as {φ }B only for | g| {μ }BB\\gg {k}B{T}K. Our auxiliary master equation approach yields highly accurate nonequilibrium results for the DOS and for the conductance all the way from within the Kondo up to the charge fluctuation regime, showing excellent agreement with a recently introduced scheme based on a combination of numerical renormalization group with time-dependent density matrix renormalization group.

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

PubMed

Rubensson, Emanuel H; Sałek, Paweł

2005-11-30

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

Dense fibrillar collagen is a potent inducer of invadopodia via a specific signaling network

PubMed Central

Swatkoski, Stephen; Matsumoto, Kazue; Campbell, Catherine B.; Petrie, Ryan J.; Dimitriadis, Emilios K.; Li, Xin; Mueller, Susette C.; Bugge, Thomas H.; Gucek, Marjan

2015-01-01

Cell interactions with the extracellular matrix (ECM) can regulate multiple cellular activities and the matrix itself in dynamic, bidirectional processes. One such process is local proteolytic modification of the ECM. Invadopodia of tumor cells are actin-rich proteolytic protrusions that locally degrade matrix molecules and mediate invasion. We report that a novel high-density fibrillar collagen (HDFC) matrix is a potent inducer of invadopodia, both in carcinoma cell lines and in primary human fibroblasts. In carcinoma cells, HDFC matrix induced formation of invadopodia via a specific integrin signaling pathway that did not require growth factors or even altered gene and protein expression. In contrast, phosphoproteomics identified major changes in a complex phosphosignaling network with kindlin2 serine phosphorylation as a key regulatory element. This kindlin2-dependent signal transduction network was required for efficient induction of invadopodia on dense fibrillar collagen and for local degradation of collagen. This novel phosphosignaling mechanism regulates cell surface invadopodia via kindlin2 for local proteolytic remodeling of the ECM. PMID:25646088

Nonequilibrium electronic transport in a one-dimensional Mott insulator

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

Heidrich-Meisner, F.; Gonzalez, Ivan; Al-Hassanieh, K. A.

2010-01-01

We calculate the nonequilibrium electronic transport properties of a one-dimensional interacting chain at half filling, coupled to noninteracting leads. The interacting chain is initially in a Mott insulator state that is driven out of equilibrium by applying a strong bias voltage between the leads. For bias voltages above a certain threshold we observe the breakdown of the Mott insulator state and the establishment of a steady-state elec- tronic current through the system. Based on extensive time-dependent density-matrix renormalization-group simulations, we show that this steady-state current always has the same functional dependence on voltage, independent of the microscopic details of themore » model and we relate the value of the threshold to the Lieb-Wu gap. We frame our results in terms of the Landau-Zener dielectric breakdown picture. Finally, we also discuss the real-time evolution of the current, and characterize the current-carrying state resulting from the breakdown of the Mott insulator by computing the double occupancy, the spin structure factor, and the entanglement entropy.« less

Hierarchical Equation of Motion Investigation of Decoherence and Relaxation Dynamics in Nonequilibrium Transport through Interacting Quantum Dots

NASA Astrophysics Data System (ADS)

Hartle, Rainer; Cohen, Guy; Reichman, David R.; Millis, Andrew J.

2014-03-01

A recently developed hierarchical quantum master equation approach is used to investigate nonequilibrium electron transport through an interacting double quantum dot system in the regime where the inter-dot coupling is weaker than the coupling to the electrodes. The corresponding eigenstates provide tunneling paths that may interfere constructively or destructively, depending on the energy of the tunneling electrons. Electron-electron interactions are shown to quench these interference effects in bias-voltage dependent ways, leading, in particular, to negative differential resistance, population inversion and an enhanced broadening of resonances in the respective transport characteristics. Relaxation times are found to be very long, and to be correlated with very slow dynamics of the inter-dot coherences (off diagonal density matrix elements). The ability of the hierarchical quantum master equation approach to access very long time scales is crucial for the study of this physics. This work is supported by the National Science Foundation (NSF DMR-1006282 and NSF CHE-1213247), the Yad Hanadiv-Rothschild Foundation (via a Rothschild Fellowship for GC) and the Alexander von Humboldt Foundation (via a Feodor Lynen fellowship for RH).

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.

The Mechanical Properties and Modeling of Creep Behavior of UHMWPE/Nano-HA Composites

NASA Astrophysics Data System (ADS)

Li, Fan; Gao, Lilan; Gao, Hong; Cui, Yun

2017-09-01

Composites with different levels of hydroxyapatite (HA) content and ultra-high molecular weight polyethylene (UHMWPE) were prepared in this work. Mechanical properties of the composites were examined here, and to evaluate the effect of HA particles on the time-dependent behavior of the pure matrix, the creep and recovery performance of composites at various stress levels were also researched. As expected, the addition of HA influenced the time-dependent response of the UHMWPE and the effect had a strong dependence on the HA content. The creep and recovery strain of the composites significantly decreased with increasing HA content, and tensile properties were also impaired, which was due to the concentration of HA fillers. The mechanism and effect of HA dispersed into the UHMWPE matrix were examined by scanning electron microscopy. Additionally, since variations in the adjusted parameters revealed the impact of HA on the creep behavior of the UHMWPE matrix, Findley's model was employed. The results indicated that the analytical model was accurate for the prediction of creep of the pure matrix and its composites.

Linear scaling computation of the Fock matrix. VI. Data parallel computation of the exchange-correlation matrix

NASA Astrophysics Data System (ADS)

Gan, Chee Kwan; Challacombe, Matt

2003-05-01

Recently, early onset linear scaling computation of the exchange-correlation matrix has been achieved using hierarchical cubature [J. Chem. Phys. 113, 10037 (2000)]. Hierarchical cubature differs from other methods in that the integration grid is adaptive and purely Cartesian, which allows for a straightforward domain decomposition in parallel computations; the volume enclosing the entire grid may be simply divided into a number of nonoverlapping boxes. In our data parallel approach, each box requires only a fraction of the total density to perform the necessary numerical integrations due to the finite extent of Gaussian-orbital basis sets. This inherent data locality may be exploited to reduce communications between processors as well as to avoid memory and copy overheads associated with data replication. Although the hierarchical cubature grid is Cartesian, naive boxing leads to irregular work loads due to strong spatial variations of the grid and the electron density. In this paper we describe equal time partitioning, which employs time measurement of the smallest sub-volumes (corresponding to the primitive cubature rule) to load balance grid-work for the next self-consistent-field iteration. After start-up from a heuristic center of mass partitioning, equal time partitioning exploits smooth variation of the density and grid between iterations to achieve load balance. With the 3-21G basis set and a medium quality grid, equal time partitioning applied to taxol (62 heavy atoms) attained a speedup of 61 out of 64 processors, while for a 110 molecule water cluster at standard density it achieved a speedup of 113 out of 128. The efficiency of equal time partitioning applied to hierarchical cubature improves as the grid work per processor increases. With a fine grid and the 6-311G(df,p) basis set, calculations on the 26 atom molecule α-pinene achieved a parallel efficiency better than 99% with 64 processors. For more coarse grained calculations, superlinear speedups are found to result from reduced computational complexity associated with data parallelism.

Applications of stochastic mechanics to polyatomic lattices

NASA Astrophysics Data System (ADS)

Beumée, J. G. B.; Vilallonga, E.; Rabitz, H.

1990-03-01

Stochastic quantization in the sense of Nelson provides an alternative interpretation of some aspects of quantum mechanics in the coordinate representation, and it was combined recently with the Ford, Kac, and Mazur (FKM) approximation [J. Math. Phys. 6, 504 (1965)] for large lattices to construct a quantum analog to the Brownian motion process. In this paper a similar approach is applied to model the effect of temperature fluctuations in a one-dimensional ordered chain of atoms with nearest-neighbor linear forces. However, we do not make use of the FKM approximation, and as a consequence the statistical properties of the involved processes are exactly determined by the lattice force field. In particular, we evaluate the covariance matrix for the fluctuations, and we examine its high- and low-temperature behavior. Because of the translation invariance of the interaction potential, the covariance matrix for the fluctuations becomes singular implying that the associated probability density has equal density along the zero eigenvector of the interaction matrix. This behavior is readily interpreted in terms of the motion of the center of mass of the system, which corresponds to a stochastically perturbed translation, while all other modes are bounded with a probability of 1. As is well known, the transformation to internal (bondlength) coordinates leads to a Hamiltonian specified by a nonsingular interaction matrix. We examine the variance of the fluctuations for the internal coordinates, and we show that in the high-temperature limit the result agrees with that of classical statistical mechanics. Both the position and bondlength of the surface atom decrease with time as is expected for a semi-infinite lattice. However, the position of the surface atom is less dependent on substrate-atom positions than is the surface bondlength on substrate bondlengths. Finally, the autocorrelation function of the surface bondlength in the case of a semi-infinite lattice limit is investigated for low- and high-temperature limits.

Excited-state absorption in tetrapyridyl porphyrins: comparing real-time and quadratic-response time-dependent density functional theory

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

Bowman, David N.; Asher, Jason C.; Fischer, Sean A.

2017-01-01

Threemeso-substituted tetrapyridyl porphyrins (free base, Ni(ii), and Cu(ii)) were investigated for their optical limiting (OL) capabilities using real-time (RT-), linear-response (LR-), and quadratic-response (QR-) time-dependent density functional theory (TDDFT) methods.

Vector meson photoproduction with a linearly polarized beam

NASA Astrophysics Data System (ADS)

Mathieu, V.; Nys, J.; Fernández-Ramírez, C.; Jackura, A.; Pilloni, A.; Sherrill, N.; Szczepaniak, A. P.; Fox, G.; Joint Physics Analysis Center

2018-05-01

We propose a model based on Regge theory to describe photoproduction of light vector mesons. We fit the SLAC data and make predictions for the energy and momentum-transfer dependence of the spin-density matrix elements in photoproduction of ω , ρ0 and ϕ mesons at Eγ˜8.5 GeV , which are soon to be measured at Jefferson Lab.

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.

Stopping dynamics of ions passing through correlated honeycomb clusters

NASA Astrophysics Data System (ADS)

Balzer, Karsten; Schlünzen, Niclas; Bonitz, Michael

2016-12-01

A combined nonequilibrium Green functions-Ehrenfest dynamics approach is developed that allows for a time-dependent study of the energy loss of a charged particle penetrating a strongly correlated system at zero and finite temperatures. Numerical results are presented for finite inhomogeneous two-dimensional Fermi-Hubbard models, where the many-electron dynamics in the target are treated fully quantum mechanically and the motion of the projectile is treated classically. The simulations are based on the solution of the two-time Dyson (Keldysh-Kadanoff-Baym) equations using the second-order Born, third-order, and T -matrix approximations of the self-energy. As application, we consider protons and helium nuclei with a kinetic energy between 1 and 500 keV/u passing through planar fragments of the two-dimensional honeycomb lattice and, in particular, examine the influence of electron-electron correlations on the energy exchange between projectile and electron system. We investigate the time dependence of the projectile's kinetic energy (stopping power), the electron density, the double occupancy, and the photoemission spectrum. Finally, we show that, for a suitable choice of the Hubbard model parameters, the results for the stopping power are in fair agreement with ab initio simulations for particle irradiation of single-layer graphene.

Discontinuities in effective permeability due to fracture percolation

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

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

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

Discontinuities in effective permeability due to fracture percolation

DOE PAGES

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

2018-01-31

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

Surface-peaked medium effects in the interaction of nucleons with finite nuclei

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

Aguayo, F. J.; Arellano, H. F.

We investigate the asymptotic separation of the optical model potential for nucleon-nucleus scattering in momentum space, where the potential is split into a medium-independent term and another depending exclusively on the gradient of the density-dependent g matrix. This decomposition confines the medium sensitivity of the nucleon-nucleus coupling to the surface of the nucleus. We examine this feature in the context of proton-nucleus scattering at beam energies between 30 and 100 MeV and find that the pn coupling accounts for most of this sensitivity. Additionally, based on this general structure of the optical potential we are able to treat both, themore » medium dependence of the effective interaction and the full mixed density as described by single-particle shell models. The calculated scattering observables agree within 10% with those obtained by Arellano, Brieva, and Love in their momentum-space g-folding approach.« less

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

PubMed

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

2012-11-01

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

The role of surface charge in the desolvation process of gelatin: implications in nanoparticle synthesis and modulation of drug release

PubMed Central

Ahsan, Saad M; Rao, Chintalagiri Mohan

2017-01-01

The process of moving hydrophobic amino acids into the core of a protein by desolvation is important in protein folding. However, a rapid and forced desolvation can lead to precipitation of proteins. Desolvation of proteins under controlled conditions generates nanoparticles – homogeneous aggregates with a narrow size distribution. The protein nanoparticles, under physiological conditions, undergo surface erosion due to the action of proteases, releasing the entrapped drug/gene. The packing density of protein nanoparticles significantly influences the release kinetics. We have investigated the desolvation process of gelatin, exploring the role of pH and desolvating agent in nanoparticle synthesis. Our results show that the desolvation process, initiated by the addition of acetone, follows distinct pathways for gelatin incubated at different pH values and results in the generation of nanoparticles with varying matrix densities. The nanoparticles synthesized with varying matrix densities show variations in drug loading and protease-dependent extra- and intracellular drug release. These results will be useful in fine-tuning the synthesis of nanoparticles with desirable drug release profiles. PMID:28182126

Exchange bias of Ni nanoparticles embedded in an antiferromagnetic IrMn matrix.

PubMed

Kuerbanjiang, Balati; Wiedwald, Ulf; Haering, Felix; Biskupek, Johannes; Kaiser, Ute; Ziemann, Paul; Herr, Ulrich

2013-11-15

The magnetic properties of Ni nanoparticles (Ni-NPs) embedded in an antiferromagnetic IrMn matrix were investigated. The Ni-NPs of 8.4 nm mean diameter were synthesized by inert gas aggregation. In a second processing step, the Ni-NPs were in situ embedded in IrMn films or SiOx films under ultrahigh vacuum (UHV) conditions. Findings showed that Ni-NPs embedded in IrMn have an exchange bias field HEB = 821 Oe at 10 K, and 50 Oe at 300 K. The extracted value of the exchange energy density is 0.06 mJ m(-2) at 10 K, which is in good accordance with the results from multilayered thin film systems. The Ni-NPs embedded in SiOx did not show exchange bias. As expected for this particle size, they are superparamagnetic at T = 300 K. A direct comparison of the Ni-NPs embedded in IrMn or SiOx reveals an increase of the blocking temperature from 210 K to around 400 K. The coercivity of the Ni-NPs exchange coupled to the IrMn matrix at 10 K is 8 times larger than the value for Ni-NPs embedded in SiOx. We studied time-dependent remanent magnetization at different temperatures. The relaxation behavior is described by a magnetic viscosity model which reflects a rather flat distribution of energy barriers. Furthermore, we investigated the effects of different field cooling processes on the magnetic properties of the embedded Ni-NPs. Exchange bias values fit to model calculations which correlate the contribution of the antiferromagnetic IrMn matrix to its grain size.

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.

Calculating Path-Dependent Travel Time Prediction Variance and Covariance for the SALSA3D Global Tomographic P-Velocity Model with a Distributed Parallel Multi-Core Computer

NASA Astrophysics Data System (ADS)

Hipp, J. R.; Encarnacao, A.; Ballard, S.; Young, C. J.; Phillips, W. S.; Begnaud, M. L.

2011-12-01

Recently our combined SNL-LANL research team has succeeded in developing a global, seamless 3D tomographic P-velocity model (SALSA3D) that provides superior first P travel time predictions at both regional and teleseismic distances. However, given the variable data quality and uneven data sampling associated with this type of model, it is essential that there be a means to calculate high-quality estimates of the path-dependent variance and covariance associated with the predicted travel times of ray paths through the model. In this paper, we show a methodology for accomplishing this by exploiting the full model covariance matrix. Our model has on the order of 1/2 million nodes, so the challenge in calculating the covariance matrix is formidable: 0.9 TB storage for 1/2 of a symmetric matrix, necessitating an Out-Of-Core (OOC) blocked matrix solution technique. With our approach the tomography matrix (G which includes Tikhonov regularization terms) is multiplied by its transpose (GTG) and written in a blocked sub-matrix fashion. We employ a distributed parallel solution paradigm that solves for (GTG)-1 by assigning blocks to individual processing nodes for matrix decomposition update and scaling operations. We first find the Cholesky decomposition of GTG which is subsequently inverted. Next, we employ OOC matrix multiply methods to calculate the model covariance matrix from (GTG)-1 and an assumed data covariance matrix. Given the model covariance matrix we solve for the travel-time covariance associated with arbitrary ray-paths by integrating the model covariance along both ray paths. Setting the paths equal gives variance for that path. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Robust stability of bidirectional associative memory neural networks with time delays

NASA Astrophysics Data System (ADS)

Park, Ju H.

2006-01-01

Based on the Lyapunov Krasovskii functionals combined with linear matrix inequality approach, a novel stability criterion is proposed for asymptotic stability of bidirectional associative memory neural networks with time delays. A novel delay-dependent stability criterion is given in terms of linear matrix inequalities, which can be solved easily by various optimization algorithms.

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.

Influence of different crosslinking treatments on the physical properties of collagen membranes.

PubMed

Charulatha, V; Rajaram, A

2003-02-01

The physical properties of collagen-based biomaterials are profoundly influenced by the method and extent of crosslinking. In this study, the influence of various crosslinking treatments on the physical properties of reconstituted collagen membranes was assessed. Five crosslinking agents viz., GTA, DMS, DTBP, a combination of DMS and GTA and acyl azide method were used to stabilize collagen matrices. Crosslinking density, swelling ratio, thermo-mechanical properties, stress-strain characteristics and resistance to collagenase digestion were determined to evaluate the physical properties of crosslinked matrices. GTA treatment induced the maximum number of crosslinks (13) while DMS treatment induced the minimum (7). Of the two diimidoesters (DMS and DTBP), DTBP was a more effective crosslinking agent due to the presence of disulphide bonds in the DTBP crosslinks. T(s) for DTBP and DMS crosslinked collagen were 80 degrees C and 70 degrees C, and their HIT values were 5.4 and 2.85MN/m(2), respectively. Low concentration of GTA (0.01%) increased the crosslinking density of an already crosslinked matrix (DMS treated matrix) from 7 to 12. Lowest fracture energy was observed for the acyl azide treated matrix (0.61MJ/m(3)) while the highest was observed for the GTA treated matrix (1.97MJ/m(3)). The tensile strength of GTA treated matrix was maximum (12.4MPa) and that of acyl azide treated matrix was minimum (7.2MPa). GTA, DTBP and acyl azide treated matrices were equally resistant to collagenase degradation with approximately 6% solubilization after 5h while the DMS treated was least stable with 52.4% solubilization after the same time period. The spatial orientation of amino acid side chain residues on collagen plays an important role in determining the crosslinking density and consequent physical properties of the collagen matrix.

Implementation of a fast digital optical matrix-vector multiplier using a holographic look-up table and residue arithmetic

NASA Technical Reports Server (NTRS)

Habiby, Sarry F.; Collins, Stuart A., Jr.

1987-01-01

The design and implementation of a digital (numerical) optical matrix-vector multiplier are presented. A Hughes liquid crystal light valve, the residue arithmetic representation, and a holographic optical memory are used to construct position coded optical look-up tables. All operations are performed in effectively one light valve response time with a potential for a high information density.

Implementation of a fast digital optical matrix-vector multiplier using a holographic look-up table and residue arithmetic.

PubMed

Habiby, S F; Collins, S A

1987-11-01

The design and implementation of a digital (numerical) optical matrix-vector multiplier are presented. A Hughes liquid crystal light valve, the residue arithmetic representation, and a holographic optical memory are used to construct position coded optical look-up tables. All operations are performed in effectively one light valve response time with a potential for a high information density.

Non-renewal statistics for electron transport in a molecular junction with electron-vibration interaction

NASA Astrophysics Data System (ADS)

Kosov, Daniel S.

2017-09-01

Quantum transport of electrons through a molecule is a series of individual electron tunneling events separated by stochastic waiting time intervals. We study the emergence of temporal correlations between successive waiting times for the electron transport in a vibrating molecular junction. Using the master equation approach, we compute the joint probability distribution for waiting times of two successive tunneling events. We show that the probability distribution is completely reset after each tunneling event if molecular vibrations are thermally equilibrated. If we treat vibrational dynamics exactly without imposing the equilibration constraint, the statistics of electron tunneling events become non-renewal. Non-renewal statistics between two waiting times τ1 and τ2 means that the density matrix of the molecule is not fully renewed after time τ1 and the probability of observing waiting time τ2 for the second electron transfer depends on the previous electron waiting time τ1. The strong electron-vibration coupling is required for the emergence of the non-renewal statistics. We show that in the Franck-Condon blockade regime, extremely rare tunneling events become positively correlated.

Terahertz and infrared transmission of an organic/inorganic hybrid thermoelectric material

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

Heyman, J. N., E-mail: heyman@macalester.edu; Alebachew, B. A.; Kaminski, Z. S.

2014-04-07

We report terahertz and infrared transmission measurements of a high-performance thermoelectric material containing tellurium nanowires in a conducting polymer poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) matrix. The DC electrical conductivity of the hybrid material (41 S/cm) is approximately one hundred times that of pure PEDOT:PSS and more than 400 times that of a film of pure tellurium nanowires, while the terahertz-frequency (THz) conductivity of PEDOT:PSS and the hybrid material are comparable at f ∼ 2THz. A frequency-dependent conductivity model indicates that the increased DC conductivity of the hybrid material results from an increase in the DC charge mobility rather than in the free charge density. We suggestmore » that the increased DC conductivity of the hybrid material results from an increase in linkage between PEDOT domains by the tellurium nanowires.« less

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.

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.

Time-dependent variational principle in matrix-product state manifolds: Pitfalls and potential

NASA Astrophysics Data System (ADS)

Kloss, Benedikt; Lev, Yevgeny Bar; Reichman, David

2018-01-01

We study the applicability of the time-dependent variational principle in matrix-product state manifolds for the long time description of quantum interacting systems. By studying integrable and nonintegrable systems for which the long time dynamics are known we demonstrate that convergence of long time observables is subtle and needs to be examined carefully. Remarkably, for the disordered nonintegrable system we consider the long time dynamics are in good agreement with the rigorously obtained short time behavior and with previous obtained numerically exact results, suggesting that at least in this case, the apparent convergence of this approach is reliable. Our study indicates that, while great care must be exercised in establishing the convergence of the method, it may still be asymptotically accurate for a class of disordered nonintegrable quantum systems.

A real-space stochastic density matrix approach for density functional electronic structure.

PubMed

Beck, Thomas L

2015-12-21

The recent development of real-space grid methods has led to more efficient, accurate, and adaptable approaches for large-scale electrostatics and density functional electronic structure modeling. With the incorporation of multiscale techniques, linear-scaling real-space solvers are possible for density functional problems if localized orbitals are used to represent the Kohn-Sham energy functional. These methods still suffer from high computational and storage overheads, however, due to extensive matrix operations related to the underlying wave function grid representation. In this paper, an alternative stochastic method is outlined that aims to solve directly for the one-electron density matrix in real space. In order to illustrate aspects of the method, model calculations are performed for simple one-dimensional problems that display some features of the more general problem, such as spatial nodes in the density matrix. This orbital-free approach may prove helpful considering a future involving increasingly parallel computing architectures. Its primary advantage is the near-locality of the random walks, allowing for simultaneous updates of the density matrix in different regions of space partitioned across the processors. In addition, it allows for testing and enforcement of the particle number and idempotency constraints through stabilization of a Feynman-Kac functional integral as opposed to the extensive matrix operations in traditional approaches.

Linear-scaling time-dependent density-functional theory beyond the Tamm-Dancoff approximation: Obtaining efficiency and accuracy with in situ optimised local orbitals.

PubMed

Zuehlsdorff, T J; Hine, N D M; Payne, M C; Haynes, P D

2015-11-28

We present a solution of the full time-dependent density-functional theory (TDDFT) eigenvalue equation in the linear response formalism exhibiting a linear-scaling computational complexity with system size, without relying on the simplifying Tamm-Dancoff approximation (TDA). The implementation relies on representing the occupied and unoccupied subspaces with two different sets of in situ optimised localised functions, yielding a very compact and efficient representation of the transition density matrix of the excitation with the accuracy associated with a systematic basis set. The TDDFT eigenvalue equation is solved using a preconditioned conjugate gradient algorithm that is very memory-efficient. The algorithm is validated on a small test molecule and a good agreement with results obtained from standard quantum chemistry packages is found, with the preconditioner yielding a significant improvement in convergence rates. The method developed in this work is then used to reproduce experimental results of the absorption spectrum of bacteriochlorophyll in an organic solvent, where it is demonstrated that the TDA fails to reproduce the main features of the low energy spectrum, while the full TDDFT equation yields results in good qualitative agreement with experimental data. Furthermore, the need for explicitly including parts of the solvent into the TDDFT calculations is highlighted, making the treatment of large system sizes necessary that are well within reach of the capabilities of the algorithm introduced here. Finally, the linear-scaling properties of the algorithm are demonstrated by computing the lowest excitation energy of bacteriochlorophyll in solution. The largest systems considered in this work are of the same order of magnitude as a variety of widely studied pigment-protein complexes, opening up the possibility of studying their properties without having to resort to any semiclassical approximations to parts of the protein environment.

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.

Correlation functions from a unified variational principle: Trial Lie groups

NASA Astrophysics Data System (ADS)

Balian, R.; Vénéroni, M.

2015-11-01

Time-dependent expectation values and correlation functions for many-body quantum systems are evaluated by means of a unified variational principle. It optimizes a generating functional depending on sources associated with the observables of interest. It is built by imposing through Lagrange multipliers constraints that account for the initial state (at equilibrium or off equilibrium) and for the backward Heisenberg evolution of the observables. The trial objects are respectively akin to a density operator and to an operator involving the observables of interest and the sources. We work out here the case where trial spaces constitute Lie groups. This choice reduces the original degrees of freedom to those of the underlying Lie algebra, consisting of simple observables; the resulting objects are labeled by the indices of a basis of this algebra. Explicit results are obtained by expanding in powers of the sources. Zeroth and first orders provide thermodynamic quantities and expectation values in the form of mean-field approximations, with dynamical equations having a classical Lie-Poisson structure. At second order, the variational expression for two-time correlation functions separates-as does its exact counterpart-the approximate dynamics of the observables from the approximate correlations in the initial state. Two building blocks are involved: (i) a commutation matrix which stems from the structure constants of the Lie algebra; and (ii) the second-derivative matrix of a free-energy function. The diagonalization of both matrices, required for practical calculations, is worked out, in a way analogous to the standard RPA. The ensuing structure of the variational formulae is the same as for a system of non-interacting bosons (or of harmonic oscillators) plus, at non-zero temperature, classical Gaussian variables. This property is explained by mapping the original Lie algebra onto a simpler Lie algebra. The results, valid for any trial Lie group, fulfill consistency properties and encompass several special cases: linear responses, static and time-dependent fluctuations, zero- and high-temperature limits, static and dynamic stability of small deviations.

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

Balian, R., E-mail: roger.balian@cea.fr; Vénéroni, M.

Time-dependent expectation values and correlation functions for many-body quantum systems are evaluated by means of a unified variational principle. It optimizes a generating functional depending on sources associated with the observables of interest. It is built by imposing through Lagrange multipliers constraints that account for the initial state (at equilibrium or off equilibrium) and for the backward Heisenberg evolution of the observables. The trial objects are respectively akin to a density operator and to an operator involving the observables of interest and the sources. We work out here the case where trial spaces constitute Lie groups. This choice reduces themore » original degrees of freedom to those of the underlying Lie algebra, consisting of simple observables; the resulting objects are labeled by the indices of a basis of this algebra. Explicit results are obtained by expanding in powers of the sources. Zeroth and first orders provide thermodynamic quantities and expectation values in the form of mean-field approximations, with dynamical equations having a classical Lie–Poisson structure. At second order, the variational expression for two-time correlation functions separates–as does its exact counterpart–the approximate dynamics of the observables from the approximate correlations in the initial state. Two building blocks are involved: (i) a commutation matrix which stems from the structure constants of the Lie algebra; and (ii) the second-derivative matrix of a free-energy function. The diagonalization of both matrices, required for practical calculations, is worked out, in a way analogous to the standard RPA. The ensuing structure of the variational formulae is the same as for a system of non-interacting bosons (or of harmonic oscillators) plus, at non-zero temperature, classical Gaussian variables. This property is explained by mapping the original Lie algebra onto a simpler Lie algebra. The results, valid for any trial Lie group, fulfill consistency properties and encompass several special cases: linear responses, static and time-dependent fluctuations, zero- and high-temperature limits, static and dynamic stability of small deviations.« less

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.

Physical Cause of Kimberlite Occurrences Clustering

NASA Astrophysics Data System (ADS)

Khazan, Y.; Aryasova, O.

2011-12-01

High abundances of incompatible elements in kimberlites are indicative of low or even infinitesimal melting degree in a source. This means that initially protokimberlite melts exist as a system of dispersed small inclusions while the kimberlite transportation to the surface assumes formation of macroscopic melt pools. In other words, an inevitable stage of the protokimberlite melt evolution is its segregation from the porous matrix inside a partially molten zone and accumulation to the zone top where the melt fraction greatly exceeds the initial melting degree. Khazan (2010), Khazan, Aryasova (2011) demonstrated that the characteristic segregation time, τ, depends on the ratio L/δ of the molten zone thickness, L, to the compaction length, δ, (McKenzie, 1984), which in its turn is defined by melt and matrix viscosities and matrix permeability. For low-viscosity melts the segregation time decreases with increasing molten zone thickness as τ≈19.5(η/ΔρgL) (η is the matrix viscosity, Δρ is the density contrast) and is independent of poorly known melt viscosity, matrix permeability, and melting degree. Since no system can exist longer than its decay time is, the decreasing segregation time dependence on the molten zone thickness constrains the latter. To illustrate, assume that the melting is due to decompression and accompanies ascent of a mantle diapir with a velocity V. In this case the molten zone thickness increases linearly with time L=Vt where t is measured from the onset of melting and cannot exceed the segregation time, so that t≤τ (Fig. 1) and L≤L*=4.4(Vη/Δρg)^0.5. Under a robust parameter choice (η=10^19 Pa s, Δρ=300 kg/m^3, V=3 cm/year) L* is about 8 km, with the corresponding segregation time τ being of 0.3 Myear (Fig. 1). After the first segregation, a new partially molten zone grows resulting in the next segregation when its thickness reaches the maximum possible value L*. This sequence of events repeats until the whole diapir passes by the melting level. One may estimate a diapir diameter D of 30 to 80 km based upon a size of low-amplitude uplifts associated with the kimberlite fields (e. g., Kaminsky et al., 1995). So the diapir ascent results in a cluster of ~D/L*=3-10 same age and composition eruptions. A total activity accociated with the cluster continues of τD/L*=1 to 3 Myear as it is really observed (Heaman et al.,2004). The described sequence of events is schematic(lly illustrated in Fig. 2. Heaman L et al., Lithos, 2004, 76, 377. Kaminsky F et al., J. Geochem. Explor. 1995, 53, 167. Khazan Y, Geoph. J. Int. 2010, 183, 601. Khazan Y, Aryasona O, Izvestiya, Phys. Solid Earth. 2011, 47, No. 5, 425. McKenzie D, J Petrol. 1984, 25, 713.

Understanding the densification process of Bi2Sr2CaCu2Ox round wires with overpressure processing and its effect on critical current density

PubMed Central

Matras, M. R.; Jiang, J.; Larbalestier, D. C.; Hellstrom, E. E.

2016-01-01

Overpressure (OP) processing increases the critical current density (JC) of Bi2Sr2CaCu2Ox (2212) round wires by shrinking the surrounding Ag matrix around the 2212 filaments, driving them close to full density and greatly increasing the 2212 grain connectivity. Indeed densification is vital for attaining the highest JC. Here, we investigate the time and temperature dependence of the wire densification. We find that the wire diameter decreases by 3.8 ± 0.3 % after full heat treatment at 50 atm and 100 atm OP. At 50 atm OP pressure, the filaments start densifying above 700 °C and reach a 3.30 ± 0.07 % smaller diameter after 2 h at 820 °C, which is below the melting point of 2212 powder. The densification is homogeneous and does not change the filament shape before melting. The growth of non-superconducting phases is observed at 820 °C, suggesting that time should be minimized at high temperature prior to melting the 2212 powder. Study of an open-ended 2.2 m long wire sample shows that full densification and the high OP JC (JC varies by about 3.1 times over the 2.2 m long wire) is reached about 1 m from the open ends, thus showing that coil-length wires can be protected from leaky seals by adding at least 1 m of sacrificial wire at each end. PMID:28479675

D2O clusters isolated in rare-gas solids: Dependence of infrared spectrum on concentration, deposition rate, heating temperature, and matrix material

NASA Astrophysics Data System (ADS)

Shimazaki, Yoichi; Arakawa, Ichiro; Yamakawa, Koichiro

2018-04-01

The infrared absorption spectra of D2O monomers and clusters isolated in rare-gas matrices were systematically reinvestigated under the control of the following factors: the D2O concentration, deposition rate, heating temperature, and rare-gas species. We clearly show that the cluster-size distribution is dependent on not only the D2O concentration but also the deposition rate of a sample; as the rate got higher, smaller clusters were preferentially formed. Under the heating procedures at different temperatures, the cluster-size growth was successfully observed. Since the monomer diffusion was not enough to balance the changes in the column densities of the clusters, the dimer diffusion was likely to contribute the cluster growth. The frequencies of the bonded-OD stretches of (D2O)k with k = 2-6 were almost linearly correlated with the square root of the critical temperature of the matrix material. Additional absorption peaks of (D2O)2 and (D2O)3 in a Xe matrix were assigned to the species trapped in tight accommodation sites.

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.

Time-dependent difference theory for noise propagation in a two-dimensional duct. [of a turbofan engine

NASA Technical Reports Server (NTRS)

Baumeister, K. J.

1979-01-01

A time dependent numerical formulation was derived for sound propagation in a two dimensional straight soft-walled duct in the absence of mean flow. The time dependent governing acoustic-difference equations and boundary conditions were developed along with the maximum stable time increment. Example calculations were presented for sound attenuation in hard and soft wall ducts. The time dependent analysis were found to be superior to the conventional steady numerical analysis because of much shorter solution times and the elimination of matrix storage requirements.

Matrix-assisted laser desorption/ionization imaging mass spectrometry for direct measurement of clozapine in rat brain tissue.

PubMed

Hsieh, Yunsheng; Casale, Roger; Fukuda, Elaine; Chen, Jiwen; Knemeyer, Ian; Wingate, Julia; Morrison, Richard; Korfmacher, Walter

2006-01-01

Matrix-assisted laser desorption/ionization hyphenated with quadrupole time-of-flight (QTOF) mass spectrometry (MS) has been used to directly determine the distribution of pharmaceuticals in rat brain tissue slices which might unravel their disposition for new drug development. Clozapine, an antipsychotic drug, and norclozapine were used as model compounds to investigate fundamental parameters such as matrix and solvent effects and irradiance dependence on MALDI intensity but also to address the issues with direct tissue imaging MS technique such as (1) uniform coating by the matrix, (2) linearity of MALDI signals, and (3) redistribution of surface analytes. The tissue sections were coated with various matrices on MALDI plates by airspray deposition prior to MS detection. MALDI signals of analytes were detected by monitoring the dissociation of the individual protonated molecules to their predominant MS/MS product ions. The matrices were chosen for tissue applications based on their ability to form a homogeneous coating of dense crystals and to yield greater sensitivity. Images revealing the spatial localization in tissue sections using MALDI-QTOF following a direct infusion of (3)H-clozapine into rat brain were found to be in good correlation with those using a radioautographic approach. The density of clozapine and its major metabolites from whole brain homogenates was further confirmed using fast high-performance liquid chromatography/tandem mass spectrometry (HPLC-MS/MS) procedures. Copyright (c) 2006 John Wiley & Sons, Ltd.

Differential cross sections and polarization observables from CLAS K* photoproduction and the search for new N* states

NASA Astrophysics Data System (ADS)

Anisovich, A. V.; Hicks, K.; Klempt, E.; Nikonov, V. A.; Sarantsev, A.; Tang, W.; Adikaram, D.; Akbar, Z.; Amaryan, M. J.; Anefalos Pereira, S.; Badui, R. A.; Ball, J.; Battaglieri, M.; Batourine, V.; Bedlinskiy, I.; Biselli, A. S.; Briscoe, W. J.; Burkert, V. D.; Carman, D. S.; Celentano, A.; Chandavar, S.; Chetry, T.; Ciullo, G.; Clark, L.; Cole, P. L.; Compton, N.; Contalbrigo, M.; Crede, V.; D'Angelo, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Deur, A.; Djalali, C.; Dugger, M.; Dupre, R.; Egiyan, H.; El Alaoui, A.; El Fassi, L.; Eugenio, P.; Fanchini, E.; Fedotov, G.; Filippi, A.; Fleming, J. A.; Gevorgyan, N.; Ghandilyan, Y.; Giovanetti, K. L.; Girod, F. X.; Gleason, C.; Gothe, R. W.; Griffioen, K. A.; Guo, L.; Hanretty, C.; Harrison, N.; Hattawy, M.; Holtrop, M.; Hughes, S. M.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Isupov, E. L.; Jenkins, D.; Jiang, H.; Jo, H. S.; Joosten, S.; Keller, D.; Khachatryan, G.; Khandaker, M.; Kim, W.; Klein, F. J.; Kubarovsky, V.; Lanza, L.; Lenisa, P.; Livingston, K.; MacGregor, I. J. D.; Markov, N.; McKinnon, B.; Meyer, C. A.; Mirazita, M.; Mokeev, V.; Montgomery, R. A.; Movsisyan, A.; Munevar, E.; Munoz Camacho, C.; Murdoch, G.; Nadel-Turonski, P.; Net, L. A.; Ni, A.; Niccolai, S.; Niculescu, I.; Osipenko, M.; Ostrovidov, A. I.; Paolone, M.; Paremuzyan, R.; Park, K.; Pasyuk, E.; Peng, P.; Phelps, W.; Pisano, S.; Pogorelko, O.; Price, J. W.; Prok, Y.; Puckett, A. J. R.; Raue, B. A.; Ripani, M.; Ritchie, B. G.; Rosner, G.; Roy, P.; Sabatié, F.; Schumacher, R. A.; Sharabian, Y. G.; Skorodumina, Iu.; Smith, G. D.; Sokhan, D.; Sparveris, N.; Stankovic, I.; Stepanyan, S.; Strauch, S.; Sytnik, V.; Tian, Ye.; Ungaro, M.; Voskanyan, H.; Voutier, E.; Walford, N. K.; Watts, D. P.; Wood, M. H.; Zachariou, N.; Zhang, J.; Zonta, I.; CLAS Collaboration

2017-08-01

The reaction γp →K*+ Λ was measured using the CLAS detector for photon energies between the threshold and 3.9 GeV at the Thomas Jefferson National Accelerator Facility. For the first time, spin-density matrix elements have been extracted for this reaction. Differential cross sections, spin density matrix elements, and the Λ recoil polarization are compared with theoretical predictions using the BnGa partial wave analysis. The main result is the evidence for significant contributions from N (1895) 1 /2- and N (2100) 1 /2+ to the reaction. Branching ratios for decays into K* Λ for these resonances and further resonances are reported.

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.

Modeling cometary photopolarimetric characteristics with Sh-matrix method

NASA Astrophysics Data System (ADS)

Kolokolova, L.; Petrov, D.

2017-12-01

Cometary dust is dominated by particles of complex shape and structure, which are often considered as fractal aggregates. Rigorous modeling of light scattering by such particles, even using parallelized codes and NASA supercomputer resources, is very computer time and memory consuming. We are presenting a new approach to modeling cometary dust that is based on the Sh-matrix technique (e.g., Petrov et al., JQSRT, 112, 2012). This method is based on the T-matrix technique (e.g., Mishchenko et al., JQSRT, 55, 1996) and was developed after it had been found that the shape-dependent factors could be separated from the size- and refractive-index-dependent factors and presented as a shape matrix, or Sh-matrix. Size and refractive index dependences are incorporated through analytical operations on the Sh-matrix to produce the elements of T-matrix. Sh-matrix method keeps all advantages of the T-matrix method, including analytical averaging over particle orientation. Moreover, the surface integrals describing the Sh-matrix elements themselves can be solvable analytically for particles of any shape. This makes Sh-matrix approach an effective technique to simulate light scattering by particles of complex shape and surface structure. In this paper, we present cometary dust as an ensemble of Gaussian random particles. The shape of these particles is described by a log-normal distribution of their radius length and direction (Muinonen, EMP, 72, 1996). Changing one of the parameters of this distribution, the correlation angle, from 0 to 90 deg., we can model a variety of particles from spheres to particles of a random complex shape. We survey the angular and spectral dependencies of intensity and polarization resulted from light scattering by such particles, studying how they depend on the particle shape, size, and composition (including porous particles to simulate aggregates) to find the best fit to the cometary observations.

SevenOperators, a Mathematica script for harmonic oscillator nuclear matrix elements arising in semileptonic electroweak interactions

NASA Astrophysics Data System (ADS)

Haxton, Wick; Lunardini, Cecilia

2008-09-01

Semi-leptonic electroweak interactions in nuclei—such as β decay, μ capture, charged- and neutral-current neutrino reactions, and electron scattering—are described by a set of multipole operators carrying definite parity and angular momentum, obtained by projection from the underlying nuclear charge and three-current operators. If these nuclear operators are approximated by their one-body forms and expanded in the nucleon velocity through order |p→|/M, where p→ and M are the nucleon momentum and mass, a set of seven multipole operators is obtained. Nuclear structure calculations are often performed in a basis of Slater determinants formed from harmonic oscillator orbitals, a choice that allows translational invariance to be preserved. Harmonic-oscillator single-particle matrix elements of the multipole operators can be evaluated analytically and expressed in terms of finite polynomials in q, where q is the magnitude of the three-momentum transfer. While results for such matrix elements are available in tabular form, with certain restriction on quantum numbers, the task of determining the analytic form of a response function can still be quite tedious, requiring the folding of the tabulated matrix elements with the nuclear density matrix, and subsequent algebra to evaluate products of operators. Here we provide a Mathematica script for generating these matrix elements, which will allow users to carry out all such calculations by symbolic manipulation. This will eliminate the errors that may accompany hand calculations and speed the calculation of electroweak nuclear cross sections and rates. We illustrate the use of the new script by calculating the cross sections for charged- and neutral-current neutrino scattering in 12C. Program summaryProgram title: SevenOperators Catalogue identifier: AEAY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAY_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.: 2227 No. of bytes in distributed program, including test data, etc.: 19 382 Distribution format: tar.gz Programming language: Mathematica Computer: Any computer running Mathematica; tested on Mac OS X PowerPC (32-bit) running Mathematica 6.0.0 Operating system: Any running Mathematica RAM: Memory requirements determined by Mathematica; 512 MB or greater RAM and hard drive space of at least 3.0 GB recommended Classification: 17.16, 17.19 Nature of problem: Algebraic evaluation of harmonic oscillator nuclear matrix elements for the one-body multipole operators governing semi-leptonic weak interactions, such as charged- or neutral-current neutrino scattering off nuclei. Solution method: Mathematica evaluation of associated angular momentum algebra and spherical Bessel function radial integrals. Running time: Depends on the complexity of the one-body density matrix employed, but times of a few seconds are typical.

Estimating Density and Temperature Dependence of Juvenile Vital Rates Using a Hidden Markov Model

PubMed Central

McElderry, Robert M.

2017-01-01

Organisms in the wild have cryptic life stages that are sensitive to changing environmental conditions and can be difficult to survey. In this study, I used mark-recapture methods to repeatedly survey Anaea aidea (Nymphalidae) caterpillars in nature, then modeled caterpillar demography as a hidden Markov process to assess if temporal variability in temperature and density influence the survival and growth of A. aidea over time. Individual encounter histories result from the joint likelihood of being alive and observed in a particular stage, and I have included hidden states by separating demography and observations into parallel and independent processes. I constructed a demographic matrix containing the probabilities of all possible fates for each stage, including hidden states, e.g., eggs and pupae. I observed both dead and live caterpillars with high probability. Peak caterpillar abundance attracted multiple predators, and survival of fifth instars declined as per capita predation rate increased through spring. A time lag between predator and prey abundance was likely the cause of improved fifth instar survival estimated at high density. Growth rates showed an increase with temperature, but the preferred model did not include temperature. This work illustrates how state-space models can include unobservable stages and hidden state processes to evaluate how environmental factors influence vital rates of cryptic life stages in the wild. PMID:28505138

Growth model for uneven-aged loblolly pine stands : simulations and management implications

Treesearch

C.-R. Lin; J. Buongiorno; Jeffrey P. Prestemon; K. E. Skog

1998-01-01

A density-dependent matrix growth model of uneven-aged loblolly pine stands was developed with data from 991 permanent plots in the southern United States. The model predicts the number of pine, soft hardwood, and hard hardwood trees in 13 diameter classes, based on equations for ingrowth, upgrowth, and mortality. Projections of 6 to 10 years agreed with the growth...

A framework for studying transient dynamics of population projection matrix models.

PubMed

Stott, Iain; Townley, Stuart; Hodgson, David James

2011-09-01

Empirical models are central to effective conservation and population management, and should be predictive of real-world dynamics. Available modelling methods are diverse, but analysis usually focuses on long-term dynamics that are unable to describe the complicated short-term time series that can arise even from simple models following ecological disturbances or perturbations. Recent interest in such transient dynamics has led to diverse methodologies for their quantification in density-independent, time-invariant population projection matrix (PPM) models, but the fragmented nature of this literature has stifled the widespread analysis of transients. We review the literature on transient analyses of linear PPM models and synthesise a coherent framework. We promote the use of standardised indices, and categorise indices according to their focus on either convergence times or transient population density, and on either transient bounds or case-specific transient dynamics. We use a large database of empirical PPM models to explore relationships between indices of transient dynamics. This analysis promotes the use of population inertia as a simple, versatile and informative predictor of transient population density, but criticises the utility of established indices of convergence times. Our findings should guide further development of analyses of transient population dynamics using PPMs or other empirical modelling techniques. © 2011 Blackwell Publishing Ltd/CNRS.

Laboratory measurements of ice tensile strength dependence on density and concentration of silicate and polymer impurities at low temperatures

NASA Astrophysics Data System (ADS)

Litwin, K. L.; Beyeler, J. D.; Polito, P. J.; Zygielbaum, B. R.; Sklar, L. S.; Collins, G. C.

2009-12-01

The tensile strength of ice bedrock on Titan should strongly influence the effectiveness of the erosional processes responsible for carving the extensive fluvial drainage networks and other surface features visible in images returned by the Cassini and Huygens probes. Recent measurements of the effect of temperature on the tensile strength of low-porosity, polycrystalline ice, without impurities, suggest that ice bedrock at the Titan surface temperature of 93 K may be as much as five times stronger than ice at terrestrial surface temperatures. However, ice bedrock on Titan and other outer solar system bodies may have significant porosity, and impurities such silicates or polymers are possible in such ices. In this laboratory investigation we are exploring the dependence of tensile strength on the density and concentration of impurities, for polycrystalline ice across a wide range of temperatures. We use the Brazilian tensile splitting test to measure strength, and control temperature with dry ice and liquid nitrogen. The 50 mm diameter ice cores are made from a log-normally distributed seed crystal mixture with a median size of 1.4 mm. To control ice density and porosity we vary the packing density of the seed grains in core molds and vary the degree of saturation of the matrix with added near-freezing distilled water. We also vary ice density by blending in a similarly-sized mixture of angular fragments of two types of impurities, a fine-grained volcanic rock and a polyethylene polymer. Because both types of impurities have greater tensile strength than ice at Earth surface temperatures, we expect higher concentrations of impurities to correlate with increased strength for ice-rock and ice-polymer mixtures. However, at the ultra-cold temperatures of the outer planets, we expect significant divergence in the temperature dependence of ice tensile strength for the various mixtures and resulting densities. These measurements will help constrain the range of possible ice tensile strengths that might occur on Titan and other solar system bodies.

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.

Intermediate disturbance in experimental landscapes improves persistence of beetle metapopulations.

PubMed

Govindan, Byju N; Feng, Zhilan; DeWoody, Yssa D; Swihart, Robert K

2015-03-01

Human-dominated landscapes often feature patches that fluctuate in suitability through space and time, but there is little experimental evidence relating the consequences of dynamic patches for species persistence. We used a spatially and temporally dynamic metapopulation model to assess and compare metapopulation capacity and persistence for red flour beetles (Tribolium castaneum) in experimental landscapes differentiated by resource structure, patch dynamics (destruction and restoration), and connectivity. High connectivity increased the colonization rate of beetles, but this effect was less pronounced in heterogeneous relative to homogeneous landscapes. Higher connectivity and faster patch dynamics increased extinction rates in landscapes. Lower connectivity promoted density-dependent emigration. Heterogeneous landscapes containing patches of different carrying capacity enhanced landscape-level occupancy probability. The highest metapopulation capacity and persistence was observed in landscapes with heterogeneous patches, low connectivity, and slow patch dynamics. Control landscapes with no patch dynamics exhibited rapid declines in abundance and approached extinction due to increased adult mortality in the matrix, higher pupal cannibalism by adults, and extremely low rates of exchange between remaining habitable patches. Our results highlight the role of intermediate patch dynamics, intermediate connectivity, and the nature of density dependence of emigration for persistence of species in heterogeneous landscapes. Our results also demonstrate the importance of incorporating local dynamics into the estimation of metapopulation capacity for conservation planning.

Photoinduced Hund excitons in the breakdown of a two-orbital Mott insulator

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

Rincon, Julian; Dagotto, Elbio R.; Feiguin, Adrian E.

We study the photoinduced breakdown of a two-orbital Mott insulator and resulting metallic state. Using time-dependent density matrix renormalization group, we scrutinize the real-time dynamics of the half-filled two-orbital Hubbard model interacting with a resonant radiation field pulse. The breakdown, caused by production of doublon-holon pairs, is enhanced by Hund's exchange, which dynamically activates large orbital fluctuations. The melting of the Mott insulator is accompanied by a high to low spin transition with a concomitant reduction of antiferromagnetic spin fluctuations. Most notably, the overall time response is driven by the photogeneration of excitons with orbital character that are stabilized bymore » Hund's coupling. These unconventional “Hund excitons” correspond to bound spin-singlet orbital-triplet doublon-holon pairs. We study exciton properties such as bandwidth, binding potential, and size within a semiclassical approach. In conclusion, the photometallic state results from a coexistence of Hund excitons and doublon-holon plasma.« less

Photoinduced Hund excitons in the breakdown of a two-orbital Mott insulator

DOE PAGES

Rincon, Julian; Dagotto, Elbio R.; Feiguin, Adrian E.

2018-06-05

We study the photoinduced breakdown of a two-orbital Mott insulator and resulting metallic state. Using time-dependent density matrix renormalization group, we scrutinize the real-time dynamics of the half-filled two-orbital Hubbard model interacting with a resonant radiation field pulse. The breakdown, caused by production of doublon-holon pairs, is enhanced by Hund's exchange, which dynamically activates large orbital fluctuations. The melting of the Mott insulator is accompanied by a high to low spin transition with a concomitant reduction of antiferromagnetic spin fluctuations. Most notably, the overall time response is driven by the photogeneration of excitons with orbital character that are stabilized bymore » Hund's coupling. These unconventional “Hund excitons” correspond to bound spin-singlet orbital-triplet doublon-holon pairs. We study exciton properties such as bandwidth, binding potential, and size within a semiclassical approach. In conclusion, the photometallic state results from a coexistence of Hund excitons and doublon-holon plasma.« less

Kohn-Sham potentials from electron densities using a matrix representation within finite atomic orbital basis sets

NASA Astrophysics Data System (ADS)

Zhang, Xing; Carter, Emily A.

2018-01-01

We revisit the static response function-based Kohn-Sham (KS) inversion procedure for determining the KS effective potential that corresponds to a given target electron density within finite atomic orbital basis sets. Instead of expanding the potential in an auxiliary basis set, we directly update the potential in its matrix representation. Through numerical examples, we show that the reconstructed density rapidly converges to the target density. Preliminary results are presented to illustrate the possibility of obtaining a local potential in real space from the optimized potential in its matrix representation. We have further applied this matrix-based KS inversion approach to density functional embedding theory. A proof-of-concept study of a solvated proton transfer reaction demonstrates the method's promise.

Time-Dependent Stress Rupture Strength Degradation of Hi-Nicalon Fiber-Reinforced Silicon Carbide Composites at Intermediate Temperatures

NASA Technical Reports Server (NTRS)

Sullivan, Roy M.

2016-01-01

The stress rupture strength of silicon carbide fiber-reinforced silicon carbide composites with a boron nitride fiber coating decreases with time within the intermediate temperature range of 700 to 950 degree Celsius. Various theories have been proposed to explain the cause of the time-dependent stress rupture strength. The objective of this paper is to investigate the relative significance of the various theories for the time-dependent strength of silicon carbide fiber-reinforced silicon carbide composites. This is achieved through the development of a numerically based progressive failure analysis routine and through the application of the routine to simulate the composite stress rupture tests. The progressive failure routine is a time-marching routine with an iterative loop between a probability of fiber survival equation and a force equilibrium equation within each time step. Failure of the composite is assumed to initiate near a matrix crack and the progression of fiber failures occurs by global load sharing. The probability of survival equation is derived from consideration of the strength of ceramic fibers with randomly occurring and slow growing flaws as well as the mechanical interaction between the fibers and matrix near a matrix crack. The force equilibrium equation follows from the global load sharing presumption. The results of progressive failure analyses of the composite tests suggest that the relationship between time and stress-rupture strength is attributed almost entirely to the slow flaw growth within the fibers. Although other mechanisms may be present, they appear to have only a minor influence on the observed time-dependent behavior.

Density-matrix simulation of small surface codes under current and projected experimental noise

NASA Astrophysics Data System (ADS)

O'Brien, T. E.; Tarasinski, B.; DiCarlo, L.

2017-09-01

We present a density-matrix simulation of the quantum memory and computing performance of the distance-3 logical qubit Surface-17, following a recently proposed quantum circuit and using experimental error parameters for transmon qubits in a planar circuit QED architecture. We use this simulation to optimize components of the QEC scheme (e.g., trading off stabilizer measurement infidelity for reduced cycle time) and to investigate the benefits of feedback harnessing the fundamental asymmetry of relaxation-dominated error in the constituent transmons. A lower-order approximate calculation extends these predictions to the distance-5 Surface-49. These results clearly indicate error rates below the fault-tolerance threshold of the surface code, and the potential for Surface-17 to perform beyond the break-even point of quantum memory. However, Surface-49 is required to surpass the break-even point of computation at state-of-the-art qubit relaxation times and readout speeds.

A transverse isotropic constitutive model for the aortic valve tissue incorporating rate-dependency and fibre dispersion: Application to biaxial deformation.

PubMed

Anssari-Benam, Afshin; Tseng, Yuan-Tsan; Bucchi, Andrea

2018-05-26

This paper presents a continuum-based transverse isotropic model incorporating rate-dependency and fibre dispersion, applied to the planar biaxial deformation of aortic valve (AV) specimens under various stretch rates. The rate dependency of the mechanical behaviour of the AV tissue under biaxial deformation, the (pseudo-) invariants of the right Cauchy-Green deformation-rate tensor Ċ associated with fibre dispersion, and a new fibre orientation density function motivated by fibre kinematics are presented for the first time. It is shown that the model captures the experimentally observed deformation of the specimens, and characterises a shear-thinning behaviour associated with the dissipative (viscous) kinematics of the matrix and the fibres. The application of the model for predicting the deformation behaviour of the AV under physiological rates is illustrated and an example of the predicted σ-λ curves is presented. While the development of the model was principally motivated by the AV biomechanics requisites, the comprehensive theoretical approach employed in the study renders the model suitable for application to other fibrous soft tissues that possess similar rate-dependent and structural attributes. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.

Random acoustic metamaterial with a subwavelength dipolar resonance.

PubMed

Duranteau, Mickaël; Valier-Brasier, Tony; Conoir, Jean-Marc; Wunenburger, Régis

2016-06-01

The effective velocity and attenuation of longitudinal waves through random dispersions of rigid, tungsten-carbide beads in an elastic matrix made of epoxy resin in the range of beads volume fraction 2%-10% are determined experimentally. The multiple scattering model proposed by Luppé, Conoir, and Norris [J. Acoust. Soc. Am. 131(2), 1113-1120 (2012)], which fully takes into account the elastic nature of the matrix and the associated mode conversions, accurately describes the measurements. Theoretical calculations show that the rigid particles display a local, dipolar resonance which shares several features with Minnaert resonance of bubbly liquids and with the dipolar resonance of core-shell particles. Moreover, for the samples under study, the main cause of smoothing of the dipolar resonance of the scatterers and the associated variations of the effective mass density of the dispersions is elastic relaxation, i.e., the finite time required for the shear stresses associated to the translational motion of the scatterers to propagate through the matrix. It is shown that its influence is governed solely by the value of the particle to matrix mass density contrast.

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.

The Cauchy Two-Matrix Model, C-Toda Lattice and CKP Hierarchy

NASA Astrophysics Data System (ADS)

Li, Chunxia; Li, Shi-Hao

2018-06-01

This paper mainly talks about the Cauchy two-matrix model and its corresponding integrable hierarchy with the help of orthogonal polynomial theory and Toda-type equations. Starting from the symmetric reduction in Cauchy biorthogonal polynomials, we derive the Toda equation of CKP type (or the C-Toda lattice) as well as its Lax pair by introducing time flows. Then, matrix integral solutions to the C-Toda lattice are extended to give solutions to the CKP hierarchy which reveals the time-dependent partition function of the Cauchy two-matrix model is nothing but the τ -function of the CKP hierarchy. At last, the connection between the Cauchy two-matrix model and Bures ensemble is established from the point of view of integrable systems.

Probing the Bond Order Wave Phase Transitions of the Ionic Hubbard Model by Superlattice Modulation Spectroscopy

NASA Astrophysics Data System (ADS)

Loida, Karla; Bernier, Jean-Sébastien; Citro, Roberta; Orignac, Edmond; Kollath, Corinna

2017-12-01

An exotic phase, the bond order wave, characterized by the spontaneous dimerization of the hopping, has been predicted to exist sandwiched between the band and Mott insulators in systems described by the ionic Hubbard model. Despite growing theoretical evidence, this phase still evades experimental detection. Given the recent realization of the ionic Hubbard model in ultracold atomic gases, we propose here to detect the bond order wave using superlattice modulation spectroscopy. We demonstrate, with the help of time-dependent density-matrix renormalization group and bosonization, that this spectroscopic approach reveals characteristics of both the Ising and Kosterlitz-Thouless transitions signaling the presence of the bond order wave phase. This scheme also provides insights into the excitation spectra of both the band and Mott insulators.

Comparisons of anomalous and collisional radial transport with a continuum kinetic edge code

NASA Astrophysics Data System (ADS)

Bodi, K.; Krasheninnikov, S.; Cohen, R.; Rognlien, T.

2009-05-01

Modeling of anomalous (turbulence-driven) radial transport in controlled-fusion plasmas is necessary for long-time transport simulations. Here the focus is continuum kinetic edge codes such as the (2-D, 2-V) transport version of TEMPEST, NEO, and the code being developed by the Edge Simulation Laboratory, but the model also has wider application. Our previously developed anomalous diagonal transport matrix model with velocity-dependent convection and diffusion coefficients allows contact with typical fluid transport models (e.g., UEDGE). Results are presented that combine the anomalous transport model and collisional transport owing to ion drift orbits utilizing a Krook collision operator that conserves density and energy. Comparison is made of the relative magnitudes and possible synergistic effects of the two processes for typical tokamak device parameters.

Breaking the theoretical scaling limit for predicting quasiparticle energies: the stochastic GW approach.

PubMed

Neuhauser, Daniel; Gao, Yi; Arntsen, Christopher; Karshenas, Cyrus; Rabani, Eran; Baer, Roi

2014-08-15

We develop a formalism to calculate the quasiparticle energy within the GW many-body perturbation correction to the density functional theory. The occupied and virtual orbitals of the Kohn-Sham Hamiltonian are replaced by stochastic orbitals used to evaluate the Green function G, the polarization potential W, and, thereby, the GW self-energy. The stochastic GW (sGW) formalism relies on novel theoretical concepts such as stochastic time-dependent Hartree propagation, stochastic matrix compression, and spatial or temporal stochastic decoupling techniques. Beyond the theoretical interest, the formalism enables linear scaling GW calculations breaking the theoretical scaling limit for GW as well as circumventing the need for energy cutoff approximations. We illustrate the method for silicon nanocrystals of varying sizes with N_{e}>3000 electrons.

Effect of growth temperature, surface type and incubation time on the resistance of Staphylococcus aureus biofilms to disinfectants.

PubMed

Abdallah, Marwan; Chataigne, Gabrielle; Ferreira-Theret, Pauline; Benoliel, Corinne; Drider, Djamel; Dhulster, Pascal; Chihib, Nour-Eddine

2014-03-01

The goal of this study was to investigate the effect of the environmental conditions such as the temperature change, incubation time and surface type on the resistance of Staphylococcus aureus biofilms to disinfectants. The antibiofilm assays were performed against biofilms grown at 20 °C, 30 °C and 37 °C, on the stainless steel and polycarbonate, during 24 and 48 h. The involvement of the biofilm matrix and the bacterial membrane fluidity in the resistance of sessile cells were investigated. Our results show that the efficiency of disinfectants was dependent on the growth temperature, the surface type and the disinfectant product. The increase of growth temperature from 20 °C to 37 °C, with an incubation time of 24 h, increased the resistance of biofilms to cationic antimicrobials. This change of growth temperature did not affect the major content of the biofilm matrix, but it decreased the membrane fluidity of sessile cells through the increase of the anteiso-C19 relative amount. The increase of the biofilm resistance to disinfectants, with the rise of the incubation time, was dependent on both growth temperature and disinfectant product. The increase of the biofilm age also promoted increases in the matrix production and the membrane fluidity of sessile cells. The resistance of S. aureus biofilm seems to depend on the environment of the biofilm formation and involves both extracellular matrix and membrane fluidity of sessile cells. Our study represents the first report describing the impact of environmental conditions on the matrix production, sessile cells membrane fluidity and resistance of S. aureus biofilms to disinfectants.

Creep-rupture of polymer-matrix composites. [graphite-epoxy laminates

NASA Technical Reports Server (NTRS)

Brinson, H. F.; Griffith, W. I.; Morris, D. H.

1980-01-01

An accelerated characterization method for resin matrix composites is reviewed. Methods for determining modulus and strength master curves are given. Creep rupture analytical models are discussed as applied to polymers and polymer matrix composites. Comparisons between creep rupture experiments and analytical models are presented. The time dependent creep rupture process in graphite epoxy laminates is examined as a function of temperature and stress level.

Predation and fragmentation portrayed in the statistical structure of prey time series

PubMed Central

Hendrichsen, Ditte K; Topping, Chris J; Forchhammer, Mads C

2009-01-01

Background Statistical autoregressive analyses of direct and delayed density dependence are widespread in ecological research. The models suggest that changes in ecological factors affecting density dependence, like predation and landscape heterogeneity are directly portrayed in the first and second order autoregressive parameters, and the models are therefore used to decipher complex biological patterns. However, independent tests of model predictions are complicated by the inherent variability of natural populations, where differences in landscape structure, climate or species composition prevent controlled repeated analyses. To circumvent this problem, we applied second-order autoregressive time series analyses to data generated by a realistic agent-based computer model. The model simulated life history decisions of individual field voles under controlled variations in predator pressure and landscape fragmentation. Analyses were made on three levels: comparisons between predated and non-predated populations, between populations exposed to different types of predators and between populations experiencing different degrees of habitat fragmentation. Results The results are unambiguous: Changes in landscape fragmentation and the numerical response of predators are clearly portrayed in the statistical time series structure as predicted by the autoregressive model. Populations without predators displayed significantly stronger negative direct density dependence than did those exposed to predators, where direct density dependence was only moderately negative. The effects of predation versus no predation had an even stronger effect on the delayed density dependence of the simulated prey populations. In non-predated prey populations, the coefficients of delayed density dependence were distinctly positive, whereas they were negative in predated populations. Similarly, increasing the degree of fragmentation of optimal habitat available to the prey was accompanied with a shift in the delayed density dependence, from strongly negative to gradually becoming less negative. Conclusion We conclude that statistical second-order autoregressive time series analyses are capable of deciphering interactions within and across trophic levels and their effect on direct and delayed density dependence. PMID:19419539

Two modulator generalized ellipsometer for complete mueller matrix measurement

DOEpatents

Jellison, Jr., Gerald E.; Modine, Frank A.

1999-01-01

A two-modulator generalized ellipsometer (2-MGE) comprising two polarizer-photoelastic modulator (PEM) pairs, an optical light source, an optical detection system, and associated data processing and control electronics, where the PEMs are free-running. The input light passes through the first polarizer-PEM pair, reflects off the sample surface or passes through the sample, passes through the second PEM-polarizer pair, and is detected. Each PEM is free running and operates at a different resonant frequency, e.g., 50 and 60 kHz. The resulting time-dependent waveform of the light intensity is a complicated function of time, and depends upon the exact operating frequency and phase of each PEM, the sample, and the azimuthal angles of the polarizer-PEM pairs, but can be resolved into a dc component and eight periodic components. In one embodiment, the waveform is analyzed using a new spectral analysis technique that is similar to Fourier analysis to determine eight sample Mueller matrix elements (normalized to the m.sub.00 Mueller matrix element). The other seven normalized elements of the general 4.times.4 Mueller matrix can be determined by changing the azimuthal angles of the PEM-polarizer pairs with respect to the plane of incidence. Since this instrument can measure all elements of the sample Mueller matrix, it is much more powerful than standard ellipsometers.

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.

Advanced Constituents and Processes for Ceramic Composite Engine Components

NASA Technical Reports Server (NTRS)

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

2004-01-01

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

On Porosity Formation in Metal Matrix Composites Made with Dual-Scale Fiber Reinforcements Using Pressure Infiltration Process

NASA Astrophysics Data System (ADS)

Etemadi, Reihaneh; Pillai, Krishna M.; Rohatgi, Pradeep K.; Hamidi, Sajad Ahmad

2015-05-01

This is the first such study on porosity formation phenomena observed in dual-scale fiber preforms during the synthesis of metal matrix composites (MMCs) using the gas pressure infiltration process. In this paper, different mechanisms of porosity formation during pressure infiltration of Al-Si alloys into Nextel™ 3D-woven ceramic fabric reinforcements (a dual-porosity or dual-scale porous medium) are studied. The effect of processing conditions on porosity content of the ceramic fabric infiltrated by the alloys through the gas PIP (PIP stands for "Pressure Infiltration Process" in which liquid metal is injected under pressure into a mold packed with reinforcing fibers.) is investigated. Relative density (RD), defined as the ratio of the actual MMC density and the density obtained at ideal 100 pct saturation of the preform, was used to quantify the overall porosity. Increasing the infiltration temperature led to an increase in RD due to reduced viscosity of liquid metal and enhanced wettability leading to improved feedability of the liquid metal. Similarly, increasing the infiltration pressure led to enhanced penetration of fiber tows and resulted in higher RD and reduced porosity. For the first time, the modified Capillary number ( Ca*), which is found to predict formation of porosity in polymer matrix composites quite well, is employed to study porosity in MMCs made using PIP. It is observed that in the high Ca* regime which is common in PIP, the overall porosity shows a strong downward trend with increasing Ca*. In addition, the effect of matrix shrinkage on porosity content of the samples is studied through using a zero-shrinkage Al-Si alloy as the matrix; usage of this alloy as the matrix led to a reduction in porosity content.

Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections.

PubMed

Karslake, Jason; Maltas, Jeff; Brumm, Peter; Wood, Kevin B

2016-10-01

The inoculum effect (IE) is an increase in the minimum inhibitory concentration (MIC) of an antibiotic as a function of the initial size of a microbial population. The IE has been observed in a wide range of bacteria, implying that antibiotic efficacy may depend on population density. Such density dependence could have dramatic effects on bacterial population dynamics and potential treatment strategies, but explicit measures of per capita growth as a function of density are generally not available. Instead, the IE measures MIC as a function of initial population size, and population density changes by many orders of magnitude on the timescale of the experiment. Therefore, the functional relationship between population density and antibiotic inhibition is generally not known, leaving many questions about the impact of the IE on different treatment strategies unanswered. To address these questions, here we directly measured real-time per capita growth of Enterococcus faecalis populations exposed to antibiotic at fixed population densities using multiplexed computer-automated culture devices. We show that density-dependent growth inhibition is pervasive for commonly used antibiotics, with some drugs showing increased inhibition and others decreased inhibition at high densities. For several drugs, the density dependence is mediated by changes in extracellular pH, a community-level phenomenon not previously linked with the IE. Using a simple mathematical model, we demonstrate how this density dependence can modulate population dynamics in constant drug environments. Then, we illustrate how time-dependent dosing strategies can mitigate the negative effects of density-dependence. Finally, we show that these density effects lead to bistable treatment outcomes for a wide range of antibiotic concentrations in a pharmacological model of antibiotic treatment. As a result, infections exceeding a critical density often survive otherwise effective treatments.

Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections

PubMed Central

Maltas, Jeff; Brumm, Peter; Wood, Kevin B.

2016-01-01

The inoculum effect (IE) is an increase in the minimum inhibitory concentration (MIC) of an antibiotic as a function of the initial size of a microbial population. The IE has been observed in a wide range of bacteria, implying that antibiotic efficacy may depend on population density. Such density dependence could have dramatic effects on bacterial population dynamics and potential treatment strategies, but explicit measures of per capita growth as a function of density are generally not available. Instead, the IE measures MIC as a function of initial population size, and population density changes by many orders of magnitude on the timescale of the experiment. Therefore, the functional relationship between population density and antibiotic inhibition is generally not known, leaving many questions about the impact of the IE on different treatment strategies unanswered. To address these questions, here we directly measured real-time per capita growth of Enterococcus faecalis populations exposed to antibiotic at fixed population densities using multiplexed computer-automated culture devices. We show that density-dependent growth inhibition is pervasive for commonly used antibiotics, with some drugs showing increased inhibition and others decreased inhibition at high densities. For several drugs, the density dependence is mediated by changes in extracellular pH, a community-level phenomenon not previously linked with the IE. Using a simple mathematical model, we demonstrate how this density dependence can modulate population dynamics in constant drug environments. Then, we illustrate how time-dependent dosing strategies can mitigate the negative effects of density-dependence. Finally, we show that these density effects lead to bistable treatment outcomes for a wide range of antibiotic concentrations in a pharmacological model of antibiotic treatment. As a result, infections exceeding a critical density often survive otherwise effective treatments. PMID:27764095

Atomically thin layers of B-N-C-O with tunable composition.

PubMed

Ozturk, Birol; de-Luna-Bugallo, Andres; Panaitescu, Eugen; Chiaramonti, Ann N; Liu, Fangze; Vargas, Anthony; Jiang, Xueping; Kharche, Neerav; Yavuzcetin, Ozgur; Alnaji, Majed; Ford, Matthew J; Lok, Jay; Zhao, Yongyi; King, Nicholas; Dhar, Nibir K; Dubey, Madan; Nayak, Saroj K; Sridhar, Srinivas; Kar, Swastik

2015-07-01

In recent times, atomically thin alloys of boron, nitrogen, and carbon have generated significant excitement as a composition-tunable two-dimensional (2D) material that demonstrates rich physics as well as application potentials. The possibility of tunably incorporating oxygen, a group VI element, into the honeycomb sp(2)-type 2D-BNC lattice is an intriguing idea from both fundamental and applied perspectives. We present the first report on an atomically thin quaternary alloy of boron, nitrogen, carbon, and oxygen (2D-BNCO). Our experiments suggest, and density functional theory (DFT) calculations corroborate, stable configurations of a honeycomb 2D-BNCO lattice. We observe micrometer-scale 2D-BNCO domains within a graphene-rich 2D-BNC matrix, and are able to control the area coverage and relative composition of these domains by varying the oxygen content in the growth setup. Macroscopic samples comprising 2D-BNCO domains in a graphene-rich 2D-BNC matrix show graphene-like gate-modulated electronic transport with mobility exceeding 500 cm(2) V(-1) s(-1), and Arrhenius-like activated temperature dependence. Spin-polarized DFT calculations for nanoscale 2D-BNCO patches predict magnetic ground states originating from the B atoms closest to the O atoms and sizable (0.6 eV < E g < 0.8 eV) band gaps in their density of states. These results suggest that 2D-BNCO with novel electronic and magnetic properties have great potential for nanoelectronics and spintronic applications in an atomically thin platform.

Equivalence principle for quantum systems: dephasing and phase shift of free-falling particles

NASA Astrophysics Data System (ADS)

Anastopoulos, C.; Hu, B. L.

2018-02-01

We ask the question of how the (weak) equivalence principle established in classical gravitational physics should be reformulated and interpreted for massive quantum objects that may also have internal degrees of freedom (dof). This inquiry is necessary because even elementary concepts like a classical trajectory are not well defined in quantum physics—trajectories originating from quantum histories become viable entities only under stringent decoherence conditions. From this investigation we posit two logically and operationally distinct statements of the equivalence principle for quantum systems. Version A: the probability distribution of position for a free-falling particle is the same as the probability distribution of a free particle, modulo a mass-independent shift of its mean. Version B: any two particles with the same velocity wave-function behave identically in free fall, irrespective of their masses. Both statements apply to all quantum states, including those without a classical correspondence, and also for composite particles with quantum internal dof. We also investigate the consequences of the interaction between internal and external dof induced by free fall. For a class of initial states, we find dephasing occurs for the translational dof, namely, the suppression of the off-diagonal terms of the density matrix, in the position basis. We also find a gravitational phase shift in the reduced density matrix of the internal dof that does not depend on the particle’s mass. For classical states, the phase shift has a natural classical interpretation in terms of gravitational red-shift and special relativistic time-dilation.

Rate-Dependent Behavior of the Amorphous Phase of Spider Dragline Silk

PubMed Central

Patil, Sandeep P.; Markert, Bernd; Gräter, Frauke

2014-01-01

The time-dependent stress-strain behavior of spider dragline silk was already observed decades ago, and has been attributed to the disordered sequences in silk proteins, which compose the soft amorphous matrix. However, the actual molecular origin and magnitude of internal friction within the amorphous matrix has remained inaccessible, because experimentally decomposing the mechanical response of the amorphous matrix from the embedded crystalline units is challenging. Here, we used atomistic molecular dynamics simulations to obtain friction forces for the relative sliding of peptide chains of Araneus diadematus spider silk within bundles of these chains as a representative unit of the amorphous matrix in silk fibers. We computed the friction coefficient and coefficient of viscosity of the amorphous phase to be in the order of 10−6 Ns/m and 104 Ns/m2, respectively, by extrapolating our simulation data to the viscous limit. Finally, we used a finite element method for the amorphous phase, solely based on parameters derived from molecular dynamics simulations including the newly determined coefficient of viscosity. With this model the time scales of stress relaxation, creep, and hysteresis were assessed, and found to be in line with the macroscopic time-dependent response of silk fibers. Our results suggest the amorphous phase to be the primary source of viscosity in silk and open up the avenue for finite element method studies of silk fiber mechanics including viscous effects. PMID:24896131

Evolutionary stability for matrix games under time constraints.

PubMed

Garay, József; Csiszár, Villő; Móri, Tamás F

2017-02-21

Game theory focuses on payoffs and typically ignores time constraints that play an important role in evolutionary processes where the repetition of games can depend on the strategies, too. We introduce a matrix game under time constraints, where each pairwise interaction has two consequences: both players receive a payoff and they cannot play the next game for a specified time duration. Thus our model is defined by two matrices: a payoff matrix and an average time duration matrix. Maynard Smith's concept of evolutionary stability is extended to this class of games. We illustrate the effect of time constraints by the well-known prisoner's dilemma game, where additional time constraints can ensure the existence of unique evolutionary stable strategies (ESS), both pure and mixed, or the coexistence of two pure ESS. Our general results may be useful in several fields of biology where evolutionary game theory is applied, principally in ecological games, where time constraints play an inevitable role. Copyright © 2016 Elsevier Ltd. All rights reserved.

Chapman Enskog-maximum entropy method on time-dependent neutron transport equation

NASA Astrophysics Data System (ADS)

Abdou, M. A.

2006-09-01

The time-dependent neutron transport equation in semi and infinite medium with linear anisotropic and Rayleigh scattering is proposed. The problem is solved by means of the flux-limited, Chapman Enskog-maximum entropy for obtaining the solution of the time-dependent neutron transport. The solution gives the neutron distribution density function which is used to compute numerically the radiant energy density E(x,t), net flux F(x,t) and reflectivity Rf. The behaviour of the approximate flux-limited maximum entropy neutron density function are compared with those found by other theories. Numerical calculations for the radiant energy, net flux and reflectivity of the proposed medium are calculated at different time and space.

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.

An isometric muscle force estimation framework based on a high-density surface EMG array and an NMF algorithm

NASA Astrophysics Data System (ADS)

Huang, Chengjun; Chen, Xiang; Cao, Shuai; Qiu, Bensheng; Zhang, Xu

2017-08-01

Objective. To realize accurate muscle force estimation, a novel framework is proposed in this paper which can extract the input of the prediction model from the appropriate activation area of the skeletal muscle. Approach. Surface electromyographic (sEMG) signals from the biceps brachii muscle during isometric elbow flexion were collected with a high-density (HD) electrode grid (128 channels) and the external force at three contraction levels was measured at the wrist synchronously. The sEMG envelope matrix was factorized into a matrix of basis vectors with each column representing an activation pattern and a matrix of time-varying coefficients by a nonnegative matrix factorization (NMF) algorithm. The activation pattern with the highest activation intensity, which was defined as the sum of the absolute values of the time-varying coefficient curve, was considered as the major activation pattern, and its channels with high weighting factors were selected to extract the input activation signal of a force estimation model based on the polynomial fitting technique. Main results. Compared with conventional methods using the whole channels of the grid, the proposed method could significantly improve the quality of force estimation and reduce the electrode number. Significance. The proposed method provides a way to find proper electrode placement for force estimation, which can be further employed in muscle heterogeneity analysis, myoelectric prostheses and the control of exoskeleton devices.

Vector meson photoproduction with a linearly polarized beam

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

Mathieu, V.; Nys, J.; Fernendez-Ramirez, C.

Here, we propose a model based on Regge theory to describe photoproduction of light vector mesons. We fit the SLAC data and make predictions for the energy and momentum transfer dependence of the spin-density matrix elements in photoproduction of ω,more » $$\\rho^0$$ and $$\\sigma$$ mesons at Ε γ ~ 8.5 GeV, which are soon to be measured at Jefferson Lab.« less

Vector meson photoproduction with a linearly polarized beam

DOE PAGES

Mathieu, V.; Nys, J.; Fernendez-Ramirez, C.; ...

2018-05-09

Here, we propose a model based on Regge theory to describe photoproduction of light vector mesons. We fit the SLAC data and make predictions for the energy and momentum transfer dependence of the spin-density matrix elements in photoproduction of ω,more » $$\\rho^0$$ and $$\\sigma$$ mesons at Ε γ ~ 8.5 GeV, which are soon to be measured at Jefferson Lab.« less

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Differential cross sections and polarization observables from CLAS K *photoproduction and the search for new N* states

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

Anisovich, A. V.

The reactionmore » $$\\gamma p \\to K^{*+} \\Lambda$$ was measured using the CLAS detector for photon energies between the threshold and 3.9 GeV at the Thomas Jefferson National Accelerator Facility. For the first time, spin-density matrix elements have been extracted for this reaction. Differential cross sections, spin density matrix elements, and the $$\\Lambda$$ recoil polarization are compared with theoretical predictions using the BnGa partial wave analysis. The main result is the evidence for significant contributions from $N(1895)1/2^-$ and $N(2100)1/2^+$ to the reaction. Branching ratios for decays into $$K^*\\Lambda$$ for these resonances and further resonances are reported.« less

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.

Differential cross sections and polarization observables from CLAS K *photoproduction and the search for new N* states

DOE PAGES

Anisovich, A. V.

2017-05-16

The reactionmore » $$\\gamma p \\to K^{*+} \\Lambda$$ was measured using the CLAS detector for photon energies between the threshold and 3.9 GeV at the Thomas Jefferson National Accelerator Facility. For the first time, spin-density matrix elements have been extracted for this reaction. Differential cross sections, spin density matrix elements, and the $$\\Lambda$$ recoil polarization are compared with theoretical predictions using the BnGa partial wave analysis. The main result is the evidence for significant contributions from $N(1895)1/2^-$ and $N(2100)1/2^+$ to the reaction. Branching ratios for decays into $$K^*\\Lambda$$ for these resonances and further resonances are reported.« less

Matrix Methods for Estimating the Coherence Functions from Estimates of the Cross-Spectral Density Matrix

DOE PAGES

Smallwood, D. O.

1996-01-01

It is shown that the usual method for estimating the coherence functions (ordinary, partial, and multiple) for a general multiple-input! multiple-output problem can be expressed as a modified form of Cholesky decomposition of the cross-spectral density matrix of the input and output records. The results can be equivalently obtained using singular value decomposition (SVD) of the cross-spectral density matrix. Using SVD suggests a new form of fractional coherence. The formulation as a SVD problem also suggests a way to order the inputs when a natural physical order of the inputs is absent.

Fatigue Lifetime of Ceramic Matrix Composites at Intermediate Temperature by Acoustic Emission

PubMed Central

Racle, Elie; Godin, Nathalie; Reynaud, Pascal; Fantozzi, Gilbert

2017-01-01

The fatigue behavior of a Ceramic Matrix Composite (CMC) at intermediate temperature under air is investigated. Because of the low density and the high tensile strength of CMC, they offer a good technical solution to design aeronautical structural components. The aim of the present study is to compare the behavior of this composite under static and cyclic loading. Comparison between incremental static and cyclic tests shows that cyclic loading with an amplitude higher than 30% of the ultimate tensile strength has significant effects on damage and material lifetimes. In order to evaluate the remaining lifetime, several damage indicators, mainly based on the investigation of the liberated energy, are introduced. These indicators highlight critical times or characteristic times, allowing an evaluation of the remaining lifetime. A link is established with the characteristic time around 25% of the total test duration and the beginning of the matrix cracking during cyclic fatigue. PMID:28773019

Tamibarotene-loaded citric acid-crosslinked alkali-treated collagen matrix as a coating material for a drug-eluting stent

NASA Astrophysics Data System (ADS)

Inoue, Motoki; Takayanagi, Mariko; Fujiu, Katsuhito; Manabe, Ichiro; Nagai, Ryozo; Taguchi, Tetsushi

2012-12-01

Tamibarotene-loaded biodegradable matrices with antithrombogenic and drug-releasing properties were prepared in a crosslinking reaction between amino groups of alkali-treated collagen (AlCol) and active ester groups of trisuccinimidyl citrate. The resulting matrices were characterized by their residual amino group concentrations, swelling ratios and thermal, antithrombogenic and drug-releasing properties. It was clarified that the addition of tamibarotene does not inhibit matrix formation. After immersion in water, the swelling ratio of a matrix became lower than that prior to immersion. Thermal analysis indicated that AlCol interacted with tamibarotene. The addition of tamibarotene to the matrix did not influence the antithrombogenic property of the resulting matrix. A matrix with a high crosslinking density had a prolonged tamibarotene elution time. These results demonstrate that tamibarotene-loaded matrices have great potential as a coating material for drug-eluting stents.

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

Quantum Stochastic Trajectories: The Fokker-Planck-Bohm Equation Driven by the Reduced Density Matrix.

PubMed

Avanzini, Francesco; Moro, Giorgio J

2018-03-15

The quantum molecular trajectory is the deterministic trajectory, arising from the Bohm theory, that describes the instantaneous positions of the nuclei of molecules by assuring the agreement with the predictions of quantum mechanics. Therefore, it provides the suitable framework for representing the geometry and the motions of molecules without neglecting their quantum nature. However, the quantum molecular trajectory is extremely demanding from the computational point of view, and this strongly limits its applications. To overcome such a drawback, we derive a stochastic representation of the quantum molecular trajectory, through projection operator techniques, for the degrees of freedom of an open quantum system. The resulting Fokker-Planck operator is parametrically dependent upon the reduced density matrix of the open system. Because of the pilot role played by the reduced density matrix, this stochastic approach is able to represent accurately the main features of the open system motions both at equilibrium and out of equilibrium with the environment. To verify this procedure, the predictions of the stochastic and deterministic representation are compared for a model system of six interacting harmonic oscillators, where one oscillator is taken as the open quantum system of interest. The undeniable advantage of the stochastic approach is that of providing a simplified and self-contained representation of the dynamics of the open system coordinates. Furthermore, it can be employed to study the out of equilibrium dynamics and the relaxation of quantum molecular motions during photoinduced processes, like photoinduced conformational changes and proton transfers.

Optimized effective potential in real time: Problems and prospects in time-dependent density-functional theory

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

Mundt, Michael; Kuemmel, Stephan

2006-08-15

The integral equation for the time-dependent optimized effective potential (TDOEP) in time-dependent density-functional theory is transformed into a set of partial-differential equations. These equations only involve occupied Kohn-Sham orbitals and orbital shifts resulting from the difference between the exchange-correlation potential and the orbital-dependent potential. Due to the success of an analog scheme in the static case, a scheme that propagates orbitals and orbital shifts in real time is a natural candidate for an exact solution of the TDOEP equation. We investigate the numerical stability of such a scheme. An approximation beyond the Krieger-Li-Iafrate approximation for the time-dependent exchange-correlation potential ismore » analyzed.« less

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.

Rapid Diffusion of Green Fluorescent Protein in the Mitochondrial Matrix

PubMed Central

Partikian, Arthur; Ölveczky, Bence; Swaminathan, R.; Li, Yuxin; Verkman, A.S.

1998-01-01

Abstract. It is thought that the high protein density in the mitochondrial matrix results in severely restricted solute diffusion and metabolite channeling from one enzyme to another without free aqueous-phase diffusion. To test this hypothesis, we measured the diffusion of green fluorescent protein (GFP) expressed in the mitochondrial matrix of fibroblast, liver, skeletal muscle, and epithelial cell lines. Spot photobleaching of GFP with a 100× objective (0.8-μm spot diam) gave half-times for fluorescence recovery of 15–19 ms with >90% of the GFP mobile. As predicted for aqueous-phase diffusion in a confined compartment, fluorescence recovery was slowed or abolished by increased laser spot size or bleach time, and by paraformaldehyde fixation. Quantitative analysis of bleach data using a mathematical model of matrix diffusion gave GFP diffusion coefficients of 2–3 × 10−7 cm2/s, only three to fourfold less than that for GFP diffusion in water. In contrast, little recovery was found for bleaching of GFP in fusion with subunits of the fatty acid β-oxidation multienzyme complex that are normally present in the matrix. Measurement of the rotation of unconjugated GFP by time-resolved anisotropy gave a rotational correlation time of 23.3 ± 1 ns, similar to that of 20 ns for GFP rotation in water. A rapid rotational correlation time of 325 ps was also found for a small fluorescent probe (BCECF, ∼0.5 kD) in the matrix of isolated liver mitochondria. The rapid and unrestricted diffusion of solutes in the mitochondrial matrix suggests that metabolite channeling may not be required to overcome diffusive barriers. We propose that the clustering of matrix enzymes in membrane-associated complexes might serve to establish a relatively uncrowded aqueous space in which solutes can freely diffuse. PMID:9472034

Implementing the SU(2) Symmetry for the DMRG

NASA Astrophysics Data System (ADS)

Alvarez, Gonzalo

2010-03-01

In the Density Matrix Renormalization Group (DMRG) algorithm (White, 1992), Hamiltonian symmetries play an important role. Using symmetries, the matrix representation of the Hamiltonian can be blocked. Diagonalizing each matrix block is more efficient than diagonalizing the original matrix. This talk will explain how the DMRG++ codefootnotetextarXiv:0902.3185 or Computer Physics Communications 180 (2009) 1572-1578. has been extended to handle the non-local SU(2) symmetry in a model independent way. Improvements in CPU times compared to runs with only local symmetries will be discussed for typical tight-binding models of strongly correlated electronic systems. The computational bottleneck of the algorithm, and the use of shared memory parallelization will also be addressed. Finally, a roadmap for future work on DMRG++ will be presented.

Implementation of the SU(2) Hamiltonian Symmetry for the DMRG Algorithm

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

Alvarez, Gonzalo

2012-01-01

In the Density Matrix Renormalization Group (DMRG) algorithm (White, 1992, 1993) and Hamiltonian symmetries play an important role. Using symmetries, the matrix representation of the Hamiltonian can be blocked. Diagonalizing each matrix block is more efficient than diagonalizing the original matrix. This paper explains how the the DMRG++ code (Alvarez, 2009) has been extended to handle the non-local SU(2) symmetry in a model independent way. Improvements in CPU times compared to runs with only local symmetries are discussed for the one-orbital Hubbard model, and for a two-orbital Hubbard model for iron-based superconductors. The computational bottleneck of the algorithm and themore » use of shared memory parallelization are also addressed.« less

Support for the existence of invertible maps between electronic densities and non-analytic 1-body external potentials in non-relativistic time-dependent quantum mechanics

NASA Astrophysics Data System (ADS)

Mosquera, Martín A.

2017-10-01

Provided the initial state, the Runge-Gross theorem establishes that the time-dependent (TD) external potential of a system of non-relativistic electrons determines uniquely their TD electronic density, and vice versa (up to a constant in the potential). This theorem requires the TD external potential and density to be Taylor-expandable around the initial time of the propagation. This paper presents an extension without this restriction. Given the initial state of the system and evolution of the density due to some TD scalar potential, we show that a perturbative (not necessarily weak) TD potential that induces a non-zero divergence of the external force-density, inside a small spatial subset and immediately after the initial propagation time, will cause a change in the density within that subset, implying that the TD potential uniquely determines the TD density. In this proof, we assume unitary evolution of wavefunctions and first-order differentiability (which does not imply analyticity) in time of the internal and external force-densities, electronic density, current density, and their spatial derivatives over the small spatial subset and short time interval.

Towards time-dependent current-density-functional theory in the non-linear regime

NASA Astrophysics Data System (ADS)

Escartín, J. M.; Vincendon, M.; Romaniello, P.; Dinh, P. M.; Reinhard, P.-G.; Suraud, E.

2015-02-01

Time-Dependent Density-Functional Theory (TDDFT) is a well-established theoretical approach to describe and understand irradiation processes in clusters and molecules. However, within the so-called adiabatic local density approximation (ALDA) to the exchange-correlation (xc) potential, TDDFT can show insufficiencies, particularly in violently dynamical processes. This is because within ALDA the xc potential is instantaneous and is a local functional of the density, which means that this approximation neglects memory effects and long-range effects. A way to go beyond ALDA is to use Time-Dependent Current-Density-Functional Theory (TDCDFT), in which the basic quantity is the current density rather than the density as in TDDFT. This has been shown to offer an adequate account of dissipation in the linear domain when the Vignale-Kohn (VK) functional is used. Here, we go beyond the linear regime and we explore this formulation in the time domain. In this case, the equations become very involved making the computation out of reach; we hence propose an approximation to the VK functional which allows us to calculate the dynamics in real time and at the same time to keep most of the physics described by the VK functional. We apply this formulation to the calculation of the time-dependent dipole moment of Ca, Mg and Na2. Our results show trends similar to what was previously observed in model systems or within linear response. In the non-linear domain, our results show that relaxation times do not decrease with increasing deposited excitation energy, which sets some limitations to the practical use of TDCDFT in such a domain of excitations.

Towards time-dependent current-density-functional theory in the non-linear regime.

PubMed

Escartín, J M; Vincendon, M; Romaniello, P; Dinh, P M; Reinhard, P-G; Suraud, E

2015-02-28

Time-Dependent Density-Functional Theory (TDDFT) is a well-established theoretical approach to describe and understand irradiation processes in clusters and molecules. However, within the so-called adiabatic local density approximation (ALDA) to the exchange-correlation (xc) potential, TDDFT can show insufficiencies, particularly in violently dynamical processes. This is because within ALDA the xc potential is instantaneous and is a local functional of the density, which means that this approximation neglects memory effects and long-range effects. A way to go beyond ALDA is to use Time-Dependent Current-Density-Functional Theory (TDCDFT), in which the basic quantity is the current density rather than the density as in TDDFT. This has been shown to offer an adequate account of dissipation in the linear domain when the Vignale-Kohn (VK) functional is used. Here, we go beyond the linear regime and we explore this formulation in the time domain. In this case, the equations become very involved making the computation out of reach; we hence propose an approximation to the VK functional which allows us to calculate the dynamics in real time and at the same time to keep most of the physics described by the VK functional. We apply this formulation to the calculation of the time-dependent dipole moment of Ca, Mg and Na2. Our results show trends similar to what was previously observed in model systems or within linear response. In the non-linear domain, our results show that relaxation times do not decrease with increasing deposited excitation energy, which sets some limitations to the practical use of TDCDFT in such a domain of excitations.

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

PubMed

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

2014-11-01

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

The role of hydrodynamic stress on the phenotypic characteristics of single and binary biofilms of Pseudomonas fluorescens.

PubMed

Simões, M; Pereira, M O; Vieira, M J

2007-01-01

This study investigates the phenotype of turbulent (Re = 5,200) and laminar (Re = 2,000) flow-generated Pseudomonas fluorescens biofilms. Three P. fluorescens strains, the type strain ATCC 13525 and two strains isolated from an industrial processing plant, D3-348 and D3-350, were used throughout this study. The isolated strains were used to form single and binary biofilms. The biofilm physiology (metabolic activity, cellular density, mass, extracellular polymeric substances, structural characteristics and outer membrane proteins [OMP] expression) was compared. The results indicate that, for every situation, turbulent flow-generated biofilms were more active (p < 0.05), had more mass per cm(2) (p < 0.05), a higher cellular density (p < 0.05), distinct morphology, similar matrix proteins (p > 0.1) and identical (isolated strains -single and binary biofilms) and higher (type strain) matrix polysaccharides contents (p < 0.05) than laminar flow-generated biofilms. Flow-generated biofilms formed by the type strain revealed a considerably higher cellular density and amount of matrix polysaccharides than single and binary biofilms formed by the isolated strains (p < 0.05). Similar OMP expression was detected for the several single strains and for the binary situation, not dependent on the hydrodynamic conditions. Binary biofilms revealed an equal coexistence of the isolated strains with apparent neutral interactions. In summary, the biofilms formed by the type strain represent, apparently, the worst situation in a context of control. The results obtained clearly illustrate the importance of considering strain variation and hydrodynamics in biofilm development, and complement previous studies which have focused on physical aspects of structural and density differences.

Tight-binding approximations to time-dependent density functional theory — A fast approach for the calculation of electronically excited states

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

Rüger, Robert, E-mail: rueger@scm.com; Department of Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam; Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Linnéstr. 2, 04103 Leipzig

2016-05-14

We propose a new method of calculating electronically excited states that combines a density functional theory based ground state calculation with a linear response treatment that employs approximations used in the time-dependent density functional based tight binding (TD-DFTB) approach. The new method termed time-dependent density functional theory TD-DFT+TB does not rely on the DFTB parametrization and is therefore applicable to systems involving all combinations of elements. We show that the new method yields UV/Vis absorption spectra that are in excellent agreement with computationally much more expensive TD-DFT calculations. Errors in vertical excitation energies are reduced by a factor of twomore » compared to TD-DFTB.« less

Electric field induced optical gain of a hydrogenic impurity in a Cd{sub 0.8}Zn{sub 0.2}Se/ZnSe parabolic quantum dot

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

Jasmine, P. Christina Lily; Peter, A. John, E-mail: a.john.peter@gmail.com

The dependence of electric field on the electronic and optical properties is investigated in a Cd{sub 0.8}Zn{sub 0.2}Se/ZnSe quantum dot. The hydrogenic binding energy, in the presence of electric field, is calculated with the spatial confinement effect. The electric field dependent optical gain with the photon energy is found using compact density matrix method. The results show that the electric field has a great influence on the optical properties of II-VI semiconductor quantum dot.

Radiatively induced neutrino mass model with flavor dependent gauge symmetry

NASA Astrophysics Data System (ADS)

Lee, SangJong; Nomura, Takaaki; Okada, Hiroshi

2018-06-01

We study a radiative seesaw model at one-loop level with a flavor dependent gauge symmetry U(1) μ - τ, in which we consider bosonic dark matter. We also analyze the constraints from lepton flavor violations, muon g - 2, relic density of dark matter, and collider physics, and carry out numerical analysis to search for allowed parameter region which satisfy all the constraints and to investigate some predictions. Furthermore we find that a simple but adhoc hypothesis induces specific two zero texture with inverse mass matrix, which provides us several predictions such as a specific pattern of Dirac CP phase.

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.

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

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.

Localized tissue mineralization regulated by bone remodelling: A computational approach

PubMed Central

Decco, Oscar; Adams, George; Cook, Richard B.; García Aznar, José Manuel

2017-01-01

Bone is a living tissue whose main mechanical function is to provide stiffness, strength and protection to the body. Both stiffness and strength depend on the mineralization of the organic matrix, which is constantly being remodelled by the coordinated action of the bone multicellular units (BMUs). Due to the dynamics of both remodelling and mineralization, each sample of bone is composed of structural units (osteons in cortical and packets in cancellous bone) created at different times, therefore presenting different levels of mineral content. In this work, a computational model is used to understand the feedback between the remodelling and the mineralization processes under different load conditions and bone porosities. This model considers that osteoclasts primarily resorb those parts of bone closer to the surface, which are younger and less mineralized than older inner ones. Under equilibrium loads, results show that bone volumes with both the highest and the lowest levels of porosity (cancellous and cortical respectively) tend to develop higher levels of mineral content compared to volumes with intermediate porosity, thus presenting higher material densities. In good agreement with recent experimental measurements, a boomerang-like pattern emerges when plotting apparent density at the tissue level versus material density at the bone material level. Overload and disuse states are studied too, resulting in a translation of the apparent–material density curve. Numerical results are discussed pointing to potential clinical applications. PMID:28306746

Understanding the densification process of Bi2Sr2CaCu2O x round wires with overpressure processing and its effect on critical current density

NASA Astrophysics Data System (ADS)

Matras, M. R.; Jiang, J.; Larbalestier, D. C.; Hellstrom, E. E.

2016-10-01

Overpressure (OP) processing increases the critical current density ({{\\boldsymbol{J}}}{{C}}) of Bi2Sr2CaCu2O x (2212) round wires by shrinking the surrounding Ag matrix around the 2212 filaments, driving them close to full density and greatly increasing the 2212 grain connectivity. Indeed densification is vital for attaining the highest {{\\boldsymbol{J}}}{{C}}. Here, we investigate the time and temperature dependence of the wire densification. We find that the wire diameter decreases by 3.8 ± 0.3% after full heat treatment at 50 atm and 100 atm OP. At 50 atm OP pressure, the filaments start densifying above 700 °C and reach a 3.30 ± 0.07% smaller diameter after 2 h at 820 °C, which is below the melting point of 2212 powder. The densification is homogeneous and does not change the filament shape before melting. The growth of non-superconducting phases is observed at 820 °C, suggesting that time should be minimized at high temperature prior to melting the 2212 powder. Study of an open-ended 2.2 m long wire sample shows that full densification and the high OP {{\\boldsymbol{J}}}{{C}} ({{\\boldsymbol{J}}}{{C}} varies by about 3.1 times over the 2.2 m long wire) is reached about 1 m from the open ends, thus showing that coil-length wires can be protected from leaky seals by adding at least 1 m of sacrificial wire at each end.

Method for making a low density polyethylene waste form for safe disposal of low level radioactive material

DOEpatents

Colombo, P.; Kalb, P.D.

1984-06-05

In the method of the invention low density polyethylene pellets are mixed in a predetermined ratio with radioactive particulate material, then the mixture is fed through a screw-type extruder that melts the low density polyethylene under a predetermined pressure and temperature to form a homogeneous matrix that is extruded and separated into solid monolithic waste forms. The solid waste forms are adapted to be safely handled, stored for a short time, and safely disposed of in approved depositories.

Compressed Sensing for Chemistry

NASA Astrophysics Data System (ADS)

Sanders, Jacob Nathan

Many chemical applications, from spectroscopy to quantum chemistry, involve measuring or computing a large amount of data, and then compressing this data to retain the most chemically-relevant information. In contrast, compressed sensing is an emergent technique that makes it possible to measure or compute an amount of data that is roughly proportional to its information content. In particular, compressed sensing enables the recovery of a sparse quantity of information from significantly undersampled data by solving an ℓ 1-optimization problem. This thesis represents the application of compressed sensing to problems in chemistry. The first half of this thesis is about spectroscopy. Compressed sensing is used to accelerate the computation of vibrational and electronic spectra from real-time time-dependent density functional theory simulations. Using compressed sensing as a drop-in replacement for the discrete Fourier transform, well-resolved frequency spectra are obtained at one-fifth the typical simulation time and computational cost. The technique is generalized to multiple dimensions and applied to two-dimensional absorption spectroscopy using experimental data collected on atomic rubidium vapor. Finally, a related technique known as super-resolution is applied to open quantum systems to obtain realistic models of a protein environment, in the form of atomistic spectral densities, at lower computational cost. The second half of this thesis deals with matrices in quantum chemistry. It presents a new use of compressed sensing for more efficient matrix recovery whenever the calculation of individual matrix elements is the computational bottleneck. The technique is applied to the computation of the second-derivative Hessian matrices in electronic structure calculations to obtain the vibrational modes and frequencies of molecules. When applied to anthracene, this technique results in a threefold speed-up, with greater speed-ups possible for larger molecules. The implementation of the method in the Q-Chem commercial software package is described. Moreover, the method provides a general framework for bootstrapping cheap low-accuracy calculations in order to reduce the required number of expensive high-accuracy calculations.

Thermalization and revivals after a quantum quench in conformal field theory.

PubMed

Cardy, John

2014-06-06

We consider a quantum quench in a finite system of length L described by a 1+1-dimensional conformal field theory (CFT), of central charge c, from a state with finite energy density corresponding to an inverse temperature β≪L. For times t such that ℓ/2

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...

Resilience of bacterial quorum sensing against fluid flow

NASA Astrophysics Data System (ADS)

Emge, Philippe; Moeller, Jens; Jang, Hongchul; Rusconi, Roberto; Yawata, Yutaka; Stocker, Roman; Vogel, Viola

2016-09-01

Quorum sensing (QS) is a population-density dependent chemical process that enables bacteria to communicate based on the production, secretion and sensing of small inducer molecules. While recombinant constructs have been widely used to decipher the molecular details of QS, how those findings translate to natural QS systems has remained an open question. Here, we compare the activation of natural and synthetic Pseudomonas aeruginosa LasI/R QS systems in bacteria exposed to quiescent conditions and controlled flows. Quantification of QS-dependent GFP expression in suspended cultures and in surface-attached microcolonies revealed that QS onset in both systems was similar under quiescent conditions but markedly differed under flow. Moderate flow (Pe > 25) was sufficient to suppress LasI/R QS recombinantly expressed in Escherichia coli, whereas only high flow (Pe > 102) suppressed QS in wild-type P. aeruginosa. We suggest that this difference stems from the differential production of extracellular matrix and that the matrix confers resilience against moderate flow to QS in wild-type organisms. These results suggest that the expression of a biofilm matrix extends the environmental conditions under which QS-based cell-cell communication is effective and that findings from synthetic QS circuits cannot be directly translated to natural systems.

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

PubMed

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

2007-04-21

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

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

Optimum 3D Matrix Stiffness for Maintenance of Cancer Stem Cells Is Dependent on Tissue Origin of Cancer Cells

PubMed Central

Jabbari, Esmaiel; Sarvestani, Samaneh K.; Daneshian, Leily; Moeinzadeh, Seyedsina

2015-01-01

Introduction The growth and expression of cancer stem cells (CSCs) depend on many factors in the tumor microenvironment. The objective of this work was to investigate the effect of cancer cells’ tissue origin on the optimum matrix stiffness for CSC growth and marker expression in a model polyethylene glycol diacrylate (PEGDA) hydrogel without the interference of other factors in the microenvironment. Methods Human MCF7 and MDA-MB-231 breast carcinoma, HCT116 colorectal and AGS gastric carcinoma, and U2OS osteosarcoma cells were used. The cells were encapsulated in PEGDA gels with compressive moduli in the 2-70 kPa range and optimized cell seeding density of 0.6x106 cells/mL. Micropatterning was used to optimize the growth of encapsulated cells with respect to average tumorsphere size. The CSC sub-population of the encapsulated cells was characterized by cell number, tumorsphere size and number density, and mRNA expression of CSC markers. Results The optimum matrix stiffness for growth and marker expression of CSC sub-population of cancer cells was 5 kPa for breast MCF7 and MDA231, 25 kPa for colorectal HCT116 and gastric AGS, and 50 kPa for bone U2OS cells. Conjugation of a CD44 binding peptide to the gel stopped tumorsphere formation by cancer cells from different tissue origin. The expression of YAP/TAZ transcription factors by the encapsulated cancer cells was highest at the optimum stiffness indicating a link between the Hippo transducers and CSC growth. The optimum average tumorsphere size for CSC growth and marker expression was 50 μm. Conclusion The marker expression results suggest that the CSC sub-population of cancer cells resides within a niche with optimum stiffness which depends on the cancer cells’ tissue origin. PMID:26168187

Numerical time evolution of ETH spin chains by means of matrix product density operators

NASA Astrophysics Data System (ADS)

White, Christopher; Zaletel, Michael; Mong, Roger; Refael, Gil

We introduce a method for approximating density operators of 1D systems that, when combined with a standard framework for time evolution (TEBD), makes possible simulation of the dynamics of strongly thermalizing systems to arbitrary times. We demonstrate that the method works on both near-equilibrium initial states (Gibbs states with spatially varying temperatures) and far-from-equilibrium initial states, including quenches across phase transitions and pure states. This work was supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE \\x901144469 and by the Caltech IQIM, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore.

Density matrix renormalization group with efficient dynamical electron correlation through range separation

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

Hedegård, Erik Donovan, E-mail: erik.hedegard@phys.chem.ethz.ch; Knecht, Stefan; Reiher, Markus, E-mail: markus.reiher@phys.chem.ethz.ch

2015-06-14

We present a new hybrid multiconfigurational method based on the concept of range-separation that combines the density matrix renormalization group approach with density functional theory. This new method is designed for the simultaneous description of dynamical and static electron-correlation effects in multiconfigurational electronic structure problems.

Photoionization of Atoms and Ions: Application of Time-Dependent Response Method within the Density Functional Theory.

DTIC Science & Technology

1987-10-13

AD-A±95 686 PHOTOIONIZATION OF ATOMS AND IONS: APPLICATION OF III TIME-DEPENDENT RESPONSE..(U) NAVAL RESEARCH LAB WASHINGTON DC U GUPTA ET AL. 13 OCT...on revere if ncemy and idmntify by block number) FIELD GROUP SUBGROUP Photoionization Density functional Atoms Time dependent 1 S. (Continue on...reverse if necenary and identify by block numnbw) The photoionization cross-section of several atoms (AT, Xe, Rn, Cs) and ions (Ne-like Ar, H-like and Li

Breast Cancer Tissue Bioreactor for Direct Interrogation and Observation of Response to Antitumor Therapies

DTIC Science & Technology

2011-07-01

into the bioreactor . Cell lines were cultured in low density 3D matrigel conditions. Mammoshere formation is dependent upon a number of...epithelial cell culture systems grown under 3D cell culture conditions that allow for mammosphere or glandular mammary acinar development. Drug...assessed whether lowering the dose would still be affective as a extracellular matrix inhibitor. For 3D cell cultures , mammospheres were allowed to

Probabilistic low-rank factorization accelerates tensor network simulations of critical quantum many-body ground states.

PubMed

Kohn, Lucas; Tschirsich, Ferdinand; Keck, Maximilian; Plenio, Martin B; Tamascelli, Dario; Montangero, Simone

2018-01-01

We provide evidence that randomized low-rank factorization is a powerful tool for the determination of the ground-state properties of low-dimensional lattice Hamiltonians through tensor network techniques. In particular, we show that randomized matrix factorization outperforms truncated singular value decomposition based on state-of-the-art deterministic routines in time-evolving block decimation (TEBD)- and density matrix renormalization group (DMRG)-style simulations, even when the system under study gets close to a phase transition: We report linear speedups in the bond or local dimension of up to 24 times in quasi-two-dimensional cylindrical systems.

Probabilistic low-rank factorization accelerates tensor network simulations of critical quantum many-body ground states

NASA Astrophysics Data System (ADS)

Kohn, Lucas; Tschirsich, Ferdinand; Keck, Maximilian; Plenio, Martin B.; Tamascelli, Dario; Montangero, Simone

2018-01-01

We provide evidence that randomized low-rank factorization is a powerful tool for the determination of the ground-state properties of low-dimensional lattice Hamiltonians through tensor network techniques. In particular, we show that randomized matrix factorization outperforms truncated singular value decomposition based on state-of-the-art deterministic routines in time-evolving block decimation (TEBD)- and density matrix renormalization group (DMRG)-style simulations, even when the system under study gets close to a phase transition: We report linear speedups in the bond or local dimension of up to 24 times in quasi-two-dimensional cylindrical systems.

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

Vu-khanh, T.; Denault, J.

The effects of the conditions of the processing of PEEK/carbon prepregs and comingled fabric on the microstructure and mechanical characteristics of the resulting composites were investigated. Results showed that, in the comingled fabric system, the fiber/matrix adhesion depends on the molding temperature, the residence time at the melt temperature, and the cooling rate. Too high molding temperature resulted in degradation of the PEEK matrix, which affected the crystallization behavior of the composites, the fiber/matrix adhesion, and the matrix properties. This effect was most important in the case of comingled systems containing sized carbon fibers. 17 refs.

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.

Study of the effect of electron irradiation on the density of the activated sludge in aqueous solution

NASA Astrophysics Data System (ADS)

Kupchishin, A. I.; Niyazov, M. N.; Taipova, B. G.; Voronova, N. A.; Khodarina, N. N.

2018-01-01

Complex experimental studies on the effect of electron irradiation on the deposition rate of active sludge in aqueous systems by the optical method have been carried out. The obtained dependences of density (ρ) on time (t) are of the same nature for different radiation sources. The experimental curves of the dependence of the active sludge density on time are satisfactorily described by an exponential model.

Corrosion susceptibility of steel drums containing cemented intermediate level nuclear wastes

NASA Astrophysics Data System (ADS)

Duffó, Gustavo S.; Farina, Silvia B.; Schulz, Fátima M.; Marotta, Francesca

2010-10-01

Cementation processes are used as immobilization techniques for low or intermediate level radioactive waste for economical and safety reasons and for being a simple operation. In particular, ion-exchange resins commonly used for purification of radioactive liquid waste from nuclear reactors are immobilized before being stored to improve the leach resistance of the waste matrix and to maintain mechanical stability. Combustible solid radioactive waste can be incinerated and the resulting ashes can also be immobilized before storage. The immobilized resins and ashes are then contained in steel drums that may undergo corrosion depending on the presence of certain contaminants. The work described in this paper was aimed at evaluating the corrosion susceptibility of steel drums in contact with cemented ion-exchange resins and incineration ashes containing different concentrations of aggressive species (mostly chloride and sulphate ions). A special type of specimen was designed to simulate the cemented waste in the drum. The evolution of the corrosion potential and the corrosion current density of the steel, as well as the electrical resistivity of the matrix were monitored over a time period of 1 year. The results show the deleterious effect of chloride on the expected lifespan of the waste containers.

Linear absorptive dielectrics

NASA Astrophysics Data System (ADS)

Tip, A.

1998-06-01

Starting from Maxwell's equations for a linear, nonconducting, absorptive, and dispersive medium, characterized by the constitutive equations D(x,t)=ɛ1(x)E(x,t)+∫t-∞dsχ(x,t-s)E(x,s) and H(x,t)=B(x,t), a unitary time evolution and canonical formalism is obtained. Given the complex, coordinate, and frequency-dependent, electric permeability ɛ(x,ω), no further assumptions are made. The procedure leads to a proper definition of band gaps in the periodic case and a new continuity equation for energy flow. An S-matrix formalism for scattering from lossy objects is presented in full detail. A quantized version of the formalism is derived and applied to the generation of Čerenkov and transition radiation as well as atomic decay. The last case suggests a useful generalization of the density of states to the absorptive situation.

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

Yu, Chongqi; Harbich, Wolfgang; Sementa, Luca

Ligand-protected Au clusters are non-bleaching fluorescence markers in bio- and medical applications. We show that their fluorescence is an intrinsic property of the Au cluster itself. We find a very intense and sharp fluorescence peak located at λ =739.2 nm (1.68 eV) for Au20 clusters in a Ne matrix held at 6 K. The fluorescence reflects the HOMO-LUMO diabatic bandgap of the cluster. The cluster shows a very rich absorption fine structure reminiscent of well defined molecule-like quantum levels. These levels are resolved since Au20 has only one stable isomer (tetrahedral), therefore our sample is mono-disperse in cluster size andmore » conformation. Density-functional theory (DFT) and time-dependent DFT calculations clarify the nature of optical absorptionand predict both main absorption peaks and intrinsic fluorescence in good agreement with experiment.« less

The Liouville equation for flavour evolution of neutrinos and neutrino wave packets

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

Hansen, Rasmus Sloth Lundkvist; Smirnov, Alexei Yu., E-mail: rasmus@mpi-hd.mpg.de, E-mail: smirnov@mpi-hd.mpg.de

We consider several aspects related to the form, derivation and applications of the Liouville equation (LE) for flavour evolution of neutrinos. To take into account the quantum nature of neutrinos we derive the evolution equation for the matrix of densities using wave packets instead of Wigner functions. The obtained equation differs from the standard LE by an additional term which is proportional to the difference of group velocities. We show that this term describes loss of the propagation coherence in the system. In absence of momentum changing collisions, the LE can be reduced to a single derivative equation over amore » trajectory coordinate. Additional time and spatial dependence may stem from initial (production) conditions. The transition from single neutrino evolution to the evolution of a neutrino gas is considered.« less

Modeling ultrafast solvated electronic dynamics using time-dependent density functional theory and polarizable continuum model.

PubMed

Liang, Wenkel; Chapman, Craig T; Ding, Feizhi; Li, Xiaosong

2012-03-01

A first-principles solvated electronic dynamics method is introduced. Solvent electronic degrees of freedom are coupled to the time-dependent electronic density of a solute molecule by means of the implicit reaction field method, and the entire electronic system is propagated in time. This real-time time-dependent approach, incorporating the polarizable continuum solvation model, is shown to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. © 2012 American Chemical Society

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.

Spectral analysis of finite-time correlation matrices near equilibrium phase transitions

NASA Astrophysics Data System (ADS)

Vinayak; Prosen, T.; Buča, B.; Seligman, T. H.

2014-10-01

We study spectral densities for systems on lattices, which, at a phase transition display, power-law spatial correlations. Constructing the spatial correlation matrix we prove that its eigenvalue density shows a power law that can be derived from the spatial correlations. In practice time series are short in the sense that they are either not stationary over long time intervals or not available over long time intervals. Also we usually do not have time series for all variables available. We shall make numerical simulations on a two-dimensional Ising model with the usual Metropolis algorithm as time evolution. Using all spins on a grid with periodic boundary conditions we find a power law, that is, for large grids, compatible with the analytic result. We still find a power law even if we choose a fairly small subset of grid points at random. The exponents of the power laws will be smaller under such circumstances. For very short time series leading to singular correlation matrices we use a recently developed technique to lift the degeneracy at zero in the spectrum and find a significant signature of critical behavior even in this case as compared to high temperature results which tend to those of random matrix models.

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.

SALSA3D: A Tomographic Model of Compressional Wave Slowness in the Earth’s Mantle for Improved Travel-Time Prediction and Travel-Time Prediction Uncertainty

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

Ballard, Sanford; Hipp, James R.; Begnaud, Michael L.

The task of monitoring the Earth for nuclear explosions relies heavily on seismic data to detect, locate, and characterize suspected nuclear tests. In this study, motivated by the need to locate suspected explosions as accurately and precisely as possible, we developed a tomographic model of the compressional wave slowness in the Earth’s mantle with primary focus on the accuracy and precision of travel-time predictions for P and Pn ray paths through the model. Path-dependent travel-time prediction uncertainties are obtained by computing the full 3D model covariance matrix and then integrating slowness variance and covariance along ray paths from source tomore » receiver. Path-dependent travel-time prediction uncertainties reflect the amount of seismic data that was used in tomography with very low values for paths represented by abundant data in the tomographic data set and very high values for paths through portions of the model that were poorly sampled by the tomography data set. The pattern of travel-time prediction uncertainty is a direct result of the off-diagonal terms of the model covariance matrix and underscores the importance of incorporating the full model covariance matrix in the determination of travel-time prediction uncertainty. In addition, the computed pattern of uncertainty differs significantly from that of 1D distance-dependent travel-time uncertainties computed using traditional methods, which are only appropriate for use with travel times computed through 1D velocity models.« less

SALSA3D: A Tomographic Model of Compressional Wave Slowness in the Earth’s Mantle for Improved Travel-Time Prediction and Travel-Time Prediction Uncertainty

DOE PAGES

Ballard, Sanford; Hipp, James R.; Begnaud, Michael L.; ...

2016-10-11

The task of monitoring the Earth for nuclear explosions relies heavily on seismic data to detect, locate, and characterize suspected nuclear tests. In this study, motivated by the need to locate suspected explosions as accurately and precisely as possible, we developed a tomographic model of the compressional wave slowness in the Earth’s mantle with primary focus on the accuracy and precision of travel-time predictions for P and Pn ray paths through the model. Path-dependent travel-time prediction uncertainties are obtained by computing the full 3D model covariance matrix and then integrating slowness variance and covariance along ray paths from source tomore » receiver. Path-dependent travel-time prediction uncertainties reflect the amount of seismic data that was used in tomography with very low values for paths represented by abundant data in the tomographic data set and very high values for paths through portions of the model that were poorly sampled by the tomography data set. The pattern of travel-time prediction uncertainty is a direct result of the off-diagonal terms of the model covariance matrix and underscores the importance of incorporating the full model covariance matrix in the determination of travel-time prediction uncertainty. In addition, the computed pattern of uncertainty differs significantly from that of 1D distance-dependent travel-time uncertainties computed using traditional methods, which are only appropriate for use with travel times computed through 1D velocity models.« less

Enhanced superconductivity in the high pressure phase of SnAs studied from first principles

NASA Astrophysics Data System (ADS)

Sreenivasa Reddy, P. V.; Kanchana, V.; Millichamp, T. E.; Vaitheeswaran, G.; Dugdale, S. B.

2017-01-01

First principles calculations are performed using density functional theory and density functional perturbation theory for SnAs. Total energy calculations show the first order phase transition from an NaCl structure to a CsCl one at around 37 GPa, which is also confirmed from enthalpy calculations and agrees well with experimental work. Calculations of the phonon structure and hence the electron-phonon coupling, λep, and superconducting transition temperature, Tc, across the phase diagram are performed. These calculations give an ambient pressure Tc, in the NaCl structure, of 3.08 K, in good agreement with experiment whilst at the transition pressure, in the CsCl structure, a drastically increased value of Tc = 12.2 K is found. Calculations also show a dramatic increase in the electronic density of states at this pressure. The lowest energy acoustic phonon branch in each structure also demonstrates some softening effects. Electronic structure calculations of the Fermi surface in both phases are presented for the first time as well as further calculations of the generalised susceptibility with the inclusion of matrix elements. These calculations indicate that the softening is not derived from Fermi surface nesting and it is concluded to be due to a wavevector-dependent enhancement of the electron-phonon coupling.

Study of thermal annealing effect on Bragg gratings photo-inscribed in step-index polymer optical fibers

NASA Astrophysics Data System (ADS)

Hu, X.; Kinet, D.; Mégret, P.; Caucheteur, C.

2016-04-01

In this paper, both non-annealed and annealed trans-4-stilbenemethanol-doped step-index polymer optical fibers were photo-inscribed using a 325 nm HeCd laser with two different beam power densities reaching the fiber core. In the high density regime where 637 mW/mm2 are used, the grating reflectivity is stable over time after the photo-writing process but the reflected spectrum is of limited quality, as the grating physical length is limited to 1.2 mm. To produce longer gratings exhibiting more interesting spectral features, the beam is enlarged to 6 mm, decreasing the power density to 127 mW/mm2. In this second regime, the grating reflectivity is not stable after the inscription process but tends to decay for both kinds of fibers. A fortunate property in this case results from the possibility to fully recover the initial reflectivity using a post-inscription thermal annealing, where the gratings are annealed at 80 °C during 2 days. The observed evolutions for both regimes are attributed to the behavior of the excited intermediate states between the excited singlet and the ground singlet state of trans- and cis-isomers as well as the temperature-dependent glassy polymer matrix.

Rate-dependent behavior of the amorphous phase of spider dragline silk.

PubMed

Patil, Sandeep P; Markert, Bernd; Gräter, Frauke

2014-06-03

The time-dependent stress-strain behavior of spider dragline silk was already observed decades ago, and has been attributed to the disordered sequences in silk proteins, which compose the soft amorphous matrix. However, the actual molecular origin and magnitude of internal friction within the amorphous matrix has remained inaccessible, because experimentally decomposing the mechanical response of the amorphous matrix from the embedded crystalline units is challenging. Here, we used atomistic molecular dynamics simulations to obtain friction forces for the relative sliding of peptide chains of Araneus diadematus spider silk within bundles of these chains as a representative unit of the amorphous matrix in silk fibers. We computed the friction coefficient and coefficient of viscosity of the amorphous phase to be in the order of 10(-6) Ns/m and 10(4) Ns/m(2), respectively, by extrapolating our simulation data to the viscous limit. Finally, we used a finite element method for the amorphous phase, solely based on parameters derived from molecular dynamics simulations including the newly determined coefficient of viscosity. With this model the time scales of stress relaxation, creep, and hysteresis were assessed, and found to be in line with the macroscopic time-dependent response of silk fibers. Our results suggest the amorphous phase to be the primary source of viscosity in silk and open up the avenue for finite element method studies of silk fiber mechanics including viscous effects. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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.

Charging in the ac Conductance of a Double Barrier Resonant Tunneling Structure

NASA Technical Reports Server (NTRS)

Anantram, M. P.; Saini, Subhash (Technical Monitor)

1998-01-01

There have been many studies of the linear response ac conductance of a double barrier resonant tunneling structure (DBRTS), both at zero and finite dc biases. While these studies are important, they fail to self consistently include the effect of the time dependent charge density in the well. In this paper, we calculate the ac conductance at both zero and finite do biases by including the effect of the time dependent charge density in the well in a self consistent manner. The charge density in the well contributes to both the flow of displacement currents in the contacts and the time dependent potential in the well. We find that including these effects can make a significant difference to the ac conductance and the total ac current is not equal to the simple average of the non-selfconsistently calculated conduction currents in the two contacts. This is illustrated by comparing the results obtained with and without the effect of the time dependent charge density included correctly. Some possible experimental scenarios to observe these effects are suggested.

Nonequilibrium evolution of scalar fields in FRW cosmologies

NASA Astrophysics Data System (ADS)

Boyanovsky, D.; de Vega, H. J.; Holman, R.

1994-03-01

We derive the effective equations for the out of equilibrium time evolution of the order parameter and the fluctuations of a scalar field theory in spatially flat FRW cosmologies. The calculation is performed both to one loop and in a nonperturbative, self-consistent Hartree approximation. The method consists of evolving an initial functional thermal density matrix in time and is suitable for studying phase transitions out of equilibrium. The renormalization aspects are studied in detail and we find that the counterterms depend on the initial state. We investigate the high temperature expansion and show that it breaks down at long times. We also obtain the time evolution of the initial Boltzmann distribution functions, and argue that to one-loop order or in the Hartree approximation the time evolved state is a ``squeezed'' state. We illustrate the departure from thermal equilibrium by numerically studying the case of a free massive scalar field in de Sitter and radiation-dominated cosmologies. It is found that a suitably defined nonequilibrium entropy per mode increases linearly with comoving time in a de Sitter cosmology, whereas it is not a monotonically increasing function in the radiation-dominated case.

Unconventional fermionic pairing states in a monochromatically tilted optical lattice

DOE PAGES

Nocera, Alberto; Polkovnikov, Anatoli; Feiguin, Adrian E.

2017-02-01

We study the one-dimensional attractive fermionic Hubbard model under the influence of periodic driving with the time-dependent density matrix renormalization group method. We show that the system can be driven into an unconventional pairing state characterized by a condensate made of Cooper pairs with a finite center-of-mass momentum similar to a Fulde-Ferrell state. We obtain results both in the laboratory and the rotating reference frames demonstrating that the momentum of the condensate can be finely tuned by changing the ratio between the amplitude and the frequency of the driving. In particular, by quenching this ratio to the value corresponding tomore » suppression of the tunneling and the Coulomb interaction strength to zero, we are able to “freeze” the condensate. We finally study the effects of different initial conditions and compare our numerical results to those obtained from a time-independent Floquet theory in the large frequency regime. Lastly, our work offers the possibility of engineering and controlling unconventional pairing states in fermionic condensates.« less

Adiabatic perturbation theory of electronic stopping in insulators

DOE PAGES

Horsfield, Andrew P.; Lim, Anthony; Foulkes, W. M. C.; ...

2016-06-02

A model able to explain the complicated structure of electronic stopping at low velocities in insulating materials is presented. It is shown to be in good agreement with results obtained from time-dependent density-functional theory for the stopping of a channeling Si atom in a Si crystal. If we define the repeat frequency f=v/λ, where λ is the periodic repeat length of the crystal along the direction the channeling atom is traveling, and v is the velocity of the channeling atom, we find that electrons experience a perturbing force that varies in time at integer multiples l of f. This enablesmore » electronic excitations at low atom velocity, but their contributions diminish rapidly with increasing values of l. The expressions for stopping power are derived using adiabatic perturbation theory for many-electron systems, and they are then specialized to the case of independent electrons. Lastly, a simple model for the nonadiabatic matrix elements is described, along with the procedure for determining its parameters.« less

Periodic matrix models for seasonal dynamics of structured populations with application to a seabird population.

PubMed

Cushing, J M; Henson, Shandelle M

2018-02-03

For structured populations with an annual breeding season, life-stage interactions and behavioral tactics may occur on a faster time scale than that of population dynamics. Motivated by recent field studies of the effect of rising sea surface temperature (SST) on within-breeding-season behaviors in colonial seabirds, we formulate and analyze a general class of discrete-time matrix models designed to account for changes in behavioral tactics within the breeding season and their dynamic consequences at the population level across breeding seasons. As a specific example, we focus on egg cannibalism and the daily reproductive synchrony observed in seabirds. Using the model, we investigate circumstances under which these life history tactics can be beneficial or non-beneficial at the population level in light of the expected continued rise in SST. Using bifurcation theoretic techniques, we study the nature of non-extinction, seasonal cycles as a function of environmental resource availability as they are created upon destabilization of the extinction state. Of particular interest are backward bifurcations in that they typically create strong Allee effects in population models which, in turn, lead to the benefit of possible (initial condition dependent) survival in adverse environments. We find that positive density effects (component Allee effects) due to increased adult survival from cannibalism and the propensity of females to synchronize daily egg laying can produce a strong Allee effect due to a backward bifurcation.

The degree and nature of radiation damage in zircon observed by 29Si nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Farnan, I.; Salje, E. K. H.

2001-02-01

A quantitative analysis of 29Si nuclear magnetic resonance spectra of radiation damaged, natural zircons showed that the local structure in crystalline and amorphous regions depend explicitly on radiation dose. Nonpercolating amorphous islands of high density "glass" within the crystalline matrix show a low interconnectivity of SiO4 tetrahedra. This structural state is quite different from that of the high dose, percolating regions of low density glass with more polymerised tetrahedra. A continuous nonlinear dose dependence between the high and low density glass states is reported. A continuous evolution of the local structure of the crystalline phase up to the percolation point is also reported. No phase separation into binary oxides was observed. The total number of permanently displaced atoms per α-recoil event is ˜3800 atoms for low radiation doses and decreases to ˜2000 atoms for 10×1018 α events/g. No indication of partitioning of paramagnetic impurities between crystalline and amorphous regions was found for these natural zircons. The amorphous fractions of the metamict zircons were determined as a function of their accumulated radiation dose. These values coincide closely with those recently determined by x-ray diffraction studies. They are much greater than previously assumed based on density measurements. The dose dependence is consistent with the concept of direct impact amorphization in the atomic cascade following an α-recoil event.

Study of decoherence in a system of superconducting flux-qubits interacting with an ensemble of electrons

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

Reboiro, M., E-mail: reboiro@fisica.unlp.edu.ar; Civitarese, O., E-mail: osvaldo.civitarese@fisica.unlp.edu.ar; Ramírez, R.

2017-03-15

The degree of coherence in a hybrid system composed of superconducting flux-qubits and an electron ensemble is analysed. Both, the interactions among the electrons and among the superconducting flux-qubits are taken into account. The time evolution of the hybrid system is solved exactly, and discussed in terms of the reduced density matrix of each subsystem. It is seen that the inclusion of a line width, for the electrons and for the superconducting flux-qubits, influences the pattern of spin-squeezing and the coherence of the superconducting flux qubits. - Highlights: • The degree of coherence in a hybrid system, composed of superconductingmore » flux qubits and an electron ensemble, is analysed. • The time evolution of the hybrid system is solved exactly and discussed in terms of the reduced density matrix of each subsystem. • It is shown that the initial state of the system evolves to a stationary squeezed state.« less

Cortical Matrix Mineral Density Measured Non-invasively in Pre- and Postmenopausal Women and a Woman with Vitamin D Dependent Rickets.

PubMed

Chiang, Cherie Y; Zebaze, Roger; Wang, Xiao-Fang; Ghasem-Zadeh, Ali; Zajac, Jeffrey D; Seeman, Ego

2018-02-28

Reduced bone mineral density (BMD) may be due to reduced mineralized bone matrix volume, incomplete secondary mineralization or reduced primary mineralization. As bone biopsy is invasive, we hypothesized that non-invasive image acquisition at high resolution can accurately quantify matrix mineral density (MMD). Quantification of MMD was confined to voxels attenuation photons above 80% of that produced by fully mineralized bone matrix because attenuation at this level is due to variation in mineralization not porosity. To assess accuracy, 9 cadaveric distal radii were imaged at a voxel size of 82 microns using high resolution peripheral quantitative computed tomography (HR-pQCT, XtremeCT, Scanco Medical AG, Switzerland) and compared with VivaCT 40 (µCT) at 19 microns voxel size. Associations between MMD and porosity were studied in 94 heathy vitamin D replete pre-menopausal, 77 post-menopausal women, and in a 27 year-old woman with vitamin-D Dependent Rickets (VDDR). Microstructure and MMD were quantified using StrAx (StraxCorp, Melbourne, Australia). MMD measured by HR-pQCT and µCT correlated (R = 0.87; p <0.0001). The precision error for MMD was 2.43%. Cortical porosity and MMD were associated with age (r 2  = 0.5 and - 0.4 respectively) and correlated inversely in pre- and post-menopausal women (both r 2  = 0.9, all p < 0.001). Porosity was higher, and MMD was lower, in post- than in pre-menopausal women (porosity 40.3% ± 7.0 versus 34.7% ± 3.5 respectively, MMD 65.4% ± 1.8 versus 66.6% ± 1.4 respectively, both p < 0.001). In the woman with VDDR, MMD was 5.6 SD lower, and porosity was 5.6 SD higher, than the respective trait means in premenopausal women. BMD was reduced (Z scores femoral neck - 4.3 SD, lumbar spine - 3.8 SD). Low radiation HR-pQCT may facilitate non-invasive quantification of bone's MMD and microstructure in health, disease and during treatment. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Horizontal Trends in Larval Fish Diversity and Abundance Along an Ocean-Estuarine Gradient on the Northern KwaZulu-Natal Coast, South Africa

NASA Astrophysics Data System (ADS)

Harris, S. A.; Cyrus, D. P.; Beckley, L. E.

2001-08-01

The structure of the larval fish assemblages along an ocean-estuarine gradient in the St Lucia region on the northern KwaZulu-Natal coast of South Africa was examined using a combination of univariate, distributional and multivariate techniques. The data was comprised of a full annual set of ichthyoplankton samples taken from three types of environment: nearshore coastal waters, surf zone and within the St Lucia Estuary itself. The mean monthly densities of each species in each environment were used in the species matrix, and the mean monthly values of salinity, temperature and turbidity were used in the physical variables matrix. The mean species diversity and eveness index was significantly higher in the nearshore waters than the surf zone and estuary. The patterns of relative species abundances in each environment (K-dominance curves) showed that the estuarine environment was dominated by a few species in large numbers, the surf zone was intermediate, and the nearshore coast was the most diverse. Classification and multidimensional scaling (MDS) ordination analyses of larval fish densities grouped together into three main clusters based on the three different environments. The species similarity matrix (inverse analysis) clustered into four groups at the 10% similarity level. The MDS analysis of the same matrix showed that the groups separated out more or less according to the type of environment they occur in, and hence the level of estuarine dependence of the various species. Species belonging to each assemblage showed similarities with regards to their reproduction modes and/or preference to a particular physical condition. Some species were restricted to one environment, whilst others were common to two or all three environments. The occurrence of partially estuarine-dependent species in all three environments suggests that ocean-estuarine coupling is an important process for the recruitment success of these species. The ' best fitting ' physical variable which explained the larval fish community patterns was turbidity on its own, with the relationship of larval densities to the physical variables being species-specific. The present study indicates that a number of factors must play a role in determining the structure and composition of larval fish assemblages occurring in different types of environments along an ocean-estuarine gradient. It is suggested that these distinct assemblages might be considered indicators for the different environments which they inhabit.

Functional differentiability in time-dependent quantum mechanics.

PubMed

Penz, Markus; Ruggenthaler, Michael

2015-03-28

In this work, we investigate the functional differentiability of the time-dependent many-body wave function and of derived quantities with respect to time-dependent potentials. For properly chosen Banach spaces of potentials and wave functions, Fréchet differentiability is proven. From this follows an estimate for the difference of two solutions to the time-dependent Schrödinger equation that evolve under the influence of different potentials. Such results can be applied directly to the one-particle density and to bounded operators, and present a rigorous formulation of non-equilibrium linear-response theory where the usual Lehmann representation of the linear-response kernel is not valid. Further, the Fréchet differentiability of the wave function provides a new route towards proving basic properties of time-dependent density-functional theory.

Dependence of two-proton radioactivity on nuclear pairing models

NASA Astrophysics Data System (ADS)

Oishi, Tomohiro; Kortelainen, Markus; Pastore, Alessandro

2017-10-01

Sensitivity of two-proton emitting decay to nuclear pairing correlation is discussed within a time-dependent three-body model. We focus on the 6Be nucleus assuming α +p +p configuration, and its decay process is described as a time evolution of the three-body resonance state. For a proton-proton subsystem, a schematic density-dependent contact (SDDC) pairing model is employed. From the time-dependent calculation, we observed the exponential decay rule of a two-proton emission. It is shown that the density dependence does not play a major role in determining the decay width, which can be controlled only by the asymptotic strength of the pairing interaction. This asymptotic pairing sensitivity can be understood in terms of the dynamics of the wave function driven by the three-body Hamiltonian, by monitoring the time-dependent density distribution. With this simple SDDC pairing model, there remains an impossible trinity problem: it cannot simultaneously reproduce the empirical Q value, decay width, and the nucleon-nucleon scattering length. This problem suggests that a further sophistication of the theoretical pairing model is necessary, utilizing the two-proton radioactivity data as the reference quantities.

Convergence of moment expansions for expectation values with embedded random matrix ensembles and quantum chaos

NASA Astrophysics Data System (ADS)

Kota, V. K. B.

2003-07-01

Smoothed forms for expectation values < K> E of positive definite operators K follow from the K-density moments either directly or in many other ways each giving a series expansion (involving polynomials in E). In large spectroscopic spaces one has to partition the many particle spaces into subspaces. Partitioning leads to new expansions for expectation values. It is shown that all the expansions converge to compact forms depending on the nature of the operator K and the operation of embedded random matrix ensembles and quantum chaos in many particle spaces. Explicit results are given for occupancies < ni> E, spin-cutoff factors < JZ2> E and strength sums < O†O> E, where O is a one-body transition operator.

Effective Thermal Conductivity of Spherical Particulate Nanocomposites: Comparison with Theoretical Models, Monte Carlo Simulations and Experiments

NASA Astrophysics Data System (ADS)

Machrafi, Hatim; Lebon, Georgy

2014-11-01

The purpose of this work is to study heat conduction in systems that are composed out of spherical micro-and nanoparticles dispersed in a bulk matrix. Special emphasis will be put on the dependence of the effective heat conductivity on various selected parameters as dimension and density of particles, interface interaction with the matrix. This is achieved by combining the effective medium approximation and extended irreversible thermodynamics, whose main feature is to elevate the heat flux vector to the status of independent variable. The model is illustrated by three examples: Silicium-Germanium, Silica-epoxy-resin and Copper-Silicium systems. Predictions of our model are in good agreement with other theoretical models, Monte-Carlo simulations and experimental data.

Volkov basis for simulation of interaction of strong laser pulses and solids

NASA Astrophysics Data System (ADS)

Kidd, Daniel; Covington, Cody; Li, Yonghui; Varga, Kálmán

2018-01-01

An efficient and accurate basis comprised of Volkov states is implemented and tested for time-dependent simulations of interactions between strong laser pulses and crystalline solids. The Volkov states are eigenstates of the free electron Hamiltonian in an electromagnetic field and analytically represent the rapidly oscillating time-dependence of the orbitals, allowing significantly faster time propagation than conventional approaches. The Volkov approach can be readily implemented in plane-wave codes by multiplying the potential energy matrix elements with a simple time-dependent phase factor.

Modeling the Elastic Modulus of 2D Woven CVI SiC Composites

NASA Technical Reports Server (NTRS)

Morscher, Gregory N.

2006-01-01

The use of fiber, interphase, CVI SiC minicomposites as structural elements for 2D-woven SiC fiber reinforced chemically vapor infiltrated (CVI) SiC matrix composites is demonstrated to be a viable approach to model the elastic modulus of these composite systems when tensile loaded in an orthogonal direction. The 0deg (loading direction) and 90deg (perpendicular to loading direction) oriented minicomposites as well as the open porosity and excess SiC associated with CVI SiC composites were all modeled as parallel elements using simple Rule of Mixtures techniques. Excellent agreement for a variety of 2D woven Hi-Nicalon(TradeMark) fiber-reinforced and Sylramic-iBN reinforced CVI SiC matrix composites that differed in numbers of plies, constituent content, thickness, density, and number of woven tows in either direction (i.e, balanced weaves versus unbalanced weaves) was achieved. It was found that elastic modulus was not only dependent on constituent content, but also the degree to which 90deg minicomposites carried load. This depended on the degree of interaction between 90deg and 0deg minicomposites which was quantified to some extent by composite density. The relationships developed here for elastic modulus only necessitated the knowledge of the fractional contents of fiber, interphase and CVI SiC as well as the tow size and shape. It was concluded that such relationships are fairly robust for orthogonally loaded 2D woven CVI SiC composite system and can be implemented by ceramic matrix composite component modelers and designers for modeling the local stiffness in simple or complex parts fabricated with variable constituent contents.

Functional Brain Networks: Does the Choice of Dependency Estimator and Binarization Method Matter?

NASA Astrophysics Data System (ADS)

Jalili, Mahdi

2016-07-01

The human brain can be modelled as a complex networked structure with brain regions as individual nodes and their anatomical/functional links as edges. Functional brain networks are constructed by first extracting weighted connectivity matrices, and then binarizing them to minimize the noise level. Different methods have been used to estimate the dependency values between the nodes and to obtain a binary network from a weighted connectivity matrix. In this work we study topological properties of EEG-based functional networks in Alzheimer’s Disease (AD). To estimate the connectivity strength between two time series, we use Pearson correlation, coherence, phase order parameter and synchronization likelihood. In order to binarize the weighted connectivity matrices, we use Minimum Spanning Tree (MST), Minimum Connected Component (MCC), uniform threshold and density-preserving methods. We find that the detected AD-related abnormalities highly depend on the methods used for dependency estimation and binarization. Topological properties of networks constructed using coherence method and MCC binarization show more significant differences between AD and healthy subjects than the other methods. These results might explain contradictory results reported in the literature for network properties specific to AD symptoms. The analysis method should be seriously taken into account in the interpretation of network-based analysis of brain signals.

A potential application to the study of microscopic energy deposition in a solid by means of heavy charged-particle induced photochromic alterations in a tissue-equivalent matrix

NASA Astrophysics Data System (ADS)

Emfietzoglou, D.; Moscovitch, M.

1999-01-01

A theoretical study was carried out to investigate the feasibility of using the radiation-induced colour decay of photochromic molecules embedded in a polymer matrix as a probe for studying the microscopic energy deposition of heavy charged particles (HCPs) in a tissue-equivalent solid. The theoretical treatment makes use of the radial dose distribution function as derived from gas-phase physics, together with the effects of the increase in temperature and of matrix degradation on the colour-decay kinetics of the photochromic molecules, according to empirical models derived for the solid state. Bearing in mind the non-stochastic nature of the model, the use of gas-phase physics at the level of radiation interaction, and the fact that some empirical quantities used have been established macroscopically, all factors which signify that extra caution is required in the interpretation of the results, it is shown that when the optimum information retrieval time (after track formation) is considered the technique may be able to resolve differences in the energy deposition pattern by different HCPs in the nanometre range (1-10 nm; material's mass density ) from the track axis. Most importantly, though, the present study aims to erect a theoretical framework for the possible application of the technique and to highlight those aspects which are likely to be critical to its practical usage, such as particle type and energy range, and spatial scale and magnitude of the expected effect together with its dependence on time, the physical characteristics of the matrix, and the kinetic behaviour of the type of photochromic molecule studied. Furthermore, it establishes a rationale for interpreting the experimentally observed (if available) colour changes in the HCP track in terms of the microscopic distribution of energy deposition in it.

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.

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.

Influence of density and environmental factors on decomposition kinetics of amorphous polylactide - Reactive molecular dynamics studies.

PubMed

Mlyniec, A; Ekiert, M; Morawska-Chochol, A; Uhl, T

2016-06-01

In this work, we investigate the influence of the surrounding environment and the initial density on the decomposition kinetics of polylactide (PLA). The decomposition of the amorphous PLA was investigated by means of reactive molecular dynamics simulations. A computational model simulates the decomposition of PLA polymer inside the bulk, due to the assumed lack of removal of reaction products from the polymer matrix. We tracked the temperature dependency of the water and carbon monoxide production to extract the activation energy of thermal decomposition of PLA. We found that an increased density results in decreased activation energy of decomposition by about 50%. Moreover, initiation of decomposition of the amorphous PLA is followed by a rapid decline in activation energy caused by reaction products which accelerates the hydrolysis of esters. The addition of water molecules decreases initial energy of activation as well as accelerates the decomposition process. Additionally, we have investigated the dependency of density on external loading. Comparison of pressures needed to obtain assumed densities shows that this relationship is bilinear and the slope changes around a density equal to 1.3g/cm(3). The conducted analyses provide an insight into the thermal decomposition process of the amorphous phase of PLA, which is particularly susceptible to decomposition in amorphous and semi-crystalline PLA polymers. Copyright © 2016 Elsevier Inc. All rights reserved.

Disentangling density-dependent dynamics using full annual cycle models and Bayesian model weight updating

USGS Publications Warehouse

Robinson, Orin J.; McGowan, Conor P.; Devers, Patrick K.

2017-01-01

Density dependence regulates populations of many species across all taxonomic groups. Understanding density dependence is vital for predicting the effects of climate, habitat loss and/or management actions on wild populations. Migratory species likely experience seasonal changes in the relative influence of density dependence on population processes such as survival and recruitment throughout the annual cycle. These effects must be accounted for when characterizing migratory populations via population models.To evaluate effects of density on seasonal survival and recruitment of a migratory species, we used an existing full annual cycle model framework for American black ducks Anas rubripes, and tested different density effects (including no effects) on survival and recruitment. We then used a Bayesian model weight updating routine to determine which population model best fit observed breeding population survey data between 1990 and 2014.The models that best fit the survey data suggested that survival and recruitment were affected by density dependence and that density effects were stronger on adult survival during the breeding season than during the non-breeding season.Analysis also suggests that regulation of survival and recruitment by density varied over time. Our results showed that different characterizations of density regulations changed every 8–12 years (three times in the 25-year period) for our population.Synthesis and applications. Using a full annual cycle, modelling framework and model weighting routine will be helpful in evaluating density dependence for migratory species in both the short and long term. We used this method to disentangle the seasonal effects of density on the continental American black duck population which will allow managers to better evaluate the effects of habitat loss and potential habitat management actions throughout the annual cycle. The method here may allow researchers to hone in on the proper form and/or strength of density dependence for use in models for conservation recommendations.

Direct calculation of liquid-vapor phase equilibria from transition matrix Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Errington, Jeffrey R.

2003-06-01

An approach for directly determining the liquid-vapor phase equilibrium of a model system at any temperature along the coexistence line is described. The method relies on transition matrix Monte Carlo ideas developed by Fitzgerald, Picard, and Silver [Europhys. Lett. 46, 282 (1999)]. During a Monte Carlo simulation attempted transitions between states along the Markov chain are monitored as opposed to tracking the number of times the chain visits a given state as is done in conventional simulations. Data collection is highly efficient and very precise results are obtained. The method is implemented in both the grand canonical and isothermal-isobaric ensemble. The main result from a simulation conducted at a given temperature is a density probability distribution for a range of densities that includes both liquid and vapor states. Vapor pressures and coexisting densities are calculated in a straightforward manner from the probability distribution. The approach is demonstrated with the Lennard-Jones fluid. Coexistence properties are directly calculated at temperatures spanning from the triple point to the critical point.

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

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.

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.

Two-leg ladder systems with dipole–dipole Fermion interactions

NASA Astrophysics Data System (ADS)

Mosadeq, Hamid; Asgari, Reza

2018-05-01

The ground-state phase diagram of a two-leg fermionic dipolar ladder with inter-site interactions is studied using density matrix renormalization group (DMRG) techniques. We use a state-of-the-art implementation of the DMRG algorithm and finite size scaling to simulate large system sizes with high accuracy. We also consider two different model systems and explore stable phases in half and quarter filling factors. We find that in the half filling, the charge and spin gaps emerge in a finite value of the dipole–dipole and on-site interactions. In the quarter filling case, s-wave superconducting state, charge density wave, homogenous insulating and phase separation phases occur depend on the interaction values. Moreover, in the dipole–dipole interaction, the D-Mott phase emerges when the hopping terms along the chain and rung are the same, whereas, this phase has been only proposed for the anisotropic Hubbard model. In the half filling case, on the other hand, there is either charge-density wave or charged Mott order phase depends on the orientation of the dipole moments of the particles with respect to the ladder geometry.

Dependence of Plastic TATB Shock-Wave Sensitivity on Temperature, Density and Technology Factors

NASA Astrophysics Data System (ADS)

Vlasov, Yu. A.; Kosolapov, V. B.; Fomicheva, L. V.; Khabarov, I. P.

1999-06-01

Mixed TATB-based HE is the most perspective because of the manufacture and exploitation safety of its items. At the same time the safety of these explosive, at high temperatures, which take place at emergencies, causes the certain anxiety. Plastic TATB shock-wave sensitivity (SWS) researches has shown that temperature as one of the important factors of external influence is not always the determining reason of SWS change. It is known that density influence on SWS significantly. At the same time density depends on temperature and technology of details manufacturing. In this connection in this work the temperature dependence of plastic TATB SWS was studied in view of convertible and irreversible changes of density (p) under heating at -50[C up to 90[C . It is shown that during these influences the dependence of threshold pressure of initiation (P) from temperature is explained, first of all, by change of HE density, caused by its thermal expansion (compression), and also by irreversible changes of p and HE structure, arising at heating. It is found also that the share of irreversible change of density depends on technology of HE details manufacturing and is explained by relaxation of residual pressure in them. The mentioned relaxation is finished after the first cycles of thermal influence. The value of density change, caused by this factor, depends on temperature and duration of heating.

Subsystem real-time time dependent density functional theory.

PubMed

Krishtal, Alisa; Ceresoli, Davide; Pavanello, Michele

2015-04-21

We present the extension of Frozen Density Embedding (FDE) formulation of subsystem Density Functional Theory (DFT) to real-time Time Dependent Density Functional Theory (rt-TDDFT). FDE is a DFT-in-DFT embedding method that allows to partition a larger Kohn-Sham system into a set of smaller, coupled Kohn-Sham systems. Additional to the computational advantage, FDE provides physical insight into the properties of embedded systems and the coupling interactions between them. The extension to rt-TDDFT is done straightforwardly by evolving the Kohn-Sham subsystems in time simultaneously, while updating the embedding potential between the systems at every time step. Two main applications are presented: the explicit excitation energy transfer in real time between subsystems is demonstrated for the case of the Na4 cluster and the effect of the embedding on optical spectra of coupled chromophores. In particular, the importance of including the full dynamic response in the embedding potential is demonstrated.

Multiphoton ionization of many-electron atoms and highly-charged ions in intense laser fields: a relativistic time-dependent density functional theory approach

NASA Astrophysics Data System (ADS)

Tumakov, Dmitry A.; Telnov, Dmitry A.; Maltsev, Ilia A.; Plunien, Günter; Shabaev, Vladimir M.

2017-10-01

We develop an efficient numerical implementation of the relativistic time-dependent density functional theory (RTDDFT) to study multielectron highly-charged ions subject to intense linearly-polarized laser fields. The interaction with the electromagnetic field is described within the electric dipole approximation. The resulting time-dependent relativistic Kohn-Sham (RKS) equations possess an axial symmetry and are solved accurately and efficiently with the help of the time-dependent generalized pseudospectral method. As a case study, we calculate multiphoton ionization probabilities of the neutral argon atom and argon-like xenon ion. Relativistic effects are assessed by comparison of our present results with existing non-relativistic data.

Spectroscopic and time-dependent density functional investigation of the role of structure on the acid-base effects of citrinin detection

USDA-ARS?s Scientific Manuscript database

A time dependent density functional (TD-DFT) study was carried out on tautomers and ionic forms of citrinin to gain insight into the role of chemical structure and micellar environments on detection. Steady state fluorescence studies of citrinin in micellar aqueous solutions produced unusual results...

Fundamental Flux Equations for Fracture-Matrix Interactions with Linear Diffusion

NASA Astrophysics Data System (ADS)

Oldenburg, C. M.; Zhou, Q.; Rutqvist, J.; Birkholzer, J. T.

2017-12-01

The conventional dual-continuum models are only applicable for late-time behavior of pressure propagation in fractured rock, while discrete-fracture-network models may explicitly deal with matrix blocks at high computational expense. To address these issues, we developed a unified-form diffusive flux equation for 1D isotropic (spheres, cylinders, slabs) and 2D/3D rectangular matrix blocks (squares, cubes, rectangles, and rectangular parallelepipeds) by partitioning the entire dimensionless-time domain (Zhou et al., 2017a, b). For each matrix block, this flux equation consists of the early-time solution up until a switch-over time after which the late-time solution is applied to create continuity from early to late time. The early-time solutions are based on three-term polynomial functions in terms of square root of dimensionless time, with the coefficients dependent on dimensionless area-to-volume ratio and aspect ratios for rectangular blocks. For the late-time solutions, one exponential term is needed for isotropic blocks, while a few additional exponential terms are needed for highly anisotropic blocks. The time-partitioning method was also used for calculating pressure/concentration/temperature distribution within a matrix block. The approximate solution contains an error-function solution for early times and an exponential solution for late times, with relative errors less than 0.003. These solutions form the kernel of multirate and multidimensional hydraulic, solute and thermal diffusion in fractured reservoirs.

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

NASA Astrophysics Data System (ADS)

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

2013-08-01

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

Sexual segregation in North American elk: the role of density dependence

PubMed Central

Stewart, Kelley M; Walsh, Danielle R; Kie, John G; Dick, Brian L; Bowyer, R Terry

2015-01-01

We investigated how density-dependent processes and subsequent variation in nutritional condition of individuals influenced both timing and duration of sexual segregation and selection of resources. During 1999–2001, we experimentally created two population densities of North American elk (Cervus elaphus), a high-density population at 20 elk/km2, and a low-density population at 4 elk/km2 to test hypotheses relative to timing and duration of sexual segregation and variation in selection of resources. We used multi-response permutation procedures to investigate patterns of sexual segregation, and resource selection functions to document differences in selection of resources by individuals in high- and low-density populations during sexual segregation and aggregation. The duration of sexual segregation was 2 months longer in the high-density population and likely was influenced by individuals in poorer nutritional condition, which corresponded with later conception and parturition, than at low density. Males and females in the high-density population overlapped in selection of resources to a greater extent than in the low-density population, probably resulting from density-dependent effects of increased intraspecific competition and lower availability of resources. PMID:25691992

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.

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.

Analysis of band structure, transmission properties, and dispersion behavior of THz wave in one-dimensional parabolic plasma photonic crystal

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

Askari, Nasim; Eslami, Esmaeil, E-mail: eeslami@iust.ac.ir; Mirzaie, Reza

2015-11-15

The photonic band gap of obliquely incident terahertz electromagnetic waves in a one-dimensional plasma photonic crystal is studied. The periodic structure consists of lossless dielectric and inhomogeneous plasma with a parabolic density profile. The dispersion relation and the THz wave transmittance are analyzed based on the electromagnetic equations and transfer matrix method. The dependence of effective plasma frequency and photonic band gap characteristics on dielectric and plasma thickness, plasma density, and incident angle are discussed in detail. A theoretical calculation for effective plasma frequency is presented and compared with numerical results. Results of these two methods are in good agreement.

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.

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.

The development of the time dependence of the nuclear EMP electric field

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

Eng, C

The nuclear electromagnetic pulse (EMP) electric field calculated with the legacy code CHAP is compared with the field given by an integral solution of Maxwell's equations, also known as the Jefimenko equation, to aid our current understanding on the factors that affect the time dependence of the EMP. For a fair comparison the CHAP current density is used as a source in the Jefimenko equation. At first, the comparison is simplified by neglecting the conduction current and replacing the standard atmosphere with a constant density air slab. The simplicity of the resultant current density aids in determining the factors thatmore » affect the rise, peak and tail of the EMP electric field versus time. The three dimensional nature of the radiating source, i.e. sources off the line-of-sight, and the time dependence of the derivative of the current density with respect to time are found to play significant roles in shaping the EMP electric field time dependence. These results are found to hold even when the conduction current and the standard atmosphere are properly accounted for. Comparison of the CHAP electric field with the Jefimenko electric field offers a direct validation of the high-frequency/outgoing wave approximation.« less

Entanglement entropy in a one-dimensional disordered interacting system: the role of localization.

PubMed

Berkovits, Richard

2012-04-27

The properties of the entanglement entropy (EE) in one-dimensional disordered interacting systems are studied. Anderson localization leaves a clear signature on the average EE, as it saturates on the length scale exceeding the localization length. This is verified by numerically calculating the EE for an ensemble of disordered realizations using the density matrix renormalization group method. A heuristic expression describing the dependence of the EE on the localization length, which takes into account finite-size effects, is proposed. This is used to extract the localization length as a function of the interaction strength. The localization length dependence on the interaction fits nicely with the expectations.

Effect of repulsive and attractive three-body forces on nucleus-nucleus elastic scattering

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

Furumoto, T.; Sakuragi, Y.; Yamamoto, Y.

2009-10-15

The effect of the three-body force (TBF) is studied in nucleus-nucleus elastic scattering on the basis of Brueckner theory for nucleon-nucleon (NN) effective interaction (complex G matrix) in the nuclear matter. A new G matrix called CEG07 proposed recently by the present authors includes the TBF effect and reproduces a realistic saturation curve in the nuclear matter, and it is shown to well reproduce proton-nucleus elastic scattering. The microscopic optical potential for the nucleus-nucleus system is obtained by folding the G matrix with nucleon density distributions in colliding nuclei. We first analyze in detail the {sup 16}O+{sup 16}O elastic scatteringmore » at E/A=70 MeV. The observed cross sections are nicely reproduced up to the most backward scattering angles only when the TBF effect is included. The use of the frozen-density approximation (FDA) is essentially important to properly estimate the effect of the TBF in nucleus-nucleus scattering. Other prescriptions for defining the local density have also been tested, but only the FDA prescription gives a proper description of the experimental cross sections as well as the effect of the TBF. The effects of the three-body attraction and the {omega}-rearrangement term are also analyzed. The CEG07 interaction is compared with CDM3Y6, which is a reliable and successful effective density-dependent NN interaction used in the double-folding model. The CEG07 G matrix is also tested in the elastic scattering of {sup 16}O by the {sup 12}C, {sup 28}Si, and {sup 40}Ca targets at E/A=93.9 MeV, and in the elastic scattering of {sup 12}C by the {sup 12}C target at E/A=135 MeV with great success. The decisive effect of the TBF is clearly seen also in those systems. Finally, we have tested CEG07a, CEG07b, and CEG07c for the {sup 16}O+{sup 16}O system at various energies.« less

Hot pressing titanium metal matrix composites reinforced with graphene nanoplatelets through an in-situ reactive method

NASA Astrophysics Data System (ADS)

Mu, X. N.; Zhang, H. M.; Cai, H. N.; Fan, Q. B.; Wu, Y.; Fu, Z. J.; Wang, Q. X.

2017-05-01

This study proposed an in-situ reactive method that uses graphene as a reinforcement to fabricate titanium metal matrix composites (TiMMCs) through powder metallurgy processing route. The volume fraction of graphene nanoplatelets was 1.8%vol, and the pure titanium was used as a matrix. The Archimedes density, hardness, microstructure and mechanical properties of specimens were compared under different ball milling times (20 min and 2.5 h) and hot pressing temperatures (900°C, 1150°C, and 1300°C,). The ultimate tensile strength of 630 MPa, which demonstrated a 27.3% increase compared with pure Ti, was achieved under a ball milling time of 20 min. Elongation increased with increasing temperature. When the ball milling time and hot pressing temperature were increased to 2.5 h and 1300 °C, respectively, the ultimate tensile strength of the composites reached 750 MPa, showing an increase of 51.5% compared with pure Ti.